Daily Papers

Language models can serve as a valuable tool for software developers to increase productivity. Large generative models can be used for code generation and code completion, while smaller encoder-only models are capable of performing code search tasks using natural language queries.These capabilities are heavily influenced by the quality and diversity of the available training data. Source code datasets used for training usually focus on the most popular languages and testing is mostly conducted on the same distributions, often overlooking low-resource programming languages. Motivated by the NLP generalization taxonomy proposed by Hupkes et.\,al., we propose a new benchmark dataset called GenCodeSearchNet (GeCS) which builds upon existing natural language code search datasets to systemically evaluate the programming language understanding generalization capabilities of language models. As part of the full dataset, we introduce a new, manually curated subset StatCodeSearch that focuses on R, a popular but so far underrepresented programming language that is often used by researchers outside the field of computer science. For evaluation and comparison, we collect several baseline results using fine-tuned BERT-style models and GPT-style large language models in a zero-shot setting.

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of errorful and error-free parallel corpora. We design custom token-level transformations to map input tokens to target corrections. Our best single-model/ensemble GEC tagger achieves an F_{0.5} of 65.3/66.5 on CoNLL-2014 (test) and F_{0.5} of 72.4/73.6 on BEA-2019 (test). Its inference speed is up to 10 times as fast as a Transformer-based seq2seq GEC system. The code and trained models are publicly available.

In code search, the Generation-Augmented Retrieval (GAR) framework, which generates exemplar code snippets to augment queries, has emerged as a promising strategy to address the principal challenge of modality misalignment between code snippets and natural language queries, particularly with the demonstrated code generation capabilities of Large Language Models (LLMs). Nevertheless, our preliminary investigations indicate that the improvements conferred by such an LLM-augmented framework are somewhat constrained. This limitation could potentially be ascribed to the fact that the generated codes, albeit functionally accurate, frequently display a pronounced stylistic deviation from the ground truth code in the codebase. In this paper, we extend the foundational GAR framework and propose a simple yet effective method that additionally Rewrites the Code (ReCo) within the codebase for style normalization. Experimental results demonstrate that ReCo significantly boosts retrieval accuracy across sparse (up to 35.7%), zero-shot dense (up to 27.6%), and fine-tuned dense (up to 23.6%) retrieval settings in diverse search scenarios. To further elucidate the advantages of ReCo and stimulate research in code style normalization, we introduce Code Style Similarity, the first metric tailored to quantify stylistic similarities in code. Notably, our empirical findings reveal the inadequacy of existing metrics in capturing stylistic nuances.

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.

Semantic code search is the task of retrieving relevant code given a natural language query. While related to other information retrieval tasks, it requires bridging the gap between the language used in code (often abbreviated and highly technical) and natural language more suitable to describe vague concepts and ideas. To enable evaluation of progress on code search, we are releasing the CodeSearchNet Corpus and are presenting the CodeSearchNet Challenge, which consists of 99 natural language queries with about 4k expert relevance annotations of likely results from CodeSearchNet Corpus. The corpus contains about 6 million functions from open-source code spanning six programming languages (Go, Java, JavaScript, PHP, Python, and Ruby). The CodeSearchNet Corpus also contains automatically generated query-like natural language for 2 million functions, obtained from mechanically scraping and preprocessing associated function documentation. In this article, we describe the methodology used to obtain the corpus and expert labels, as well as a number of simple baseline solutions for the task. We hope that CodeSearchNet Challenge encourages researchers and practitioners to study this interesting task further and will host a competition and leaderboard to track the progress on the challenge. We are also keen on extending CodeSearchNet Challenge to more queries and programming languages in the future.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

Code search is crucial for code reuse, enabling developers to efficiently locate relevant snippets. Current methods rely on encoder-based models, which suffer from limitations such as poor generalization and restricted input lengths. Decoder-only large language models (LLMs), with their extensive pre-training, larger size, and longer input capabilities, offer potential solutions to these issues, yet their effectiveness in code search remains underexplored. To fill this gap, our study presents the first systematic exploration of decoder-only LLMs for code search. We evaluate nine state-of-the-art decoder-only models using two fine-tuning methods, two datasets (CSN and CoSQA^+), and three model sizes. Our findings reveal that fine-tuned CodeGemma significantly outperforms encoder-only models like UniXcoder, achieving a 5.57% improvement in MRR on CSN and a 49.6% increase in MAP on CoSQA^+ compared to zero-shot UniXcoder. These results highlight the superior performance and adaptability of decoder-only models. Additionally, we provide valuable insights into optimizing these models for code search, covering aspects such as model selection, fine-tuning methods, training data, and model size, and discussing their strengths and limitations.

We introduce a prototyping testbed, GenSC-6G, developed to generate a comprehensive dataset that supports the integration of generative artificial intelligence (AI), quantum computing, and semantic communication for emerging sixth-generation (6G) applications. The GenSC-6G dataset is designed with noise-augmented synthetic data optimized for semantic decoding, classification, and localization tasks, significantly enhancing flexibility for diverse AI-driven communication applications. This adaptable prototype supports seamless modifications across baseline models, communication modules, and goal-oriented decoders. Case studies demonstrate its application in lightweight classification, semantic upsampling, and edge-based language inference under noise conditions. The GenSC-6G dataset serves as a scalable and robust resource for developing goal-oriented communication systems tailored to the growing demands of 6G networks.

How to evaluate Large Language Models (LLMs) in code generation is an open question. Existing benchmarks demonstrate poor alignment with real-world code repositories and are insufficient to evaluate the coding abilities of LLMs. This paper proposes a new benchmark - EvoCodeBench to address the preceding problems, which has three primary advances. (1) EvoCodeBench aligns with real-world repositories in multiple dimensions, e.g., code distributions and dependency distributions. (2) EvoCodeBench offers comprehensive annotations (e.g., requirements, reference code, and reference dependencies), and robust evaluation metrics (e.g., Pass@k and Recall@k). (3) EvoCodeBench is an evolving benchmark to avoid data leakage. We build an automatic pipeline to update EvoCodeBench from the latest repositories. We release the first version - EvoCodeBench-2403, containing 275 samples from 25 real-world repositories. Based on EvoCodeBench, we propose repository-level code generation and evaluate 10 popular LLMs (e.g., gpt-4, gpt-3.5, DeepSeek Coder, StarCoder 2, CodeLLaMa, Gemma, and Qwen 1.5). Our experiments reveal the coding abilities of these LLMs in real-world repositories. For example, the highest Pass@1 of gpt-4 only is 20.73% in our experiments. We also analyze failed cases and summarize the shortcomings of existing LLMs in EvoCodeBench. We release EvoCodeBench, all prompts, and LLMs' completions for further community analysis.

Code search is a task to find programming codes that semantically match the given natural language queries. Even though some of the existing datasets for this task are multilingual on the programming language side, their query data are only in English. In this research, we create a multilingual code search dataset in four natural and four programming languages using a neural machine translation model. Using our dataset, we pre-train and fine-tune the Transformer-based models and then evaluate them on multiple code search test sets. Our results show that the model pre-trained with all natural and programming language data has performed best in most cases. By applying back-translation data filtering to our dataset, we demonstrate that the translation quality affects the model's performance to a certain extent, but the data size matters more.

The advent of large language models (LLMs) has ushered in a new paradigm of search engines that use generative models to gather and summarize information to answer user queries. This emerging technology, which we formalize under the unified framework of generative engines (GEs), can generate accurate and personalized responses, rapidly replacing traditional search engines like Google and Bing. Generative Engines typically satisfy queries by synthesizing information from multiple sources and summarizing them using LLMs. While this shift significantly improves user utility and generative search engine traffic, it poses a huge challenge for the third stakeholder - website and content creators. Given the black-box and fast-moving nature of generative engines, content creators have little to no control over when and how their content is displayed. With generative engines here to stay, we must ensure the creator economy is not disadvantaged. To address this, we introduce Generative Engine Optimization (GEO), the first novel paradigm to aid content creators in improving their content visibility in GE responses through a flexible black-box optimization framework for optimizing and defining visibility metrics. We facilitate systematic evaluation by introducing GEO-bench, a large-scale benchmark of diverse user queries across multiple domains, along with relevant web sources to answer these queries. Through rigorous evaluation, we demonstrate that GEO can boost visibility by up to 40\% in GE responses. Moreover, we show the efficacy of these strategies varies across domains, underscoring the need for domain-specific optimization methods. Our work opens a new frontier in information discovery systems, with profound implications for both developers of GEs and content creators.

Generative Flow Networks (GFlowNets) are amortized sampling methods that learn a distribution over discrete objects proportional to their rewards. GFlowNets exhibit a remarkable ability to generate diverse samples, yet occasionally struggle to consistently produce samples with high rewards due to over-exploration on wide sample space. This paper proposes to train GFlowNets with local search, which focuses on exploiting high-rewarded sample space to resolve this issue. Our main idea is to explore the local neighborhood via backtracking and reconstruction guided by backward and forward policies, respectively. This allows biasing the samples toward high-reward solutions, which is not possible for a typical GFlowNet solution generation scheme, which uses the forward policy to generate the solution from scratch. Extensive experiments demonstrate a remarkable performance improvement in several biochemical tasks. Source code is available: https://github.com/dbsxodud-11/ls_gfn.

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

Competition-level code generation tasks pose significant challenges for current state-of-the-art large language models (LLMs). For example, on the LiveCodeBench-Hard dataset, models such as O1-Mini and O1-Preview achieve pass@1 rates of only 0.366 and 0.143, respectively. While tree search techniques have proven effective in domains like mathematics and general coding, their potential in competition-level code generation remains under-explored. In this work, we propose a novel token-level tree search method specifically designed for code generation. Leveraging Qwen2.5-Coder-32B-Instruct, our approach achieves a pass rate of 0.305 on LiveCodeBench-Hard, surpassing the pass@100 performance of GPT4o-0513 (0.245). Furthermore, by integrating Chain-of-Thought (CoT) prompting, we improve our method's performance to 0.351, approaching O1-Mini's pass@1 rate. To ensure reproducibility, we report the average number of generations required per problem by our tree search method on the test set. Our findings underscore the potential of tree search to significantly enhance performance on competition-level code generation tasks. This opens up new possibilities for large-scale synthesis of challenging code problems supervised fine-tuning (SFT) data, advancing competition-level code generation tasks.

Code generation aims to automatically generate code snippets of specific programming language according to natural language descriptions. The continuous advancements in deep learning, particularly pre-trained models, have empowered the code generation task to achieve remarkable performance. One main challenge of pre-trained models for code generation is the semantic gap between natural language requirements and source code. To address the issue, prior studies typically adopt a retrieval-augmented framework for the task, where the similar code snippets collected by a retrieval process can be leveraged to help understand the requirements and provide guidance for the generation process. However, there is a lack of systematic study on the application of this framework for code generation, including the impact of the final generated results and the specific usage of the framework. In this paper, we choose three popular pre-trained code models, namely CodeGen, UniXcoder, and CodeT5, to assess the impact of the quality and utilization of retrieved code on the retrieval-augmented framework. Our analysis shows that the retrieval-augmented framework is beneficial for improving the performance of the existing pre-trained models. We also provide suggestions on the utilization of the retrieval-augmented code generation framework: BM25 and Sequential Integration Fusion are recommended due to their convenience and superior performance. Sketch Filling Fusion, which extracts a sketch of relevant code, could help the model improve its performance further. Additionally, we conduct experiments to investigate the influence of the retrieval-augmented framework on large language models for code generation, showing the effectiveness of the framework, and we discuss the trade-off between performance improvement and computational costs in each phase within the framework.

While scaling training compute has led to remarkable improvements in large language models (LLMs), scaling inference compute has not yet yielded analogous gains. We hypothesize that a core missing component is a lack of diverse LLM outputs, leading to inefficient search due to models repeatedly sampling highly similar, yet incorrect generations. We empirically demonstrate that this lack of diversity can be mitigated by searching over candidate plans for solving a problem in natural language. Based on this insight, we propose PLANSEARCH, a novel search algorithm which shows strong results across HumanEval+, MBPP+, and LiveCodeBench (a contamination-free benchmark for competitive coding). PLANSEARCH generates a diverse set of observations about the problem and then uses these observations to construct plans for solving the problem. By searching over plans in natural language rather than directly over code solutions, PLANSEARCH explores a significantly more diverse range of potential solutions compared to baseline search methods. Using PLANSEARCH on top of Claude 3.5 Sonnet achieves a state-of-the-art pass@200 of 77.0% on LiveCodeBench, outperforming both the best score achieved without search (pass@1 = 41.4%) and using standard repeated sampling (pass@200 = 60.6%). Finally, we show that, across all models, search algorithms, and benchmarks analyzed, we can accurately predict performance gains due to search as a direct function of the diversity over generated ideas.

Generative Error Correction (GEC) has emerged as a powerful post-processing method to enhance the performance of Automatic Speech Recognition (ASR) systems. However, we show that GEC models struggle to generalize beyond the specific types of errors encountered during training, limiting their ability to correct new, unseen errors at test time, particularly in out-of-domain (OOD) scenarios. This phenomenon amplifies with named entities (NEs), where, in addition to insufficient contextual information or knowledge about the NEs, novel NEs keep emerging. To address these issues, we propose DARAG (Data- and Retrieval-Augmented Generative Error Correction), a novel approach designed to improve GEC for ASR in in-domain (ID) and OOD scenarios. We augment the GEC training dataset with synthetic data generated by prompting LLMs and text-to-speech models, thereby simulating additional errors from which the model can learn. For OOD scenarios, we simulate test-time errors from new domains similarly and in an unsupervised fashion. Additionally, to better handle named entities, we introduce retrieval-augmented correction by augmenting the input with entities retrieved from a database. Our approach is simple, scalable, and both domain- and language-agnostic. We experiment on multiple datasets and settings, showing that DARAG outperforms all our baselines, achieving 8\% -- 30\% relative WER improvements in ID and 10\% -- 33\% improvements in OOD settings.

Decompilation aims to recover the source code form of a binary executable. It has many security applications such as malware analysis, vulnerability detection and code hardening. A prominent challenge in decompilation is to recover variable names. We propose a novel technique that leverages the strengths of generative models while mitigating model biases and potential hallucinations. We build a prototype, GenNm, from pre-trained generative models CodeGemma-2B and CodeLlama-7B. We finetune GenNm on decompiled functions, and mitigate model biases by incorporating symbol preference to the training pipeline. GenNm includes names from callers and callees while querying a function, providing rich contextual information within the model's input token limitation. It further leverages program analysis to validate the consistency of names produced by the generative model. Our results show that GenNm improves the state-of-the-art name recovery accuracy by 8.6 and 11.4 percentage points on two commonly used datasets, and improves the state-of-the-art from 8.5% to 22.8% in the most challenging setup where ground-truth variable names are not seen in the training dataset.

Semantic code search is the task of retrieving a code snippet given a textual description of its functionality. Recent work has been focused on using similarity metrics between neural embeddings of text and code. However, current language models are known to struggle with longer, compositional text, and multi-step reasoning. To overcome this limitation, we propose supplementing the query sentence with a layout of its semantic structure. The semantic layout is used to break down the final reasoning decision into a series of lower-level decisions. We use a Neural Module Network architecture to implement this idea. We compare our model - NS3 (Neuro-Symbolic Semantic Search) - to a number of baselines, including state-of-the-art semantic code retrieval methods, and evaluate on two datasets - CodeSearchNet and Code Search and Question Answering. We demonstrate that our approach results in more precise code retrieval, and we study the effectiveness of our modular design when handling compositional queries.

Code search with natural language plays a crucial role in reusing existing code snippets and accelerating software development. Thanks to the Transformer-based pretraining models, the performance of code search has been improved significantly compared to traditional information retrieval (IR) based models. However, due to the quadratic complexity of multi-head self-attention, there is a limit on the input token length. For efficient training on standard GPUs like V100, existing pretrained code models, including GraphCodeBERT, CodeBERT, RoBERTa (code), take the first 256 tokens by default, which makes them unable to represent the complete information of long code that is greater than 256 tokens. Unlike long text paragraph that can be regarded as a whole with complete semantics, the semantics of long code is discontinuous as a piece of long code may contain different code modules. Therefore, it is unreasonable to directly apply the long text processing methods to long code. To tackle the long code problem, we propose SEA (Split, Encode and Aggregate for Long Code Search), which splits long code into code blocks, encodes these blocks into embeddings, and aggregates them to obtain a comprehensive long code representation. With SEA, we could directly use Transformer-based pretraining models to model long code without changing their internal structure and repretraining. Leveraging abstract syntax tree (AST) based splitting and attention-based aggregation methods, SEA achieves significant improvements in long code search performance. We also compare SEA with two sparse Trasnformer methods. With GraphCodeBERT as the encoder, SEA achieves an overall mean reciprocal ranking score of 0.785, which is 10.1% higher than GraphCodeBERT on the CodeSearchNet benchmark.

Code search is an important task that has seen many developments in recent years. However, previous attempts have mostly considered the problem of searching for code by a text query. We argue that using a code snippet (and possibly an associated traceback) as a query and looking for answers with bugfixing instructions and code samples is a natural use case that is not covered by existing approaches. Moreover, existing datasets use comments extracted from code rather than full-text descriptions as text, making them unsuitable for this use case. We present a new SearchBySnippet dataset implementing the search-by-code use case based on StackOverflow data; it turns out that in this setting, existing architectures fall short of the simplest BM25 baseline even after fine-tuning. We present a new single encoder model SnippeR that outperforms several strong baselines on the SearchBySnippet dataset with a result of 0.451 Recall@10; we propose the SearchBySnippet dataset and SnippeR as a new important benchmark for code search evaluation.

Semantic code search, retrieving code that matches a given natural language query, is an important task to improve productivity in software engineering. Existing code search datasets are problematic: either using unrealistic queries, or with mismatched codes, and typically using one-to-one query-code pairing, which fails to reflect the reality that a query might have multiple valid code matches. This paper introduces CoSQA+, pairing high-quality queries (reused from CoSQA) with multiple suitable codes. We collect code candidates from diverse sources and form candidate pairs by pairing queries with these codes. Utilizing the power of large language models (LLMs), we automate pair annotation, filtering, and code generation for queries without suitable matches. Through extensive experiments, CoSQA+ has demonstrated superior quality over CoSQA. Models trained on CoSQA+ exhibit improved performance. Furthermore, we propose a new metric Mean Multi-choice Reciprocal Rank (MMRR), to assess one-to-N code search performance. We provide the code and data at https://github.com/DeepSoftwareAnalytics/CoSQA_Plus.

Thanks to unprecedented language understanding and generation capabilities of large language model (LLM), Retrieval-augmented Code Generation (RaCG) has recently been widely utilized among software developers. While this has increased productivity, there are still frequent instances of incorrect codes being provided. In particular, there are cases where plausible yet incorrect codes are generated for queries from users that cannot be answered with the given queries and API descriptions. This study proposes a task for evaluating answerability, which assesses whether valid answers can be generated based on users' queries and retrieved APIs in RaCG. Additionally, we build a benchmark dataset called Retrieval-augmented Code Generability Evaluation (RaCGEval) to evaluate the performance of models performing this task. Experimental results show that this task remains at a very challenging level, with baseline models exhibiting a low performance of 46.7%. Furthermore, this study discusses methods that could significantly improve performance.

Code search aims to retrieve semantically relevant code snippets for a given natural language query. Recently, many approaches employing contrastive learning have shown promising results on code representation learning and greatly improved the performance of code search. However, there is still a lot of room for improvement in using contrastive learning for code search. In this paper, we propose CoCoSoDa to effectively utilize contrastive learning for code search via two key factors in contrastive learning: data augmentation and negative samples. Specifically, soft data augmentation is to dynamically masking or replacing some tokens with their types for input sequences to generate positive samples. Momentum mechanism is used to generate large and consistent representations of negative samples in a mini-batch through maintaining a queue and a momentum encoder. In addition, multimodal contrastive learning is used to pull together representations of code-query pairs and push apart the unpaired code snippets and queries. We conduct extensive experiments to evaluate the effectiveness of our approach on a large-scale dataset with six programming languages. Experimental results show that: (1) CoCoSoDa outperforms 14 baselines and especially exceeds CodeBERT, GraphCodeBERT, and UniXcoder by 13.3%, 10.5%, and 5.9% on average MRR scores, respectively. (2) The ablation studies show the effectiveness of each component of our approach. (3) We adapt our techniques to several different pre-trained models such as RoBERTa, CodeBERT, and GraphCodeBERT and observe a significant boost in their performance in code search. (4) Our model performs robustly under different hyper-parameters. Furthermore, we perform qualitative and quantitative analyses to explore reasons behind the good performance of our model.

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

The goals of this research were to search for Convolutional Neural Network (CNN) architectures, suitable for an on-device processor with limited computing resources, performing at substantially lower Network Architecture Search (NAS) costs. A new algorithm entitled an Early Exit Population Initialisation (EE-PI) for Evolutionary Algorithm (EA) was developed to achieve both goals. The EE-PI reduces the total number of parameters in the search process by filtering the models with fewer parameters than the maximum threshold. It will look for a new model to replace those models with parameters more than the threshold. Thereby, reducing the number of parameters, memory usage for model storage and processing time while maintaining the same performance or accuracy. The search time was reduced to 0.52 GPU day. This is a huge and significant achievement compared to the NAS of 4 GPU days achieved using NSGA-Net, 3,150 GPU days by the AmoebaNet model, and the 2,000 GPU days by the NASNet model. As well, Early Exit Evolutionary Algorithm networks (EEEA-Nets) yield network architectures with minimal error and computational cost suitable for a given dataset as a class of network algorithms. Using EEEA-Net on CIFAR-10, CIFAR-100, and ImageNet datasets, our experiments showed that EEEA-Net achieved the lowest error rate among state-of-the-art NAS models, with 2.46% for CIFAR-10, 15.02% for CIFAR-100, and 23.8% for ImageNet dataset. Further, we implemented this image recognition architecture for other tasks, such as object detection, semantic segmentation, and keypoint detection tasks, and, in our experiments, EEEA-Net-C2 outperformed MobileNet-V3 on all of these various tasks. (The algorithm code is available at https://github.com/chakkritte/EEEA-Net).

