new

Get trending papers in your email inbox!

Subscribe

byAK and the research community

Mar 17

Word-Level Representation From Bytes For Language Modeling

Modern language models mostly take sub-words as input, a design that balances the trade-off between vocabulary size, number of parameters, and performance. However, sub-word tokenization still has disadvantages like not being robust to noise and difficult to generalize to new languages. Also, the current trend of scaling up models reveals that larger models require larger embeddings but that makes parallelization hard. Previous work on image classification proves splitting raw input into a sequence of chucks is a strong, model-agnostic inductive bias. Based on this observation, we rethink the existing character-aware method that takes character-level inputs but makes word-level sequence modeling and prediction. We overhaul this method by introducing a cross-attention network that builds word-level representation directly from bytes, and a sub-word level prediction based on word-level hidden states to avoid the time and space requirement of word-level prediction. With these two improvements combined, we have a token free model with slim input embeddings for downstream tasks. We name our method Byte2Word and perform evaluations on language modeling and text classification. Experiments show that Byte2Word is on par with the strong sub-word baseline BERT but only takes up 10\% of embedding size. We further test our method on synthetic noise and cross-lingual transfer and find it competitive to baseline methods on both settings.

Embed-Search-Align: DNA Sequence Alignment using Transformer Models

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.

Uni$\textbf{F}^2$ace: Fine-grained Face Understanding and Generation with Unified Multimodal Models

Unified multimodal models (UMMs) have emerged as a powerful paradigm in foundational computer vision research, demonstrating significant potential in both image understanding and generation. However, existing research in the face domain primarily focuses on coarse facial attribute understanding, with limited capacity to handle fine-grained facial attributes and without addressing generation capabilities. To overcome these limitations, we propose UniF^2ace, the first UMM tailored specifically for fine-grained face understanding and generation. In general, we train UniF^2ace on a self-constructed, specialized dataset utilizing two mutually beneficial diffusion techniques and a two-level mixture-of-experts architecture. Specifically, we first build a large-scale facial dataset, UniF^2ace-130K, which contains 130K image-text pairs with one million question-answering pairs that span a wide range of facial attributes. Second, we establish a theoretical connection between discrete diffusion score matching and masked generative models, optimizing both evidence lower bounds simultaneously, which significantly improves the model's ability to synthesize facial details. Finally, we introduce both token-level and sequence-level mixture-of-experts, enabling efficient fine-grained representation learning for both understanding and generation tasks. Extensive experiments on UniF^2ace-130K demonstrate that UniF^2ace outperforms existing UMMs and generative models, achieving superior performance across both understanding and generation tasks.

Financial Risk Assessment via Long-term Payment Behavior Sequence Folding

Online inclusive financial services encounter significant financial risks due to their expansive user base and low default costs. By real-world practice, we reveal that utilizing longer-term user payment behaviors can enhance models' ability to forecast financial risks. However, learning long behavior sequences is non-trivial for deep sequential models. Additionally, the diverse fields of payment behaviors carry rich information, requiring thorough exploitation. These factors collectively complicate the task of long-term user behavior modeling. To tackle these challenges, we propose a Long-term Payment Behavior Sequence Folding method, referred to as LBSF. In LBSF, payment behavior sequences are folded based on merchants, using the merchant field as an intrinsic grouping criterion, which enables informative parallelism without reliance on external knowledge. Meanwhile, we maximize the utility of payment details through a multi-field behavior encoding mechanism. Subsequently, behavior aggregation at the merchant level followed by relational learning across merchants facilitates comprehensive user financial representation. We evaluate LBSF on the financial risk assessment task using a large-scale real-world dataset. The results demonstrate that folding long behavior sequences based on internal behavioral cues effectively models long-term patterns and changes, thereby generating more accurate user financial profiles for practical applications.

Harnessing the Power of Prompt-based Techniques for Generating School-Level Questions using Large Language Models

Designing high-quality educational questions is a challenging and time-consuming task. In this work, we propose a novel approach that utilizes prompt-based techniques to generate descriptive and reasoning-based questions. However, current question-answering (QA) datasets are inadequate for conducting our experiments on prompt-based question generation (QG) in an educational setting. Therefore, we curate a new QG dataset called EduProbe for school-level subjects, by leveraging the rich content of NCERT textbooks. We carefully annotate this dataset as quadruples of 1) Context: a segment upon which the question is formed; 2) Long Prompt: a long textual cue for the question (i.e., a longer sequence of words or phrases, covering the main theme of the context); 3) Short Prompt: a short textual cue for the question (i.e., a condensed representation of the key information or focus of the context); 4) Question: a deep question that aligns with the context and is coherent with the prompts. We investigate several prompt-based QG methods by fine-tuning pre-trained transformer-based large language models (LLMs), namely PEGASUS, T5, MBART, and BART. Moreover, we explore the performance of two general-purpose pre-trained LLMs such as Text-Davinci-003 and GPT-3.5-Turbo without any further training. By performing automatic evaluation, we show that T5 (with long prompt) outperforms all other models, but still falls short of the human baseline. Under human evaluation criteria, TextDavinci-003 usually shows better results than other models under various prompt settings. Even in the case of human evaluation criteria, QG models mostly fall short of the human baseline. Our code and dataset are available at: https://github.com/my625/PromptQG

Order Matters: Sequence to sequence for sets

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

Efficiently Modeling Long Sequences with Structured State Spaces

A central goal of sequence modeling is designing a single principled model that can address sequence data across a range of modalities and tasks, particularly on long-range dependencies. Although conventional models including RNNs, CNNs, and Transformers have specialized variants for capturing long dependencies, they still struggle to scale to very long sequences of 10000 or more steps. A promising recent approach proposed modeling sequences by simulating the fundamental state space model (SSM) \( x'(t) = Ax(t) + Bu(t), y(t) = Cx(t) + Du(t) \), and showed that for appropriate choices of the state matrix \( A \), this system could handle long-range dependencies mathematically and empirically. However, this method has prohibitive computation and memory requirements, rendering it infeasible as a general sequence modeling solution. We propose the Structured State Space sequence model (S4) based on a new parameterization for the SSM, and show that it can be computed much more efficiently than prior approaches while preserving their theoretical strengths. Our technique involves conditioning \( A \) with a low-rank correction, allowing it to be diagonalized stably and reducing the SSM to the well-studied computation of a Cauchy kernel. S4 achieves strong empirical results across a diverse range of established benchmarks, including (i) 91\% accuracy on sequential CIFAR-10 with no data augmentation or auxiliary losses, on par with a larger 2-D ResNet, (ii) substantially closing the gap to Transformers on image and language modeling tasks, while performing generation 60times faster (iii) SoTA on every task from the Long Range Arena benchmark, including solving the challenging Path-X task of length 16k that all prior work fails on, while being as efficient as all competitors.

Text Is All You Need: Learning Language Representations for Sequential Recommendation

Sequential recommendation aims to model dynamic user behavior from historical interactions. Existing methods rely on either explicit item IDs or general textual features for sequence modeling to understand user preferences. While promising, these approaches still struggle to model cold-start items or transfer knowledge to new datasets. In this paper, we propose to model user preferences and item features as language representations that can be generalized to new items and datasets. To this end, we present a novel framework, named Recformer, which effectively learns language representations for sequential recommendation. Specifically, we propose to formulate an item as a "sentence" (word sequence) by flattening item key-value attributes described by text so that an item sequence for a user becomes a sequence of sentences. For recommendation, Recformer is trained to understand the "sentence" sequence and retrieve the next "sentence". To encode item sequences, we design a bi-directional Transformer similar to the model Longformer but with different embedding layers for sequential recommendation. For effective representation learning, we propose novel pretraining and finetuning methods which combine language understanding and recommendation tasks. Therefore, Recformer can effectively recommend the next item based on language representations. Extensive experiments conducted on six datasets demonstrate the effectiveness of Recformer for sequential recommendation, especially in low-resource and cold-start settings.

