Daily Papers

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.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.

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.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

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.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment) and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (i) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (ii) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (ii) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https://github.com/elttaes/Revisiting-PLMs.

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

The language model (LM) approach based on acoustic and linguistic prompts, such as VALL-E, has achieved remarkable progress in the field of zero-shot audio generation. However, existing methods still have some limitations: 1) repetitions, transpositions, and omissions in the output synthesized speech due to limited alignment constraints between audio and phoneme tokens; 2) challenges of fine-grained control over the synthesized speech with autoregressive (AR) language model; 3) infinite silence generation due to the nature of AR-based decoding, especially under the greedy strategy. To alleviate these issues, we propose ELLA-V, a simple but efficient LM-based zero-shot text-to-speech (TTS) framework, which enables fine-grained control over synthesized audio at the phoneme level. The key to ELLA-V is interleaving sequences of acoustic and phoneme tokens, where phoneme tokens appear ahead of the corresponding acoustic tokens. The experimental findings reveal that our model outperforms VALL-E in terms of accuracy and delivers more stable results using both greedy and sampling-based decoding strategies. The code of ELLA-V will be open-sourced after cleanups. Audio samples are available at https://ereboas.github.io/ELLAV/.

Real world deployments of word alignment are almost certain to cover both high and low resource languages. However, the state-of-the-art for this task recommends a different model class depending on the availability of gold alignment training data for a particular language pair. We propose BinaryAlign, a novel word alignment technique based on binary sequence labeling that outperforms existing approaches in both scenarios, offering a unifying approach to the task. Additionally, we vary the specific choice of multilingual foundation model, perform stratified error analysis over alignment error type, and explore the performance of BinaryAlign on non-English language pairs. We make our source code publicly available.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

Diffusion models have achieved state-of-the-art performance across multiple domains, with recent advancements extending their applicability to discrete data. However, aligning discrete diffusion models with task-specific preferences remains challenging, particularly in scenarios where explicit reward functions are unavailable. In this work, we introduce Discrete Diffusion DPO (D3PO), the first adaptation of Direct Preference Optimization (DPO) to discrete diffusion models formulated as continuous-time Markov chains. Our approach derives a novel loss function that directly fine-tunes the generative process using preference data while preserving fidelity to a reference distribution. We validate D3PO on a structured binary sequence generation task, demonstrating that the method effectively aligns model outputs with preferences while maintaining structural validity. Our results highlight that D3PO enables controlled fine-tuning without requiring explicit reward models, making it a practical alternative to reinforcement learning-based approaches. Future research will explore extending D3PO to more complex generative tasks, including language modeling and protein sequence generation, as well as investigating alternative noise schedules, such as uniform noising, to enhance flexibility across different applications.

Reinforcement Learning (RL) has been used to finetune Large Language Models (LLMs) using a reward model trained from preference data, to better align with human judgment. The recently introduced direct alignment methods, which are often simpler, more stable, and computationally lighter, can more directly achieve this. However, these approaches cannot optimize arbitrary rewards, and the preference-based ones are not the only rewards of interest for LLMs (eg., unit tests for code generation or textual entailment for summarization, among others). RL-finetuning is usually done with a variation of policy gradient, which calls for on-policy or near-on-policy samples, requiring costly generations. We introduce Contrastive Policy Gradient, or CoPG, a simple and mathematically principled new RL algorithm that can estimate the optimal policy even from off-policy data. It can be seen as an off-policy policy gradient approach that does not rely on important sampling techniques and highlights the importance of using (the right) state baseline. We show this approach to generalize the direct alignment method IPO (identity preference optimization) and classic policy gradient. We experiment with the proposed CoPG on a toy bandit problem to illustrate its properties, as well as for finetuning LLMs on a summarization task, using a learned reward function considered as ground truth for the purpose of the experiments.

Pretext training followed by task-specific fine-tuning has been a successful approach in vision and language domains. This paper proposes a self-supervised pretext training framework tailored to event sequence data. We introduce a novel alignment verification task that is specialized to event sequences, building on good practices in masked reconstruction and contrastive learning. Our pretext tasks unlock foundational representations that are generalizable across different down-stream tasks, including next-event prediction for temporal point process models, event sequence classification, and missing event interpolation. Experiments on popular public benchmarks demonstrate the potential of the proposed method across different tasks and data domains.

Long-context models(LCMs) have shown great potential in processing long input sequences(even more than 100M tokens) conveniently and effectively. With significant progress, recent research has pointed out that LCMs can accurately locate token-level salient information within the context. Yet, the generation performance of these LCMs is far from satisfactory and might result in misaligned responses, such as hallucinations. To enhance the generation capability of LCMs, existing works have investigated the effects of data size and quality for both pre-training and instruction tuning. Though achieving meaningful improvement, previous methods fall short in either effectiveness or efficiency. In this paper, we introduce LOGO(Long cOntext aliGnment via efficient preference Optimization), a training strategy that first introduces preference optimization for long-context alignment. To overcome the GPU memory-bound issue caused by the long sequence, LOGO employs a reference-free preference optimization strategy and adopts a position synthesis method to construct the training data. By training with only 0.3B data on a single 8timesA800 GPU machine for 16 hours, LOGO allows the Llama-3-8B-Instruct-80K model to achieve comparable performance with GPT-4 in real-world long-context tasks while preserving the model's original capabilities on other tasks, e.g., language modeling and MMLU. Moreover, LOGO can extend the model's context window size while enhancing its generation performance.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

Character animation is a transformative field in computer graphics and vision, enabling dynamic and realistic video animations from static images. Despite advancements, maintaining appearance consistency in animations remains a challenge. Our approach addresses this by introducing a training-free framework that ensures the generated video sequence preserves the reference image's subtleties, such as physique and proportions, through a dual alignment strategy. We decouple skeletal and motion priors from pose information, enabling precise control over animation generation. Our method also improves pixel-level alignment for conditional control from the reference character, enhancing the temporal consistency and visual cohesion of animations. Our method significantly enhances the quality of video generation without the need for large datasets or expensive computational resources.