Neural architecture search (NAS) with an accuracy predictor that predicts the accuracy of candidate architectures has drawn increasing attention due to its simplicity and effectiveness. Previous works usually employ neural network-based predictors which require more delicate design and are easy to overfit. Considering that most architectures are represented as sequences of discrete symbols which are more like tabular data and preferred by non-neural predictors, in this paper, we study an alternative approach which uses non-neural model for accuracy prediction. Specifically, as decision tree based models can better handle tabular data, we leverage gradient boosting decision tree (GBDT) as the predictor for NAS. We demonstrate that the GBDT predictor can achieve comparable (if not better) prediction accuracy than neural network based predictors. Moreover, considering that a compact search space can ease the search process, we propose to prune the search space gradually according to important features derived from GBDT. In this way, NAS can be performed by first pruning the search space and then searching a neural architecture, which is more efficient and effective. Experiments on NASBench-101 and ImageNet demonstrate the effectiveness of using GBDT as predictor for NAS: (1) On NASBench-101, it is 22x, 8x, and 6x more sample efficient than random search, regularized evolution, and Monte Carlo Tree Search (MCTS) in finding the global optimum; (2) It achieves 24.2% top-1 error rate on ImageNet, and further achieves 23.4% top-1 error rate on ImageNet when enhanced with search space pruning. Code is provided at https://github.com/renqianluo/GBDT-NAS.

There has been an increase of interest in code search using natural language. Assessing the performance of such code search models can be difficult without a readily available evaluation suite. In this paper, we present an evaluation dataset consisting of natural language query and code snippet pairs, with the hope that future work in this area can use this dataset as a common benchmark. We also provide the results of two code search models ([1] and [6]) from recent work. The evaluation dataset is available at https://github.com/facebookresearch/Neural-Code-Search-Evaluation-Dataset

Quality estimation models have been developed to assess the corrections made by grammatical error correction (GEC) models when the reference or gold-standard corrections are not available. An ideal quality estimator can be utilized to combine the outputs of multiple GEC systems by choosing the best subset of edits from the union of all edits proposed by the GEC base systems. However, we found that existing GEC quality estimation models are not good enough in differentiating good corrections from bad ones, resulting in a low F0.5 score when used for system combination. In this paper, we propose GRECO, a new state-of-the-art quality estimation model that gives a better estimate of the quality of a corrected sentence, as indicated by having a higher correlation to the F0.5 score of a corrected sentence. It results in a combined GEC system with a higher F0.5 score. We also propose three methods for utilizing GEC quality estimation models for system combination with varying generality: model-agnostic, model-agnostic with voting bias, and model-dependent method. The combined GEC system outperforms the state of the art on the CoNLL-2014 test set and the BEA-2019 test set, achieving the highest F0.5 scores published to date.

This paper presents EasyRAG, a simple, lightweight, and efficient retrieval-augmented generation framework for automated network operations. Our framework has three advantages. The first is accurate question answering. We designed a straightforward RAG scheme based on (1) a specific data processing workflow (2) dual-route sparse retrieval for coarse ranking (3) LLM Reranker for reranking (4) LLM answer generation and optimization. This approach achieved first place in the GLM4 track in the preliminary round and second place in the GLM4 track in the semifinals. The second is simple deployment. Our method primarily consists of BM25 retrieval and BGE-reranker reranking, requiring no fine-tuning of any models, occupying minimal VRAM, easy to deploy, and highly scalable; we provide a flexible code library with various search and generation strategies, facilitating custom process implementation. The last one is efficient inference. We designed an efficient inference acceleration scheme for the entire coarse ranking, reranking, and generation process that significantly reduces the inference latency of RAG while maintaining a good level of accuracy; each acceleration scheme can be plug-and-play into any component of the RAG process, consistently enhancing the efficiency of the RAG system. Our code and data are released at https://github.com/BUAADreamer/EasyRAG.

Code embeddings are essential for semantic code search; however, current approaches often struggle to capture the precise syntactic and contextual nuances inherent in code. Open-source models such as CodeBERT and UniXcoder exhibit limitations in scalability and efficiency, while high-performing proprietary systems impose substantial computational costs. We introduce a parameter-efficient fine-tuning method based on Low-Rank Adaptation (LoRA) to construct task-specific adapters for code retrieval. Our approach reduces the number of trainable parameters to less than two percent of the base model, enabling rapid fine-tuning on extensive code corpora (2 million samples in 25 minutes on two H100 GPUs). Experiments demonstrate an increase of up to 9.1% in Mean Reciprocal Rank (MRR) for Code2Code search, and up to 86.69% for Text2Code search tasks across multiple programming languages. Distinction in task-wise and language-wise adaptation helps explore the sensitivity of code retrieval for syntactical and linguistic variations.

The Non-Local Network (NLNet) presents a pioneering approach for capturing long-range dependencies, via aggregating query-specific global context to each query position. However, through a rigorous empirical analysis, we have found that the global contexts modeled by non-local network are almost the same for different query positions within an image. In this paper, we take advantage of this finding to create a simplified network based on a query-independent formulation, which maintains the accuracy of NLNet but with significantly less computation. We further observe that this simplified design shares similar structure with Squeeze-Excitation Network (SENet). Hence we unify them into a three-step general framework for global context modeling. Within the general framework, we design a better instantiation, called the global context (GC) block, which is lightweight and can effectively model the global context. The lightweight property allows us to apply it for multiple layers in a backbone network to construct a global context network (GCNet), which generally outperforms both simplified NLNet and SENet on major benchmarks for various recognition tasks. The code and configurations are released at https://github.com/xvjiarui/GCNet.

Despite the recent advancements in Large Language Models (LLMs), which have significantly enhanced the generative capabilities for various NLP tasks, LLMs still face limitations in directly handling retrieval tasks. However, many practical applications demand the seamless integration of both retrieval and generation. This paper introduces a novel and efficient One-pass Generation and retrieval framework (OneGen), designed to improve LLMs' performance on tasks that require both generation and retrieval. The proposed framework bridges the traditionally separate training approaches for generation and retrieval by incorporating retrieval tokens generated autoregressively. This enables a single LLM to handle both tasks simultaneously in a unified forward pass. We conduct experiments on two distinct types of composite tasks, RAG and Entity Linking, to validate the pluggability, effectiveness, and efficiency of OneGen in training and inference. Furthermore, our results show that integrating generation and retrieval within the same context preserves the generative capabilities of LLMs while improving retrieval performance. To the best of our knowledge, OneGen is the first to enable LLMs to conduct vector retrieval during the generation.

Despite the remarkable progress in the development of predictive models for healthcare, applying these algorithms on a large scale has been challenging. Algorithms trained on a particular task, based on specific data formats available in a set of medical records, tend to not generalize well to other tasks or databases in which the data fields may differ. To address this challenge, we propose General Healthcare Predictive Framework (GenHPF), which is applicable to any EHR with minimal preprocessing for multiple prediction tasks. GenHPF resolves heterogeneity in medical codes and schemas by converting EHRs into a hierarchical textual representation while incorporating as many features as possible. To evaluate the efficacy of GenHPF, we conduct multi-task learning experiments with single-source and multi-source settings, on three publicly available EHR datasets with different schemas for 12 clinically meaningful prediction tasks. Our framework significantly outperforms baseline models that utilize domain knowledge in multi-source learning, improving average AUROC by 1.2%P in pooled learning and 2.6%P in transfer learning while also showing comparable results when trained on a single EHR dataset. Furthermore, we demonstrate that self-supervised pretraining using multi-source datasets is effective when combined with GenHPF, resulting in a 0.6%P AUROC improvement compared to models without pretraining. By eliminating the need for preprocessing and feature engineering, we believe that this work offers a solid framework for multi-task and multi-source learning that can be leveraged to speed up the scaling and usage of predictive algorithms in healthcare.

Jupyter notebook allows data scientists to write machine learning code together with its documentation in cells. In this paper, we propose a new task of code documentation generation (CDG) for computational notebooks. In contrast to the previous CDG tasks which focus on generating documentation for single code snippets, in a computational notebook, one documentation in a markdown cell often corresponds to multiple code cells, and these code cells have an inherent structure. We proposed a new model (HAConvGNN) that uses a hierarchical attention mechanism to consider the relevant code cells and the relevant code tokens information when generating the documentation. Tested on a new corpus constructed from well-documented Kaggle notebooks, we show that our model outperforms other baseline models.

This paper presents the system description of our entry for the COLING 2025 RegNLP RIRAG (Regulatory Information Retrieval and Answer Generation) challenge, focusing on leveraging advanced information retrieval and answer generation techniques in regulatory domains. We experimented with a combination of embedding models, including Stella, BGE, CDE, and Mpnet, and leveraged fine-tuning and reranking for retrieving relevant documents in top ranks. We utilized a novel approach, LeSeR, which achieved competitive results with a recall@10 of 0.8201 and map@10 of 0.6655 for retrievals. This work highlights the transformative potential of natural language processing techniques in regulatory applications, offering insights into their capabilities for implementing a retrieval augmented generation system while identifying areas for future improvement in robustness and domain adaptation.

This paper presents a simple recipe to train state-of-the-art multilingual Grammatical Error Correction (GEC) models. We achieve this by first proposing a language-agnostic method to generate a large number of synthetic examples. The second ingredient is to use large-scale multilingual language models (up to 11B parameters). Once fine-tuned on language-specific supervised sets we surpass the previous state-of-the-art results on GEC benchmarks in four languages: English, Czech, German and Russian. Having established a new set of baselines for GEC, we make our results easily reproducible and accessible by releasing a cLang-8 dataset. It is produced by using our best model, which we call gT5, to clean the targets of a widely used yet noisy lang-8 dataset. cLang-8 greatly simplifies typical GEC training pipelines composed of multiple fine-tuning stages -- we demonstrate that performing a single fine-tuning step on cLang-8 with the off-the-shelf language models yields further accuracy improvements over an already top-performing gT5 model for English.

Code embeddings capture the semantic representations of code and are crucial for various code-related large language model (LLM) applications, such as code search. Previous training primarily relies on optimizing the InfoNCE loss by comparing positive natural language (NL)-code pairs with in-batch negatives. However, due to the sparse nature of code contexts, training solely by comparing the major differences between positive and negative pairs may fail to capture deeper semantic nuances. To address this issue, we propose a novel order-augmented strategy for improved code search (OASIS). It leverages order-based similarity labels to train models to capture subtle differences in similarity among negative pairs. Extensive benchmark evaluations demonstrate that our OASIS model significantly outperforms previous state-of-the-art models focusing solely on major positive-negative differences. It underscores the value of exploiting subtle differences among negative pairs with order labels for effective code embedding training.

Large language models (LLMs) require lengthy prompts as the input context to produce output aligned with user intentions, a process that incurs extra costs during inference. In this paper, we propose the Gist COnditioned deCOding (Gist-COCO) model, introducing a novel method for compressing prompts which also can assist the prompt interpretation and engineering. Gist-COCO employs an encoder-decoder based language model and then incorporates an additional encoder as a plugin module to compress prompts with inputs using gist tokens. It finetunes the compression plugin module and uses the representations of gist tokens to emulate the raw prompts in the vanilla language model. By verbalizing the representations of gist tokens into gist prompts, the compression ability of Gist-COCO can be generalized to different LLMs with high compression rates. Our experiments demonstrate that Gist-COCO outperforms previous prompt compression models in both passage and instruction compression tasks. Further analysis on gist verbalization results suggests that our gist prompts serve different functions in aiding language models. They may directly provide potential answers, generate the chain-of-thought, or simply repeat the inputs. All data and codes are available at https://github.com/OpenMatch/Gist-COCO .

Code generation with large language models has shown significant promise, especially when employing retrieval-augmented generation (RAG) with few-shot examples. However, selecting effective examples that enhance generation quality remains a challenging task, particularly when the target programming language (PL) is underrepresented. In this study, we present two key findings: (1) retrieving examples whose presented algorithmic plans can be referenced for generating the desired behavior significantly improves generation accuracy, and (2) converting code into pseudocode effectively captures such algorithmic plans, enhancing retrieval quality even when the source and the target PLs are different. Based on these findings, we propose Plan-as-query Example Retrieval for few-shot prompting in Code generation (PERC), a novel framework that utilizes algorithmic plans to identify and retrieve effective examples. We validate the effectiveness of PERC through extensive experiments on the CodeContests, HumanEval and MultiPL-E benchmarks: PERC consistently outperforms the state-of-the-art RAG methods in code generation, both when the source and target programming languages match or differ, highlighting its adaptability and robustness in diverse coding environments.

Recommender Systems are built to retrieve relevant items to satisfy users' information needs. The candidate corpus usually consists of a finite set of items that are ready to be served, such as videos, products, or articles. With recent advances in Generative AI such as GPT and Diffusion models, a new form of recommendation task is yet to be explored where items are to be created by generative models with personalized prompts. Taking image generation as an example, with a single prompt from the user and access to a generative model, it is possible to generate hundreds of new images in a few minutes. How shall we attain personalization in the presence of "infinite" items? In this preliminary study, we propose a two-stage framework, namely Prompt-Model Retrieval and Generated Item Ranking, to approach this new task formulation. We release GEMRec-18K, a prompt-model interaction dataset with 18K images generated by 200 publicly-available generative models paired with a diverse set of 90 textual prompts. Our findings demonstrate the promise of generative model recommendation as a novel personalization problem and the limitations of existing evaluation metrics. We highlight future directions for the RecSys community to advance towards generative recommender systems. Our code and dataset are available at https://github.com/MAPS-research/GEMRec.

A common and fundamental limitation of Generative AI (GenAI) is its propensity to hallucinate. While large language models (LLM) have taken the world by storm, without eliminating or at least reducing hallucinations, real-world GenAI systems may face challenges in user adoption. In the process of deploying an enterprise application that produces workflows based on natural language requirements, we devised a system leveraging Retrieval Augmented Generation (RAG) to greatly improve the quality of the structured output that represents such workflows. Thanks to our implementation of RAG, our proposed system significantly reduces hallucinations in the output and improves the generalization of our LLM in out-of-domain settings. In addition, we show that using a small, well-trained retriever encoder can reduce the size of the accompanying LLM, thereby making deployments of LLM-based systems less resource-intensive.

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our larger model BioGPT-Large achieves 81.0% on PubMedQA. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT.

Large Language Models (LLMs) have demonstrated remarkable success in various natural language processing and software engineering tasks, such as code generation. The LLMs are mainly utilized in the prompt-based zero/few-shot paradigm to guide the model in accomplishing the task. GPT-based models are one of the popular ones studied for tasks such as code comment generation or test generation. These tasks are `generative' tasks. However, there is limited research on the usage of LLMs for `non-generative' tasks such as classification using the prompt-based paradigm. In this preliminary exploratory study, we investigated the applicability of LLMs for Code Clone Detection (CCD), a non-generative task. By building a mono-lingual and cross-lingual CCD dataset derived from CodeNet, we first investigated two different prompts using ChatGPT to detect Type-4 code clones in Java-Java and Java-Ruby pairs in a zero-shot setting. We then conducted an analysis to understand the strengths and weaknesses of ChatGPT in CCD. ChatGPT surpasses the baselines in cross-language CCD attaining an F1-score of 0.877 and achieves comparable performance to fully fine-tuned models for mono-lingual CCD, with an F1-score of 0.878. Also, the prompt and the difficulty level of the problems has an impact on the performance of ChatGPT. Finally we provide insights and future directions based on our initial analysis

Every human has their own name, a fundamental aspect of their identity and cultural heritage. The name often conveys a wealth of information, including details about an individual's background, ethnicity, and, especially, their gender. By detecting gender through the analysis of names, researchers can unlock valuable insights into linguistic patterns and cultural norms, which can be applied to practical applications. Hence, this work presents a novel dataset for Japanese name gender detection comprising 64,139 full names in romaji, hiragana, and kanji forms, along with their biological genders. Moreover, we propose Gendec, a framework for gender detection from Japanese names that leverages diverse approaches, including traditional machine learning techniques or cutting-edge transfer learning models, to predict the gender associated with Japanese names accurately. Through a thorough investigation, the proposed framework is expected to be effective and serve potential applications in various domains.

A common architectural choice for deep metric learning is a convolutional neural network followed by global average pooling (GAP). Albeit simple, GAP is a highly effective way to aggregate information. One possible explanation for the effectiveness of GAP is considering each feature vector as representing a different semantic entity and GAP as a convex combination of them. Following this perspective, we generalize GAP and propose a learnable generalized sum pooling method (GSP). GSP improves GAP with two distinct abilities: i) the ability to choose a subset of semantic entities, effectively learning to ignore nuisance information, and ii) learning the weights corresponding to the importance of each entity. Formally, we propose an entropy-smoothed optimal transport problem and show that it is a strict generalization of GAP, i.e., a specific realization of the problem gives back GAP. We show that this optimization problem enjoys analytical gradients enabling us to use it as a direct learnable replacement for GAP. We further propose a zero-shot loss to ease the learning of GSP. We show the effectiveness of our method with extensive evaluations on 4 popular metric learning benchmarks. Code is available at: GSP-DML Framework

Despite the substantial success of Information Retrieval (IR) in various NLP tasks, most IR systems predominantly handle queries and corpora in natural language, neglecting the domain of code retrieval. Code retrieval is critically important yet remains under-explored, with existing methods and benchmarks inadequately representing the diversity of code in various domains and tasks. Addressing this gap, we present \name (Code Information Retrieval Benchmark), a robust and comprehensive benchmark specifically designed to assess code retrieval capabilities. \name comprises ten meticulously curated code datasets, spanning eight distinctive retrieval tasks across seven diverse domains. We first discuss the construction of \name and its diverse dataset composition. Further, we evaluate nine widely used retrieval models using \name, uncovering significant difficulties in performing code retrieval tasks even with state-of-the-art systems. To facilitate easy adoption and integration within existing research workflows, \name has been developed as a user-friendly Python framework, readily installable via pip. It shares same data schema as other popular benchmarks like MTEB and BEIR, enabling seamless cross-benchmark evaluations. Through \name, we aim to invigorate research in the code retrieval domain, providing a versatile benchmarking tool that encourages further development and exploration of code retrieval systems\url{ https://github.com/CoIR-team/coir}.

Language models of code (LMs) work well when the surrounding code in the vicinity of generation provides sufficient context. This is not true when it becomes necessary to use types or functionality defined in another module or library, especially those not seen during training. LMs suffer from limited awareness of such global context and end up hallucinating, e.g., using types defined in other files incorrectly. Recent work tries to overcome this issue by retrieving global information to augment the local context. However, this bloats the prompt or requires architecture modifications and additional training. Integrated development environments (IDEs) assist developers by bringing the global context at their fingertips using static analysis. We extend this assistance, enjoyed by developers, to the LMs. We propose a notion of monitors that use static analysis in the background to guide the decoding. Unlike a priori retrieval, static analysis is invoked iteratively during the entire decoding process, providing the most relevant suggestions on demand. We demonstrate the usefulness of our proposal by monitoring for type-consistent use of identifiers whenever an LM generates code for object dereference. To evaluate our approach, we curate PragmaticCode, a dataset of open-source projects with their development environments. On models of varying parameter scale, we show that monitor-guided decoding consistently improves the ability of an LM to not only generate identifiers that match the ground truth but also improves compilation rates and agreement with ground truth. We find that LMs with fewer parameters, when guided with our monitor, can outperform larger LMs. With monitor-guided decoding, SantaCoder-1.1B achieves better compilation rate and next-identifier match than the much larger text-davinci-003 model. The datasets and code will be released at https://aka.ms/monitors4codegen .

Large pre-trained code generation models, such as OpenAI Codex, can generate syntax- and function-correct code, making the coding of programmers more productive and our pursuit of artificial general intelligence closer. In this paper, we introduce CodeGeeX, a multilingual model with 13 billion parameters for code generation. CodeGeeX is pre-trained on 850 billion tokens of 23 programming languages as of June 2022. Our extensive experiments suggest that CodeGeeX outperforms multilingual code models of similar scale for both the tasks of code generation and translation on HumanEval-X. Building upon HumanEval (Python only), we develop the HumanEval-X benchmark for evaluating multilingual models by hand-writing the solutions in C++, Java, JavaScript, and Go. In addition, we build CodeGeeX-based extensions on Visual Studio Code, JetBrains, and Cloud Studio, generating 4.7 billion tokens for tens of thousands of active users per week. Our user study demonstrates that CodeGeeX can help to increase coding efficiency for 83.4% of its users. Finally, CodeGeeX is publicly accessible and in Sep. 2022, we open-sourced its code, model weights (the version of 850B tokens), API, extensions, and HumanEval-X at https://github.com/THUDM/CodeGeeX.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Code large language models mark a pivotal breakthrough in artificial intelligence. They are specifically crafted to understand and generate programming languages, significantly boosting the efficiency of coding development workflows. In this technical report, we present CodeShell-Base, a seven billion-parameter foundation model with 8K context length, showcasing exceptional proficiency in code comprehension. By incorporating Grouped-Query Attention and Rotary Positional Embedding into GPT-2, CodeShell-Base integrates the structural merits of StarCoder and CodeLlama and forms its unique architectural design. We then carefully built a comprehensive data pre-processing process, including similar data deduplication, perplexity-based data filtering, and model-based data filtering. Through this process, We have curated 100 billion high-quality pre-training data from GitHub. Benefiting from the high-quality data, CodeShell-Base outperforms CodeLlama in Humaneval after training on just 500 billion tokens (5 epochs). We have conducted extensive experiments across multiple language datasets, including Python, Java, and C++, and the results indicate that our model possesses robust foundational capabilities in code comprehension and generation.