Best of Both Worlds: Advantages of Hybrid Graph Sequence Models

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Diverse Beam Search: Decoding Diverse Solutions from Neural Sequence Models

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

Autoregressive Models in Vision: A Survey

Autoregressive modeling has been a huge success in the field of natural language processing (NLP). Recently, autoregressive models have emerged as a significant area of focus in computer vision, where they excel in producing high-quality visual content. Autoregressive models in NLP typically operate on subword tokens. However, the representation strategy in computer vision can vary in different levels, i.e., pixel-level, token-level, or scale-level, reflecting the diverse and hierarchical nature of visual data compared to the sequential structure of language. This survey comprehensively examines the literature on autoregressive models applied to vision. To improve readability for researchers from diverse research backgrounds, we start with preliminary sequence representation and modeling in vision. Next, we divide the fundamental frameworks of visual autoregressive models into three general sub-categories, including pixel-based, token-based, and scale-based models based on the strategy of representation. We then explore the interconnections between autoregressive models and other generative models. Furthermore, we present a multi-faceted categorization of autoregressive models in computer vision, including image generation, video generation, 3D generation, and multi-modal generation. We also elaborate on their applications in diverse domains, including emerging domains such as embodied AI and 3D medical AI, with about 250 related references. Finally, we highlight the current challenges to autoregressive models in vision with suggestions about potential research directions. We have also set up a Github repository to organize the papers included in this survey at: https://github.com/ChaofanTao/Autoregressive-Models-in-Vision-Survey.

Representation, Exploration and Recommendation of Music Playlists

Playlists have become a significant part of our listening experience because of the digital cloud-based services such as Spotify, Pandora, Apple Music. Owing to the meteoric rise in the usage of playlists, recommending playlists is crucial to music services today. Although there has been a lot of work done in playlist prediction, the area of playlist representation hasn't received that level of attention. Over the last few years, sequence-to-sequence models, especially in the field of natural language processing, have shown the effectiveness of learned embeddings in capturing the semantic characteristics of sequences. We can apply similar concepts to music to learn fixed length representations for playlists and use those representations for downstream tasks such as playlist discovery, browsing, and recommendation. In this work, we formulate the problem of learning a fixed-length playlist representation in an unsupervised manner, using Sequence-to-sequence (Seq2seq) models, interpreting playlists as sentences and songs as words. We compare our model with two other encoding architectures for baseline comparison. We evaluate our work using the suite of tasks commonly used for assessing sentence embeddings, along with a few additional tasks pertaining to music, and a recommendation task to study the traits captured by the playlist embeddings and their effectiveness for the purpose of music recommendation.

Sequence to Sequence Learning with Neural Networks

Deep Neural Networks (DNNs) are powerful models that have achieved excellent performance on difficult learning tasks. Although DNNs work well whenever large labeled training sets are available, they cannot be used to map sequences to sequences. In this paper, we present a general end-to-end approach to sequence learning that makes minimal assumptions on the sequence structure. Our method uses a multilayered Long Short-Term Memory (LSTM) to map the input sequence to a vector of a fixed dimensionality, and then another deep LSTM to decode the target sequence from the vector. Our main result is that on an English to French translation task from the WMT'14 dataset, the translations produced by the LSTM achieve a BLEU score of 34.8 on the entire test set, where the LSTM's BLEU score was penalized on out-of-vocabulary words. Additionally, the LSTM did not have difficulty on long sentences. For comparison, a phrase-based SMT system achieves a BLEU score of 33.3 on the same dataset. When we used the LSTM to rerank the 1000 hypotheses produced by the aforementioned SMT system, its BLEU score increases to 36.5, which is close to the previous best result on this task. The LSTM also learned sensible phrase and sentence representations that are sensitive to word order and are relatively invariant to the active and the passive voice. Finally, we found that reversing the order of the words in all source sentences (but not target sentences) improved the LSTM's performance markedly, because doing so introduced many short term dependencies between the source and the target sentence which made the optimization problem easier.

A Critical Review of Recurrent Neural Networks for Sequence Learning

Countless learning tasks require dealing with sequential data. Image captioning, speech synthesis, and music generation all require that a model produce outputs that are sequences. In other domains, such as time series prediction, video analysis, and musical information retrieval, a model must learn from inputs that are sequences. Interactive tasks, such as translating natural language, engaging in dialogue, and controlling a robot, often demand both capabilities. Recurrent neural networks (RNNs) are connectionist models that capture the dynamics of sequences via cycles in the network of nodes. Unlike standard feedforward neural networks, recurrent networks retain a state that can represent information from an arbitrarily long context window. Although recurrent neural networks have traditionally been difficult to train, and often contain millions of parameters, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful large-scale learning with them. In recent years, systems based on long short-term memory (LSTM) and bidirectional (BRNN) architectures have demonstrated ground-breaking performance on tasks as varied as image captioning, language translation, and handwriting recognition. In this survey, we review and synthesize the research that over the past three decades first yielded and then made practical these powerful learning models. When appropriate, we reconcile conflicting notation and nomenclature. Our goal is to provide a self-contained explication of the state of the art together with a historical perspective and references to primary research.

HMT: Hierarchical Memory Transformer for Long Context Language Processing

Transformer-based large language models (LLM) have been widely used in language processing applications. However, most of them restrict the context window that permits the model to attend to every token in the inputs. Previous works in recurrent models can memorize past tokens to enable unlimited context and maintain effectiveness. However, they have "flat" memory architectures, which have limitations in selecting and filtering information. Since humans are good at learning and self-adjustment, we speculate that imitating brain memory hierarchy is beneficial for model memorization. We propose the Hierarchical Memory Transformer (HMT), a novel framework that enables and improves models' long-context processing ability by imitating human memorization behavior. Leveraging memory-augmented segment-level recurrence, we organize the memory hierarchy by preserving tokens from early input token segments, passing memory embeddings along the sequence, and recalling relevant information from history. Evaluating general language modeling (Wikitext-103, PG-19) and question-answering tasks (PubMedQA), we show that HMT steadily improves the long-context processing ability of context-constrained and long-context models. With an additional 0.5% - 2% of parameters, HMT can easily plug in and augment future LLMs to handle long context effectively. Our code is open-sourced on Github: https://github.com/OswaldHe/HMT-pytorch.

Read, Highlight and Summarize: A Hierarchical Neural Semantic Encoder-based Approach

Traditional sequence-to-sequence (seq2seq) models and other variations of the attention-mechanism such as hierarchical attention have been applied to the text summarization problem. Though there is a hierarchy in the way humans use language by forming paragraphs from sentences and sentences from words, hierarchical models have usually not worked that much better than their traditional seq2seq counterparts. This effect is mainly because either the hierarchical attention mechanisms are too sparse using hard attention or noisy using soft attention. In this paper, we propose a method based on extracting the highlights of a document; a key concept that is conveyed in a few sentences. In a typical text summarization dataset consisting of documents that are 800 tokens in length (average), capturing long-term dependencies is very important, e.g., the last sentence can be grouped with the first sentence of a document to form a summary. LSTMs (Long Short-Term Memory) proved useful for machine translation. However, they often fail to capture long-term dependencies while modeling long sequences. To address these issues, we have adapted Neural Semantic Encoders (NSE) to text summarization, a class of memory-augmented neural networks by improving its functionalities and proposed a novel hierarchical NSE that outperforms similar previous models significantly. The quality of summarization was improved by augmenting linguistic factors, namely lemma, and Part-of-Speech (PoS) tags, to each word in the dataset for improved vocabulary coverage and generalization. The hierarchical NSE model on factored dataset outperformed the state-of-the-art by nearly 4 ROUGE points. We further designed and used the first GPU-based self-critical Reinforcement Learning model.