An ideal length-extrapolatable Transformer language model can handle sequences longer than the training length without any fine-tuning. Such long-context utilization capability relies heavily on a flexible positional embedding design. Upon investigating the flexibility of existing large pre-trained Transformer language models, we find that the T5 family deserves a closer look, as its positional embeddings capture rich and flexible attention patterns. However, T5 suffers from the dispersed attention issue: the longer the input sequence, the flatter the attention distribution. To alleviate the issue, we propose two attention alignment strategies via temperature scaling. Our findings show improvement on the long-context utilization capability of T5 on language modeling, retrieval, multi-document question answering, and code completion tasks without any fine-tuning. This suggests that a flexible positional embedding design and attention alignment can go a long way toward Transformer length extrapolation.

3D super-resolution aims to reconstruct high-fidelity 3D models from low-resolution (LR) multi-view images. Early studies primarily focused on single-image super-resolution (SISR) models to upsample LR images into high-resolution images. However, these methods often lack view consistency because they operate independently on each image. Although various post-processing techniques have been extensively explored to mitigate these inconsistencies, they have yet to fully resolve the issues. In this paper, we perform a comprehensive study of 3D super-resolution by leveraging video super-resolution (VSR) models. By utilizing VSR models, we ensure a higher degree of spatial consistency and can reference surrounding spatial information, leading to more accurate and detailed reconstructions. Our findings reveal that VSR models can perform remarkably well even on sequences that lack precise spatial alignment. Given this observation, we propose a simple yet practical approach to align LR images without involving fine-tuning or generating 'smooth' trajectory from the trained 3D models over LR images. The experimental results show that the surprisingly simple algorithms can achieve the state-of-the-art results of 3D super-resolution tasks on standard benchmark datasets, such as the NeRF-synthetic and MipNeRF-360 datasets. Project page: https://ko-lani.github.io/Sequence-Matters

We introduce AnyGPT, an any-to-any multimodal language model that utilizes discrete representations for the unified processing of various modalities, including speech, text, images, and music. AnyGPT can be trained stably without any alterations to the current large language model (LLM) architecture or training paradigms. Instead, it relies exclusively on data-level preprocessing, facilitating the seamless integration of new modalities into LLMs, akin to the incorporation of new languages. We build a multimodal text-centric dataset for multimodal alignment pre-training. Utilizing generative models, we synthesize the first large-scale any-to-any multimodal instruction dataset. It consists of 108k samples of multi-turn conversations that intricately interweave various modalities, thus equipping the model to handle arbitrary combinations of multimodal inputs and outputs. Experimental results demonstrate that AnyGPT is capable of facilitating any-to-any multimodal conversation while achieving performance comparable to specialized models across all modalities, proving that discrete representations can effectively and conveniently unify multiple modalities within a language model. Demos are shown in https://junzhan2000.github.io/AnyGPT.github.io/

Aligning the behavior of Large language models (LLMs) with human intentions and values remains a critical challenge. Reinforcement learning from human feedback (RLHF) aligns LLMs by training a reward model (RM) on human preferences and fine-tuning the LLMs to maximize RM feedback. Despite its effectiveness and popularity, RLHF is prone to biased local optimization. It means RM fails to provide feedback that accurately aligns with human preference, causing LLMs to explore unexpected generalizations, and failing to achieve alignment objectives. To mitigate this issue, we propose a novel sequence-to-sequence (seq2seq) reward modeling method. Its key insight is that learning from language feedback rather than scalar feedback improves RLHF without additional annotations. We replaced the reward modeling target from binary maximum likelihood estimation (MLE) with sequence MLE. This method enables richer and fine-grained language feedback without additional annotations, models, or training stages. Our experiments demonstrated its effectiveness, specifically, reducing the refusal-to-response paradigm in single-turn safety dialogues and the long-response bias in text summarization tasks. We provide further analysis that seq2seq RM improves RLHF performance across 2B and 7B LLMs on 3 NLP tasks, achieving an average win rate of 76.9\%. We further show that seq2seq RM can still improve the performance of RLHF under out-of-distribution prompts.

Ensuring alignment of language models' outputs with human preferences is critical to guarantee a useful, safe, and pleasant user experience. Thus, human alignment has been extensively studied recently and several methods such as Reinforcement Learning from Human Feedback (RLHF), Direct Policy Optimisation (DPO) and Sequence Likelihood Calibration (SLiC) have emerged. In this paper, our contribution is two-fold. First, we show the equivalence between two recent alignment methods, namely Identity Policy Optimisation (IPO) and Nash Mirror Descent (Nash-MD). Second, we introduce a generalisation of IPO, named IPO-MD, that leverages the regularised sampling approach proposed by Nash-MD. This equivalence may seem surprising at first sight, since IPO is an offline method whereas Nash-MD is an online method using a preference model. However, this equivalence can be proven when we consider the online version of IPO, that is when both generations are sampled by the online policy and annotated by a trained preference model. Optimising the IPO loss with such a stream of data becomes then equivalent to finding the Nash equilibrium of the preference model through self-play. Building on this equivalence, we introduce the IPO-MD algorithm that generates data with a mixture policy (between the online and reference policy) similarly as the general Nash-MD algorithm. We compare online-IPO and IPO-MD to different online versions of existing losses on preference data such as DPO and SLiC on a summarisation task.

Existing end-to-end speech large language models (LLMs) usually rely on large-scale annotated data for training, while data-efficient training has not been discussed in depth. We focus on two fundamental problems between speech and text: the representation space gap and sequence length inconsistency. We propose Soundwave, which utilizes an efficient training strategy and a novel architecture to address these issues. Results show that Soundwave outperforms the advanced Qwen2-Audio in speech translation and AIR-Bench speech tasks, using only one-fiftieth of the training data. Further analysis shows that Soundwave still retains its intelligence during conversation. The project is available at https://github.com/FreedomIntelligence/Soundwave.