While language models (LMs) have proven remarkably adept at generating code, many programs are challenging for LMs to generate using their parametric knowledge alone. Providing external contexts such as library documentation can facilitate generating accurate and functional code. Despite the success of retrieval-augmented generation (RAG) in various text-oriented tasks, its potential for improving code generation remains under-explored. In this work, we conduct a systematic, large-scale analysis by asking: in what scenarios can retrieval benefit code generation models? and what challenges remain? We first curate a comprehensive evaluation benchmark, CodeRAG-Bench, encompassing three categories of code generation tasks, including basic programming, open-domain, and repository-level problems. We aggregate documents from five sources for models to retrieve contexts: competition solutions, online tutorials, library documentation, StackOverflow posts, and GitHub repositories. We examine top-performing models on CodeRAG-Bench by providing contexts retrieved from one or multiple sources. While notable gains are made in final code generation by retrieving high-quality contexts across various settings, our analysis reveals room for improvement -- current retrievers still struggle to fetch useful contexts especially with limited lexical overlap, and generators fail to improve with limited context lengths or abilities to integrate additional contexts. We hope CodeRAG-Bench serves as an effective testbed to encourage further development of advanced code-oriented RAG methods.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

Grammatical Error Detection and Correction (GEC) tools have proven useful for native speakers and second language learners. Developing such tools requires a large amount of parallel, annotated data, which is unavailable for most languages. Synthetic data generation is a common practice to overcome the scarcity of such data. However, it is not straightforward for morphologically rich languages like Turkish due to complex writing rules that require phonological, morphological, and syntactic information. In this work, we present a flexible and extensible synthetic data generation pipeline for Turkish covering more than 20 expert-curated grammar and spelling rules (a.k.a., writing rules) implemented through complex transformation functions. Using this pipeline, we derive 130,000 high-quality parallel sentences from professionally edited articles. Additionally, we create a more realistic test set by manually annotating a set of movie reviews. We implement three baselines formulating the task as i) neural machine translation, ii) sequence tagging, and iii) prefix tuning with a pretrained decoder-only model, achieving strong results. Furthermore, we perform exhaustive experiments on out-of-domain datasets to gain insights on the transferability and robustness of the proposed approaches. Our results suggest that our corpus, GECTurk, is high-quality and allows knowledge transfer for the out-of-domain setting. To encourage further research on Turkish GEC, we release our datasets, baseline models, and the synthetic data generation pipeline at https://github.com/GGLAB-KU/gecturk.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Multi-hop QA (MHQA) involves step-by-step reasoning to answer complex questions and find multiple relevant supporting facts. However, Existing large language models'(LLMs) reasoning ability in multi-hop question answering remains exploration, which is inadequate in answering multi-hop questions. Moreover, it is unclear whether LLMs follow a desired reasoning chain to reach the right final answer. In this paper, we propose a generative question decomposition method (GenDec) from the perspective of explainable QA by generating independent and complete sub-questions based on incorporating additional extracted evidence for enhancing LLMs' reasoning ability in RAG. To demonstrate the impact, generalization, and robustness of Gendec, we conduct two experiments, the first is combining GenDec with small QA systems on paragraph retrieval and QA tasks. We secondly examine the reasoning capabilities of various state-of-the-art LLMs including GPT-4 and GPT-3.5 combined with GenDec. We experiment on the HotpotQA, 2WikihopMultiHopQA, MuSiQue, and PokeMQA datasets.

Neural Architecture Search (NAS) has been a source of dramatic improvements in neural network design, with recent results meeting or exceeding the performance of hand-tuned architectures. However, our understanding of how to represent the search space for neural net architectures and how to search that space efficiently are both still in their infancy. We have performed an in-depth analysis to identify limitations in a widely used search space and a recent architecture search method, Differentiable Architecture Search (DARTS). These findings led us to introduce novel network blocks with a more general, balanced, and consistent design; a better-optimized Cosine Power Annealing learning rate schedule; and other improvements. Our resulting sharpDARTS search is 50% faster with a 20-30% relative improvement in final model error on CIFAR-10 when compared to DARTS. Our best single model run has 1.93% (1.98+/-0.07) validation error on CIFAR-10 and 5.5% error (5.8+/-0.3) on the recently released CIFAR-10.1 test set. To our knowledge, both are state of the art for models of similar size. This model also generalizes competitively to ImageNet at 25.1% top-1 (7.8% top-5) error. We found improvements for existing search spaces but does DARTS generalize to new domains? We propose Differentiable Hyperparameter Grid Search and the HyperCuboid search space, which are representations designed to leverage DARTS for more general parameter optimization. Here we find that DARTS fails to generalize when compared against a human's one shot choice of models. We look back to the DARTS and sharpDARTS search spaces to understand why, and an ablation study reveals an unusual generalization gap. We finally propose Max-W regularization to solve this problem, which proves significantly better than the handmade design. Code will be made available.

Query Reformulation (QR) is a set of techniques used to transform a user's original search query to a text that better aligns with the user's intent and improves their search experience. Recently, zero-shot QR has been a promising approach due to its ability to exploit knowledge inherent in large language models. Inspired by the success of ensemble prompting strategies which have benefited other tasks, we investigate if they can improve query reformulation. In this context, we propose two ensemble-based prompting techniques, GenQREnsemble and GenQRFusion which leverage paraphrases of a zero-shot instruction to generate multiple sets of keywords to improve retrieval performance ultimately. We further introduce their post-retrieval variants to incorporate relevance feedback from a variety of sources, including an oracle simulating a human user and a "critic" LLM. We demonstrate that an ensemble of query reformulations can improve retrieval effectiveness by up to 18% on nDCG@10 in pre-retrieval settings and 9% on post-retrieval settings on multiple benchmarks, outperforming all previously reported SOTA results. We perform subsequent analyses to investigate the effects of feedback documents, incorporate domain-specific instructions, filter reformulations, and generate fluent reformulations that might be more beneficial to human searchers. Together, the techniques and the results presented in this paper establish a new state of the art in automated query reformulation for retrieval and suggest promising directions for future research.

Over the last several decades, software has been woven into the fabric of every aspect of our society. As software development surges and code infrastructure of enterprise applications ages, it is now more critical than ever to increase software development productivity and modernize legacy applications. Advances in deep learning and machine learning algorithms have enabled numerous breakthroughs, motivating researchers to leverage AI techniques to improve software development efficiency. Thus, the fast-emerging research area of AI for Code has garnered new interest and gathered momentum. In this paper, we present a large-scale dataset CodeNet, consisting of over 14 million code samples and about 500 million lines of code in 55 different programming languages, which is aimed at teaching AI to code. In addition to its large scale, CodeNet has a rich set of high-quality annotations to benchmark and help accelerate research in AI techniques for a variety of critical coding tasks, including code similarity and classification, code translation between a large variety of programming languages, and code performance (runtime and memory) improvement techniques. Additionally, CodeNet provides sample input and output test sets for 98.5% of the code samples, which can be used as an oracle for determining code correctness and potentially guide reinforcement learning for code quality improvements. As a usability feature, we provide several pre-processing tools in CodeNet to transform source code into representations that can be readily used as inputs into machine learning models. Results of code classification and code similarity experiments using the CodeNet dataset are provided as a reference. We hope that the scale, diversity and rich, high-quality annotations of CodeNet will offer unprecedented research opportunities at the intersection of AI and Software Engineering.

Large-scale embedding-based retrieval (EBR) is the cornerstone of search-related industrial applications. Given a user query, the system of EBR aims to identify relevant information from a large corpus of documents that may be tens or hundreds of billions in size. The storage and computation turn out to be expensive and inefficient with massive documents and high concurrent queries, making it difficult to further scale up. To tackle the challenge, we propose a binary embedding-based retrieval (BEBR) engine equipped with a recurrent binarization algorithm that enables customized bits per dimension. Specifically, we compress the full-precision query and document embeddings, formulated as float vectors in general, into a composition of multiple binary vectors using a lightweight transformation model with residual multilayer perception (MLP) blocks. We can therefore tailor the number of bits for different applications to trade off accuracy loss and cost savings. Importantly, we enable task-agnostic efficient training of the binarization model using a new embedding-to-embedding strategy. We also exploit the compatible training of binary embeddings so that the BEBR engine can support indexing among multiple embedding versions within a unified system. To further realize efficient search, we propose Symmetric Distance Calculation (SDC) to achieve lower response time than Hamming codes. We successfully employed the introduced BEBR to Tencent products, including Sogou, Tencent Video, QQ World, etc. The binarization algorithm can be seamlessly generalized to various tasks with multiple modalities. Extensive experiments on offline benchmarks and online A/B tests demonstrate the efficiency and effectiveness of our method, significantly saving 30%~50% index costs with almost no loss of accuracy at the system level.

LLM agents enhanced by tree search algorithms have yielded notable performances in code generation. However, current search algorithms in this domain suffer from low search quality due to several reasons: 1) Ineffective design of the search space for the high-reasoning demands of code generation tasks, 2) Inadequate integration of code feedback with the search algorithm, and 3) Poor handling of negative feedback during the search, leading to reduced search efficiency and quality. To address these challenges, we propose to search for the reasoning process of the code and use the detailed feedback of code execution to refine erroneous thoughts during the search. In this paper, we introduce RethinkMCTS, which employs the Monte Carlo Tree Search (MCTS) algorithm to conduct thought-level searches before generating code, thereby exploring a wider range of strategies. More importantly, we construct verbal feedback from fine-grained code execution feedback to refine erroneous thoughts during the search. This ensures that the search progresses along the correct reasoning paths, thus improving the overall search quality of the tree by leveraging execution feedback. Through extensive experiments, we demonstrate that RethinkMCTS outperforms previous search-based and feedback-based code generation baselines. On the HumanEval dataset, it improves the pass@1 of GPT-3.5-turbo from 70.12 to 89.02 and GPT-4o-mini from 87.20 to 94.51. It effectively conducts more thorough exploration through thought-level searches and enhances the search quality of the entire tree by incorporating rethink operation.

Query reformulation is a well-known problem in Information Retrieval (IR) aimed at enhancing single search successful completion rate by automatically modifying user's input query. Recent methods leverage Large Language Models (LLMs) to improve query reformulation, but often generate limited and redundant expansions, potentially constraining their effectiveness in capturing diverse intents. In this paper, we propose GenCRF: a Generative Clustering and Reformulation Framework to capture diverse intentions adaptively based on multiple differentiated, well-generated queries in the retrieval phase for the first time. GenCRF leverages LLMs to generate variable queries from the initial query using customized prompts, then clusters them into groups to distinctly represent diverse intents. Furthermore, the framework explores to combine diverse intents query with innovative weighted aggregation strategies to optimize retrieval performance and crucially integrates a novel Query Evaluation Rewarding Model (QERM) to refine the process through feedback loops. Empirical experiments on the BEIR benchmark demonstrate that GenCRF achieves state-of-the-art performance, surpassing previous query reformulation SOTAs by up to 12% on nDCG@10. These techniques can be adapted to various LLMs, significantly boosting retriever performance and advancing the field of Information Retrieval.

Current model quantization methods have shown their promising capability in reducing storage space and computation complexity. However, due to the diversity of quantization forms supported by different hardware, one limitation of existing solutions is that usually require repeated optimization for different scenarios. How to construct a model with flexible quantization forms has been less studied. In this paper, we explore a one-shot network quantization regime, named Elastic Quantization Neural Networks (EQ-Net), which aims to train a robust weight-sharing quantization supernet. First of all, we propose an elastic quantization space (including elastic bit-width, granularity, and symmetry) to adapt to various mainstream quantitative forms. Secondly, we propose the Weight Distribution Regularization Loss (WDR-Loss) and Group Progressive Guidance Loss (GPG-Loss) to bridge the inconsistency of the distribution for weights and output logits in the elastic quantization space gap. Lastly, we incorporate genetic algorithms and the proposed Conditional Quantization-Aware Accuracy Predictor (CQAP) as an estimator to quickly search mixed-precision quantized neural networks in supernet. Extensive experiments demonstrate that our EQ-Net is close to or even better than its static counterparts as well as state-of-the-art robust bit-width methods. Code can be available at https://github.com/xuke225/EQ-Net.git{https://github.com/xuke225/EQ-Net}.

Although large pre-trained models of code have delivered significant advancements in various code processing tasks, there is an impediment to the wide and fluent adoption of these powerful models in software developers' daily workflow: these large models consume hundreds of megabytes of memory and run slowly on personal devices, which causes problems in model deployment and greatly degrades the user experience. It motivates us to propose Compressor, a novel approach that can compress the pre-trained models of code into extremely small models with negligible performance sacrifice. Our proposed method formulates the design of tiny models as simplifying the pre-trained model architecture: searching for a significantly smaller model that follows an architectural design similar to the original pre-trained model. Compressor proposes a genetic algorithm (GA)-based strategy to guide the simplification process. Prior studies found that a model with higher computational cost tends to be more powerful. Inspired by this insight, the GA algorithm is designed to maximize a model's Giga floating-point operations (GFLOPs), an indicator of the model computational cost, to satisfy the constraint of the target model size. Then, we use the knowledge distillation technique to train the small model: unlabelled data is fed into the large model and the outputs are used as labels to train the small model. We evaluate Compressor with two state-of-the-art pre-trained models, i.e., CodeBERT and GraphCodeBERT, on two important tasks, i.e., vulnerability prediction and clone detection. We use our method to compress pre-trained models to a size (3 MB), which is 160times smaller than the original size. The results show that compressed CodeBERT and GraphCodeBERT are 4.31times and 4.15times faster than the original model at inference, respectively. More importantly, ...

Open-domain question answering (QA) tasks usually require the retrieval of relevant information from a large corpus to generate accurate answers. We propose a novel approach called Generator-Retriever-Generator (GRG) that combines document retrieval techniques with a large language model (LLM), by first prompting the model to generate contextual documents based on a given question. In parallel, a dual-encoder network retrieves documents that are relevant to the question from an external corpus. The generated and retrieved documents are then passed to the second LLM, which generates the final answer. By combining document retrieval and LLM generation, our approach addresses the challenges of open-domain QA, such as generating informative and contextually relevant answers. GRG outperforms the state-of-the-art generate-then-read and retrieve-then-read pipelines (GENREAD and RFiD) improving their performance by at least by +5.2, +4.2, and +1.6 on TriviaQA, NQ, and WebQ datasets, respectively. We provide code, datasets, and checkpoints at https://github.com/abdoelsayed2016/GRG.

Semantic search for candidate retrieval is an important yet neglected problem in retrieval-based Chatbots, which aims to select a bunch of candidate responses efficiently from a large pool. The existing bottleneck is to ensure the model architecture having two points: 1) rich interactions between a query and a response to produce query-relevant responses; 2) ability of separately projecting the query and the response into latent spaces to apply efficiently in semantic search during online inference. To tackle this problem, we propose a novel approach, called Multitask-based Semantic Search Neural Network (MSSNN) for candidate retrieval, which accomplishes query-response interactions through multi-tasks. The method employs a Seq2Seq modeling task to learn a good query encoder, and then performs a word prediction task to build response embeddings, finally conducts a simple matching model to form the dot-product scorer. Experimental studies have demonstrated the potential of the proposed approach.

Despite remarkable progress achieved, most neural architecture search (NAS) methods focus on searching for one single accurate and robust architecture. To further build models with better generalization capability and performance, model ensemble is usually adopted and performs better than stand-alone models. Inspired by the merits of model ensemble, we propose to search for multiple diverse models simultaneously as an alternative way to find powerful models. Searching for ensembles is non-trivial and has two key challenges: enlarged search space and potentially more complexity for the searched model. In this paper, we propose a one-shot neural ensemble architecture search (NEAS) solution that addresses the two challenges. For the first challenge, we introduce a novel diversity-based metric to guide search space shrinking, considering both the potentiality and diversity of candidate operators. For the second challenge, we enable a new search dimension to learn layer sharing among different models for efficiency purposes. The experiments on ImageNet clearly demonstrate that our solution can improve the supernet's capacity of ranking ensemble architectures, and further lead to better search results. The discovered architectures achieve superior performance compared with state-of-the-arts such as MobileNetV3 and EfficientNet families under aligned settings. Moreover, we evaluate the generalization ability and robustness of our searched architecture on the COCO detection benchmark and achieve a 3.1% improvement on AP compared with MobileNetV3. Codes and models are available at https://github.com/researchmm/NEAS.

Retrieval-Augmented Generation (RAG) enhances coding tasks by incorporating retrieved code examples into prompts. However, lengthy prompts, often exceeding tens of thousands of tokens, introduce challenges related to limited context windows of language models (LMs) and high computational costs. Existing prompt compression techniques focus on natural language, lacking tailored solutions for code. To address the gap, we propose CodePromptZip, a framework that compresses code examples before integrating into RAG workflows. Our framework employs a type-aware, priority-driven strategy to construct training samples for training code compression model. By using program analysis, we identify token types (e.g., Identifier) and perform ablation analysis to rank their removal priorities based on their impact on task performance. We then train a small LM as the compressor on these samples, enabling flexible compression conditioned on specified ratios while minimizing performance degradation. Specially, the compressor is augmented with a copy mechanism, allowing tokens to be directly copied from the original code snippets. Evaluation results show that CodePromptZip surpasses SOTA entropy-based and distillation-based baselines, improving by 23.4%, 28.7%, and 8.7% over the best baseline for Assertion Generation, Bugs2Fix, and Code Suggestion, respectively.

We propose Generation-Augmented Retrieval (GAR) for answering open-domain questions, which augments a query through text generation of heuristically discovered relevant contexts without external resources as supervision. We demonstrate that the generated contexts substantially enrich the semantics of the queries and GAR with sparse representations (BM25) achieves comparable or better performance than state-of-the-art dense retrieval methods such as DPR. We show that generating diverse contexts for a query is beneficial as fusing their results consistently yields better retrieval accuracy. Moreover, as sparse and dense representations are often complementary, GAR can be easily combined with DPR to achieve even better performance. GAR achieves state-of-the-art performance on Natural Questions and TriviaQA datasets under the extractive QA setup when equipped with an extractive reader, and consistently outperforms other retrieval methods when the same generative reader is used.

Large Language Models (LLMs) have shown great success in code generation. LLMs take as the input a prompt and output the code. A key question is how to make prompts (i.e., Prompting Techniques). Existing prompting techniques are designed for natural language generation and have low accuracy in code generation. In this paper, we propose a new prompting technique named AceCoder. Our motivation is that code generation meets two unique challenges (i.e., requirement understanding and code implementation). AceCoder contains two novel mechanisms (i.e., guided code generation and example retrieval) to solve these challenges. (1) Guided code generation asks LLMs first to analyze requirements and output an intermediate preliminary (e.g., test cases). The preliminary is used to clarify requirements and tell LLMs "what to write". (2) Example retrieval selects similar programs as examples in prompts, which provide lots of relevant content (e.g., algorithms, APIs) and teach LLMs "how to write". We apply AceCoder to three LLMs (e.g., Codex) and evaluate it on three public benchmarks using the Pass@k. Results show that AceCoder can significantly improve the performance of LLMs on code generation. (1) In terms of Pass@1, AceCoder outperforms the state-of-the-art baseline by up to 56.4% in MBPP, 70.7% in MBJP, and 88.4% in MBJSP. (2) AceCoder is effective in LLMs with different sizes (i.e., 6B to 13B) and different languages (i.e., Python, Java, and JavaScript). (3) Human evaluation shows human developers prefer programs from AceCoder.

Recently the retrieval-augmented generation (RAG) paradigm has raised much attention for its potential in incorporating external knowledge into large language models (LLMs) without further training. While widely explored in natural language applications, its utilization in code generation remains under-explored. In this paper, we introduce Active Retrieval in Knowledge Soup (ARKS), an advanced strategy for generalizing large language models for code. In contrast to relying on a single source, we construct a knowledge soup integrating web search, documentation, execution feedback, and evolved code snippets. We employ an active retrieval strategy that iteratively refines the query and updates the knowledge soup. To assess the performance of ARKS, we compile a new benchmark comprising realistic coding problems associated with frequently updated libraries and long-tail programming languages. Experimental results on ChatGPT and CodeLlama demonstrate a substantial improvement in the average execution accuracy of ARKS on LLMs. The analysis confirms the effectiveness of our proposed knowledge soup and active retrieval strategies, offering rich insights into the construction of effective retrieval-augmented code generation (RACG) pipelines. Our model, code, and data are available at https://arks-codegen.github.io.

A code generation model generates code by taking a prompt from a code comment, existing code, or a combination of both. Although code generation models (e.g. GitHub Copilot) are increasingly being adopted in practice, it is unclear whether they can successfully be used for unit test generation without fine-tuning. We investigated how well three generative models (Codex, GPT-3.5-Turbo, and StarCoder) can generate test cases to fill this gap. We used two benchmarks (HumanEval and Evosuite SF110) to investigate the context generation's effect in the unit test generation process. We evaluated the models based on compilation rates, test correctness, coverage, and test smells. We found that the Codex model achieved above 80% coverage for the HumanEval dataset, but no model had more than 2% coverage for the EvoSuite SF110 benchmark. The generated tests also suffered from test smells, such as Duplicated Asserts and Empty Tests.