Linguistic Structure Induction from Language Models

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

Combiner: Full Attention Transformer with Sparse Computation Cost

Transformers provide a class of expressive architectures that are extremely effective for sequence modeling. However, the key limitation of transformers is their quadratic memory and time complexity O(L^2) with respect to the sequence length in attention layers, which restricts application in extremely long sequences. Most existing approaches leverage sparsity or low-rank assumptions in the attention matrix to reduce cost, but sacrifice expressiveness. Instead, we propose Combiner, which provides full attention capability in each attention head while maintaining low computation and memory complexity. The key idea is to treat the self-attention mechanism as a conditional expectation over embeddings at each location, and approximate the conditional distribution with a structured factorization. Each location can attend to all other locations, either via direct attention, or through indirect attention to abstractions, which are again conditional expectations of embeddings from corresponding local regions. We show that most sparse attention patterns used in existing sparse transformers are able to inspire the design of such factorization for full attention, resulting in the same sub-quadratic cost (O(Llog(L)) or O(LL)). Combiner is a drop-in replacement for attention layers in existing transformers and can be easily implemented in common frameworks. An experimental evaluation on both autoregressive and bidirectional sequence tasks demonstrates the effectiveness of this approach, yielding state-of-the-art results on several image and text modeling tasks.

Copyright Traps for Large Language Models

Questions of fair use of copyright-protected content to train Large Language Models (LLMs) are being very actively debated. Document-level inference has been proposed as a new task: inferring from black-box access to the trained model whether a piece of content has been seen during training. SOTA methods however rely on naturally occurring memorization of (part of) the content. While very effective against models that memorize a lot, we hypothesize--and later confirm--that they will not work against models that do not naturally memorize, e.g. medium-size 1B models. We here propose to use copyright traps, the inclusion of fictitious entries in original content, to detect the use of copyrighted materials in LLMs with a focus on models where memorization does not naturally occur. We carefully design an experimental setup, randomly inserting traps into original content (books) and train a 1.3B LLM. We first validate that the use of content in our target model would be undetectable using existing methods. We then show, contrary to intuition, that even medium-length trap sentences repeated a significant number of times (100) are not detectable using existing methods. However, we show that longer sequences repeated a large number of times can be reliably detected (AUC=0.75) and used as copyright traps. We further improve these results by studying how the number of times a sequence is seen improves detectability, how sequences with higher perplexity tend to be memorized more, and how taking context into account further improves detectability.

Decoder-Only or Encoder-Decoder? Interpreting Language Model as a Regularized Encoder-Decoder

The sequence-to-sequence (seq2seq) task aims at generating the target sequence based on the given input source sequence. Traditionally, most of the seq2seq task is resolved by the Encoder-Decoder framework which requires an encoder to encode the source sequence and a decoder to generate the target text. Recently, a bunch of new approaches have emerged that apply decoder-only language models directly to the seq2seq task. Despite the significant advancements in applying language models to the seq2seq task, there is still a lack of thorough analysis on the effectiveness of the decoder-only language model architecture. This paper aims to address this gap by conducting a detailed comparison between the encoder-decoder architecture and the decoder-only language model framework through the analysis of a regularized encoder-decoder structure. This structure is designed to replicate all behaviors in the classical decoder-only language model but has an encoder and a decoder making it easier to be compared with the classical encoder-decoder structure. Based on the analysis, we unveil the attention degeneration problem in the language model, namely, as the generation step number grows, less and less attention is focused on the source sequence. To give a quantitative understanding of this problem, we conduct a theoretical sensitivity analysis of the attention output with respect to the source input. Grounded on our analysis, we propose a novel partial attention language model to solve the attention degeneration problem. Experimental results on machine translation, summarization, and data-to-text generation tasks support our analysis and demonstrate the effectiveness of our proposed model.

An Interdisciplinary Comparison of Sequence Modeling Methods for Next-Element Prediction

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Efficient Content-Based Sparse Attention with Routing Transformers

Self-attention has recently been adopted for a wide range of sequence modeling problems. Despite its effectiveness, self-attention suffers from quadratic compute and memory requirements with respect to sequence length. Successful approaches to reduce this complexity focused on attending to local sliding windows or a small set of locations independent of content. Our work proposes to learn dynamic sparse attention patterns that avoid allocating computation and memory to attend to content unrelated to the query of interest. This work builds upon two lines of research: it combines the modeling flexibility of prior work on content-based sparse attention with the efficiency gains from approaches based on local, temporal sparse attention. Our model, the Routing Transformer, endows self-attention with a sparse routing module based on online k-means while reducing the overall complexity of attention to Oleft(n^{1.5}dright) from Oleft(n^2dright) for sequence length n and hidden dimension d. We show that our model outperforms comparable sparse attention models on language modeling on Wikitext-103 (15.8 vs 18.3 perplexity) as well as on image generation on ImageNet-64 (3.43 vs 3.44 bits/dim) while using fewer self-attention layers. Additionally, we set a new state-of-the-art on the newly released PG-19 data-set, obtaining a test perplexity of 33.2 with a 22 layer Routing Transformer model trained on sequences of length 8192.

Hierarchical Autoregressive Transformers: Combining Byte-~and Word-Level Processing for Robust, Adaptable Language Models

Tokenization is a fundamental step in natural language processing, breaking text into units that computational models can process. While learned subword tokenizers have become the de-facto standard, they present challenges such as large vocabularies, limited adaptability to new domains or languages, and sensitivity to spelling errors and variations. To overcome these limitations, we investigate a hierarchical architecture for autoregressive language modelling that combines character-level and word-level processing. It employs a lightweight character-level encoder to convert character sequences into word embeddings, which are then processed by a word-level backbone model and decoded back into characters via a compact character-level decoder. This method retains the sequence compression benefits of word-level tokenization without relying on a rigid, predefined vocabulary. We demonstrate, at scales up to 7 billion parameters, that hierarchical transformers match the downstream task performance of subword-tokenizer-based models while exhibiting significantly greater robustness to input perturbations. Additionally, during continued pretraining on an out-of-domain language, our model trains almost twice as fast, achieves superior performance on the target language, and retains more of its previously learned knowledge. Hierarchical transformers pave the way for NLP systems that are more robust, flexible, and generalizable across languages and domains.

Sparse Modular Activation for Efficient Sequence Modeling

Linear State Space Models (SSMs) have demonstrated strong performance in a variety of sequence modeling tasks due to their efficient encoding of the recurrent structure. However, in more comprehensive tasks like language modeling and machine translation, self-attention-based models still outperform SSMs. Hybrid models employing both SSM and self-attention generally show promising performance, but current approaches apply attention modules statically and uniformly to all elements in the input sequences, leading to sub-optimal quality-efficiency trade-offs. In this work, we introduce Sparse Modular Activation (SMA), a general mechanism enabling neural networks to sparsely and dynamically activate sub-modules for sequence elements in a differentiable manner. Through allowing each element to skip non-activated sub-modules, SMA reduces computation and memory consumption at both training and inference stages of sequence modeling. As a specific instantiation of SMA, we design a novel neural architecture, SeqBoat, which employs SMA to sparsely activate a Gated Attention Unit (GAU) based on the state representations learned from an SSM. By constraining the GAU to only conduct local attention on the activated inputs, SeqBoat can achieve linear inference complexity with theoretically infinite attention span, and provide substantially better quality-efficiency trade-off than the chunking-based models. With experiments on a wide range of tasks, including language modeling, speech classification and long-range arena, SeqBoat brings new state-of-the-art results among hybrid models with linear complexity and reveals the amount of attention needed for each task through the learned sparse activation patterns.