The past year has witnessed the significant advancement of video-based large language models. However, the challenge of developing a unified model for both short and long video understanding remains unresolved. Most existing video LLMs cannot handle hour-long videos, while methods custom for long videos tend to be ineffective for shorter videos and images. In this paper, we identify the key issue as the redundant content in videos. To address this, we propose a novel pooling strategy that simultaneously achieves token compression and instruction-aware visual feature aggregation. Our model is termed Prompt-guided Pooling LLaVA, or PPLLaVA for short. Specifically, PPLLaVA consists of three core components: the CLIP-based visual-prompt alignment that extracts visual information relevant to the user's instructions, the prompt-guided pooling that compresses the visual sequence to arbitrary scales using convolution-style pooling, and the clip context extension designed for lengthy prompt common in visual dialogue. Moreover, our codebase also integrates the most advanced video Direct Preference Optimization (DPO) and visual interleave training. Extensive experiments have validated the performance of our model. With superior throughput and only 1024 visual context, PPLLaVA achieves better results on image benchmarks as a video LLM, while achieving state-of-the-art performance across various video benchmarks, excelling in tasks ranging from caption generation to multiple-choice questions, and handling video lengths from seconds to hours. Codes have been available at https://github.com/farewellthree/PPLLaVA.

Encoder-decoder models have become an effective approach for sequence learning tasks like machine translation, image captioning and speech recognition, but have yet to show competitive results for handwritten text recognition. To this end, we propose an attention-based sequence-to-sequence model. It combines a convolutional neural network as a generic feature extractor with a recurrent neural network to encode both the visual information, as well as the temporal context between characters in the input image, and uses a separate recurrent neural network to decode the actual character sequence. We make experimental comparisons between various attention mechanisms and positional encodings, in order to find an appropriate alignment between the input and output sequence. The model can be trained end-to-end and the optional integration of a hybrid loss allows the encoder to retain an interpretable and usable output, if desired. We achieve competitive results on the IAM and ICFHR2016 READ data sets compared to the state-of-the-art without the use of a language model, and we significantly improve over any recent sequence-to-sequence approaches.

Preference Optimization (PO) has proven an effective step for aligning language models to human-desired behaviors. Current variants, following the offline Direct Preference Optimization objective, have focused on a strict setting where all tokens are contributing signals of KL divergence and rewards to the loss function. However, human preference is not affected by each word in a sequence equally but is often dependent on specific words or phrases, e.g. existence of toxic terms leads to non-preferred responses. Based on this observation, we argue that not all tokens should be weighted equally during PO and propose a flexible objective termed SparsePO, that aims to automatically learn to weight the KL divergence and reward corresponding to each token during PO training. We propose two different variants of weight-masks that can either be derived from the reference model itself or learned on the fly. Notably, our method induces sparsity in the learned masks, allowing the model to learn how to best weight reward and KL divergence contributions at the token level, learning an optimal level of mask sparsity. Extensive experiments on multiple domains, including sentiment control, dialogue, text summarization and text-to-code generation, illustrate that our approach assigns meaningful weights to tokens according to the target task, generates more responses with the desired preference and improves reasoning tasks by up to 2 percentage points compared to other token- and response-level PO methods.

This paper presents a solution for the Multilingual Text Detoxification task in the PAN-2024 competition of the SmurfCat team. Using data augmentation through machine translation and a special filtering procedure, we collected an additional multilingual parallel dataset for text detoxification. Using the obtained data, we fine-tuned several multilingual sequence-to-sequence models, such as mT0 and Aya, on a text detoxification task. We applied the ORPO alignment technique to the final model. Our final model has only 3.7 billion parameters and achieves state-of-the-art results for the Ukrainian language and near state-of-the-art results for other languages. In the competition, our team achieved first place in the automated evaluation with a score of 0.52 and second place in the final human evaluation with a score of 0.74.

The reward model has become increasingly important in alignment, assessment, and data construction for large language models (LLMs). Most existing researchers focus on enhancing reward models through data improvements, following the conventional training framework for reward models that directly optimizes the predicted rewards. In this paper, we propose a hybrid alignment framework HaF-RM for reward model training by introducing an additional constraint on token-level policy probabilities in addition to the reward score. It can simultaneously supervise the internal preference model at the token level and optimize the mapping layer of the reward model at the sequence level. Theoretical justifications and experiment results on five datasets show the validity and effectiveness of our proposed hybrid framework for training a high-quality reward model. By decoupling the reward modeling procedure and incorporating hybrid supervision, our HaF-RM framework offers a principled and effective approach to enhancing the performance and alignment of reward models, a critical component in the responsible development of powerful language models. We release our code at https://haf-rm.github.io.

Retrosynthesis planning poses a formidable challenge in the organic chemical industry, particularly in pharmaceuticals. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, Our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.

This paper proposes singing voice synthesis (SVS) based on frame-level sequence-to-sequence models considering vocal timing deviation. In SVS, it is essential to synchronize the timing of singing with temporal structures represented by scores, taking into account that there are differences between actual vocal timing and note start timing. In many SVS systems including our previous work, phoneme-level score features are converted into frame-level ones on the basis of phoneme boundaries obtained by external aligners to take into account vocal timing deviations. Therefore, the sound quality is affected by the aligner accuracy in this system. To alleviate this problem, we introduce an attention mechanism with frame-level features. In the proposed system, the attention mechanism absorbs alignment errors in phoneme boundaries. Additionally, we evaluate the system with pseudo-phoneme-boundaries defined by heuristic rules based on musical scores when there is no aligner. The experimental results show the effectiveness of the proposed system.

The last year has seen astonishing progress in text-prompted image generation premised on the idea of a cross-modal representation space in which the text and image domains are represented jointly. In ASR, this idea has found application as joint speech-text encoders that can scale to the capacities of very large parameter models by being trained on both unpaired speech and text. While these methods show promise, they have required special treatment of the sequence-length mismatch inherent in speech and text, either by up-sampling heuristics or an explicit alignment model. In this work, we offer evidence that joint speech-text encoders naturally achieve consistent representations across modalities by disregarding sequence length, and argue that consistency losses could forgive length differences and simply assume the best alignment. We show that such a loss improves downstream WER in both a large-parameter monolingual and multilingual system.