Program synthesis with language models (LMs) has unlocked a large set of reasoning abilities; code-tuned LMs have proven adept at generating programs that solve a wide variety of algorithmic symbolic manipulation tasks (e.g. word concatenation). However, not all reasoning tasks are easily expressible as code, e.g. tasks involving commonsense reasoning, moral decision-making, and sarcasm understanding. Our goal is to extend an LM's program synthesis skills to such tasks and evaluate the results via pseudo-programs, namely Python programs where some leaf function calls are left undefined. To that end, we propose, Code Generation and Emulated EXecution (CoGEX). CoGEX works by (1) training LMs to generate their own pseudo-programs, (2) teaching them to emulate their generated program's execution, including those leaf functions, allowing the LM's knowledge to fill in the execution gaps; and (3) using them to search over many programs to find an optimal one. To adapt the CoGEX model to a new task, we introduce a method for performing program search to find a single program whose pseudo-execution yields optimal performance when applied to all the instances of a given dataset. We show that our approach yields large improvements compared to standard in-context learning approaches on a battery of tasks, both algorithmic and soft reasoning. This result thus demonstrates that code synthesis can be applied to a much broader class of problems than previously considered. Our released dataset, fine-tuned models, and implementation can be found at https://github.com/nweir127/CoGEX.

G-code (Geometric code) or RS-274 is the most widely used computer numerical control (CNC) and 3D printing programming language. G-code provides machine instructions for the movement of the 3D printer, especially for the nozzle, stage, and extrusion of material for extrusion-based additive manufacturing. Currently there does not exist a large repository of curated CAD models along with their corresponding G-code files for additive manufacturing. To address this issue, we present SLICE-100K, a first-of-its-kind dataset of over 100,000 G-code files, along with their tessellated CAD model, LVIS (Large Vocabulary Instance Segmentation) categories, geometric properties, and renderings. We build our dataset from triangulated meshes derived from Objaverse-XL and Thingi10K datasets. We demonstrate the utility of this dataset by finetuning GPT-2 on a subset of the dataset for G-code translation from a legacy G-code format (Sailfish) to a more modern, widely used format (Marlin). SLICE-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

The success of the GPT series proves that GPT can extract general information from sequences, thereby benefiting all downstream tasks. This motivates us to use pre-trained models to explore the hidden information in DNA sequences. However, data and task requirements in DNA sequence analysis are complexity and diversity as DNA relevant data includes different types of information, such as sequences, expression levels, etc, while there is currently no model specifically designed for these characteristics. Hereby, we present DNAGPT, a generalized foundation model pre-trained on over 10 billion base pairs from 9 species which can be fine-tuned for any DNA sequence analysis task. Our model can simultaneously process or output DNA sequences and numbers. In addition, our unique token design allows users to design prompts according to their own task requirements, making it applicable to any type of task. We have evaluated our model on classification, regression, and generation tasks. We demonstrate that DNAGPT benefits from pre-training, and therefore can bring performance gains to any downstream task. Our model is not only a new attempt in the field of genomes analysis, but also provides a new direction for the application of foundation models in biology.

Grammatical error correction (GEC) is the task of correcting typos, spelling, punctuation and grammatical issues in text. Approaching the problem as a sequence-to-sequence task, we compare the use of a common subword unit vocabulary and byte-level encoding. Initial synthetic training data is created using an error-generating pipeline, and used for finetuning two subword-level models and one byte-level model. Models are then finetuned further on hand-corrected error corpora, including texts written by children, university students, dyslexic and second-language writers, and evaluated over different error types and origins. We show that a byte-level model enables higher correction quality than a subword approach, not only for simple spelling errors, but also for more complex semantic, stylistic and grammatical issues. In particular, initial training on synthetic corpora followed by finetuning on a relatively small parallel corpus of real-world errors helps the byte-level model correct a wide range of commonly occurring errors. Our experiments are run for the Icelandic language but should hold for other similar languages, particularly morphologically rich ones.

Text embedding models play a crucial role in natural language processing, particularly in information retrieval, and their importance is further highlighted with the recent utilization of RAG (Retrieval- Augmented Generation). This study presents an efficient fine-tuning methodology encompassing data selection, loss function, and model architecture to enhance the information retrieval performance of pre-trained text embedding models. In particular, this study proposes a novel Contrastive Learning Penalty function that overcomes the limitations of existing Contrastive Learning. The proposed methodology achieves significant performance improvements over existing methods in document retrieval tasks. This study is expected to contribute to improving the performance of information retrieval systems through fine-tuning of text embedding models. The code for this study can be found at https://github.com/CreaLabs/Enhanced-BGE-M3-with-CLP-and-MoE, and the best-performing model can be found at https://huggingface.co/CreaLabs.

In this work, we make the first attempt to evaluate LLMs in a more challenging code generation scenario, i.e. class-level code generation. We first manually construct the first class-level code generation benchmark ClassEval of 100 class-level Python code generation tasks with approximately 500 person-hours. Based on it, we then perform the first study of 11 state-of-the-art LLMs on class-level code generation. Based on our results, we have the following main findings. First, we find that all existing LLMs show much worse performance on class-level code generation compared to on standalone method-level code generation benchmarks like HumanEval; and the method-level coding ability cannot equivalently reflect the class-level coding ability among LLMs. Second, we find that GPT-4 and GPT-3.5 still exhibit dominate superior than other LLMs on class-level code generation, and the second-tier models includes Instruct-Starcoder, Instruct-Codegen, and Wizardcoder with very similar performance. Third, we find that generating the entire class all at once (i.e. holistic generation strategy) is the best generation strategy only for GPT-4 and GPT-3.5, while method-by-method generation (i.e. incremental and compositional) is better strategies for the other models with limited ability of understanding long instructions and utilizing the middle information. Lastly, we find the limited model ability of generating method-dependent code and discuss the frequent error types in generated classes. Our benchmark is available at https://github.com/FudanSELab/ClassEval.

The rapid development of generative AI (GenAI) models in computer vision necessitates effective evaluation methods to ensure their quality and fairness. Existing tools primarily focus on dataset quality assurance and model explainability, leaving a significant gap in GenAI output evaluation during model development. Current practices often depend on developers' subjective visual assessments, which may lack scalability and generalizability. This paper bridges this gap by conducting a formative study with GenAI model developers in an industrial setting. Our findings led to the development of GenLens, a visual analytic interface designed for the systematic evaluation of GenAI model outputs during the early stages of model development. GenLens offers a quantifiable approach for overviewing and annotating failure cases, customizing issue tags and classifications, and aggregating annotations from multiple users to enhance collaboration. A user study with model developers reveals that GenLens effectively enhances their workflow, evidenced by high satisfaction rates and a strong intent to integrate it into their practices. This research underscores the importance of robust early-stage evaluation tools in GenAI development, contributing to the advancement of fair and high-quality GenAI models.

Document retrieval techniques form the foundation for the development of large-scale information systems. The prevailing methodology is to construct a bi-encoder and compute the semantic similarity. However, such scalar similarity is difficult to reflect enough information and impedes our comprehension of the retrieval results. In addition, this computational process mainly emphasizes the global semantics and ignores the fine-grained semantic relationship between the query and the complex text in the document. In this paper, we propose a new method called Generation Augmented Retrieval (GeAR) that incorporates well-designed fusion and decoding modules. This enables GeAR to generate the relevant text from documents based on the fused representation of the query and the document, thus learning to "focus on" the fine-grained information. Also when used as a retriever, GeAR does not add any computational burden over bi-encoders. To support the training of the new framework, we have introduced a pipeline to efficiently synthesize high-quality data by utilizing large language models. GeAR exhibits competitive retrieval and localization performance across diverse scenarios and datasets. Moreover, the qualitative analysis and the results generated by GeAR provide novel insights into the interpretation of retrieval results. The code, data, and models will be released after completing technical review to facilitate future research.

Information Extraction (IE) aims to extract structural knowledge (e.g., entities, relations, events) from natural language texts, which brings challenges to existing methods due to task-specific schemas and complex text expressions. Code, as a typical kind of formalized language, is capable of describing structural knowledge under various schemas in a universal way. On the other hand, Large Language Models (LLMs) trained on both codes and texts have demonstrated powerful capabilities of transforming texts into codes, which provides a feasible solution to IE tasks. Therefore, in this paper, we propose a universal retrieval-augmented code generation framework based on LLMs, called Code4UIE, for IE tasks. Specifically, Code4UIE adopts Python classes to define task-specific schemas of various structural knowledge in a universal way. By so doing, extracting knowledge under these schemas can be transformed into generating codes that instantiate the predefined Python classes with the information in texts. To generate these codes more precisely, Code4UIE adopts the in-context learning mechanism to instruct LLMs with examples. In order to obtain appropriate examples for different tasks, Code4UIE explores several example retrieval strategies, which can retrieve examples semantically similar to the given texts. Extensive experiments on five representative IE tasks across nine datasets demonstrate the effectiveness of the Code4UIE framework.

Named Entity Recognition (NER) models play a crucial role in various NLP tasks, including information extraction (IE) and text understanding. In academic writing, references to machine learning models and datasets are fundamental components of various computer science publications and necessitate accurate models for identification. Despite the advancements in NER, existing ground truth datasets do not treat fine-grained types like ML model and model architecture as separate entity types, and consequently, baseline models cannot recognize them as such. In this paper, we release a corpus of 100 manually annotated full-text scientific publications and a first baseline model for 10 entity types centered around ML models and datasets. In order to provide a nuanced understanding of how ML models and datasets are mentioned and utilized, our dataset also contains annotations for informal mentions like "our BERT-based model" or "an image CNN". You can find the ground truth dataset and code to replicate model training at https://data.gesis.org/gsap/gsap-ner.

To extend the scope of coding queries to more realistic settings, we propose ODEX, the first Open-Domain EXecution-based natural language (NL) to Python code generation dataset. ODEX has 945 NL-Code pairs spanning 79 diverse libraries, along with 1,707 human-written test cases for execution. Our NL-Code pairs are harvested from StackOverflow forums to encourage natural and practical coding queries. Moreover, ODEX supports four natural languages as intents, in English, Spanish, Japanese, and Russian. ODEX unveils intriguing behavioral differences among top-performing code language models (LM). While CODEX achieves better overall results, CODEGEN improves effectively via scaling -- CODEGEN 6.1B performs comparably with CODEX 12B. Both models show substantial gaps between open and closed domains, but CODEGEN gaps tend to decrease with model size while CODEX gaps increase. We release ODEX to facilitate research into open-domain problems for the code generation community.

Retrieval-Augmented Generation (RAG) has become ubiquitous when deploying Large Language Models (LLMs), as it can address typical limitations such as generating hallucinated or outdated information. However, when building real-world RAG applications, practical issues arise. First, the retrieved information is generally domain-specific. Since it is computationally expensive to fine-tune LLMs, it is more feasible to fine-tune the retriever to improve the quality of the data included in the LLM input. Second, as more applications are deployed in the same real-world system, one cannot afford to deploy separate retrievers. Moreover, these RAG applications normally retrieve different kinds of data. Our solution is to instruction fine-tune a small retriever encoder on a variety of domain-specific tasks to allow us to deploy one encoder that can serve many use cases, thereby achieving low-cost, scalability, and speed. We show how this encoder generalizes to out-of-domain settings as well as to an unseen retrieval task on real-world enterprise use cases.

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning since we are expecting from deep learning a superhuman intelligence that explores beyond our knowledge to interpret the genome. A powerful deep learning model should rely on insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with a proper deep architecture, and remark on practical considerations of developing modern deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research, as well as pointing out potential opportunities and obstacles for future genomics applications.

Knowledge-intensive language tasks (KILTs) benefit from retrieving high-quality relevant contexts from large external knowledge corpora. Learning task-specific retrievers that return relevant contexts at an appropriate level of semantic granularity, such as a document retriever, passage retriever, sentence retriever, and entity retriever, may help to achieve better performance on the end-to-end task. But a task-specific retriever usually has poor generalization ability to new domains and tasks, and it may be costly to deploy a variety of specialised retrievers in practice. We propose a unified generative retriever (UGR) that combines task-specific effectiveness with robust performance over different retrieval tasks in KILTs. To achieve this goal, we make two major contributions: (i) To unify different retrieval tasks into a single generative form, we introduce an n-gram-based identifier for relevant contexts at different levels of granularity in KILTs. And (ii) to address different retrieval tasks with a single model, we employ a prompt learning strategy and investigate three methods to design prompt tokens for each task. In this way, the proposed UGR model can not only share common knowledge across tasks for better generalization, but also perform different retrieval tasks effectively by distinguishing task-specific characteristics. We train UGR on a heterogeneous set of retrieval corpora with well-designed prompts in a supervised and multi-task fashion. Experimental results on the KILT benchmark demonstrate the effectiveness of UGR on in-domain datasets, out-of-domain datasets, and unseen tasks.

Decoder transformers have continued increasing in scale reaching hundreds of billions of parameters. Due to their scale the same decoder sets state-of-the-art results on various language tasks via prompting or fine-tuning. Yet, these large foundation models remain unusable for the related fields of semantic search and sentence embeddings. This prevents possibly new state-of-the-art results and forces organizations to train and maintain separate models. To this end, we propose SGPT to use decoders for sentence embeddings and semantic search via prompting or fine-tuning. At 5.8 billion parameters SGPT improves on the previously best sentence embeddings by a margin of 7% and outperforms a concurrent method with 175 billion parameters as measured on the BEIR search benchmark. Code, models and result files are freely available at https://github.com/Muennighoff/sgpt.

Recent advancements in the field of natural language generation have facilitated the use of large language models to assess the quality of generated text. Although these models have shown promising results in tasks such as machine translation and summarization, their applicability in code generation tasks remains limited without human involvement. The complexity of programming concepts required for such tasks makes it difficult to develop evaluation metrics that align with human judgment. Token-matching-based metrics, such as BLEU, have demonstrated weak correlations with human practitioners in code generation tasks. Moreover, the utilization of human-written test suites to evaluate functional correctness can be challenging in domains with low resources. To overcome these obstacles, we propose a new evaluation framework based on the GPT-3.5 (GPT-3.5-turbo), for code generation assessments. Our framework addresses the limitations of existing approaches by achieving superior correlations with functional correctness and human preferences, without the need for test oracles or references. We evaluate the efficacy of our framework on two different tasks and four programming languages, comparing its performance with the state-of-the-art CodeBERTScore metric, which relies on a pre-trained model. Our results demonstrate that our framework surpasses CodeBERTScore, delivering high levels of accuracy and consistency across various programming languages and tasks. We also make our evaluation framework and datasets available to the public at https://github.com/terryyz/llm-code-eval, encouraging further research in the evaluation of code generation.

This paper introduces Neurocache, an approach to extend the effective context size of large language models (LLMs) using an external vector cache to store its past states. Like recent vector retrieval approaches, Neurocache uses an efficient k-nearest-neighbor (kNN) algorithm to retrieve relevant past states and incorporate them into the attention process. Neurocache improves upon previous methods by (1) storing compressed states, which reduces cache size; (2) performing a single retrieval operation per token which increases inference speed; and (3) extending the retrieval window to neighboring states, which improves both language modeling and downstream task accuracy. Our experiments show the effectiveness of Neurocache both for models trained from scratch and for pre-trained models such as Llama2-7B and Mistral-7B when enhanced with the cache mechanism. We also compare Neurocache with text retrieval methods and show improvements in single-document question-answering and few-shot learning tasks. We made the source code available under: https://github.com/alisafaya/neurocache

When a human requests an LLM to complete a coding task using functionality from a large code repository, how do we provide context from the repo to the LLM? One approach is to add the entire repo to the LLM's context window. However, most tasks involve only fraction of symbols from a repo, longer contexts are detrimental to the LLM's reasoning abilities, and context windows are not unlimited. Alternatively, we could emulate the human ability to navigate a large repo, pick out the right functionality, and form a plan to solve the task. We propose MutaGReP (Mutation-guided Grounded Repository Plan Search), an approach to search for plans that decompose a user request into natural language steps grounded in the codebase. MutaGReP performs neural tree search in plan space, exploring by mutating plans and using a symbol retriever for grounding. On the challenging LongCodeArena benchmark, our plans use less than 5% of the 128K context window for GPT-4o but rival the coding performance of GPT-4o with a context window filled with the repo. Plans produced by MutaGReP allow Qwen 2.5 Coder 32B and 72B to match the performance of GPT-4o with full repo context and enable progress on the hardest LongCodeArena tasks. Project page: zaidkhan.me/MutaGReP

Programming with Generative AI (GenAI) models is a type of Neurosymbolic programming and has seen tremendous adoption across many domains. However, leveraging GenAI models in code today can be complex, counter-intuitive and often require specialized frameworks, leading to increased complexity. This is because it is currently unclear as to the right abstractions through which we should marry GenAI models with the nature of traditional programming code constructs. In this paper, we introduce a set of novel abstractions to help bridge the gap between Neuro- and symbolic programming. We introduce Meaning, a new specialized type that represents the underlying semantic value of traditional types (e.g., string). We make the case that GenAI models, LLMs in particular, should be reasoned as a meaning-type wrapped code construct at the language level. We formulate the problem of translation between meaning and traditional types and propose Automatic Meaning-Type Transformation (A-MTT), a runtime feature that abstracts this translation away from the developers by automatically converting between M eaning and types at the interface of LLM invocation. Leveraging this new set of code constructs and OTT, we demonstrate example implementation of neurosymbolic programs that seamlessly utilizes LLMs to solve problems in place of potentially complex traditional programming logic.

Prediction sets have recently been shown to be a promising strategy for quantifying the uncertainty of deep neural networks in a way that provides theoretical guarantees. However, existing techniques have largely targeted settings where the space of labels is simple, so prediction sets can be arbitrary subsets of labels. For structured prediction problems where the space of labels is exponential in size, even prediction sets containing a small fraction of all labels can be exponentially large. In the context of code generation, we propose a solution that considers a restricted set of prediction sets that can compactly be represented as partial programs, which are programs with portions replaced with holes. Given a trained code generation model, our algorithm leverages a programming language's abstract syntax tree to generate a set of programs such that the correct program is in the set with high-confidence. Valuable applications of our algorithm include a Codex-style code generator with holes in uncertain parts of the generated code, which provides a partial program with theoretical guarantees. We evaluate our approach on PICARD (a T5 model for SQL semantic parsing) and Codex (a GPT model for over a dozen programming languages, including Python), demonstrating that our approach generates compact PAC prediction sets. This is the first research contribution that generates PAC prediction sets for generative code models.

In this paper, we describe our end-to-end content-based image retrieval system built upon Elasticsearch, a well-known and popular textual search engine. As far as we know, this is the first time such a system has been implemented in eCommerce, and our efforts have turned out to be highly worthwhile. We end up with a novel and exciting visual search solution that is extremely easy to be deployed, distributed, scaled and monitored in a cost-friendly manner. Moreover, our platform is intrinsically flexible in supporting multimodal searches, where visual and textual information can be jointly leveraged in retrieval. The core idea is to encode image feature vectors into a collection of string tokens in a way such that closer vectors will share more string tokens in common. By doing that, we can utilize Elasticsearch to efficiently retrieve similar images based on similarities within encoded sting tokens. As part of the development, we propose a novel vector to string encoding method, which is shown to substantially outperform the previous ones in terms of both precision and latency. First-hand experiences in implementing this Elasticsearch-based platform are extensively addressed, which should be valuable to practitioners also interested in building visual search engine on top of Elasticsearch.

How to evaluate Large Language Models (LLMs) in code generation remains an open question. Existing benchmarks have two limitations - data leakage and lack of domain-specific evaluation. The former hurts the fairness of benchmarks, and the latter hinders practitioners from selecting superior LLMs for specific programming domains. To address these two limitations, we propose a new benchmark - EvoCodeBench, which has the following advances: (1) Evolving data. EvoCodeBench will be dynamically updated every period (e.g., 6 months) to avoid data leakage. This paper releases the first version - EvoCodeBench-2403, containing 275 samples from 25 repositories. (2) A domain taxonomy and domain labels. Based on the statistics of open-source communities, we design a programming domain taxonomy consisting of 10 popular domains. Based on the taxonomy, we annotate each sample in EvoCodeBench with a domain label. (3) Domain-specific evaluations. Besides the Pass@k, we compute the Domain-Specific Improvement (DSI) and define LLMs' comfort and strange domains. These evaluations help practitioners select superior LLMs in specific domains and discover the shortcomings of existing LLMs. We evaluate 8 popular LLMs (e.g., gpt-4, DeepSeek Coder) on EvoCodeBench and summarize some insights. EvoCodeBench reveals the actual abilities of these LLMs in real-world repositories. For example, the highest Pass@1 of gpt-4 on EvoCodeBench-2403 is only 20.74%. Besides, we evaluate LLMs in different domains and discover their comfort and strange domains. For example, gpt-4 performs best in most domains but falls behind others in the Internet domain. StarCoder 2-15B unexpectedly performs well in the Database domain and even outperforms 33B LLMs. EvoCodeBench has been released.

Vision Transformer (ViT) extracts the final representation from either class token or an average of all patch tokens, following the architecture of Transformer in Natural Language Processing (NLP) or Convolutional Neural Networks (CNNs) in computer vision. However, studies for the best way of aggregating the patch tokens are still limited to average pooling, while widely-used pooling strategies, such as max and GeM pooling, can be considered. Despite their effectiveness, the existing pooling strategies do not consider the architecture of ViT and the channel-wise difference in the activation maps, aggregating the crucial and trivial channels with the same importance. In this paper, we present Group Generalized Mean (GGeM) pooling as a simple yet powerful pooling strategy for ViT. GGeM divides the channels into groups and computes GeM pooling with a shared pooling parameter per group. As ViT groups the channels via a multi-head attention mechanism, grouping the channels by GGeM leads to lower head-wise dependence while amplifying important channels on the activation maps. Exploiting GGeM shows 0.1%p to 0.7%p performance boosts compared to the baselines and achieves state-of-the-art performance for ViT-Base and ViT-Large models in ImageNet-1K classification task. Moreover, GGeM outperforms the existing pooling strategies on image retrieval and multi-modal representation learning tasks, demonstrating the superiority of GGeM for a variety of tasks. GGeM is a simple algorithm in that only a few lines of code are necessary for implementation.