Combining Recurrent, Convolutional, and Continuous-time Models with Linear State-Space Layers

Recurrent neural networks (RNNs), temporal convolutions, and neural differential equations (NDEs) are popular families of deep learning models for time-series data, each with unique strengths and tradeoffs in modeling power and computational efficiency. We introduce a simple sequence model inspired by control systems that generalizes these approaches while addressing their shortcomings. The Linear State-Space Layer (LSSL) maps a sequence u mapsto y by simply simulating a linear continuous-time state-space representation x = Ax + Bu, y = Cx + Du. Theoretically, we show that LSSL models are closely related to the three aforementioned families of models and inherit their strengths. For example, they generalize convolutions to continuous-time, explain common RNN heuristics, and share features of NDEs such as time-scale adaptation. We then incorporate and generalize recent theory on continuous-time memorization to introduce a trainable subset of structured matrices A that endow LSSLs with long-range memory. Empirically, stacking LSSL layers into a simple deep neural network obtains state-of-the-art results across time series benchmarks for long dependencies in sequential image classification, real-world healthcare regression tasks, and speech. On a difficult speech classification task with length-16000 sequences, LSSL outperforms prior approaches by 24 accuracy points, and even outperforms baselines that use hand-crafted features on 100x shorter sequences.

Characterizing Verbatim Short-Term Memory in Neural Language Models

When a language model is trained to predict natural language sequences, its prediction at each moment depends on a representation of prior context. What kind of information about the prior context can language models retrieve? We tested whether language models could retrieve the exact words that occurred previously in a text. In our paradigm, language models (transformers and an LSTM) processed English text in which a list of nouns occurred twice. We operationalized retrieval as the reduction in surprisal from the first to the second list. We found that the transformers retrieved both the identity and ordering of nouns from the first list. Further, the transformers' retrieval was markedly enhanced when they were trained on a larger corpus and with greater model depth. Lastly, their ability to index prior tokens was dependent on learned attention patterns. In contrast, the LSTM exhibited less precise retrieval, which was limited to list-initial tokens and to short intervening texts. The LSTM's retrieval was not sensitive to the order of nouns and it improved when the list was semantically coherent. We conclude that transformers implemented something akin to a working memory system that could flexibly retrieve individual token representations across arbitrary delays; conversely, the LSTM maintained a coarser and more rapidly-decaying semantic gist of prior tokens, weighted toward the earliest items.

Vector representations of text data in deep learning

In this dissertation we report results of our research on dense distributed representations of text data. We propose two novel neural models for learning such representations. The first model learns representations at the document level, while the second model learns word-level representations. For document-level representations we propose Binary Paragraph Vector: a neural network models for learning binary representations of text documents, which can be used for fast document retrieval. We provide a thorough evaluation of these models and demonstrate that they outperform the seminal method in the field in the information retrieval task. We also report strong results in transfer learning settings, where our models are trained on a generic text corpus and then used to infer codes for documents from a domain-specific dataset. In contrast to previously proposed approaches, Binary Paragraph Vector models learn embeddings directly from raw text data. For word-level representations we propose Disambiguated Skip-gram: a neural network model for learning multi-sense word embeddings. Representations learned by this model can be used in downstream tasks, like part-of-speech tagging or identification of semantic relations. In the word sense induction task Disambiguated Skip-gram outperforms state-of-the-art models on three out of four benchmarks datasets. Our model has an elegant probabilistic interpretation. Furthermore, unlike previous models of this kind, it is differentiable with respect to all its parameters and can be trained with backpropagation. In addition to quantitative results, we present qualitative evaluation of Disambiguated Skip-gram, including two-dimensional visualisations of selected word-sense embeddings.

Large Concept Models: Language Modeling in a Sentence Representation Space

LLMs have revolutionized the field of artificial intelligence and have emerged as the de-facto tool for many tasks. The current established technology of LLMs is to process input and generate output at the token level. This is in sharp contrast to humans who operate at multiple levels of abstraction, well beyond single words, to analyze information and to generate creative content. In this paper, we present an attempt at an architecture which operates on an explicit higher-level semantic representation, which we name a concept. Concepts are language- and modality-agnostic and represent a higher level idea or action in a flow. Hence, we build a "Large Concept Model". In this study, as proof of feasibility, we assume that a concept corresponds to a sentence, and use an existing sentence embedding space, SONAR, which supports up to 200 languages in both text and speech modalities. The Large Concept Model is trained to perform autoregressive sentence prediction in an embedding space. We explore multiple approaches, namely MSE regression, variants of diffusion-based generation, and models operating in a quantized SONAR space. These explorations are performed using 1.6B parameter models and training data in the order of 1.3T tokens. We then scale one architecture to a model size of 7B parameters and training data of about 2.7T tokens. We perform an experimental evaluation on several generative tasks, namely summarization and a new task of summary expansion. Finally, we show that our model exhibits impressive zero-shot generalization performance to many languages, outperforming existing LLMs of the same size. The training code of our models is freely available.

Making the Most of your Model: Methods for Finetuning and Applying Pretrained Transformers

This thesis provides methods and analysis of models which make progress on this goal. The techniques outlined are task agnostic, and should provide benefit when used with nearly any transformer LM. We introduce two new finetuning methods which add new capabilities to the models they are used on. The first adds a recurrence mechanism, which removes the fixed-window sized constraint and improves the efficiency of a transformer decoder. The second allows masked language models (MLMs) to be used for initialization of both the encoder and decoder of a non-autoregressive sequence-to-sequence transformer, opening up generative applications of models which were previously only used for natural language understanding tasks. We also introduce two new techniques for improving the quality of predictions of any transformer decoder without additional finetuning. One, hidden state optimization, can be applied to any transformer decoder to improve the quality of predictions at inference time, especially for few-shot classification. The other, conditional beam search, allows practitioners to search for natural language generation (NLG) model outputs with high likelihood while conditioning on the event that the output is not degenerate (e.g. empty, repetitive, etc.). Finally, we provide theoretical and empirical insights on the divergence of model-likelihood and output quality which has widely been observed in prior work. These insights apply to any model which represents a distribution over text, and apply to language models which are not transformers or even autoregressive. We argue that the NLP community has, to some extent, misunderstood the implications of these findings, and encourage a point of view which has more nuance.

Pointer Networks

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

Set-Based Prompting: Provably Solving the Language Model Order Dependency Problem

The development of generative language models that can create long and coherent textual outputs via autoregression has lead to a proliferation of uses and a corresponding sweep of analyses as researches work to determine the limitations of this new paradigm. Unlike humans, these 'Large Language Models' (LLMs) are highly sensitive to small changes in their inputs, leading to unwanted inconsistency in their behavior. One problematic inconsistency when LLMs are used to answer multiple-choice questions or analyze multiple inputs is order dependency: the output of an LLM can (and often does) change significantly when sub-sequences are swapped, despite both orderings being semantically identical. In this paper we present , a technique that guarantees the output of an LLM will not have order dependence on a specified set of sub-sequences. We show that this method provably eliminates order dependency, and that it can be applied to any transformer-based LLM to enable text generation that is unaffected by re-orderings. Delving into the implications of our method, we show that, despite our inputs being out of distribution, the impact on expected accuracy is small, where the expectation is over the order of uniformly chosen shuffling of the candidate responses, and usually significantly less in practice. Thus, can be used as a 'dropped-in' method on fully trained models. Finally, we discuss how our method's success suggests that other strong guarantees can be obtained on LLM performance via modifying the input representations.