The rapid development of Large Language Models (LLMs) has substantially expanded the range of tasks they can address. In the field of Natural Language Processing (NLP), researchers have shifted their focus from conventional NLP tasks (e.g., sequence tagging and parsing) towards tasks that revolve around aligning with human needs (e.g., brainstorming and email writing). This shift in task distribution imposes new requirements on evaluating these aligned models regarding generality (i.e., assessing performance across diverse scenarios), flexibility (i.e., examining under different protocols), and interpretability (i.e., scrutinizing models with explanations). In this paper, we propose a generative judge with 13B parameters, Auto-J, designed to address these challenges. Our model is trained on user queries and LLM-generated responses under massive real-world scenarios and accommodates diverse evaluation protocols (e.g., pairwise response comparison and single-response evaluation) with well-structured natural language critiques. To demonstrate the efficacy of our approach, we construct a new testbed covering 58 different scenarios. Experimentally, Auto-J outperforms a series of strong competitors, including both open-source and closed-source models, by a large margin. We also provide detailed analysis and case studies to further reveal the potential of our method and make a variety of resources public at https://github.com/GAIR-NLP/auto-j.

Advancements in Large Language Models (LLMs) inspire various strategies for integrating video modalities. A key approach is Video-LLMs, which incorporate an optimizable interface linking sophisticated video encoders to LLMs. However, due to computation and data limitations, these Video-LLMs are typically pre-trained to process only short videos, limiting their broader application for understanding longer video content. Additionally, fine-tuning Video-LLMs to handle longer videos is cost-prohibitive. Consequently, it becomes essential to explore the interpolation of Video-LLMs under a completely training-free setting. In this paper, we first identify the primary challenges in interpolating Video-LLMs: (1) the video encoder and modality alignment projector are fixed, preventing the integration of additional frames into Video-LLMs, and (2) the LLM backbone is limited in its content length capabilities, which complicates the processing of an increased number of video tokens. To address these challenges, we propose a specific INTerPolation method for Video-LLMs (INTP-Video-LLMs). We introduce an alternative video token rearrangement technique that circumvents limitations imposed by the fixed video encoder and alignment projector. Furthermore, we introduce a training-free LLM context window extension method to enable Video-LLMs to understand a correspondingly increased number of visual tokens.

Retrieval augmented generation (RAG) with large language models (LLMs) for Question Answering (QA) entails furnishing relevant context within the prompt to facilitate the LLM in answer generation. During the generation, inaccuracies or hallucinations frequently occur due to two primary factors: inadequate or distracting context in the prompts, and the inability of LLMs to effectively reason through the facts. In this paper, we investigate whether providing aligned context via a carefully selected passage sequence leads to better answer generation by the LLM for multi-hop QA. We introduce, "GenSco", a novel approach of selecting passages based on the predicted decomposition of the multi-hop questions}. The framework consists of two distinct LLMs: (i) Generator LLM, which is used for question decomposition and final answer generation; (ii) an auxiliary open-sourced LLM, used as the scorer, to semantically guide the Generator for passage selection. The generator is invoked only once for the answer generation, resulting in a cost-effective and efficient approach. We evaluate on three broadly established multi-hop question answering datasets: 2WikiMultiHop, Adversarial HotPotQA and MuSiQue and achieve an absolute gain of 15.1 and 5.9 points in Exact Match score with respect to the best performing baselines over MuSiQue and 2WikiMultiHop respectively.

Targeting at both high efficiency and performance, we propose AlignTTS to predict the mel-spectrum in parallel. AlignTTS is based on a Feed-Forward Transformer which generates mel-spectrum from a sequence of characters, and the duration of each character is determined by a duration predictor.Instead of adopting the attention mechanism in Transformer TTS to align text to mel-spectrum, the alignment loss is presented to consider all possible alignments in training by use of dynamic programming. Experiments on the LJSpeech dataset show that our model achieves not only state-of-the-art performance which outperforms Transformer TTS by 0.03 in mean option score (MOS), but also a high efficiency which is more than 50 times faster than real-time.

Large Language Models (LLMs) achieve state-of-the-art performance across various NLP tasks but face deployment challenges due to high computational costs and memory constraints. Knowledge distillation (KD) is a promising solution, transferring knowledge from large teacher models to smaller student models. However, existing KD methods often assume shared vocabularies and tokenizers, limiting their flexibility. While approaches like Universal Logit Distillation (ULD) and Dual-Space Knowledge Distillation (DSKD) address vocabulary mismatches, they overlook the critical reasoning-aware distillation aspect. To bridge this gap, we propose CoT2Align a universal KD framework that integrates Chain-of-Thought (CoT) augmentation and introduces Cross-CoT Alignment to enhance reasoning transfer. Additionally, we extend Optimal Transport beyond token-wise alignment to a sequence-level and layer-wise alignment approach that adapts to varying sequence lengths while preserving contextual integrity. Comprehensive experiments demonstrate that CoT2Align outperforms existing KD methods across different vocabulary settings, improving reasoning capabilities and robustness in domain-specific tasks.

Automatic song writing aims to compose a song (lyric and/or melody) by machine, which is an interesting topic in both academia and industry. In automatic song writing, lyric-to-melody generation and melody-to-lyric generation are two important tasks, both of which usually suffer from the following challenges: 1) the paired lyric and melody data are limited, which affects the generation quality of the two tasks, considering a lot of paired training data are needed due to the weak correlation between lyric and melody; 2) Strict alignments are required between lyric and melody, which relies on specific alignment modeling. In this paper, we propose SongMASS to address the above challenges, which leverages masked sequence to sequence (MASS) pre-training and attention based alignment modeling for lyric-to-melody and melody-to-lyric generation. Specifically, 1) we extend the original sentence-level MASS pre-training to song level to better capture long contextual information in music, and use a separate encoder and decoder for each modality (lyric or melody); 2) we leverage sentence-level attention mask and token-level attention constraint during training to enhance the alignment between lyric and melody. During inference, we use a dynamic programming strategy to obtain the alignment between each word/syllable in lyric and note in melody. We pre-train SongMASS on unpaired lyric and melody datasets, and both objective and subjective evaluations demonstrate that SongMASS generates lyric and melody with significantly better quality than the baseline method without pre-training or alignment constraint.