Neural architecture search (NAS) for Graph neural networks (GNNs), called NAS-GNNs, has achieved significant performance over manually designed GNN architectures. However, these methods inherit issues from the conventional NAS methods, such as high computational cost and optimization difficulty. More importantly, previous NAS methods have ignored the uniqueness of GNNs, where GNNs possess expressive power without training. With the randomly-initialized weights, we can then seek the optimal architecture parameters via the sparse coding objective and derive a novel NAS-GNNs method, namely neural architecture coding (NAC). Consequently, our NAC holds a no-update scheme on GNNs and can efficiently compute in linear time. Empirical evaluations on multiple GNN benchmark datasets demonstrate that our approach leads to state-of-the-art performance, which is up to 200times faster and 18.8% more accurate than the strong baselines.

In the automatic evaluation of generative question answering (GenQA) systems, it is difficult to assess the correctness of generated answers due to the free-form of the answer. Especially, widely used n-gram similarity metrics often fail to discriminate the incorrect answers since they equally consider all of the tokens. To alleviate this problem, we propose KPQA-metric, a new metric for evaluating the correctness of GenQA. Specifically, our new metric assigns different weights to each token via keyphrase prediction, thereby judging whether a generated answer sentence captures the key meaning of the reference answer. To evaluate our metric, we create high-quality human judgments of correctness on two GenQA datasets. Using our human-evaluation datasets, we show that our proposed metric has a significantly higher correlation with human judgments than existing metrics. The code is available at https://github.com/hwanheelee1993/KPQA.

Despite the success of text retrieval in many NLP tasks, code retrieval remains a largely underexplored area. Most text retrieval systems are tailored for natural language queries, often neglecting the specific challenges of retrieving code. This gap leaves existing models unable to effectively capture the diversity of programming languages and tasks across different domains, highlighting the need for more focused research in code retrieval. To address this, we introduce CodeXEmbed, a family of large-scale code embedding models ranging from 400M to 7B parameters. Our novel training pipeline unifies multiple programming languages and transforms various code-related tasks into a common retrieval framework, enhancing model generalizability and retrieval performance. Our 7B model sets a new state-of-the-art (SOTA) in code retrieval, outperforming the previous leading model, Voyage-Code, by over 20% on CoIR benchmark. In addition to excelling in code retrieval, our models demonstrate competitive performance on the widely adopted BeIR text retrieval benchmark, offering versatility across domains. Experimental results demonstrate that improving retrieval performance significantly enhances end-to-end Retrieval-Augmented Generation (RAG) performance for code-related tasks.

Recent work has shown that small distilled language models are strong competitors to models that are orders of magnitude larger and slower in a wide range of information retrieval tasks. This has made distilled and dense models, due to latency constraints, the go-to choice for deployment in real-world retrieval applications. In this work, we question this practice by showing that the number of parameters and early query-document interaction play a significant role in the generalization ability of retrieval models. Our experiments show that increasing model size results in marginal gains on in-domain test sets, but much larger gains in new domains never seen during fine-tuning. Furthermore, we show that rerankers largely outperform dense ones of similar size in several tasks. Our largest reranker reaches the state of the art in 12 of the 18 datasets of the Benchmark-IR (BEIR) and surpasses the previous state of the art by 3 average points. Finally, we confirm that in-domain effectiveness is not a good indicator of zero-shot effectiveness. Code is available at https://github.com/guilhermemr04/scaling-zero-shot-retrieval.git

Recent advances in retrieval-augmented generation (RAG) have initiated a new era in repository-level code completion. However, the invariable use of retrieval in existing methods exposes issues in both efficiency and robustness, with a large proportion of the retrieved contexts proving unhelpful or harmful to code language models (code LMs). In this paper, we propose a selective RAG framework to avoid retrieval when unnecessary. To power this framework, we design a self-supervised learning approach to enable a code LM to accurately self-evaluate whether retrieval can improve its output quality and robustly leverage the potentially noisy retrieved contexts. Using this LM as both the selective RAG policy and the generation model, our framework achieves state-of-the-art repository-level code completion performance on diverse benchmarks including RepoEval, CrossCodeEval, and CrossCodeLongEval, a new long-form code completion benchmark. Meanwhile, our analyses show that selectively retrieving brings as much as 70% inference speedup in the online serving setting without harming the performance. We further demonstrate that our framework is able to accommodate different generation models, retrievers, and programming languages. These advancements position our framework as an important step towards more accurate and efficient repository-level code completion.

Code Large Language Models (CodeLLMs) have ushered in a new era of code generation advancements. However, selecting the best solutions from among all possible CodeLLM solutions remains a challenge. Previous methods frequently overlooked the intricate functional similarities and interactions between clusters, resulting in suboptimal results. In this work, we introduce SRank, a novel reranking strategy for selecting the best solution from code generation that focuses on modeling inter-cluster relationship. By quantifying the functional overlap between clusters, our approach provides a better ranking strategy of code solutions. Empirical results show that our method achieves a remarkable results on pass@1 score. For instance, on the Human-Eval benchmark, we achieve 69.66\% in pass@1 with Codex002, 75.31\% for WizardCoder, 53.99\% for StarCoder and 60.55\% for CodeGen, which surpass the state-of-the-arts solution ranking methods, such as CodeT and Coder-Reviewer on the same CodeLLM with significant margin (approx 6.1% improvement on average). Comparing to the random sampling method, we can achieve an average improvement of approx 23.07% on Human-Eval and 17.64\% on MBPP. Even in scenarios with limited test inputs, our approach demonstrates robustness and superiority, marking a new state-of-the-arts in code generation reranking.

We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mapping, symbolic NLP and classification are unscalable and cannot accommodate large scale EHR datasets. In this work, we present Text2Node, a cross-domain mapping system capable of mapping medical phrases to concepts in a large taxonomy (such as SNOMED CT). The system is designed to generalize from a limited set of training samples and map phrases to elements of the taxonomy that are not covered by training data. As a result, our system is scalable, robust to wording variants between coding systems and can output highly relevant concepts when no exact concept exists in the target taxonomy. Text2Node operates in three main stages: first, the lexicon is mapped to word embeddings; second, the taxonomy is vectorized using node embeddings; and finally, the mapping function is trained to connect the two embedding spaces. We compared multiple algorithms and architectures for each stage of the training, including GloVe and FastText word embeddings, CNN and Bi-LSTM mapping functions, and node2vec for node embeddings. We confirmed the robustness and generalisation properties of Text2Node by mapping ICD-9-CM Diagnosis phrases to SNOMED CT and by zero-shot training at comparable accuracy. This system is a novel methodological contribution to the task of normalizing and linking phrases to a taxonomy, advancing data interchangeability in healthcare. When applied, the system can use electronic health records to generate an embedding that incorporates taxonomical medical knowledge to improve clinical predictive models.

Code is seldom written in a single left-to-right pass and is instead repeatedly edited and refined. We introduce InCoder, a unified generative model that can perform program synthesis (via left-to-right generation) as well as editing (via infilling). InCoder is trained to generate code files from a large corpus of permissively licensed code, where regions of code have been randomly masked and moved to the end of each file, allowing code infilling with bidirectional context. Our model is the first generative model that is able to directly perform zero-shot code infilling, which we evaluate on challenging tasks such as type inference, comment generation, and variable re-naming. We find that the ability to condition on bidirectional context substantially improves performance on these tasks, while still performing comparably on standard program synthesis benchmarks in comparison to left-to-right only models pretrained at similar scale. The InCoder models and code are publicly released. https://sites.google.com/view/incoder-code-models

We provide a reproducible, end-to-end demonstration of vector search with OpenAI embeddings using Lucene on the popular MS MARCO passage ranking test collection. The main goal of our work is to challenge the prevailing narrative that a dedicated vector store is necessary to take advantage of recent advances in deep neural networks as applied to search. Quite the contrary, we show that hierarchical navigable small-world network (HNSW) indexes in Lucene are adequate to provide vector search capabilities in a standard bi-encoder architecture. This suggests that, from a simple cost-benefit analysis, there does not appear to be a compelling reason to introduce a dedicated vector store into a modern "AI stack" for search, since such applications have already received substantial investments in existing, widely deployed infrastructure.

Learning to search is the task of building artificial agents that learn to autonomously use a search box to find information. So far, it has been shown that current language models can learn symbolic query reformulation policies, in combination with traditional term-based retrieval, but fall short of outperforming neural retrievers. We extend the previous learning to search setup to a hybrid environment, which accepts discrete query refinement operations, after a first-pass retrieval step via a dual encoder. Experiments on the BEIR task show that search agents, trained via behavioral cloning, outperform the underlying search system based on a combined dual encoder retriever and cross encoder reranker. Furthermore, we find that simple heuristic Hybrid Retrieval Environments (HRE) can improve baseline performance by several nDCG points. The search agent based on HRE (HARE) matches state-of-the-art performance, balanced in both zero-shot and in-domain evaluations, via interpretable actions, and at twice the speed.

We investigate the potential of GPT-4~gpt4 to perform Neural Architecture Search (NAS) -- the task of designing effective neural architectures. Our proposed approach, GPT-4 Enhanced Neural archItectUre Search (GENIUS), leverages the generative capabilities of GPT-4 as a black-box optimiser to quickly navigate the architecture search space, pinpoint promising candidates, and iteratively refine these candidates to improve performance. We assess GENIUS across several benchmarks, comparing it with existing state-of-the-art NAS techniques to illustrate its effectiveness. Rather than targeting state-of-the-art performance, our objective is to highlight GPT-4's potential to assist research on a challenging technical problem through a simple prompting scheme that requires relatively limited domain expertiseCode available at \href{https://github.com/mingkai-zheng/GENIUS{https://github.com/mingkai-zheng/GENIUS}.}. More broadly, we believe our preliminary results point to future research that harnesses general purpose language models for diverse optimisation tasks. We also highlight important limitations to our study, and note implications for AI safety.

Generative search engines directly generate responses to user queries, along with in-line citations. A prerequisite trait of a trustworthy generative search engine is verifiability, i.e., systems should cite comprehensively (high citation recall; all statements are fully supported by citations) and accurately (high citation precision; every cite supports its associated statement). We conduct human evaluation to audit four popular generative search engines -- Bing Chat, NeevaAI, perplexity.ai, and YouChat -- across a diverse set of queries from a variety of sources (e.g., historical Google user queries, dynamically-collected open-ended questions on Reddit, etc.). We find that responses from existing generative search engines are fluent and appear informative, but frequently contain unsupported statements and inaccurate citations: on average, a mere 51.5% of generated sentences are fully supported by citations and only 74.5% of citations support their associated sentence. We believe that these results are concerningly low for systems that may serve as a primary tool for information-seeking users, especially given their facade of trustworthiness. We hope that our results further motivate the development of trustworthy generative search engines and help researchers and users better understand the shortcomings of existing commercial systems.

Retrieval-augmented generation (RAG) techniques leverage the in-context learning capabilities of large language models (LLMs) to produce more accurate and relevant responses. Originating from the simple 'retrieve-then-read' approach, the RAG framework has evolved into a highly flexible and modular paradigm. A critical component, the Query Rewriter module, enhances knowledge retrieval by generating a search-friendly query. This method aligns input questions more closely with the knowledge base. Our research identifies opportunities to enhance the Query Rewriter module to Query Rewriter+ by generating multiple queries to overcome the Information Plateaus associated with a single query and by rewriting questions to eliminate Ambiguity, thereby clarifying the underlying intent. We also find that current RAG systems exhibit issues with Irrelevant Knowledge; to overcome this, we propose the Knowledge Filter. These two modules are both based on the instruction-tuned Gemma-2B model, which together enhance response quality. The final identified issue is Redundant Retrieval; we introduce the Memory Knowledge Reservoir and the Retriever Trigger to solve this. The former supports the dynamic expansion of the RAG system's knowledge base in a parameter-free manner, while the latter optimizes the cost for accessing external knowledge, thereby improving resource utilization and response efficiency. These four RAG modules synergistically improve the response quality and efficiency of the RAG system. The effectiveness of these modules has been validated through experiments and ablation studies across six common QA datasets. The source code can be accessed at https://github.com/Ancientshi/ERM4.

Generative Retrieval (GR), autoregressively decoding relevant document identifiers given a query, has been shown to perform well under the setting of small-scale corpora. By memorizing the document corpus with model parameters, GR implicitly achieves deep interaction between query and document. However, such a memorizing mechanism faces three drawbacks: (1) Poor memory accuracy for fine-grained features of documents; (2) Memory confusion gets worse as the corpus size increases; (3) Huge memory update costs for new documents. To alleviate these problems, we propose the Generative Dense Retrieval (GDR) paradigm. Specifically, GDR first uses the limited memory volume to achieve inter-cluster matching from query to relevant document clusters. Memorizing-free matching mechanism from Dense Retrieval (DR) is then introduced to conduct fine-grained intra-cluster matching from clusters to relevant documents. The coarse-to-fine process maximizes the advantages of GR's deep interaction and DR's scalability. Besides, we design a cluster identifier constructing strategy to facilitate corpus memory and a cluster-adaptive negative sampling strategy to enhance the intra-cluster mapping ability. Empirical results show that GDR obtains an average of 3.0 R@100 improvement on NQ dataset under multiple settings and has better scalability.

The rapid growth of scientific literature imposes significant challenges for researchers endeavoring to stay updated with the latest advancements in their fields and delve into new areas. We introduce OpenResearcher, an innovative platform that leverages Artificial Intelligence (AI) techniques to accelerate the research process by answering diverse questions from researchers. OpenResearcher is built based on Retrieval-Augmented Generation (RAG) to integrate Large Language Models (LLMs) with up-to-date, domain-specific knowledge. Moreover, we develop various tools for OpenResearcher to understand researchers' queries, search from the scientific literature, filter retrieved information, provide accurate and comprehensive answers, and self-refine these answers. OpenResearcher can flexibly use these tools to balance efficiency and effectiveness. As a result, OpenResearcher enables researchers to save time and increase their potential to discover new insights and drive scientific breakthroughs. Demo, video, and code are available at: https://github.com/GAIR-NLP/OpenResearcher.

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

Code generation models have increasingly become integral to aiding software development, offering assistance in tasks such as code completion, debugging, and code translation. Although current research has thoroughly examined the correctness of code produced by code generation models, a vital aspect, i.e., the efficiency of the generated code, has often been neglected. This paper presents EffiBench, a benchmark with 1,000 efficiency-critical coding problems for assessing the efficiency of code generated by code generation models. EffiBench contains a diverse set of LeetCode coding problems. Each problem is paired with an executable human-written canonical solution. With EffiBench, we empirically examine the capability of 21 Large Language Models (13 open-sourced and 8 closed-sourced) in generating efficient code. The results demonstrate that GPT-4-turbo generates the most efficient code, significantly outperforming Palm-2-chat-bison, Claude-instant-1, Gemini-pro, GPT-4, and GPT-3.5. Nevertheless, its code efficiency is still worse than the efficiency of human-written canonical solutions. In particular, the average and worst execution time of GPT-4-turbo generated code is 1.69 and 45.49 times that of the canonical solutions.

The paper describes a system designed by Advacheck team to recognise machine-generated and human-written texts in the monolingual subtask of GenAI Detection Task 1 competition. Our developed system is a multi-task architecture with shared Transformer Encoder between several classification heads. One head is responsible for binary classification between human-written and machine-generated texts, while the other heads are auxiliary multiclass classifiers for texts of different domains from particular datasets. As multiclass heads were trained to distinguish the domains presented in the data, they provide a better understanding of the samples. This approach led us to achieve the first place in the official ranking with 83.07% macro F1-score on the test set and bypass the baseline by 10%. We further study obtained system through ablation, error and representation analyses, finding that multi-task learning outperforms single-task mode and simultaneous tasks form a cluster structure in embeddings space.

In the past few years, Differentiable Neural Architecture Search (DNAS) rapidly imposed itself as the trending approach to automate the discovery of deep neural network architectures. This rise is mainly due to the popularity of DARTS, one of the first major DNAS methods. In contrast with previous works based on Reinforcement Learning or Evolutionary Algorithms, DNAS is faster by several orders of magnitude and uses fewer computational resources. In this comprehensive survey, we focus specifically on DNAS and review recent approaches in this field. Furthermore, we propose a novel challenge-based taxonomy to classify DNAS methods. We also discuss the contributions brought to DNAS in the past few years and its impact on the global NAS field. Finally, we conclude by giving some insights into future research directions for the DNAS field.

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Large Language Models (LLMs) trained on code are revolutionizing the software development process. Increasingly, code LLMs are being integrated into software development environments to improve the productivity of human programmers, and LLM-based agents are beginning to show promise for handling complex tasks autonomously. Realizing the full potential of code LLMs requires a wide range of capabilities, including code generation, fixing bugs, explaining and documenting code, maintaining repositories, and more. In this work, we introduce the Granite series of decoder-only code models for code generative tasks, trained with code written in 116 programming languages. The Granite Code models family consists of models ranging in size from 3 to 34 billion parameters, suitable for applications ranging from complex application modernization tasks to on-device memory-constrained use cases. Evaluation on a comprehensive set of tasks demonstrates that Granite Code models consistently reaches state-of-the-art performance among available open-source code LLMs. The Granite Code model family was optimized for enterprise software development workflows and performs well across a range of coding tasks (e.g. code generation, fixing and explanation), making it a versatile all around code model. We release all our Granite Code models under an Apache 2.0 license for both research and commercial use.

Since language models (LMs) now outperform average humans on many challenging tasks, it has become increasingly difficult to develop challenging, high-quality, and realistic evaluations. We address this issue by examining LMs' capabilities to generate code for solving real scientific research problems. Incorporating input from scientists and AI researchers in 16 diverse natural science sub-fields, including mathematics, physics, chemistry, biology, and materials science, we created a scientist-curated coding benchmark, SciCode. The problems in SciCode naturally factorize into multiple subproblems, each involving knowledge recall, reasoning, and code synthesis. In total, SciCode contains 338 subproblems decomposed from 80 challenging main problems. It offers optional descriptions specifying useful scientific background information and scientist-annotated gold-standard solutions and test cases for evaluation. Claude3.5-Sonnet, the best-performing model among those tested, can solve only 4.6% of the problems in the most realistic setting. We believe that SciCode demonstrates both contemporary LMs' progress towards becoming helpful scientific assistants and sheds light on the development and evaluation of scientific AI in the future.

We generalize the class vectors found in neural networks to linear subspaces (i.e.~points in the Grassmann manifold) and show that the Grassmann Class Representation (GCR) enables the simultaneous improvement in accuracy and feature transferability. In GCR, each class is a subspace and the logit is defined as the norm of the projection of a feature onto the class subspace. We integrate Riemannian SGD into deep learning frameworks such that class subspaces in a Grassmannian are jointly optimized with the rest model parameters. Compared to the vector form, the representative capability of subspaces is more powerful. We show that on ImageNet-1K, the top-1 error of ResNet50-D, ResNeXt50, Swin-T and Deit3-S are reduced by 5.6%, 4.5%, 3.0% and 3.5%, respectively. Subspaces also provide freedom for features to vary and we observed that the intra-class feature variability grows when the subspace dimension increases. Consequently, we found the quality of GCR features is better for downstream tasks. For ResNet50-D, the average linear transfer accuracy across 6 datasets improves from 77.98% to 79.70% compared to the strong baseline of vanilla softmax. For Swin-T, it improves from 81.5% to 83.4% and for Deit3, it improves from 73.8% to 81.4%. With these encouraging results, we believe that more applications could benefit from the Grassmann class representation. Code is released at https://github.com/innerlee/GCR.

AI technologies are moving rapidly from research to production. With the popularity of Foundation Models (FMs) that generate text, images, and video, AI-based systems are increasing their complexity. Compared to traditional AI-based software, systems employing FMs, or GenAI-based systems, are more difficult to design due to their scale and versatility. This makes it necessary to document best practices, known as design patterns in software engineering, that can be used across GenAI applications. Our first contribution is to formalize two techniques, Task Decomposition and Retrieval-Augmented Generation (RAG), as design patterns for GenAI-based systems. We discuss their trade-offs in terms of software quality attributes and comment on alternative approaches. We recommend to AI practitioners to consider these techniques not only from a scientific perspective but also from the standpoint of desired engineering properties such as flexibility, maintainability, safety, and security. As a second contribution, we describe our industry experience applying Task Decomposition and RAG to build a complex real-world GenAI application for enterprise users: Workflow Generation. The task of generating workflows entails generating a specific plan using data from the system environment, taking as input a user requirement. As these two patterns affect the entire AI development cycle, we explain how they impacted the dataset creation, model training, model evaluation, and deployment phases.

A proper code evaluation metric (CEM) profoundly impacts the evolution of code generation, which is an important research field in NLP and software engineering. Prevailing match-based CEMs (e.g., BLEU, Accuracy, and CodeBLEU) suffer from two significant drawbacks. 1. They primarily measure the surface differences between codes without considering their functional equivalence. However, functional equivalence is pivotal in evaluating the effectiveness of code generation, as different codes can perform identical operations. 2. They are predominantly designed for the Ref-only input format. However, code evaluation necessitates versatility in input formats. Aside from Ref-only, there are NL-only and Ref\&NL formats, which existing match-based CEMs cannot effectively accommodate. In this paper, we propose CodeScore, a large language model (LLM)-based CEM, which estimates the functional correctness of generated code on three input types. To acquire CodeScore, we present UniCE, a unified code generation learning framework, for LLMs to learn code execution (i.e., learning PassRatio and Executability of generated code) with unified input. Extensive experimental results on multiple code evaluation datasets demonstrate that CodeScore absolutely improves up to 58.87% correlation with functional correctness compared to other CEMs, achieves state-of-the-art performance, and effectively handles three input formats.