Mamba-360: Survey of State Space Models as Transformer Alternative for Long Sequence Modelling: Methods, Applications, and Challenges

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

InfLLM: Unveiling the Intrinsic Capacity of LLMs for Understanding Extremely Long Sequences with Training-Free Memory

Large language models (LLMs) have emerged as a cornerstone in real-world applications with lengthy streaming inputs, such as LLM-driven agents. However, existing LLMs, pre-trained on sequences with restricted maximum length, cannot generalize to longer sequences due to the out-of-domain and distraction issues. To alleviate these issues, existing efforts employ sliding attention windows and discard distant tokens to achieve the processing of extremely long sequences. Unfortunately, these approaches inevitably fail to capture long-distance dependencies within sequences to deeply understand semantics. This paper introduces a training-free memory-based method, InfLLM, to unveil the intrinsic ability of LLMs to process streaming long sequences. Specifically, InfLLM stores distant contexts into additional memory units and employs an efficient mechanism to lookup token-relevant units for attention computation. Thereby, InfLLM allows LLMs to efficiently process long sequences while maintaining the ability to capture long-distance dependencies. Without any training, InfLLM enables LLMs pre-trained on sequences of a few thousand tokens to achieve superior performance than competitive baselines continually training these LLMs on long sequences. Even when the sequence length is scaled to 1,024K, InfLLM still effectively captures long-distance dependencies.

You Only Scan Once: Efficient Multi-dimension Sequential Modeling with LightNet

Linear attention mechanisms have gained prominence in causal language models due to their linear computational complexity and enhanced speed. However, the inherent decay mechanism in linear attention presents challenges when applied to multi-dimensional sequence modeling tasks, such as image processing and multi-modal learning. In these scenarios, the utilization of sequential scanning to establish a global receptive field necessitates multiple scans for multi-dimensional data, thereby leading to inefficiencies. This paper identifies the inefficiency caused by a multiplicative linear recurrence and proposes an efficient alternative additive linear recurrence to avoid the issue, as it can handle multi-dimensional data within a single scan. We further develop an efficient multi-dimensional sequential modeling framework called LightNet based on the new recurrence. Moreover, we present two new multi-dimensional linear relative positional encoding methods, MD-TPE and MD-LRPE to enhance the model's ability to discern positional information in multi-dimensional scenarios. Our empirical evaluations across various tasks, including image classification, image generation, bidirectional language modeling, and autoregressive language modeling, demonstrate the efficacy of LightNet, showcasing its potential as a versatile and efficient solution for multi-dimensional sequential modeling.

Contextual Memory Reweaving in Large Language Models Using Layered Latent State Reconstruction

Memory retention challenges in deep neural architectures have ongoing limitations in the ability to process and recall extended contextual information. Token dependencies degrade as sequence length increases, leading to a decline in coherence and factual consistency across longer outputs. A structured approach is introduced to mitigate this issue through the reweaving of latent states captured at different processing layers, reinforcing token representations over extended sequences. The proposed Contextual Memory Reweaving framework incorporates a Layered Latent State Reconstruction mechanism to systematically integrate past contextual embeddings without introducing external memory modules. Experimental results demonstrate improvements in recall accuracy across a range of sequence lengths, with notable gains in the retention of rarely occurring tokens and numerical reasoning consistency. Further analysis of computational efficiency indicates that the additional processing overhead remains within acceptable thresholds, enabling scalability across different model sizes. Evaluations in long-form text generation and ambiguous query resolution highlight the capacity of memory reweaving to enhance continuity and reduce inconsistencies over extended outputs. Attention weight distributions reveal more structured allocation patterns, suggesting that reweaved latent states contribute to improved contextual awareness. The findings establish a framework for refining memory retention mechanisms in language models, addressing long-standing challenges in handling complex, multi-step reasoning tasks.

Learn or Recall? Revisiting Incremental Learning with Pre-trained Language Models

Incremental Learning (IL) has been a long-standing problem in both vision and Natural Language Processing (NLP) communities. In recent years, as Pre-trained Language Models (PLMs) have achieved remarkable progress in various NLP downstream tasks, utilizing PLMs as backbones has become a common practice in recent research of IL in NLP. Most assume that catastrophic forgetting is the biggest obstacle to achieving superior IL performance and propose various techniques to overcome this issue. However, we find that this assumption is problematic. Specifically, we revisit more than 20 methods on four classification tasks (Text Classification, Intent Classification, Relation Extraction, and Named Entity Recognition) under the two most popular IL settings (Class-Incremental and Task-Incremental) and reveal that most of them severely underestimate the inherent anti-forgetting ability of PLMs. Based on the observation, we propose a frustratingly easy method called SEQ* for IL with PLMs. The results show that SEQ* has competitive or superior performance compared to state-of-the-art (SOTA) IL methods and requires considerably less trainable parameters and training time. These findings urge us to revisit the IL with PLMs and encourage future studies to have a fundamental understanding of the catastrophic forgetting in PLMs. The data, code and scripts are publicly available at https://github.com/zzz47zzz/codebase-for-incremental-learning-with-llm.

RankGen: Improving Text Generation with Large Ranking Models

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

BERT4Rec: Sequential Recommendation with Bidirectional Encoder Representations from Transformer

Modeling users' dynamic and evolving preferences from their historical behaviors is challenging and crucial for recommendation systems. Previous methods employ sequential neural networks (e.g., Recurrent Neural Network) to encode users' historical interactions from left to right into hidden representations for making recommendations. Although these methods achieve satisfactory results, they often assume a rigidly ordered sequence which is not always practical. We argue that such left-to-right unidirectional architectures restrict the power of the historical sequence representations. For this purpose, we introduce a Bidirectional Encoder Representations from Transformers for sequential Recommendation (BERT4Rec). However, jointly conditioning on both left and right context in deep bidirectional model would make the training become trivial since each item can indirectly "see the target item". To address this problem, we train the bidirectional model using the Cloze task, predicting the masked items in the sequence by jointly conditioning on their left and right context. Comparing with predicting the next item at each position in a sequence, the Cloze task can produce more samples to train a more powerful bidirectional model. Extensive experiments on four benchmark datasets show that our model outperforms various state-of-the-art sequential models consistently.

Learn Your Tokens: Word-Pooled Tokenization for Language Modeling

Language models typically tokenize text into subwords, using a deterministic, hand-engineered heuristic of combining characters into longer surface-level strings such as 'ing' or whole words. Recent literature has repeatedly shown the limitations of such a tokenization strategy, particularly for documents not written in English and for representing numbers. On the other extreme, byte/character-level language models are much less restricted but suffer from increased sequence description lengths and a subsequent quadratic expansion in self-attention computation. Recent attempts to compress and limit these context lengths with fixed size convolutions is helpful but completely ignores the word boundary. This paper considers an alternative 'learn your tokens' scheme which utilizes the word boundary to pool bytes/characters into word representations, which are fed to the primary language model, before again decoding individual characters/bytes per word in parallel. We find that our moderately expressive and moderately fast end-to-end tokenizer outperform by over 300% both subwords and byte/character models over the intrinsic language modeling metric of next-word prediction across datasets. It particularly outshines on rare words, outperforming by a factor of 30! We extensively study the language modeling setup for all three categories of tokenizers and theoretically analyze how our end-to-end models can also be a strong trade-off in efficiency and robustness.