Object removal, as a sub-task of image inpainting, has garnered significant attention in recent years. Existing datasets related to object removal serve a valuable foundation for model validation and optimization. However, they mainly rely on inpainting techniques to generate pseudo-removed results, leading to distribution gaps between synthetic and real-world data. While some real-world datasets mitigate these issues, they face challenges such as limited scalability, high annotation costs, and unrealistic representations of lighting and shadows. To address these limitations, we propose a novel video-based annotation pipeline for constructing a realistic illumination-aware object removal dataset. Leveraging this pipeline, we introduce VDOR, a dataset specifically designed for object removal tasks, which comprises triplets of original frame images with objects, background images without objects, and corresponding masks. By leveraging continuous real-world video frames, we minimize distribution gaps and accurately capture realistic lighting and shadow variations, ensuring close alignment with real-world scenarios. Our approach significantly reduces annotation effort while providing a robust foundation for advancing object removal research.

With the help of discrete neural audio codecs, large language models (LLM) have increasingly been recognized as a promising methodology for zero-shot Text-to-Speech (TTS) synthesis. However, sampling based decoding strategies bring astonishing diversity to generation, but also pose robustness issues such as typos, omissions and repetition. In addition, the high sampling rate of audio also brings huge computational overhead to the inference process of autoregression. To address these issues, we propose VALL-E R, a robust and efficient zero-shot TTS system, building upon the foundation of VALL-E. Specifically, we introduce a phoneme monotonic alignment strategy to strengthen the connection between phonemes and acoustic sequence, ensuring a more precise alignment by constraining the acoustic tokens to match their associated phonemes. Furthermore, we employ a codec-merging approach to downsample the discrete codes in shallow quantization layer, thereby accelerating the decoding speed while preserving the high quality of speech output. Benefiting from these strategies, VALL-E R obtains controllablity over phonemes and demonstrates its strong robustness by approaching the WER of ground truth. In addition, it requires fewer autoregressive steps, with over 60% time reduction during inference. This research has the potential to be applied to meaningful projects, including the creation of speech for those affected by aphasia. Audio samples will be available at: https://aka.ms/valler.

For multilingual sequence-to-sequence pretrained language models (multilingual Seq2Seq PLMs), e.g. mBART, the self-supervised pretraining task is trained on a wide range of monolingual languages, e.g. 25 languages from CommonCrawl, while the downstream cross-lingual tasks generally progress on a bilingual language subset, e.g. English-German, making there exists the data discrepancy, namely domain discrepancy, and cross-lingual learning objective discrepancy, namely task discrepancy, between the pretraining and finetuning stages. To bridge the above cross-lingual domain and task gaps, we extend the vanilla pretrain-finetune pipeline with extra code-switching restore task. Specifically, the first stage employs the self-supervised code-switching restore task as a pretext task, allowing the multilingual Seq2Seq PLMs to acquire some in-domain alignment information. And for the second stage, we fine-tune the model on downstream data normally. Experiments on both NLG evaluation (12 bilingual translation tasks, 30 zero-shot translation tasks, and 2 cross-lingual summarization tasks) and NLU evaluation (7 cross-lingual natural language inference tasks) show our model outperforms the strong baseline mBART with standard finetuning strategy, consistently. Analyses indicate our approach could narrow the Euclidean distance of cross-lingual sentence representations, and improve the model generalization with trivial computational cost. We release the code at: https://github.com/zanchangtong/CSR4mBART.

Many real-world applications require the prediction of long sequence time-series, such as electricity consumption planning. Long sequence time-series forecasting (LSTF) demands a high prediction capacity of the model, which is the ability to capture precise long-range dependency coupling between output and input efficiently. Recent studies have shown the potential of Transformer to increase the prediction capacity. However, there are several severe issues with Transformer that prevent it from being directly applicable to LSTF, including quadratic time complexity, high memory usage, and inherent limitation of the encoder-decoder architecture. To address these issues, we design an efficient transformer-based model for LSTF, named Informer, with three distinctive characteristics: (i) a ProbSparse self-attention mechanism, which achieves O(L log L) in time complexity and memory usage, and has comparable performance on sequences' dependency alignment. (ii) the self-attention distilling highlights dominating attention by halving cascading layer input, and efficiently handles extreme long input sequences. (iii) the generative style decoder, while conceptually simple, predicts the long time-series sequences at one forward operation rather than a step-by-step way, which drastically improves the inference speed of long-sequence predictions. Extensive experiments on four large-scale datasets demonstrate that Informer significantly outperforms existing methods and provides a new solution to the LSTF problem.

We present PreF3R, Pose-Free Feed-forward 3D Reconstruction from an image sequence of variable length. Unlike previous approaches, PreF3R removes the need for camera calibration and reconstructs the 3D Gaussian field within a canonical coordinate frame directly from a sequence of unposed images, enabling efficient novel-view rendering. We leverage DUSt3R's ability for pair-wise 3D structure reconstruction, and extend it to sequential multi-view input via a spatial memory network, eliminating the need for optimization-based global alignment. Additionally, PreF3R incorporates a dense Gaussian parameter prediction head, which enables subsequent novel-view synthesis with differentiable rasterization. This allows supervising our model with the combination of photometric loss and pointmap regression loss, enhancing both photorealism and structural accuracy. Given a sequence of ordered images, PreF3R incrementally reconstructs the 3D Gaussian field at 20 FPS, therefore enabling real-time novel-view rendering. Empirical experiments demonstrate that PreF3R is an effective solution for the challenging task of pose-free feed-forward novel-view synthesis, while also exhibiting robust generalization to unseen scenes.

With the release of large-scale motion datasets with textual annotations, the task of establishing a robust latent space for language and 3D human motion has recently witnessed a surge of interest. Methods have been proposed to convert human motion and texts into features to achieve accurate correspondence between them. Despite these efforts to align language and motion representations, we claim that the temporal element is often overlooked, especially for compound actions, resulting in chronological inaccuracies. To shed light on the temporal alignment in motion-language latent spaces, we propose Chronologically Accurate Retrieval (CAR) to evaluate the chronological understanding of the models. We decompose textual descriptions into events, and prepare negative text samples by shuffling the order of events in compound action descriptions. We then design a simple task for motion-language models to retrieve the more likely text from the ground truth and its chronologically shuffled version. CAR reveals many cases where current motion-language models fail to distinguish the event chronology of human motion, despite their impressive performance in terms of conventional evaluation metrics. To achieve better temporal alignment between text and motion, we further propose to use these texts with shuffled sequence of events as negative samples during training to reinforce the motion-language models. We conduct experiments on text-motion retrieval and text-to-motion generation using the reinforced motion-language models, which demonstrate improved performance over conventional approaches, indicating the necessity to consider temporal elements in motion-language alignment.