In this work, we provide a thorough investigation of gist-based context compression methods to improve long-context processing in large language models. We focus on two key questions: (1) How well can these methods replace full attention models? and (2) What potential failure patterns arise due to compression? Through extensive experiments, we show that while gist-based compression can achieve near-lossless performance on tasks like retrieval-augmented generation and long-document QA, it faces challenges in tasks like synthetic recall. Furthermore, we identify three key failure patterns: lost by the boundary, lost if surprise, and lost along the way. To mitigate these issues, we propose two effective strategies: fine-grained autoencoding, which enhances the reconstruction of original token information, and segment-wise token importance estimation, which adjusts optimization based on token dependencies. Our work provides valuable insights into the understanding of gist token-based context compression and offers practical strategies for improving compression capabilities.

Finding codes given natural language query isb eneficial to the productivity of software developers. Future progress towards better semantic matching between query and code requires richer supervised training resources. To remedy this, we introduce the CoSQA dataset.It includes 20,604 labels for pairs of natural language queries and codes, each annotated by at least 3 human annotators. We further introduce a contrastive learning method dubbed CoCLR to enhance query-code matching, which works as a data augmenter to bring more artificially generated training instances. We show that evaluated on CodeXGLUE with the same CodeBERT model, training on CoSQA improves the accuracy of code question answering by 5.1%, and incorporating CoCLR brings a further improvement of 10.5%.

Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model encoders perform better semantic retrieval, training such models requires abundant query-article annotations that are difficult to obtain in biomedicine. As a result, most biomedical IR systems only conduct lexical matching. In response, we introduce BioCPT, a first-of-its-kind Contrastively Pre-trained Transformer model for zero-shot biomedical IR. To train BioCPT, we collected an unprecedented scale of 255 million user click logs from PubMed. With such data, we use contrastive learning to train a pair of closely-integrated retriever and re-ranker. Experimental results show that BioCPT sets new state-of-the-art performance on five biomedical IR tasks, outperforming various baselines including much larger models such as GPT-3-sized cpt-text-XL. In addition, BioCPT also generates better biomedical article and sentence representations for semantic evaluations. As such, BioCPT can be readily applied to various real-world biomedical IR tasks. BioCPT API and code are publicly available at https://github.com/ncbi/BioCPT.

Extreme Classification (XC) seeks to tag data points with the most relevant subset of labels from an extremely large label set. Performing deep XC with dense, learnt representations for data points and labels has attracted much attention due to its superiority over earlier XC methods that used sparse, hand-crafted features. Negative mining techniques have emerged as a critical component of all deep XC methods that allow them to scale to millions of labels. However, despite recent advances, training deep XC models with large encoder architectures such as transformers remains challenging. This paper identifies that memory overheads of popular negative mining techniques often force mini-batch sizes to remain small and slow training down. In response, this paper introduces NGAME, a light-weight mini-batch creation technique that offers provably accurate in-batch negative samples. This allows training with larger mini-batches offering significantly faster convergence and higher accuracies than existing negative sampling techniques. NGAME was found to be up to 16% more accurate than state-of-the-art methods on a wide array of benchmark datasets for extreme classification, as well as 3% more accurate at retrieving search engine queries in response to a user webpage visit to show personalized ads. In live A/B tests on a popular search engine, NGAME yielded up to 23% gains in click-through-rates.

Testing is an integral part of the software development process. Yet, writing tests is time-consuming and therefore often neglected. Classical test generation tools such as EvoSuite generate behavioral test suites by optimizing for coverage, but tend to produce tests that are hard to understand. Language models trained on code can generate code that is highly similar to that written by humans, but current models are trained to generate each file separately, as is standard practice in natural language processing, and thus fail to consider the code-under-test context when producing a test file. In this work, we propose the Aligned Code And Tests Language Model (CAT-LM), a GPT-style language model with 2.7 Billion parameters, trained on a corpus of Python and Java projects. We utilize a novel pretraining signal that explicitly considers the mapping between code and test files when available. We also drastically increase the maximum sequence length of inputs to 8,192 tokens, 4x more than typical code generation models, to ensure that the code context is available to the model when generating test code. We analyze its usefulness for realistic applications, showing that sampling with filtering (e.g., by compilability, coverage) allows it to efficiently produce tests that achieve coverage similar to ones written by developers while resembling their writing style. By utilizing the code context, CAT-LM generates more valid tests than even much larger language models trained with more data (CodeGen 16B and StarCoder) and substantially outperforms a recent test-specific model (TeCo) at test completion. Overall, our work highlights the importance of incorporating software-specific insights when training language models for code and paves the way to more powerful automated test generation.

Repository-level code completion aims to generate code for unfinished code snippets within the context of a specified repository. Existing approaches mainly rely on retrieval-augmented generation strategies due to limitations in input sequence length. However, traditional lexical-based retrieval methods like BM25 struggle to capture code semantics, while model-based retrieval methods face challenges due to the lack of labeled data for training. Therefore, we propose RLCoder, a novel reinforcement learning framework, which can enable the retriever to learn to retrieve useful content for code completion without the need for labeled data. Specifically, we iteratively evaluate the usefulness of retrieved content based on the perplexity of the target code when provided with the retrieved content as additional context, and provide feedback to update the retriever parameters. This iterative process enables the retriever to learn from its successes and failures, gradually improving its ability to retrieve relevant and high-quality content. Considering that not all situations require information beyond code files and not all retrieved context is helpful for generation, we also introduce a stop signal mechanism, allowing the retriever to decide when to retrieve and which candidates to retain autonomously. Extensive experimental results demonstrate that RLCoder consistently outperforms state-of-the-art methods on CrossCodeEval and RepoEval, achieving 12.2% EM improvement over previous methods. Moreover, experiments show that our framework can generalize across different programming languages and further improve previous methods like RepoCoder. We provide the code and data at https://github.com/DeepSoftwareAnalytics/RLCoder.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

We present trellis networks, a new architecture for sequence modeling. On the one hand, a trellis network is a temporal convolutional network with special structure, characterized by weight tying across depth and direct injection of the input into deep layers. On the other hand, we show that truncated recurrent networks are equivalent to trellis networks with special sparsity structure in their weight matrices. Thus trellis networks with general weight matrices generalize truncated recurrent networks. We leverage these connections to design high-performing trellis networks that absorb structural and algorithmic elements from both recurrent and convolutional models. Experiments demonstrate that trellis networks outperform the current state of the art methods on a variety of challenging benchmarks, including word-level language modeling and character-level language modeling tasks, and stress tests designed to evaluate long-term memory retention. The code is available at https://github.com/locuslab/trellisnet .

Code generation is a latency-sensitive task that demands high timeliness, but the autoregressive decoding mechanism of Large Language Models (LLMs) leads to poor inference efficiency. Existing LLM inference acceleration methods mainly focus on standalone functions using only built-in components. Moreover, they treat code like natural language sequences, ignoring its unique syntax and semantic characteristics. As a result, the effectiveness of these approaches in code generation tasks remains limited and fails to align with real-world programming scenarios. To alleviate this issue, we propose CodeSwift, a simple yet highly efficient inference acceleration approach specifically designed for code generation, without comprising the quality of the output. CodeSwift constructs a multi-source datastore, providing access to both general and project-specific knowledge, facilitating the retrieval of high-quality draft sequences. Moreover, CodeSwift reduces retrieval cost by controlling retrieval timing, and enhances efficiency through parallel retrieval and a context- and LLM preference-aware cache. Experimental results show that CodeSwift can reach up to 2.53x and 2.54x speedup compared to autoregressive decoding in repository-level and standalone code generation tasks, respectively, outperforming state-of-the-art inference acceleration approaches by up to 88%.

The advent of deep machine learning platforms such as Tensorflow and Pytorch, developed in expressive high-level languages such as Python, have allowed more expressive representations of deep neural network architectures. We argue that such a powerful formalism is missing in information retrieval (IR), and propose a framework called PyTerrier that allows advanced retrieval pipelines to be expressed, and evaluated, in a declarative manner close to their conceptual design. Like the aforementioned frameworks that compile deep learning experiments into primitive GPU operations, our framework targets IR platforms as backends in order to execute and evaluate retrieval pipelines. Further, we can automatically optimise the retrieval pipelines to increase their efficiency to suite a particular IR platform backend. Our experiments, conducted on TREC Robust and ClueWeb09 test collections, demonstrate the efficiency benefits of these optimisations for retrieval pipelines involving both the Anserini and Terrier IR platforms.

Ad-hoc search calls for the selection of appropriate answers from a massive-scale corpus. Nowadays, the embedding-based retrieval (EBR) becomes a promising solution, where deep learning based document representation and ANN search techniques are allied to handle this task. However, a major challenge is that the ANN index can be too large to fit into memory, given the considerable size of answer corpus. In this work, we tackle this problem with Bi-Granular Document Representation, where the lightweight sparse embeddings are indexed and standby in memory for coarse-grained candidate search, and the heavyweight dense embeddings are hosted in disk for fine-grained post verification. For the best of retrieval accuracy, a Progressive Optimization framework is designed. The sparse embeddings are learned ahead for high-quality search of candidates. Conditioned on the candidate distribution induced by the sparse embeddings, the dense embeddings are continuously learned to optimize the discrimination of ground-truth from the shortlisted candidates. Besides, two techniques: the contrastive quantization and the locality-centric sampling are introduced for the learning of sparse and dense embeddings, which substantially contribute to their performances. Thanks to the above features, our method effectively handles massive-scale EBR with strong advantages in accuracy: with up to +4.3% recall gain on million-scale corpus, and up to +17.5% recall gain on billion-scale corpus. Besides, Our method is applied to a major sponsored search platform with substantial gains on revenue (+1.95%), Recall (+1.01%) and CTR (+0.49%). Our code is available at https://github.com/microsoft/BiDR.

Much recent research on information retrieval has focused on how to transfer from one task (typically with abundant supervised data) to various other tasks where supervision is limited, with the implicit assumption that it is possible to generalize from one task to all the rest. However, this overlooks the fact that there are many diverse and unique retrieval tasks, each targeting different search intents, queries, and search domains. In this paper, we suggest to work on Few-shot Dense Retrieval, a setting where each task comes with a short description and a few examples. To amplify the power of a few examples, we propose Prompt-base Query Generation for Retriever (Promptagator), which leverages large language models (LLM) as a few-shot query generator, and creates task-specific retrievers based on the generated data. Powered by LLM's generalization ability, Promptagator makes it possible to create task-specific end-to-end retrievers solely based on a few examples {without} using Natural Questions or MS MARCO to train %question generators or dual encoders. Surprisingly, LLM prompting with no more than 8 examples allows dual encoders to outperform heavily engineered models trained on MS MARCO like ColBERT v2 by more than 1.2 nDCG on average on 11 retrieval sets. Further training standard-size re-rankers using the same generated data yields another 5.0 point nDCG improvement. Our studies determine that query generation can be far more effective than previously observed, especially when a small amount of task-specific knowledge is given.

In spite of the outstanding performance, Neural Architecture Search (NAS) is criticized for massive computation. Recently, Zero-shot NAS has emerged as a promising approach by exploiting Zero-cost (ZC) proxies, which markedly reduce computational demands. Despite this, existing ZC proxies heavily rely on expert knowledge and incur significant trial-and-error costs. Particularly in NLP tasks, most existing ZC proxies fail to surpass the performance of the naive baseline. To address these challenges, we introduce a novel framework, LPZero, which is the first to automatically design ZC proxies for various tasks, achieving higher ranking consistency than human-designed proxies. Specifically, we model the ZC proxy as a symbolic equation and incorporate a unified proxy search space that encompasses existing ZC proxies, which are composed of a predefined set of mathematical symbols. To heuristically search for the best ZC proxy, LPZero incorporates genetic programming to find the optimal symbolic composition. We propose a Rule-based Pruning Strategy (RPS), which preemptively eliminates unpromising proxies, thereby mitigating the risk of proxy degradation. Extensive experiments on FlexiBERT, GPT-2, and LLaMA-7B demonstrate LPZero's superior ranking ability and performance on downstream tasks compared to current approaches.

Graph neural architecture search has sparked much attention as Graph Neural Networks (GNNs) have shown powerful reasoning capability in many relational tasks. However, the currently used graph search space overemphasizes learning node features and neglects mining hierarchical relational information. Moreover, due to diverse mechanisms in the message passing, the graph search space is much larger than that of CNNs. This hinders the straightforward application of classical search strategies for exploring complicated graph search space. We propose Automatic Relation-aware Graph Network Proliferation (ARGNP) for efficiently searching GNNs with a relation-guided message passing mechanism. Specifically, we first devise a novel dual relation-aware graph search space that comprises both node and relation learning operations. These operations can extract hierarchical node/relational information and provide anisotropic guidance for message passing on a graph. Second, analogous to cell proliferation, we design a network proliferation search paradigm to progressively determine the GNN architectures by iteratively performing network division and differentiation. The experiments on six datasets for four graph learning tasks demonstrate that GNNs produced by our method are superior to the current state-of-the-art hand-crafted and search-based GNNs. Codes are available at https://github.com/phython96/ARGNP.

Recent work demonstrates that, after being fine-tuned on a high-quality instruction dataset, the resulting model can obtain impressive capabilities to address a wide range of tasks. However, existing methods for instruction data generation often produce duplicate data and are not controllable enough on data quality. In this paper, we extend the generalization of instruction tuning by classifying the instruction data to 4 code-related tasks and propose a LLM-based Generator-Discriminator data process framework to generate diverse, high-quality instruction data from open source code. Hence, we introduce CodeOcean, a dataset comprising 20,000 instruction instances across 4 universal code-related tasks,which is aimed at augmenting the effectiveness of instruction tuning and improving the generalization ability of fine-tuned model. Subsequently, we present WaveCoder, a fine-tuned Code LLM with Widespread And Versatile Enhanced instruction tuning. This model is specifically designed for enhancing instruction tuning of Code Language Models (LLMs). Our experiments demonstrate that Wavecoder models outperform other open-source models in terms of generalization ability across different code-related tasks at the same level of fine-tuning scale. Moreover, Wavecoder exhibits high efficiency in previous code generation tasks. This paper thus offers a significant contribution to the field of instruction data generation and fine-tuning models, providing new insights and tools for enhancing performance in code-related tasks.

We assessed the performance of commercial Large Language Models (LLMs) GPT-3.5-Turbo and GPT-4 on tasks from the 2023 BioASQ challenge. In Task 11b Phase B, which is focused on answer generation, both models demonstrated competitive abilities with leading systems. Remarkably, they achieved this with simple zero-shot learning, grounded with relevant snippets. Even without relevant snippets, their performance was decent, though not on par with the best systems. Interestingly, the older and cheaper GPT-3.5-Turbo system was able to compete with GPT-4 in the grounded Q&A setting on factoid and list answers. In Task 11b Phase A, focusing on retrieval, query expansion through zero-shot learning improved performance, but the models fell short compared to other systems. The code needed to rerun these experiments is available through GitHub.

Generative Artificial Intelligence (AI) has enabled the development of sophisticated models that are capable of producing high-caliber text, images, and other outputs through the utilization of large pre-trained models. Nevertheless, assessing the quality of the generation is an even more arduous task than the generation itself, and this issue has not been given adequate consideration recently. This paper proposes a novel evaluation framework, GPTScore, which utilizes the emergent abilities (e.g., zero-shot instruction) of generative pre-trained models to score generated texts. There are 19 pre-trained models explored in this paper, ranging in size from 80M (e.g., FLAN-T5-small) to 175B (e.g., GPT3). Experimental results on four text generation tasks, 22 evaluation aspects, and corresponding 37 datasets demonstrate that this approach can effectively allow us to achieve what one desires to evaluate for texts simply by natural language instructions. This nature helps us overcome several long-standing challenges in text evaluation--how to achieve customized, multi-faceted evaluation without the need for annotated samples. We make our code publicly available at https://github.com/jinlanfu/GPTScore.

Dense retrieval approaches can overcome the lexical gap and lead to significantly improved search results. However, they require large amounts of training data which is not available for most domains. As shown in previous work (Thakur et al., 2021b), the performance of dense retrievers severely degrades under a domain shift. This limits the usage of dense retrieval approaches to only a few domains with large training datasets. In this paper, we propose the novel unsupervised domain adaptation method Generative Pseudo Labeling (GPL), which combines a query generator with pseudo labeling from a cross-encoder. On six representative domain-specialized datasets, we find the proposed GPL can outperform an out-of-the-box state-of-the-art dense retrieval approach by up to 9.3 points nDCG@10. GPL requires less (unlabeled) data from the target domain and is more robust in its training than previous methods. We further investigate the role of six recent pre-training methods in the scenario of domain adaptation for retrieval tasks, where only three could yield improved results. The best approach, TSDAE (Wang et al., 2021) can be combined with GPL, yielding another average improvement of 1.4 points nDCG@10 across the six tasks. The code and the models are available at https://github.com/UKPLab/gpl.

Neural Code Intelligence -- leveraging deep learning to understand, generate, and optimize code -- holds immense potential for transformative impacts on the whole society. Bridging the gap between Natural Language and Programming Language, this domain has drawn significant attention from researchers in both research communities over the past few years. This survey presents a systematic and chronological review of the advancements in code intelligence, encompassing over 50 representative models and their variants, more than 20 categories of tasks, and an extensive coverage of over 680 related works. We follow the historical progression to trace the paradigm shifts across different research phases (e.g., from modeling code with recurrent neural networks to the era of Large Language Models). Concurrently, we highlight the major technical transitions in models, tasks, and evaluations spanning through different stages. For applications, we also observe a co-evolving shift. It spans from initial endeavors to tackling specific scenarios, through exploring a diverse array of tasks during its rapid expansion, to currently focusing on tackling increasingly complex and varied real-world challenges. Building on our examination of the developmental trajectories, we further investigate the emerging synergies between code intelligence and broader machine intelligence, uncovering new cross-domain opportunities and illustrating the substantial influence of code intelligence across various domains. Finally, we delve into both the opportunities and challenges associated with this field, alongside elucidating our insights on the most promising research directions. An ongoing, dynamically updated project and resources associated with this survey have been released at https://github.com/QiushiSun/NCISurvey.

With the advent of Large Language Models (LLMs), the potential of Retrieval Augmented Generation (RAG) techniques have garnered considerable research attention. Numerous novel algorithms and models have been introduced to enhance various aspects of RAG systems. However, the absence of a standardized framework for implementation, coupled with the inherently intricate RAG process, makes it challenging and time-consuming for researchers to compare and evaluate these approaches in a consistent environment. Existing RAG toolkits like LangChain and LlamaIndex, while available, are often heavy and unwieldy, failing to meet the personalized needs of researchers. In response to this challenge, we propose FlashRAG, an efficient and modular open-source toolkit designed to assist researchers in reproducing existing RAG methods and in developing their own RAG algorithms within a unified framework. Our toolkit implements 12 advanced RAG methods and has gathered and organized 32 benchmark datasets. Our toolkit has various features, including customizable modular framework, rich collection of pre-implemented RAG works, comprehensive datasets, efficient auxiliary pre-processing scripts, and extensive and standard evaluation metrics. Our toolkit and resources are available at https://github.com/RUC-NLPIR/FlashRAG.

Modern recommender systems leverage large-scale retrieval models consisting of two stages: training a dual-encoder model to embed queries and candidates in the same space, followed by an Approximate Nearest Neighbor (ANN) search to select top candidates given a query's embedding. In this paper, we propose a new single-stage paradigm: a generative retrieval model which autoregressively decodes the identifiers for the target candidates in one phase. To do this, instead of assigning randomly generated atomic IDs to each item, we generate Semantic IDs: a semantically meaningful tuple of codewords for each item that serves as its unique identifier. We use a hierarchical method called RQ-VAE to generate these codewords. Once we have the Semantic IDs for all the items, a Transformer based sequence-to-sequence model is trained to predict the Semantic ID of the next item. Since this model predicts the tuple of codewords identifying the next item directly in an autoregressive manner, it can be considered a generative retrieval model. We show that our recommender system trained in this new paradigm improves the results achieved by current SOTA models on the Amazon dataset. Moreover, we demonstrate that the sequence-to-sequence model coupled with hierarchical Semantic IDs offers better generalization and hence improves retrieval of cold-start items for recommendations.

Automated code generation can be a powerful technique for software development, significantly reducing developers' efforts and time required to create new code by generating it automatically based on requirements. Recently, OpenAI's language model ChatGPT has emerged as a powerful tool for generating human-like responses to a wide range of textual inputs (i.e., prompts), including those related to code generation. However, the effectiveness of ChatGPT for code generation is not well understood, and the generation performance could be heavily influenced by the choice of prompt. To answer these questions, we conducted experiments using the CodeXGlue dataset to evaluate ChatGPT's capabilities for two code generation tasks, including text-to-code and code-to-code generation. We designed prompts by leveraging the chain-of-thought strategy with multi-step optimizations. Our results showed that by carefully designing prompts to guide ChatGPT, the generation performance can be improved substantially. We also analyzed the factors that influenced the prompt design and provided insights that could guide future research.

In this work we systematically review the recent advancements in code processing with language models, covering 50+ models, 30+ evaluation tasks, and 500 related works. We break down code processing models into general language models represented by the GPT family and specialized models that are specifically pretrained on code, often with tailored objectives. We discuss the relations and differences between these models, and highlight the historical transition of code modeling from statistical models and RNNs to pretrained Transformers and LLMs, which is exactly the same course that had been taken by NLP. We also discuss code-specific features such as AST, CFG, and unit tests, along with their application in training code language models, and identify key challenges and potential future directions in this domain. We keep the survey open and updated on github repository at https://github.com/codefuse-ai/Awesome-Code-LLM.