Hydra: Bidirectional State Space Models Through Generalized Matrix Mixers

A wide array of sequence models are built on a framework modeled after Transformers, comprising alternating sequence mixer and channel mixer layers. This paper studies a unifying matrix mixer view of sequence mixers that can be conceptualized as a linear map on the input sequence. This framework encompasses a broad range of well-known sequence models, including the self-attention of Transformers as well as recent strong alternatives such as structured state space models (SSMs), and allows understanding downstream characteristics such as efficiency and expressivity through properties of their structured matrix class. We identify a key axis of matrix parameterizations termed sequence alignment, which increases the flexibility and performance of matrix mixers, providing insights into the strong performance of Transformers and recent SSMs such as Mamba. Furthermore, the matrix mixer framework offers a systematic approach to developing sequence mixers with desired properties, allowing us to develop several new sub-quadratic sequence models. In particular, we propose a natural bidirectional extension of the Mamba model (Hydra), parameterized as a quasiseparable matrix mixer, which demonstrates superior performance over other sequence models including Transformers on non-causal tasks. As a drop-in replacement for attention layers, Hydra outperforms BERT by 0.8 points on the GLUE benchmark and ViT by 2% Top-1 accuracy on ImageNet.

Computation-Efficient Era: A Comprehensive Survey of State Space Models in Medical Image Analysis

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the O(N^2) complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textbf{Mamba} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.

Autoregressive Search Engines: Generating Substrings as Document Identifiers

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.

MoM: Linear Sequence Modeling with Mixture-of-Memories

Linear sequence modeling methods, such as linear attention, state space modeling, and linear RNNs, offer significant efficiency improvements by reducing the complexity of training and inference. However, these methods typically compress the entire input sequence into a single fixed-size memory state, which leads to suboptimal performance on recall-intensive downstream tasks. Drawing inspiration from neuroscience, particularly the brain's ability to maintain robust long-term memory while mitigating "memory interference", we introduce a novel architecture called Mixture-of-Memories (MoM). MoM utilizes multiple independent memory states, with a router network directing input tokens to specific memory states. This approach greatly enhances the overall memory capacity while minimizing memory interference. As a result, MoM performs exceptionally well on recall-intensive tasks, surpassing existing linear sequence modeling techniques. Despite incorporating multiple memory states, the computation of each memory state remains linear in complexity, allowing MoM to retain the linear-complexity advantage during training, while constant-complexity during inference. Our experimental results show that MoM significantly outperforms current linear sequence models on downstream language tasks, particularly recall-intensive tasks, and even achieves performance comparable to Transformer models. The code is released at https://github.com/OpenSparseLLMs/MoM and is also released as a part of https://github.com/OpenSparseLLMs/Linear-MoE.

Hierarchical Spatio-Temporal Representation Learning for Gait Recognition

Gait recognition is a biometric technique that identifies individuals by their unique walking styles, which is suitable for unconstrained environments and has a wide range of applications. While current methods focus on exploiting body part-based representations, they often neglect the hierarchical dependencies between local motion patterns. In this paper, we propose a hierarchical spatio-temporal representation learning (HSTL) framework for extracting gait features from coarse to fine. Our framework starts with a hierarchical clustering analysis to recover multi-level body structures from the whole body to local details. Next, an adaptive region-based motion extractor (ARME) is designed to learn region-independent motion features. The proposed HSTL then stacks multiple ARMEs in a top-down manner, with each ARME corresponding to a specific partition level of the hierarchy. An adaptive spatio-temporal pooling (ASTP) module is used to capture gait features at different levels of detail to perform hierarchical feature mapping. Finally, a frame-level temporal aggregation (FTA) module is employed to reduce redundant information in gait sequences through multi-scale temporal downsampling. Extensive experiments on CASIA-B, OUMVLP, GREW, and Gait3D datasets demonstrate that our method outperforms the state-of-the-art while maintaining a reasonable balance between model accuracy and complexity.

Long-Sequence Recommendation Models Need Decoupled Embeddings

Lifelong user behavior sequences, comprising up to tens of thousands of history behaviors, are crucial for capturing user interests and predicting user responses in modern recommendation systems. A two-stage paradigm is typically adopted to handle these long sequences: a few relevant behaviors are first searched from the original long sequences via an attention mechanism in the first stage and then aggregated with the target item to construct a discriminative representation for prediction in the second stage. In this work, we identify and characterize, for the first time, a neglected deficiency in existing long-sequence recommendation models: a single set of embeddings struggles with learning both attention and representation, leading to interference between these two processes. Initial attempts to address this issue using linear projections -- a technique borrowed from language processing -- proved ineffective, shedding light on the unique challenges of recommendation models. To overcome this, we propose the Decoupled Attention and Representation Embeddings (DARE) model, where two distinct embedding tables are initialized and learned separately to fully decouple attention and representation. Extensive experiments and analysis demonstrate that DARE provides more accurate search of correlated behaviors and outperforms baselines with AUC gains up to 0.9% on public datasets and notable online system improvements. Furthermore, decoupling embedding spaces allows us to reduce the attention embedding dimension and accelerate the search procedure by 50% without significant performance impact, enabling more efficient, high-performance online serving.

The Hyperfitting Phenomenon: Sharpening and Stabilizing LLMs for Open-Ended Text Generation

This paper introduces the counter-intuitive generalization results of overfitting pre-trained large language models (LLMs) on very small datasets. In the setting of open-ended text generation, it is well-documented that LLMs tend to generate repetitive and dull sequences, a phenomenon that is especially apparent when generating using greedy decoding. This issue persists even with state-of-the-art LLMs containing billions of parameters, trained via next-token prediction on large datasets. We find that by further fine-tuning these models to achieve a near-zero training loss on a small set of samples -- a process we refer to as hyperfitting -- the long-sequence generative capabilities are greatly enhanced. Greedy decoding with these Hyperfitted models even outperform Top-P sampling over long-sequences, both in terms of diversity and human preferences. This phenomenon extends to LLMs of various sizes, different domains, and even autoregressive image generation. We further find this phenomena to be distinctly different from that of Grokking and double descent. Surprisingly, our experiments indicate that hyperfitted models rarely fall into repeating sequences they were trained on, and even explicitly blocking these sequences results in high-quality output. All hyperfitted models produce extremely low-entropy predictions, often allocating nearly all probability to a single token.