Neural network based end-to-end text to speech (TTS) has significantly improved the quality of synthesized speech. Prominent methods (e.g., Tacotron 2) usually first generate mel-spectrogram from text, and then synthesize speech from the mel-spectrogram using vocoder such as WaveNet. Compared with traditional concatenative and statistical parametric approaches, neural network based end-to-end models suffer from slow inference speed, and the synthesized speech is usually not robust (i.e., some words are skipped or repeated) and lack of controllability (voice speed or prosody control). In this work, we propose a novel feed-forward network based on Transformer to generate mel-spectrogram in parallel for TTS. Specifically, we extract attention alignments from an encoder-decoder based teacher model for phoneme duration prediction, which is used by a length regulator to expand the source phoneme sequence to match the length of the target mel-spectrogram sequence for parallel mel-spectrogram generation. Experiments on the LJSpeech dataset show that our parallel model matches autoregressive models in terms of speech quality, nearly eliminates the problem of word skipping and repeating in particularly hard cases, and can adjust voice speed smoothly. Most importantly, compared with autoregressive Transformer TTS, our model speeds up mel-spectrogram generation by 270x and the end-to-end speech synthesis by 38x. Therefore, we call our model FastSpeech.

We introduce Long-VITA, a simple yet effective large multi-modal model for long-context visual-language understanding tasks. It is adept at concurrently processing and analyzing modalities of image, video, and text over 4K frames or 1M tokens while delivering advanced performances on short-context multi-modal tasks. We propose an effective multi-modal training schema that starts with large language models and proceeds through vision-language alignment, general knowledge learning, and two sequential stages of long-sequence fine-tuning. We further implement context-parallelism distributed inference and logits-masked language modeling head to scale Long-VITA to infinitely long inputs of images and texts during model inference. Regarding training data, Long-VITA is built on a mix of 17M samples from public datasets only and demonstrates the state-of-the-art performance on various multi-modal benchmarks, compared against recent cutting-edge models with internal data. Long-VITA is fully reproducible and supports both NPU and GPU platforms for training and testing. By leveraging our inference designs, Long-VITA models achieve a remarkable 2x prefill speedup and 4x context length extension in single node with 8 GPUs. We hope Long-VITA can serve as a competitive baseline and offer valuable insights for the open-source community in advancing long-context multi-modal understanding.

Retrieval-augmented language models (RALMs) have shown strong performance and wide applicability in knowledge-intensive tasks. However, there are significant trustworthiness concerns as RALMs are prone to generating unfaithful outputs, including baseless information or contradictions with the retrieved context. This paper proposes SynCheck, a lightweight monitor that leverages fine-grained decoding dynamics including sequence likelihood, uncertainty quantification, context influence, and semantic alignment to synchronously detect unfaithful sentences. By integrating efficiently measurable and complementary signals, SynCheck enables accurate and immediate feedback and intervention, achieving 0.85 AUROC in detecting faithfulness errors across six long-form retrieval-augmented generation tasks, improving prior best method by 4%. Leveraging SynCheck, we further introduce FOD, a faithfulness-oriented decoding algorithm guided by beam search for long-form retrieval-augmented generation. Empirical results demonstrate that FOD outperforms traditional strategies such as abstention, reranking, or contrastive decoding significantly in terms of faithfulness, achieving over 10% improvement across six datasets.

CTC compressor can be an effective approach to integrate audio encoders to decoder-only models, which has gained growing interest for different speech applications. In this work, we propose a novel CTC compressor based joint speech and text training (CJST) framework for decoder-only ASR. CJST matches speech and text modalities from both directions by exploring a simple modality adaptor and several features of the CTC compressor, including sequence compression, on-the-fly forced peaky alignment and CTC class embeddings. Experimental results on the Librispeech and TED-LIUM2 corpora show that the proposed CJST achieves an effective text injection without the need of duration handling, leading to the best performance for both in-domain and cross-domain scenarios. We also provide a comprehensive study on CTC compressor, covering various compression modes, edge case handling and behavior under both clean and noisy data conditions, which reveals the most robust setting to use CTC compressor for decoder-only models.

Neural sequence-to-sequence TTS has achieved significantly better output quality than statistical speech synthesis using HMMs. However, neural TTS is generally not probabilistic and uses non-monotonic attention. Attention failures increase training time and can make synthesis babble incoherently. This paper describes how the old and new paradigms can be combined to obtain the advantages of both worlds, by replacing attention in neural TTS with an autoregressive left-right no-skip hidden Markov model defined by a neural network. Based on this proposal, we modify Tacotron 2 to obtain an HMM-based neural TTS model with monotonic alignment, trained to maximise the full sequence likelihood without approximation. We also describe how to combine ideas from classical and contemporary TTS for best results. The resulting example system is smaller and simpler than Tacotron 2, and learns to speak with fewer iterations and less data, whilst achieving comparable naturalness prior to the post-net. Our approach also allows easy control over speaking rate.

We propose UniTAB that Unifies Text And Box outputs for grounded vision-language (VL) modeling. Grounded VL tasks such as grounded captioning require the model to generate a text description and align predicted words with object regions. To achieve this, models must generate desired text and box outputs together, and meanwhile indicate the alignments between words and boxes. In contrast to existing solutions that use multiple separate modules for different outputs, UniTAB represents both text and box outputs with a shared token sequence, and introduces a special <obj> token to naturally indicate word-box alignments in the sequence. UniTAB thus could provide a more comprehensive and interpretable image description, by freely grounding generated words to object regions. On grounded captioning, UniTAB presents a simpler solution with a single output head, and significantly outperforms state of the art in both grounding and captioning evaluations. On general VL tasks that have different desired output formats (i.e., text, box, or their combination), UniTAB with a single network achieves better or comparable performance than task-specific state of the art. Experiments cover 7 VL benchmarks, including grounded captioning, visual grounding, image captioning, and visual question answering. Furthermore, UniTAB's unified multi-task network and the task-agnostic output sequence design make the model parameter efficient and generalizable to new tasks.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

The most common tools for word-alignment rely on a large amount of parallel sentences, which are then usually processed according to one of the IBM model algorithms. The training data is, however, the same as for machine translation (MT) systems, especially for neural MT (NMT), which itself is able to produce word-alignments using the trained attention heads. This is convenient because word-alignment is theoretically a viable byproduct of any attention-based NMT, which is also able to provide decoder scores for a translated sentence pair. We summarize different approaches on how word-alignment can be extracted from alignment scores and then explore ways in which scores can be extracted from NMT, focusing on inferring the word-alignment scores based on output sentence and token probabilities. We compare this to the extraction of alignment scores from attention. We conclude with aggregating all of the sources of alignment scores into a simple feed-forward network which achieves the best results when combined alignment extractors are used.