We present SuperCoder2.0, an advanced autonomous system designed to enhance software development through artificial intelligence. The system combines an AI-native development approach with intelligent agents to enable fully autonomous coding. Key focus areas include a retry mechanism with error output traceback, comprehensive code rewriting and replacement using Abstract Syntax Tree (ast) parsing to minimize linting issues, code embedding technique for retrieval-augmented generation, and a focus on localizing methods for problem-solving rather than identifying specific line numbers. The methodology employs a three-step hierarchical search space reduction approach for code base navigation and bug localization:utilizing Retrieval Augmented Generation (RAG) and a Repository File Level Map to identify candidate files, (2) narrowing down to the most relevant files using a File Level Schematic Map, and (3) extracting 'relevant locations' within these files. Code editing is performed through a two-part module comprising CodeGeneration and CodeEditing, which generates multiple solutions at different temperature values and replaces entire methods or classes to maintain code integrity. A feedback loop executes repository-level test cases to validate and refine solutions. Experiments conducted on the SWE-bench Lite dataset demonstrate SuperCoder2.0's effectiveness, achieving correct file localization in 84.33% of cases within the top 5 candidates and successfully resolving 34% of test instances. This performance places SuperCoder2.0 fourth globally on the SWE-bench leaderboard. The system's ability to handle diverse repositories and problem types highlights its potential as a versatile tool for autonomous software development. Future work will focus on refining the code editing process and exploring advanced embedding models for improved natural language to code mapping.

Continual Learning (CL) for malware classification tackles the rapidly evolving nature of malware threats and the frequent emergence of new types. Generative Replay (GR)-based CL systems utilize a generative model to produce synthetic versions of past data, which are then combined with new data to retrain the primary model. Traditional machine learning techniques in this domain often struggle with catastrophic forgetting, where a model's performance on old data degrades over time. In this paper, we introduce a GR-based CL system that employs Generative Adversarial Networks (GANs) with feature matching loss to generate high-quality malware samples. Additionally, we implement innovative selection schemes for replay samples based on the model's hidden representations. Our comprehensive evaluation across Windows and Android malware datasets in a class-incremental learning scenario -- where new classes are introduced continuously over multiple tasks -- demonstrates substantial performance improvements over previous methods. For example, our system achieves an average accuracy of 55% on Windows malware samples, significantly outperforming other GR-based models by 28%. This study provides practical insights for advancing GR-based malware classification systems. The implementation is available at https://github.com/MalwareReplayGAN/MalCLThe code will be made public upon the presentation of the paper.

Knowledge-intensive language tasks require NLP systems to both provide the correct answer and retrieve supporting evidence for it in a given corpus. Autoregressive language models are emerging as the de-facto standard for generating answers, with newer and more powerful systems emerging at an astonishing pace. In this paper we argue that all this (and future) progress can be directly applied to the retrieval problem with minimal intervention to the models' architecture. Previous work has explored ways to partition the search space into hierarchical structures and retrieve documents by autoregressively generating their unique identifier. In this work we propose an alternative that doesn't force any structure in the search space: using all ngrams in a passage as its possible identifiers. This setup allows us to use an autoregressive model to generate and score distinctive ngrams, that are then mapped to full passages through an efficient data structure. Empirically, we show this not only outperforms prior autoregressive approaches but also leads to an average improvement of at least 10 points over more established retrieval solutions for passage-level retrieval on the KILT benchmark, establishing new state-of-the-art downstream performance on some datasets, while using a considerably lighter memory footprint than competing systems. Code and pre-trained models at https://github.com/facebookresearch/SEAL.

Large language models (LLMs) typically utilize the top-k contexts from a retriever in retrieval-augmented generation (RAG). In this work, we propose a novel instruction fine-tuning framework RankRAG, which instruction-tunes a single LLM for the dual purpose of context ranking and answer generation in RAG. In particular, the instruction-tuned LLMs work surprisingly well by adding a small fraction of ranking data into the training blend, and outperform existing expert ranking models, including the same LLM exclusively fine-tuned on a large amount of ranking data. For generation, we compare our model with many strong baselines, including GPT-4-0613, GPT-4-turbo-2024-0409, and ChatQA-1.5, an open-sourced model with the state-of-the-art performance on RAG benchmarks. Specifically, our Llama3-RankRAG significantly outperforms Llama3-ChatQA-1.5 and GPT-4 models on nine knowledge-intensive benchmarks. In addition, it also performs comparably to GPT-4 on five RAG benchmarks in the biomedical domain without instruction fine-tuning on biomedical data, demonstrating its superb capability for generalization to new domains.

Using Large Language Models (LLMs) has gained popularity among software developers for generating source code. However, the use of LLM-generated code can introduce risks of adding suboptimal, defective, and vulnerable code. This makes it necessary to devise methods for the accurate detection of LLM-generated code. Toward this goal, we perform a case study of Claude 3 Haiku (or Claude 3 for brevity) on CodeSearchNet dataset. We divide our analyses into two parts: function-level and class-level. We extract 22 software metric features, such as Code Lines and Cyclomatic Complexity, for each level of granularity. We then analyze code snippets generated by Claude 3 and their human-authored counterparts using the extracted features to understand how unique the code generated by Claude 3 is. In the following step, we use the unique characteristics of Claude 3-generated code to build Machine Learning (ML) models and identify which features of the code snippets make them more detectable by ML models. Our results indicate that Claude 3 tends to generate longer functions, but shorter classes than humans, and this characteristic can be used to detect Claude 3-generated code with ML models with 82% and 66% accuracies for function-level and class-level snippets, respectively.

Code Large Language Models (Code LLMs) have excelled at tasks like code completion but often miss deeper semantics such as execution effects and dynamic states. This paper aims to bridge the gap between Code LLMs' reliance on static text data and the need for thorough semantic understanding for complex tasks like debugging and program repair. We introduce a novel strategy to train Code LLMs with comprehensive semantics, encompassing high-level functional descriptions, local execution effects of individual statements, and overall input/output behavior, thereby linking static code text with dynamic execution states. We begin by collecting PyX, a clean code corpus of fully executable samples with functional descriptions and execution tracing. We propose training Code LLMs to write code and represent and reason about execution behaviors using natural language, mimicking human verbal debugging. This approach led to the development of SemCoder, a Code LLM with only 6.7B parameters, which shows competitive performance with GPT-3.5-turbo on code generation and execution reasoning tasks. SemCoder achieves 81.1% on HumanEval (GPT-3.5-turbo: 76.8%) and 54.5% on CRUXEval-I (GPT-3.5-turbo: 50.3%). We also study the effectiveness of SemCoder's monologue-style execution reasoning compared to concrete scratchpad reasoning, showing that our approach integrates semantics from multiple dimensions more smoothly. Finally, we demonstrate the potential of applying learned semantics to improve Code LLMs' debugging and self-refining capabilities.

Existing methods fail to effectively steer Large Language Models (LLMs) between textual reasoning and code generation, leaving symbolic computing capabilities underutilized. We introduce CodeSteer, an effective method for guiding LLM code/text generation. We construct a comprehensive benchmark SymBench comprising 37 symbolic tasks with adjustable complexity and also synthesize datasets of 12k multi-round guidance/generation trajectories and 5.5k guidance comparison pairs. We fine-tune the Llama-3-8B model with a newly designed multi-round supervised fine-tuning (SFT) and direct preference optimization (DPO). The resulting model, CodeSteerLLM, augmented with the proposed symbolic and self-answer checkers, effectively guides the code/text generation of larger models. Augmenting GPT-4o with CodeSteer raises its average performance score from 53.3 to 86.4, even outperforming the existing best LLM OpenAI o1 (82.7), o1-preview (74.8), and DeepSeek R1 (76.8) across all 37 tasks (28 seen, 9 unseen). Trained for GPT-4o, CodeSteer demonstrates superior generalizability, providing an average 41.8 performance boost on Claude, Mistral, and GPT-3.5. CodeSteer-guided LLMs fully harness symbolic computing to maintain strong performance on highly complex tasks. Models, Datasets, and Codes are available at https://github.com/yongchao98/CodeSteer-v1.0.

Stack Overflow (SO) has been a great source of natural language questions and their code solutions (i.e., question-code pairs), which are critical for many tasks including code retrieval and annotation. In most existing research, question-code pairs were collected heuristically and tend to have low quality. In this paper, we investigate a new problem of systematically mining question-code pairs from Stack Overflow (in contrast to heuristically collecting them). It is formulated as predicting whether or not a code snippet is a standalone solution to a question. We propose a novel Bi-View Hierarchical Neural Network which can capture both the programming content and the textual context of a code snippet (i.e., two views) to make a prediction. On two manually annotated datasets in Python and SQL domain, our framework substantially outperforms heuristic methods with at least 15% higher F1 and accuracy. Furthermore, we present StaQC (Stack Overflow Question-Code pairs), the largest dataset to date of ~148K Python and ~120K SQL question-code pairs, automatically mined from SO using our framework. Under various case studies, we demonstrate that StaQC can greatly help develop data-hungry models for associating natural language with programming language.

Despite rapid advancement in the field of Constrained Natural Language Generation, little time has been spent on exploring the potential of language models which have had their vocabularies lexically, semantically, and/or phonetically constrained. We find that most language models generate compelling text even under significant constraints. We present a simple and universally applicable technique for modifying the output of a language model by compositionally applying filter functions to the language models vocabulary before a unit of text is generated. This approach is plug-and-play and requires no modification to the model. To showcase the value of this technique, we present an easy to use AI writing assistant called Constrained Text Generation Studio (CTGS). CTGS allows users to generate or choose from text with any combination of a wide variety of constraints, such as banning a particular letter, forcing the generated words to have a certain number of syllables, and/or forcing the words to be partial anagrams of another word. We introduce a novel dataset of prose that omits the letter e. We show that our method results in strictly superior performance compared to fine-tuning alone on this dataset. We also present a Huggingface space web-app presenting this technique called Gadsby. The code is available to the public here: https://github.com/Hellisotherpeople/Constrained-Text-Generation-Studio

Generalized Continual Category Discovery (GCCD) tackles learning from sequentially arriving, partially labeled datasets while uncovering new categories. Traditional methods depend on feature distillation to prevent forgetting the old knowledge. However, this strategy restricts the model's ability to adapt and effectively distinguish new categories. To address this, we introduce a novel technique integrating a learnable projector with feature distillation, thus enhancing model adaptability without sacrificing past knowledge. The resulting distribution shift of the previously learned categories is mitigated with the auxiliary category adaptation network. We demonstrate that while each component offers modest benefits individually, their combination - dubbed CAMP (Category Adaptation Meets Projected distillation) - significantly improves the balance between learning new information and retaining old. CAMP exhibits superior performance across several GCCD and Class Incremental Learning scenarios. The code is available at https://github.com/grypesc/CAMP.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

The rapid evolution of software libraries presents a significant challenge for code generation models, which must adapt to frequent version updates while maintaining compatibility with previous versions. Existing code completion benchmarks often overlook this dynamic aspect, and the one that does consider it relies on static code prediction tasks without execution-based evaluation, offering a limited perspective on a model's practical usability. To address this gap, we introduce \GitChameleon{}, a novel, manually curated dataset comprising 116 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. is designed to rigorously assess the ability of modern large language models (LLMs) to generate version-specific code that is not only syntactically correct but also functionally accurate upon execution. Our comprehensive evaluations reveal that state-of-the-art LLMs struggle with this task; for instance, GPT-4o achieves a pass@10 of only 39.9\% (43.7\% when provided with error feedback), highlighting the complexity of the problem and the limitations of current models. By providing an execution-based benchmark that emphasizes the dynamic nature of code libraries, serves as a critical tool to advance the development of more adaptable and reliable code generation models. For facilitation for further exploration of version-conditioned code generation, we make our code repository publicly accessible at https://github.com/NizarIslah/GitChameleon.

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.

We present Grid Beam Search (GBS), an algorithm which extends beam search to allow the inclusion of pre-specified lexical constraints. The algorithm can be used with any model that generates a sequence hat{y} = {y_{0}ldots y_{T}} , by maximizing p(y | x) = prodlimits_{t}p(y_{t} | x; {y_{0} ldots y_{t-1}}) . Lexical constraints take the form of phrases or words that must be present in the output sequence. This is a very general way to incorporate additional knowledge into a model's output without requiring any modification of the model parameters or training data. We demonstrate the feasibility and flexibility of Lexically Constrained Decoding by conducting experiments on Neural Interactive-Predictive Translation, as well as Domain Adaptation for Neural Machine Translation. Experiments show that GBS can provide large improvements in translation quality in interactive scenarios, and that, even without any user input, GBS can be used to achieve significant gains in performance in domain adaptation scenarios.

In this paper, we investigate the instability in the standard dense retrieval training, which iterates between model training and hard negative selection using the being-trained model. We show the catastrophic forgetting phenomena behind the training instability, where models learn and forget different negative groups during training iterations. We then propose ANCE-Tele, which accumulates momentum negatives from past iterations and approximates future iterations using lookahead negatives, as "teleportations" along the time axis to smooth the learning process. On web search and OpenQA, ANCE-Tele outperforms previous state-of-the-art systems of similar size, eliminates the dependency on sparse retrieval negatives, and is competitive among systems using significantly more (50x) parameters. Our analysis demonstrates that teleportation negatives reduce catastrophic forgetting and improve convergence speed for dense retrieval training. Our code is available at https://github.com/OpenMatch/ANCE-Tele.

Effective code retrieval plays a crucial role in advancing code generation, bug fixing, and software maintenance, particularly as software systems increase in complexity. While current code embedding models have demonstrated promise in retrieving code snippets for small-scale, well-defined tasks, they often underperform in more demanding real-world applications such as bug localization within GitHub repositories. We hypothesize that a key issue is their reliance on noisy and inconsistent datasets for training, which impedes their ability to generalize to more complex retrieval scenarios. To address these limitations, we introduce CoRNStack, a large-scale, high-quality contrastive training dataset for code that spans multiple programming languages. This dataset is curated using consistency filtering to eliminate noisy positives and is further enriched with mined hard negatives, thereby facilitating more effective learning. We demonstrate that contrastive training of embedding models using CoRNStack leads to state-of-the-art performance across a variety of code retrieval tasks. Furthermore, the dataset can be leveraged for training code reranking models, a largely underexplored area compared to text reranking. Our finetuned code reranking model significantly improves the ranking quality over the retrieved results. Finally, by employing our code retriever and reranker together, we demonstrate significant improvements in function localization for GitHub issues, an important component of real-world software development.

In this paper, we propose KnowCoder, a Large Language Model (LLM) to conduct Universal Information Extraction (UIE) via code generation. KnowCoder aims to develop a kind of unified schema representation that LLMs can easily understand and an effective learning framework that encourages LLMs to follow schemas and extract structured knowledge accurately. To achieve these, KnowCoder introduces a code-style schema representation method to uniformly transform different schemas into Python classes, with which complex schema information, such as constraints among tasks in UIE, can be captured in an LLM-friendly manner. We further construct a code-style schema library covering over 30,000 types of knowledge, which is the largest one for UIE, to the best of our knowledge. To ease the learning process of LLMs, KnowCoder contains a two-phase learning framework that enhances its schema understanding ability via code pretraining and its schema following ability via instruction tuning. After code pretraining on around 1.5B automatically constructed data, KnowCoder already attains remarkable generalization ability and achieves relative improvements by 49.8% F1, compared to LLaMA2, under the few-shot setting. After instruction tuning, KnowCoder further exhibits strong generalization ability on unseen schemas and achieves up to 12.5% and 21.9%, compared to sota baselines, under the zero-shot setting and the low resource setting, respectively. Additionally, based on our unified schema representations, various human-annotated datasets can simultaneously be utilized to refine KnowCoder, which achieves significant improvements up to 7.5% under the supervised setting.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

This research paper presents a comprehensive analysis of integrating advanced language models with search and retrieval systems in the fields of information retrieval and natural language processing. The objective is to evaluate and compare various state-of-the-art methods based on their performance in terms of accuracy and efficiency. The analysis explores different combinations of technologies, including Azure Cognitive Search Retriever with GPT-4, Pinecone's Canopy framework, Langchain with Pinecone and different language models (OpenAI, Cohere), LlamaIndex with Weaviate Vector Store's hybrid search, Google's RAG implementation on Cloud VertexAI-Search, Amazon SageMaker's RAG, and a novel approach called KG-FID Retrieval. The motivation for this analysis arises from the increasing demand for robust and responsive question-answering systems in various domains. The RobustQA metric is used to evaluate the performance of these systems under diverse paraphrasing of questions. The report aims to provide insights into the strengths and weaknesses of each method, facilitating informed decisions in the deployment and development of AI-driven search and retrieval systems.

Graph neural networks (GNN) has been successfully applied to operate on the graph-structured data. Given a specific scenario, rich human expertise and tremendous laborious trials are usually required to identify a suitable GNN architecture. It is because the performance of a GNN architecture is significantly affected by the choice of graph convolution components, such as aggregate function and hidden dimension. Neural architecture search (NAS) has shown its potential in discovering effective deep architectures for learning tasks in image and language modeling. However, existing NAS algorithms cannot be directly applied to the GNN search problem. First, the search space of GNN is different from the ones in existing NAS work. Second, the representation learning capacity of GNN architecture changes obviously with slight architecture modifications. It affects the search efficiency of traditional search methods. Third, widely used techniques in NAS such as parameter sharing might become unstable in GNN. To bridge the gap, we propose the automated graph neural networks (AGNN) framework, which aims to find an optimal GNN architecture within a predefined search space. A reinforcement learning based controller is designed to greedily validate architectures via small steps. AGNN has a novel parameter sharing strategy that enables homogeneous architectures to share parameters, based on a carefully-designed homogeneity definition. Experiments on real-world benchmark datasets demonstrate that the GNN architecture identified by AGNN achieves the best performance, comparing with existing handcrafted models and tradistional search methods.

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

We explore different ways to utilize position-based cross-attention in seq2seq networks to enable length generalization in algorithmic tasks. We show that a simple approach of interpolating the original and reversed encoded representations combined with relative attention allows near-perfect length generalization for both forward and reverse lookup tasks or copy tasks that had been generally hard to tackle. We also devise harder diagnostic tasks where the relative distance of the ideal attention position varies with timestep. In such settings, the simple interpolation trick with relative attention is not sufficient. We introduce novel variants of location attention building on top of Dubois et al. (2020) to address the new diagnostic tasks. We also show the benefits of our approaches for length generalization in SCAN (Lake & Baroni, 2018) and CFQ (Keysers et al., 2020). Our code is available on GitHub.

Dense retrieval requires high-quality text sequence embeddings to support effective search in the representation space. Autoencoder-based language models are appealing in dense retrieval as they train the encoder to output high-quality embedding that can reconstruct the input texts. However, in this paper, we provide theoretical analyses and show empirically that an autoencoder language model with a low reconstruction loss may not provide good sequence representations because the decoder may take shortcuts by exploiting language patterns. To address this, we propose a new self-learning method that pre-trains the autoencoder using a weak decoder, with restricted capacity and attention flexibility to push the encoder to provide better text representations. Our experiments on web search, news recommendation, and open domain question answering show that our pre-trained model significantly boosts the effectiveness and few-shot ability of dense retrieval models. Our code is available at https://github.com/microsoft/SEED-Encoder/.

Generative large language models (LLMs) pre-trained on code have shown impressive effectiveness in code generation, program repair, and document analysis. However, existing generative LLMs focus on source code and are not specialized for binaries. There are three main challenges for LLMs to model and learn binary code: hex-decimal values, complex global dependencies, and compiler optimization levels. To bring the benefit of LLMs to the binary domain, we develop Nova and Nova^+, which are LLMs pre-trained on binary corpora. Nova is pre-trained with the standard language modeling task, showing significantly better capability on five benchmarks for three downstream tasks: binary code similarity detection (BCSD), binary code translation (BCT), and binary code recovery (BCR), over GPT-3.5 and other existing techniques. We build Nova^+ to further boost Nova using two new pre-training tasks, i.e., optimization generation and optimization level prediction, which are designed to learn binary optimization and align equivalent binaries. Nova^+ shows overall the best performance for all three downstream tasks on five benchmarks, demonstrating the contributions of the new pre-training tasks.

Subject-driven generation has garnered significant interest recently due to its ability to personalize text-to-image generation. Typical works focus on learning the new subject's private attributes. However, an important fact has not been taken seriously that a subject is not an isolated new concept but should be a specialization of a certain category in the pre-trained model. This results in the subject failing to comprehensively inherit the attributes in its category, causing poor attribute-related generations. In this paper, motivated by object-oriented programming, we model the subject as a derived class whose base class is its semantic category. This modeling enables the subject to inherit public attributes from its category while learning its private attributes from the user-provided example. Specifically, we propose a plug-and-play method, Subject-Derived regularization (SuDe). It constructs the base-derived class modeling by constraining the subject-driven generated images to semantically belong to the subject's category. Extensive experiments under three baselines and two backbones on various subjects show that our SuDe enables imaginative attribute-related generations while maintaining subject fidelity. Codes will be open sourced soon at FaceChain (https://github.com/modelscope/facechain).

Large Language Models (LLMs) are gaining popularity among software engineers. A crucial aspect of developing effective code generation LLMs is to evaluate these models using a robust benchmark. Evaluation benchmarks with quality issues can provide a false sense of performance. In this work, we conduct the first-of-its-kind study of the quality of prompts within benchmarks used to compare the performance of different code generation models. To conduct this study, we analyzed 3,566 prompts from 9 code generation benchmarks to identify quality issues in them. We also investigated whether fixing the identified quality issues in the benchmarks' prompts affects a model's performance. We also studied memorization issues of the evaluation dataset, which can put into question a benchmark's trustworthiness. We found that code generation evaluation benchmarks mainly focused on Python and coding exercises and had very limited contextual dependencies to challenge the model. These datasets and the developers' prompts suffer from quality issues like spelling and grammatical errors, unclear sentences to express developers' intent, and not using proper documentation style. Fixing all these issues in the benchmarks can lead to a better performance for Python code generation, but not a significant improvement was observed for Java code generation. We also found evidence that GPT-3.5-Turbo and CodeGen-2.5 models may have data contamination issues.