Pixel Sentence Representation Learning

Pretrained language models are long known to be subpar in capturing sentence and document-level semantics. Though heavily investigated, transferring perturbation-based methods from unsupervised visual representation learning to NLP remains an unsolved problem. This is largely due to the discreteness of subword units brought by tokenization of language models, limiting small perturbations of inputs to form semantics-preserved positive pairs. In this work, we conceptualize the learning of sentence-level textual semantics as a visual representation learning process. Drawing from cognitive and linguistic sciences, we introduce an unsupervised visual sentence representation learning framework, employing visually-grounded text perturbation methods like typos and word order shuffling, resonating with human cognitive patterns, and enabling perturbation to texts to be perceived as continuous. Our approach is further bolstered by large-scale unsupervised topical alignment training and natural language inference supervision, achieving comparable performance in semantic textual similarity (STS) to existing state-of-the-art NLP methods. Additionally, we unveil our method's inherent zero-shot cross-lingual transferability and a unique leapfrogging pattern across languages during iterative training. To our knowledge, this is the first representation learning method devoid of traditional language models for understanding sentence and document semantics, marking a stride closer to human-like textual comprehension. Our code is available at https://github.com/gowitheflow-1998/Pixel-Linguist

In-Context Language Learning: Architectures and Algorithms

Large-scale neural language models exhibit a remarkable capacity for in-context learning (ICL): they can infer novel functions from datasets provided as input. Most of our current understanding of when and how ICL arises comes from LMs trained on extremely simple learning problems like linear regression and associative recall. There remains a significant gap between these model problems and the "real" ICL exhibited by LMs trained on large text corpora, which involves not just retrieval and function approximation but free-form generation of language and other structured outputs. In this paper, we study ICL through the lens of a new family of model problems we term in context language learning (ICLL). In ICLL, LMs are presented with a set of strings from a formal language, and must generate additional strings from the same language. We focus on in-context learning of regular languages generated by random finite automata. We evaluate a diverse set of neural sequence models (including several RNNs, Transformers, and state-space model variants) on regular ICLL tasks, aiming to answer three questions: (1) Which model classes are empirically capable of ICLL? (2) What algorithmic solutions do successful models implement to perform ICLL? (3) What architectural changes can improve ICLL in less performant models? We first show that Transformers significantly outperform neural sequence models with recurrent or convolutional representations on ICLL tasks. Next, we provide evidence that their ability to do so relies on specialized "n-gram heads" (higher-order variants of induction heads) that compute input-conditional next-token distributions. Finally, we show that hard-wiring these heads into neural models improves performance not just on ICLL, but natural language modeling -- improving the perplexity of 340M-parameter models by up to 1.14 points (6.7%) on the SlimPajama dataset.

2D Matryoshka Sentence Embeddings

Common approaches rely on fixed-length embedding vectors from language models as sentence embeddings for downstream tasks such as semantic textual similarity (STS). Such methods are limited in their flexibility due to unknown computational constraints and budgets across various applications. Matryoshka Representation Learning (MRL) (Kusupati et al., 2022) encodes information at finer granularities, i.e., with lower embedding dimensions, to adaptively accommodate ad hoc tasks. Similar accuracy can be achieved with a smaller embedding size, leading to speedups in downstream tasks. Despite its improved efficiency, MRL still requires traversing all Transformer layers before obtaining the embedding, which remains the dominant factor in time and memory consumption. This prompts consideration of whether the fixed number of Transformer layers affects representation quality and whether using intermediate layers for sentence representation is feasible. In this paper, we introduce a novel sentence embedding model called Two-dimensional Matryoshka Sentence Embedding (2DMSE). It supports elastic settings for both embedding sizes and Transformer layers, offering greater flexibility and efficiency than MRL. We conduct extensive experiments on STS tasks and downstream applications. The experimental results demonstrate the effectiveness of our proposed model in dynamically supporting different embedding sizes and Transformer layers, allowing it to be highly adaptable to various scenarios.

Sequence Parallelism: Long Sequence Training from System Perspective

Transformer achieves promising results on various tasks. However, self-attention suffers from quadratic memory requirements with respect to the sequence length. Existing work focuses on reducing time and space complexity from an algorithm perspective. In this work, we propose sequence parallelism, a memory-efficient parallelism method to help us break input sequence length limitation and train with longer sequences on GPUs efficiently. Our approach is compatible with most existing parallelisms (e.g. data parallelism, pipeline parallelism and tensor parallelism), which means our sequence parallelism makes 4D parallelism possible. More importantly, we no longer require a single device to hold the whole sequence. That is, with sparse attention, our sequence parallelism enables us to train transformer with infinite long sequence. Specifically, we split the input sequence into multiple chunks and feed each chunk into its corresponding device (i.e. GPU). To compute the attention output, we integrated ring-style communication with self-attention calculation and proposed Ring Self-Attention (RSA). Experiments show that sequence parallelism performs well when scaling with batch size and sequence length. Compared with tensor parallelism, our approach achieved 13.7times and 3.0times maximum batch size and sequence length respectively when scaling up to 64 NVIDIA P100 GPUs. With sparse attention, sequence can handle sequence with over 114K tokens, which is over 27times longer than existing sparse attention works holding the whole sequence on a single device.

Theme Transformer: Symbolic Music Generation with Theme-Conditioned Transformer

Attention-based Transformer models have been increasingly employed for automatic music generation. To condition the generation process of such a model with a user-specified sequence, a popular approach is to take that conditioning sequence as a priming sequence and ask a Transformer decoder to generate a continuation. However, this prompt-based conditioning cannot guarantee that the conditioning sequence would develop or even simply repeat itself in the generated continuation. In this paper, we propose an alternative conditioning approach, called theme-based conditioning, that explicitly trains the Transformer to treat the conditioning sequence as a thematic material that has to manifest itself multiple times in its generation result. This is achieved with two main technical contributions. First, we propose a deep learning-based approach that uses contrastive representation learning and clustering to automatically retrieve thematic materials from music pieces in the training data. Second, we propose a novel gated parallel attention module to be used in a sequence-to-sequence (seq2seq) encoder/decoder architecture to more effectively account for a given conditioning thematic material in the generation process of the Transformer decoder. We report on objective and subjective evaluations of variants of the proposed Theme Transformer and the conventional prompt-based baseline, showing that our best model can generate, to some extent, polyphonic pop piano music with repetition and plausible variations of a given condition.

Just read twice: closing the recall gap for recurrent language models

Recurrent large language models that compete with Transformers in language modeling perplexity are emerging at a rapid rate (e.g., Mamba, RWKV). Excitingly, these architectures use a constant amount of memory during inference. However, due to the limited memory, recurrent LMs cannot recall and use all the information in long contexts leading to brittle in-context learning (ICL) quality. A key challenge for efficient LMs is selecting what information to store versus discard. In this work, we observe the order in which information is shown to the LM impacts the selection difficulty. To formalize this, we show that the hardness of information recall reduces to the hardness of a problem called set disjointness (SD), a quintessential problem in communication complexity that requires a streaming algorithm (e.g., recurrent model) to decide whether inputted sets are disjoint. We empirically and theoretically show that the recurrent memory required to solve SD changes with set order, i.e., whether the smaller set appears first in-context. Our analysis suggests, to mitigate the reliance on data order, we can put information in the right order in-context or process prompts non-causally. Towards that end, we propose: (1) JRT-Prompt, where context gets repeated multiple times in the prompt, effectively showing the model all data orders. This gives 11.0 pm 1.3 points of improvement, averaged across 16 recurrent LMs and the 6 ICL tasks, with 11.9times higher throughput than FlashAttention-2 for generation prefill (length 32k, batch size 16, NVidia H100). We then propose (2) JRT-RNN, which uses non-causal prefix-linear-attention to process prompts and provides 99% of Transformer quality at 360M params., 30B tokens and 96% at 1.3B params., 50B tokens on average across the tasks, with 19.2times higher throughput for prefill than FA2.