Recent studies have shown that post-aligning multilingual pretrained language models (mPLMs) using alignment objectives on both original and transliterated data can improve crosslingual alignment. This improvement further leads to better crosslingual transfer performance. However, it remains unclear how and why a better crosslingual alignment is achieved, as this technique only involves transliterations, and does not use any parallel data. This paper attempts to explicitly evaluate the crosslingual alignment and identify the key elements in transliteration-based approaches that contribute to better performance. For this, we train multiple models under varying setups for two pairs of related languages: (1) Polish and Ukrainian and (2) Hindi and Urdu. To assess alignment, we define four types of similarities based on sentence representations. Our experiments show that adding transliterations alone improves the overall similarities, even for random sentence pairs. With the help of auxiliary alignment objectives, especially the contrastive objective, the model learns to distinguish matched from random pairs, leading to better alignments. However, we also show that better alignment does not always yield better downstream performance, suggesting that further research is needed to clarify the connection between alignment and performance.

Monolingual word alignment is crucial to model semantic interactions between sentences. In particular, null alignment, a phenomenon in which words have no corresponding counterparts, is pervasive and critical in handling semantically divergent sentences. Identification of null alignment is useful on its own to reason about the semantic similarity of sentences by indicating there exists information inequality. To achieve unbalanced word alignment that values both alignment and null alignment, this study shows that the family of optimal transport (OT), i.e., balanced, partial, and unbalanced OT, are natural and powerful approaches even without tailor-made techniques. Our extensive experiments covering unsupervised and supervised settings indicate that our generic OT-based alignment methods are competitive against the state-of-the-arts specially designed for word alignment, remarkably on challenging datasets with high null alignment frequencies.

Aligning large language models with human objectives is paramount, yet common approaches including RLHF suffer from unstable and resource-intensive training. In response to this challenge, we introduce ARGS, Alignment as Reward-Guided Search, a novel framework that integrates alignment into the decoding process, eliminating the need for expensive RL training. By adjusting the model's probabilistic predictions using a reward signal, ARGS generates texts with semantic diversity while being aligned with human preferences, offering a promising and flexible solution for aligning language models. Notably, ARGS demonstrates consistent enhancements in average reward compared to baselines across diverse alignment tasks and various model dimensions. For example, under the same greedy-based decoding strategy, our method improves the average reward by 19.56% relative to the baseline and secures a preference or tie score of 64.33% in GPT-4 evaluation. We believe that our framework, emphasizing decoding-time alignment, paves the way for more responsive language models in the future. Code is publicly available at: https://github.com/deeplearning-wisc/args.

Big models, exemplified by Large Language Models (LLMs), are models typically pre-trained on massive data and comprised of enormous parameters, which not only obtain significantly improved performance across diverse tasks but also present emergent capabilities absent in smaller models. However, the growing intertwining of big models with everyday human lives poses potential risks and might cause serious social harm. Therefore, many efforts have been made to align LLMs with humans to make them better follow user instructions and satisfy human preferences. Nevertheless, `what to align with' has not been fully discussed, and inappropriate alignment goals might even backfire. In this paper, we conduct a comprehensive survey of different alignment goals in existing work and trace their evolution paths to help identify the most essential goal. Particularly, we investigate related works from two perspectives: the definition of alignment goals and alignment evaluation. Our analysis encompasses three distinct levels of alignment goals and reveals a goal transformation from fundamental abilities to value orientation, indicating the potential of intrinsic human values as the alignment goal for enhanced LLMs. Based on such results, we further discuss the challenges of achieving such intrinsic value alignment and provide a collection of available resources for future research on the alignment of big models.

Alignment with human preference is a desired property of large language models (LLMs). Currently, the main alignment approach is based on reinforcement learning from human feedback (RLHF). Despite the effectiveness of RLHF, it is intricate to implement and train, thus recent studies explore how to develop alternative alignment approaches based on supervised fine-tuning (SFT). A major limitation of SFT is that it essentially does imitation learning, which cannot fully understand what are the expected behaviors. To address this issue, we propose an improved alignment approach named FIGA. Different from prior methods, we incorporate fine-grained (i.e., token or phrase level) quality signals that are derived by contrasting good and bad responses. Our approach has made two major contributions. Firstly, we curate a refined alignment dataset that pairs initial responses and the corresponding revised ones. Secondly, we devise a new loss function can leverage fine-grained quality signals to instruct the learning of LLMs for alignment. Extensive experiments have demonstrated the effectiveness of our approaches by comparing a number of competitive baselines.

Large Language Models (LLMs) exhibit remarkably powerful capabilities. One of the crucial factors to achieve success is aligning the LLM's output with human preferences. This alignment process often requires only a small amount of data to efficiently enhance the LLM's performance. While effective, research in this area spans multiple domains, and the methods involved are relatively complex to understand. The relationships between different methods have been under-explored, limiting the development of the preference alignment. In light of this, we break down the existing popular alignment strategies into different components and provide a unified framework to study the current alignment strategies, thereby establishing connections among them. In this survey, we decompose all the strategies in preference learning into four components: model, data, feedback, and algorithm. This unified view offers an in-depth understanding of existing alignment algorithms and also opens up possibilities to synergize the strengths of different strategies. Furthermore, we present detailed working examples of prevalent existing algorithms to facilitate a comprehensive understanding for the readers. Finally, based on our unified perspective, we explore the challenges and future research directions for aligning large language models with human preferences.