The in-memory algorithms for approximate nearest neighbor search (ANNS) have achieved great success for fast high-recall search, but are extremely expensive when handling very large scale database. Thus, there is an increasing request for the hybrid ANNS solutions with small memory and inexpensive solid-state drive (SSD). In this paper, we present a simple but efficient memory-disk hybrid indexing and search system, named SPANN, that follows the inverted index methodology. It stores the centroid points of the posting lists in the memory and the large posting lists in the disk. We guarantee both disk-access efficiency (low latency) and high recall by effectively reducing the disk-access number and retrieving high-quality posting lists. In the index-building stage, we adopt a hierarchical balanced clustering algorithm to balance the length of posting lists and augment the posting list by adding the points in the closure of the corresponding clusters. In the search stage, we use a query-aware scheme to dynamically prune the access of unnecessary posting lists. Experiment results demonstrate that SPANN is 2times faster than the state-of-the-art ANNS solution DiskANN to reach the same recall quality 90% with same memory cost in three billion-scale datasets. It can reach 90% recall@1 and recall@10 in just around one millisecond with only 32GB memory cost. Code is available at: {\footnotesizeblue{https://github.com/microsoft/SPTAG}}.

Code generation aims to understand the problem description and generate corresponding code snippets, where existing works generally decompose such complex tasks into intermediate steps by prompting strategies, such as Chain-of-Thought and its variants. While these studies have achieved some success, their effectiveness is highly dependent on the capabilities of advanced Large Language Models (LLMs) such as GPT-4, particularly in terms of API calls, which significantly limits their practical applicability. Consequently, how to enhance the code generation capabilities of small and medium-scale code LLMs without significantly increasing training costs is an appealing challenge. In this paper, we suggest that code comments are the natural logic pivot between natural language and code language and propose using comments to boost the code generation ability of code LLMs. Concretely, we propose MANGO (comMents As Natural loGic pivOts), including a comment contrastive training strategy and a corresponding logical comment decoding strategy. Experiments are performed on HumanEval and MBPP, utilizing StarCoder and WizardCoder as backbone models, and encompassing model parameter sizes between 3B and 7B. The results indicate that MANGO significantly improves the code pass rate based on the strong baselines. Meanwhile, the robustness of the logical comment decoding strategy is notably higher than the Chain-of-thoughts prompting. The code is publicly available at https://github.com/pppa2019/Mango.

Knowledge-intensive language tasks (KILT) usually require a large body of information to provide correct answers. A popular paradigm to solve this problem is to combine a search system with a machine reader, where the former retrieves supporting evidences and the latter examines them to produce answers. Recently, the reader component has witnessed significant advances with the help of large-scale pre-trained generative models. Meanwhile most existing solutions in the search component rely on the traditional ``index-retrieve-then-rank'' pipeline, which suffers from large memory footprint and difficulty in end-to-end optimization. Inspired by recent efforts in constructing model-based IR models, we propose to replace the traditional multi-step search pipeline with a novel single-step generative model, which can dramatically simplify the search process and be optimized in an end-to-end manner. We show that a strong generative retrieval model can be learned with a set of adequately designed pre-training tasks, and be adopted to improve a variety of downstream KILT tasks with further fine-tuning. We name the pre-trained generative retrieval model as CorpusBrain as all information about the corpus is encoded in its parameters without the need of constructing additional index. Empirical results show that CorpusBrain can significantly outperform strong baselines for the retrieval task on the KILT benchmark and establish new state-of-the-art downstream performances. We also show that CorpusBrain works well under zero- and low-resource settings.

Both graph structures and textual information play a critical role in Knowledge Graph Completion (KGC). With the success of Pre-trained Language Models (PLMs) such as BERT, they have been applied for text encoding for KGC. However, the current methods mostly prefer to fine-tune PLMs, leading to huge training costs and limited scalability to larger PLMs. In contrast, we propose to utilize prompts and perform KGC on a frozen PLM with only the prompts trained. Accordingly, we propose a new KGC method named PDKGC with two prompts -- a hard task prompt which is to adapt the KGC task to the PLM pre-training task of token prediction, and a disentangled structure prompt which learns disentangled graph representation so as to enable the PLM to combine more relevant structure knowledge with the text information. With the two prompts, PDKGC builds a textual predictor and a structural predictor, respectively, and their combination leads to more comprehensive entity prediction. Solid evaluation on two widely used KGC datasets has shown that PDKGC often outperforms the baselines including the state-of-the-art, and its components are all effective. Our codes and data are available at https://github.com/genggengcss/PDKGC.

In recent years, the use of automated source code generation utilizing transformer-based generative models has expanded, and these models can generate functional code according to the requirements of the developers. However, recent research revealed that these automatically generated source codes can contain vulnerabilities and other quality issues. Despite researchers' and practitioners' attempts to enhance code generation models, retraining and fine-tuning large language models is time-consuming and resource-intensive. Thus, we describe FRANC, a lightweight framework for recommending more secure and high-quality source code derived from transformer-based code generation models. FRANC includes a static filter to make the generated code compilable with heuristics and a quality-aware ranker to sort the code snippets based on a quality score. Moreover, the framework uses prompt engineering to fix persistent quality issues. We evaluated the framework with five Python and Java code generation models and six prompt datasets, including a newly created one in this work (SOEval). The static filter improves 9% to 46% Java suggestions and 10% to 43% Python suggestions regarding compilability. The average improvement over the NDCG@10 score for the ranking system is 0.0763, and the repairing techniques repair the highest 80% of prompts. FRANC takes, on average, 1.98 seconds for Java; for Python, it takes 0.08 seconds.

Given the recent impressive accomplishments of language models (LMs) for code generation, we explore the use of LMs as adaptive mutation and crossover operators for an evolutionary neural architecture search (NAS) algorithm. While NAS still proves too difficult a task for LMs to succeed at solely through prompting, we find that the combination of evolutionary prompt engineering with soft prompt-tuning, a method we term EvoPrompting, consistently finds diverse and high performing models. We first demonstrate that EvoPrompting is effective on the computationally efficient MNIST-1D dataset, where EvoPrompting produces convolutional architecture variants that outperform both those designed by human experts and naive few-shot prompting in terms of accuracy and model size. We then apply our method to searching for graph neural networks on the CLRS Algorithmic Reasoning Benchmark, where EvoPrompting is able to design novel architectures that outperform current state-of-the-art models on 21 out of 30 algorithmic reasoning tasks while maintaining similar model size. EvoPrompting is successful at designing accurate and efficient neural network architectures across a variety of machine learning tasks, while also being general enough for easy adaptation to other tasks beyond neural network design.

Software engineers are increasingly adding semantic search capabilities to applications using a strategy known as Retrieval Augmented Generation (RAG). A RAG system involves finding documents that semantically match a query and then passing the documents to a large language model (LLM) such as ChatGPT to extract the right answer using an LLM. RAG systems aim to: a) reduce the problem of hallucinated responses from LLMs, b) link sources/references to generated responses, and c) remove the need for annotating documents with meta-data. However, RAG systems suffer from limitations inherent to information retrieval systems and from reliance on LLMs. In this paper, we present an experience report on the failure points of RAG systems from three case studies from separate domains: research, education, and biomedical. We share the lessons learned and present 7 failure points to consider when designing a RAG system. The two key takeaways arising from our work are: 1) validation of a RAG system is only feasible during operation, and 2) the robustness of a RAG system evolves rather than designed in at the start. We conclude with a list of potential research directions on RAG systems for the software engineering community.

Retrieval-Augmented Generation (RAG) systems have recently shown remarkable advancements by integrating retrieval mechanisms into language models, enhancing their ability to produce more accurate and contextually relevant responses. However, the influence of various components and configurations within RAG systems remains underexplored. A comprehensive understanding of these elements is essential for tailoring RAG systems to complex retrieval tasks and ensuring optimal performance across diverse applications. In this paper, we develop several advanced RAG system designs that incorporate query expansion, various novel retrieval strategies, and a novel Contrastive In-Context Learning RAG. Our study systematically investigates key factors, including language model size, prompt design, document chunk size, knowledge base size, retrieval stride, query expansion techniques, Contrastive In-Context Learning knowledge bases, multilingual knowledge bases, and Focus Mode retrieving relevant context at sentence-level. Through extensive experimentation, we provide a detailed analysis of how these factors influence response quality. Our findings offer actionable insights for developing RAG systems, striking a balance between contextual richness and retrieval-generation efficiency, thereby paving the way for more adaptable and high-performing RAG frameworks in diverse real-world scenarios. Our code and implementation details are publicly available.

We investigate the usefulness of generative Large Language Models (LLMs) in generating training data for cross-encoder re-rankers in a novel direction: generating synthetic documents instead of synthetic queries. We introduce a new dataset, ChatGPT-RetrievalQA, and compare the effectiveness of models fine-tuned on LLM-generated and human-generated data. Data generated with generative LLMs can be used to augment training data, especially in domains with smaller amounts of labeled data. We build ChatGPT-RetrievalQA based on an existing dataset, human ChatGPT Comparison Corpus (HC3), consisting of public question collections with human responses and answers from ChatGPT. We fine-tune a range of cross-encoder re-rankers on either human-generated or ChatGPT-generated data. Our evaluation on MS MARCO DEV, TREC DL'19, and TREC DL'20 demonstrates that cross-encoder re-ranking models trained on ChatGPT responses are statistically significantly more effective zero-shot re-rankers than those trained on human responses. In a supervised setting, the human-trained re-rankers outperform the LLM-trained re-rankers. Our novel findings suggest that generative LLMs have high potential in generating training data for neural retrieval models. Further work is needed to determine the effect of factually wrong information in the generated responses and test our findings' generalizability with open-source LLMs. We release our data, code, and cross-encoders checkpoints for future work.

Noticing the urgent need to provide tools for fast and user-friendly qualitative analysis of large-scale textual corpora of the modern NLP, we propose to turn to the mature and well-tested methods from the domain of Information Retrieval (IR) - a research field with a long history of tackling TB-scale document collections. We discuss how Pyserini - a widely used toolkit for reproducible IR research can be integrated with the Hugging Face ecosystem of open-source AI libraries and artifacts. We leverage the existing functionalities of both platforms while proposing novel features further facilitating their integration. Our goal is to give NLP researchers tools that will allow them to develop retrieval-based instrumentation for their data analytics needs with ease and agility. We include a Jupyter Notebook-based walk through the core interoperability features, available on GitHub at https://github.com/huggingface/gaia. We then demonstrate how the ideas we present can be operationalized to create a powerful tool for qualitative data analysis in NLP. We present GAIA Search - a search engine built following previously laid out principles, giving access to four popular large-scale text collections. GAIA serves a dual purpose of illustrating the potential of methodologies we discuss but also as a standalone qualitative analysis tool that can be leveraged by NLP researchers aiming to understand datasets prior to using them in training. GAIA is hosted live on Hugging Face Spaces - https://huggingface.co/spaces/spacerini/gaia.

We consider a scenario where we have access to the target domain, but cannot afford on-the-fly training data annotation, and instead would like to construct an alternative training set from a large-scale data pool such that a competitive model can be obtained. We propose a search and pruning (SnP) solution to this training data search problem, tailored to object re-identification (re-ID), an application aiming to match the same object captured by different cameras. Specifically, the search stage identifies and merges clusters of source identities which exhibit similar distributions with the target domain. The second stage, subject to a budget, then selects identities and their images from the Stage I output, to control the size of the resulting training set for efficient training. The two steps provide us with training sets 80\% smaller than the source pool while achieving a similar or even higher re-ID accuracy. These training sets are also shown to be superior to a few existing search methods such as random sampling and greedy sampling under the same budget on training data size. If we release the budget, training sets resulting from the first stage alone allow even higher re-ID accuracy. We provide interesting discussions on the specificity of our method to the re-ID problem and particularly its role in bridging the re-ID domain gap. The code is available at https://github.com/yorkeyao/SnP.

Background: AI-powered code generation, fueled by Large Language Models (LLMs), is revolutionizing software development. Models like OpenAI's Codex and GPT-4, alongside DeepSeek, leverage vast code and natural language datasets. However, ensuring code quality, correctness, and managing complex tasks remains challenging, necessitating thorough evaluation. Methodology: This research compares ChatGPT (version o1) and DeepSeek (version R1) for Python code generation using online judge coding challenges. It evaluates correctness (online judge verdicts, up to three attempts), code quality (Pylint/Flake8), and efficiency (execution time/memory usage). Results: DeepSeek demonstrated higher correctness, particularly on algorithmic tasks, often achieving 'Accepted' on the first attempt. ChatGPT sometimes requires multiple attempts or failures. ChatGPT encountered fewer issues, used comparable or slightly less memory, consumed less execution times and wrote fewer lines of code. Conclusion: DeepSeek exhibited superior correctness in Python code generation, often requiring fewer attempts, suggesting an advantage in algorithmic problem-solving. Both models showed almost similar efficiency in execution time and memory use. Finally, this research provides insights for developers choosing AI coding assistants and informs future AI-driven software development research.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

Transformer is a transformative framework that models sequential data and has achieved remarkable performance on a wide range of tasks, but with high computational and energy cost. To improve its efficiency, a popular choice is to compress the models via binarization which constrains the floating-point values into binary ones to save resource consumption owing to cheap bitwise operations significantly. However, existing binarization methods only aim at minimizing the information loss for the input distribution statistically, while ignoring the pairwise similarity modeling at the core of the attention. To this end, we propose a new binarization paradigm customized to high-dimensional softmax attention via kernelized hashing, called EcoFormer, to map the original queries and keys into low-dimensional binary codes in Hamming space. The kernelized hash functions are learned to match the ground-truth similarity relations extracted from the attention map in a self-supervised way. Based on the equivalence between the inner product of binary codes and the Hamming distance as well as the associative property of matrix multiplication, we can approximate the attention in linear complexity by expressing it as a dot-product of binary codes. Moreover, the compact binary representations of queries and keys enable us to replace most of the expensive multiply-accumulate operations in attention with simple accumulations to save considerable on-chip energy footprint on edge devices. Extensive experiments on both vision and language tasks show that EcoFormer consistently achieves comparable performance with standard attentions while consuming much fewer resources. For example, based on PVTv2-B0 and ImageNet-1K, Ecoformer achieves a 73% on-chip energy footprint reduction with only a 0.33% performance drop compared to the standard attention. Code is available at https://github.com/ziplab/EcoFormer.

Recent advances in machine learning have significantly improved the understanding of source code data and achieved good performance on a number of downstream tasks. Open source repositories like GitHub enable this process with rich unlabeled code data. However, the lack of high quality labeled data has largely hindered the progress of several code related tasks, such as program translation, summarization, synthesis, and code search. This paper introduces XLCoST, Cross-Lingual Code SnippeT dataset, a new benchmark dataset for cross-lingual code intelligence. Our dataset contains fine-grained parallel data from 8 languages (7 commonly used programming languages and English), and supports 10 cross-lingual code tasks. To the best of our knowledge, it is the largest parallel dataset for source code both in terms of size and the number of languages. We also provide the performance of several state-of-the-art baseline models for each task. We believe this new dataset can be a valuable asset for the research community and facilitate the development and validation of new methods for cross-lingual code intelligence.

Neural networks are sensitive to hyper-parameter and architecture choices. Automated Machine Learning (AutoML) is a promising paradigm for automating these choices. Current ML software libraries, however, are quite limited in handling the dynamic interactions among the components of AutoML. For example, efficientNAS algorithms, such as ENAS and DARTS, typically require an implementation coupling between the search space and search algorithm, the two key components in AutoML. Furthermore, implementing a complex search flow, such as searching architectures within a loop of searching hardware configurations, is difficult. To summarize, changing the search space, search algorithm, or search flow in current ML libraries usually requires a significant change in the program logic. In this paper, we introduce a new way of programming AutoML based on symbolic programming. Under this paradigm, ML programs are mutable, thus can be manipulated easily by another program. As a result, AutoML can be reformulated as an automated process of symbolic manipulation. With this formulation, we decouple the triangle of the search algorithm, the search space and the child program. This decoupling makes it easy to change the search space and search algorithm (without and with weight sharing), as well as to add search capabilities to existing code and implement complex search flows. We then introduce PyGlove, a new Python library that implements this paradigm. Through case studies on ImageNet and NAS-Bench-101, we show that with PyGlove users can easily convert a static program into a search space, quickly iterate on the search spaces and search algorithms, and craft complex search flows to achieve better results.

Retrieving and extracting knowledge from extensive research documents and large databases presents significant challenges for researchers, students, and professionals in today's information-rich era. Existing retrieval systems, which rely on general-purpose Large Language Models (LLMs), often fail to provide accurate responses to domain-specific inquiries. Additionally, the high cost of pretraining or fine-tuning LLMs for specific domains limits their widespread adoption. To address these limitations, we propose a novel methodology that combines the generative capabilities of LLMs with the fast and accurate retrieval capabilities of vector databases. This advanced retrieval system can efficiently handle both tabular and non-tabular data, understand natural language user queries, and retrieve relevant information without fine-tuning. The developed model, Generative Text Retrieval (GTR), is adaptable to both unstructured and structured data with minor refinement. GTR was evaluated on both manually annotated and public datasets, achieving over 90% accuracy and delivering truthful outputs in 87% of cases. Our model achieved state-of-the-art performance with a Rouge-L F1 score of 0.98 on the MSMARCO dataset. The refined model, Generative Tabular Text Retrieval (GTR-T), demonstrated its efficiency in large database querying, achieving an Execution Accuracy (EX) of 0.82 and an Exact-Set-Match (EM) accuracy of 0.60 on the Spider dataset, using an open-source LLM. These efforts leverage Generative AI and In-Context Learning to enhance human-text interaction and make advanced AI capabilities more accessible. By integrating robust retrieval systems with powerful LLMs, our approach aims to democratize access to sophisticated AI tools, improving the efficiency, accuracy, and scalability of AI-driven information retrieval and database querying.

Multi-hop Question Answering (QA) necessitates complex reasoning by integrating multiple pieces of information to resolve intricate questions. However, existing QA systems encounter challenges such as outdated information, context window length limitations, and an accuracy-quantity trade-off. To address these issues, we propose a novel framework, the Hierarchical Retrieval-Augmented Generation Model with Rethink (HiRAG), comprising Decomposer, Definer, Retriever, Filter, and Summarizer five key modules. We introduce a new hierarchical retrieval strategy that incorporates both sparse retrieval at the document level and dense retrieval at the chunk level, effectively integrating their strengths. Additionally, we propose a single-candidate retrieval method to mitigate the limitations of multi-candidate retrieval. We also construct two new corpora, Indexed Wikicorpus and Profile Wikicorpus, to address the issues of outdated and insufficient knowledge. Our experimental results on four datasets demonstrate that HiRAG outperforms state-of-the-art models across most metrics, and our Indexed Wikicorpus is effective. The code for HiRAG is available at https://github.com/2282588541a/HiRAG

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

Diffusion models have recently exhibited remarkable performance on synthetic data. After a diffusion path is selected, a base model, such as UNet, operates as a denoising autoencoder, primarily predicting noises that need to be eliminated step by step. Consequently, it is crucial to employ a model that aligns with the expected budgets to facilitate superior synthetic performance. In this paper, we meticulously analyze the diffusion model and engineer a base model search approach, denoted "DiffNAS". Specifically, we leverage GPT-4 as a supernet to expedite the search, supplemented with a search memory to enhance the results. Moreover, we employ RFID as a proxy to promptly rank the experimental outcomes produced by GPT-4. We also adopt a rapid-convergence training strategy to boost search efficiency. Rigorous experimentation corroborates that our algorithm can augment the search efficiency by 2 times under GPT-based scenarios, while also attaining a performance of 2.82 with 0.37 improvement in FID on CIFAR10 relative to the benchmark IDDPM algorithm.

Large Language Models (LLMs) like GPT-4, LLaMA, and Qwen have demonstrated remarkable success across a wide range of applications. However, these models remain inherently vulnerable to prompt injection attacks, which can bypass existing safety mechanisms, highlighting the urgent need for more robust attack detection methods and comprehensive evaluation benchmarks. To address these challenges, we introduce GenTel-Safe, a unified framework that includes a novel prompt injection attack detection method, GenTel-Shield, along with a comprehensive evaluation benchmark, GenTel-Bench, which compromises 84812 prompt injection attacks, spanning 3 major categories and 28 security scenarios. To prove the effectiveness of GenTel-Shield, we evaluate it together with vanilla safety guardrails against the GenTel-Bench dataset. Empirically, GenTel-Shield can achieve state-of-the-art attack detection success rates, which reveals the critical weakness of existing safeguarding techniques against harmful prompts. For reproducibility, we have made the code and benchmarking dataset available on the project page at https://gentellab.github.io/gentel-safe.github.io/.

This paper presents an experience report on the development of Retrieval Augmented Generation (RAG) systems using PDF documents as the primary data source. The RAG architecture combines generative capabilities of Large Language Models (LLMs) with the precision of information retrieval. This approach has the potential to redefine how we interact with and augment both structured and unstructured knowledge in generative models to enhance transparency, accuracy, and contextuality of responses. The paper details the end-to-end pipeline, from data collection, preprocessing, to retrieval indexing and response generation, highlighting technical challenges and practical solutions. We aim to offer insights to researchers and practitioners developing similar systems using two distinct approaches: OpenAI's Assistant API with GPT Series and Llama's open-source models. The practical implications of this research lie in enhancing the reliability of generative AI systems in various sectors where domain-specific knowledge and real-time information retrieval is important. The Python code used in this work is also available at: https://github.com/GPT-Laboratory/RAG-LLM-Development-Guidebook-from-PDFs.