M4LE: A Multi-Ability Multi-Range Multi-Task Multi-Domain Long-Context Evaluation Benchmark for Large Language Models

Managing long sequences has become an important and necessary feature for large language models (LLMs). However, it is still an open question of how to comprehensively and systematically evaluate the long-sequence capability of LLMs. One of the reasons is that conventional and widely-used benchmarks mainly consist of short sequences. In this paper, we propose M4LE, a Multi-ability, Multi-range, Multi-task, Multi-domain benchmark for Long-context Evaluation. M4LE is based on a diverse NLP task pool comprising 36 NLP datasets, 11 task types and 12 domains. To alleviate the scarcity of tasks with naturally long sequences and incorporate multiple-ability assessment, we propose an automatic approach (but with negligible human annotations) to convert short-sequence tasks into a unified long-sequence scenario where LLMs have to identify single or multiple relevant spans in long contexts based on explicit or semantic hints. Specifically, the scenario includes five different types of abilities: (1) explicit single-span; (2) semantic single-span; (3) explicit multiple-span; (4) semantic multiple-span; and (5) global context understanding. The resulting samples in M4LE are evenly distributed from 1k to 8k input length. We conducted a systematic evaluation on 11 well-established LLMs, especially those optimized for long-sequence inputs. Our results reveal that: 1) Current LLMs struggle to understand long context, particularly when tasks require multiple-span attention. 2) Semantic retrieval task is more difficult for competent LLMs. 3) Models fine-tuned on longer text with position interpolation have comparable performance to those using Neural Tangent Kernel (NTK) aware scaling methods without fine-tuning. We make our benchmark publicly available to encourage future research in this challenging area.

Unified Generative and Discriminative Training for Multi-modal Large Language Models

In recent times, Vision-Language Models (VLMs) have been trained under two predominant paradigms. Generative training has enabled Multimodal Large Language Models (MLLMs) to tackle various complex tasks, yet issues such as hallucinations and weak object discrimination persist. Discriminative training, exemplified by models like CLIP, excels in zero-shot image-text classification and retrieval, yet struggles with complex scenarios requiring fine-grained semantic differentiation. This paper addresses these challenges by proposing a unified approach that integrates the strengths of both paradigms. Considering interleaved image-text sequences as the general format of input samples, we introduce a structure-induced training strategy that imposes semantic relationships between input samples and the MLLM's hidden state. This approach enhances the MLLM's ability to capture global semantics and distinguish fine-grained semantics. By leveraging dynamic sequence alignment within the Dynamic Time Warping framework and integrating a novel kernel for fine-grained semantic differentiation, our method effectively balances generative and discriminative tasks. Extensive experiments demonstrate the effectiveness of our approach, achieving state-of-the-art results in multiple generative tasks, especially those requiring cognitive and discrimination abilities. Additionally, our method surpasses discriminative benchmarks in interleaved and fine-grained retrieval tasks. By employing a retrieval-augmented generation strategy, our approach further enhances performance in some generative tasks within one model, offering a promising direction for future research in vision-language modeling.

Neural-Symbolic Recursive Machine for Systematic Generalization

Despite the tremendous success, existing machine learning models still fall short of human-like systematic generalization -- learning compositional rules from limited data and applying them to unseen combinations in various domains. We propose Neural-Symbolic Recursive Machine (NSR) to tackle this deficiency. The core representation of NSR is a Grounded Symbol System (GSS) with combinatorial syntax and semantics, which entirely emerges from training data. Akin to the neuroscience studies suggesting separate brain systems for perceptual, syntactic, and semantic processing, NSR implements analogous separate modules of neural perception, syntactic parsing, and semantic reasoning, which are jointly learned by a deduction-abduction algorithm. We prove that NSR is expressive enough to model various sequence-to-sequence tasks. Superior systematic generalization is achieved via the inductive biases of equivariance and recursiveness embedded in NSR. In experiments, NSR achieves state-of-the-art performance in three benchmarks from different domains: SCAN for semantic parsing, PCFG for string manipulation, and HINT for arithmetic reasoning. Specifically, NSR achieves 100% generalization accuracy on SCAN and PCFG and outperforms state-of-the-art models on HINT by about 23%. Our NSR demonstrates stronger generalization than pure neural networks due to its symbolic representation and inductive biases. NSR also demonstrates better transferability than existing neural-symbolic approaches due to less domain-specific knowledge required.

SequenceMatch: Imitation Learning for Autoregressive Sequence Modelling with Backtracking

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-chi^2 divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

An End-to-End Trainable Neural Network for Image-based Sequence Recognition and Its Application to Scene Text Recognition

Image-based sequence recognition has been a long-standing research topic in computer vision. In this paper, we investigate the problem of scene text recognition, which is among the most important and challenging tasks in image-based sequence recognition. A novel neural network architecture, which integrates feature extraction, sequence modeling and transcription into a unified framework, is proposed. Compared with previous systems for scene text recognition, the proposed architecture possesses four distinctive properties: (1) It is end-to-end trainable, in contrast to most of the existing algorithms whose components are separately trained and tuned. (2) It naturally handles sequences in arbitrary lengths, involving no character segmentation or horizontal scale normalization. (3) It is not confined to any predefined lexicon and achieves remarkable performances in both lexicon-free and lexicon-based scene text recognition tasks. (4) It generates an effective yet much smaller model, which is more practical for real-world application scenarios. The experiments on standard benchmarks, including the IIIT-5K, Street View Text and ICDAR datasets, demonstrate the superiority of the proposed algorithm over the prior arts. Moreover, the proposed algorithm performs well in the task of image-based music score recognition, which evidently verifies the generality of it.

Learning semantic sentence representations from visually grounded language without lexical knowledge

Current approaches to learning semantic representations of sentences often use prior word-level knowledge. The current study aims to leverage visual information in order to capture sentence level semantics without the need for word embeddings. We use a multimodal sentence encoder trained on a corpus of images with matching text captions to produce visually grounded sentence embeddings. Deep Neural Networks are trained to map the two modalities to a common embedding space such that for an image the corresponding caption can be retrieved and vice versa. We show that our model achieves results comparable to the current state-of-the-art on two popular image-caption retrieval benchmark data sets: MSCOCO and Flickr8k. We evaluate the semantic content of the resulting sentence embeddings using the data from the Semantic Textual Similarity benchmark task and show that the multimodal embeddings correlate well with human semantic similarity judgements. The system achieves state-of-the-art results on several of these benchmarks, which shows that a system trained solely on multimodal data, without assuming any word representations, is able to capture sentence level semantics. Importantly, this result shows that we do not need prior knowledge of lexical level semantics in order to model sentence level semantics. These findings demonstrate the importance of visual information in semantics.

Can Transformers Learn Sequential Function Classes In Context?

In-context learning (ICL) has revolutionized the capabilities of transformer models in NLP. In our project, we extend the understanding of the mechanisms underpinning ICL by exploring whether transformers can learn from sequential, non-textual function class data distributions. We introduce a novel sliding window sequential function class and employ toy-sized transformers with a GPT-2 architecture to conduct our experiments. Our analysis indicates that these models can indeed leverage ICL when trained on non-textual sequential function classes. Additionally, our experiments with randomized y-label sequences highlights that transformers retain some ICL capabilities even when the label associations are obfuscated. We provide evidence that transformers can reason with and understand sequentiality encoded within function classes, as reflected by the effective learning of our proposed tasks. Our results also show that the performance deteriorated with increasing randomness in the labels, though not to the extent one might expect, implying a potential robustness of learned sequentiality against label noise. Future research may want to look into how previous explanations of transformers, such as induction heads and task vectors, relate to sequentiality in ICL in these toy examples. Our investigation lays the groundwork for further research into how transformers process and perceive sequential data.

Transformer-Based Models Are Not Yet Perfect At Learning to Emulate Structural Recursion

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

GNN-Coder: Boosting Semantic Code Retrieval with Combined GNNs and Transformer

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.

ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.