Non-autoregressive translation (NAT) models are typically trained with the cross-entropy loss, which forces the model outputs to be aligned verbatim with the target sentence and will highly penalize small shifts in word positions. Latent alignment models relax the explicit alignment by marginalizing out all monotonic latent alignments with the CTC loss. However, they cannot handle non-monotonic alignments, which is non-negligible as there is typically global word reordering in machine translation. In this work, we explore non-monotonic latent alignments for NAT. We extend the alignment space to non-monotonic alignments to allow for the global word reordering and further consider all alignments that overlap with the target sentence. We non-monotonically match the alignments to the target sentence and train the latent alignment model to maximize the F1 score of non-monotonic matching. Extensive experiments on major WMT benchmarks show that our method substantially improves the translation performance of CTC-based models. Our best model achieves 30.06 BLEU on WMT14 En-De with only one-iteration decoding, closing the gap between non-autoregressive and autoregressive models.

Word alignment, which aims to align translationally equivalent words between source and target sentences, plays an important role in many natural language processing tasks. Current unsupervised neural alignment methods focus on inducing alignments from neural machine translation models, which does not leverage the full context in the target sequence. In this paper, we propose Mask-Align, a self-supervised word alignment model that takes advantage of the full context on the target side. Our model masks out each target token and predicts it conditioned on both source and the remaining target tokens. This two-step process is based on the assumption that the source token contributing most to recovering the masked target token should be aligned. We also introduce an attention variant called leaky attention, which alleviates the problem of unexpected high cross-attention weights on special tokens such as periods. Experiments on four language pairs show that our model outperforms previous unsupervised neural aligners and obtains new state-of-the-art results.

Word alignments are useful for tasks like statistical and neural machine translation (NMT) and cross-lingual annotation projection. Statistical word aligners perform well, as do methods that extract alignments jointly with translations in NMT. However, most approaches require parallel training data, and quality decreases as less training data is available. We propose word alignment methods that require no parallel data. The key idea is to leverage multilingual word embeddings, both static and contextualized, for word alignment. Our multilingual embeddings are created from monolingual data only without relying on any parallel data or dictionaries. We find that alignments created from embeddings are superior for four and comparable for two language pairs compared to those produced by traditional statistical aligners, even with abundant parallel data; e.g., contextualized embeddings achieve a word alignment F1 for English-German that is 5 percentage points higher than eflomal, a high-quality statistical aligner, trained on 100k parallel sentences.

We introduce Aligner, a novel Parameter-Efficient Fine-Tuning (PEFT) method for aligning multi-billion-parameter-sized Large Language Models (LLMs). Aligner employs a unique design that constructs a globally shared set of tunable tokens that modify the attention of every layer. Remarkably with this method, even when using one token accounting for a mere 5,000 parameters, Aligner can still perform comparably well to state-of-the-art LLM adaptation methods like LoRA that require millions of parameters. This capacity is substantiated in both instruction following and value alignment tasks. Besides the multiple order-of-magnitude improvement in parameter efficiency, the insight Aligner provides into the internal mechanisms of LLMs is also valuable. The architectural features and efficacy of our method, in addition to our experiments demonstrate that an LLM separates its internal handling of "form" and "knowledge" in a somewhat orthogonal manner. This finding promises to motivate new research into LLM mechanism understanding and value alignment.

Large language models (LLMs) can handle a wide variety of general tasks with simple prompts, without the need for task-specific training. Multimodal Large Language Models (MLLMs), built upon LLMs, have demonstrated impressive potential in tackling complex tasks involving visual, auditory, and textual data. However, critical issues related to truthfulness, safety, o1-like reasoning, and alignment with human preference remain insufficiently addressed. This gap has spurred the emergence of various alignment algorithms, each targeting different application scenarios and optimization goals. Recent studies have shown that alignment algorithms are a powerful approach to resolving the aforementioned challenges. In this paper, we aim to provide a comprehensive and systematic review of alignment algorithms for MLLMs. Specifically, we explore four key aspects: (1) the application scenarios covered by alignment algorithms, including general image understanding, multi-image, video, and audio, and extended multimodal applications; (2) the core factors in constructing alignment datasets, including data sources, model responses, and preference annotations; (3) the benchmarks used to evaluate alignment algorithms; and (4) a discussion of potential future directions for the development of alignment algorithms. This work seeks to help researchers organize current advancements in the field and inspire better alignment methods. The project page of this paper is available at https://github.com/BradyFU/Awesome-Multimodal-Large-Language-Models/tree/Alignment.

Alignment is a crucial step to enhance the instruction-following and conversational abilities of language models. Despite many recent work proposing new algorithms, datasets, and training pipelines, there is a lack of comprehensive studies measuring the impact of various design choices throughout the whole training process. We first conduct a rigorous analysis over a three-stage training pipeline consisting of supervised fine-tuning, offline preference learning, and online preference learning. We have found that using techniques like sequence packing, loss masking in SFT, increasing the preference dataset size in DPO, and online DPO training can significantly improve the performance of language models. We then train from Gemma-2b-base and LLama-3-8b-base, and find that our best models exceed the performance of the official instruct models tuned with closed-source data and algorithms. Our code and models can be found at https://github.com/Columbia-NLP-Lab/LionAlignment.

The word alignment task, despite its prominence in the era of statistical machine translation (SMT), is niche and under-explored today. In this two-part tutorial, we argue for the continued relevance for word alignment. The first part provides a historical background to word alignment as a core component of the traditional SMT pipeline. We zero-in on GIZA++, an unsupervised, statistical word aligner with surprising longevity. Jumping forward to the era of neural machine translation (NMT), we show how insights from word alignment inspired the attention mechanism fundamental to present-day NMT. The second part shifts to a survey approach. We cover neural word aligners, showing the slow but steady progress towards surpassing GIZA++ performance. Finally, we cover the present-day applications of word alignment, from cross-lingual annotation projection, to improving translation.

The widespread applicability and increasing omnipresence of LLMs have instigated a need to align LLM responses to user and stakeholder preferences. Many preference optimization approaches have been proposed that fine-tune LLM parameters to achieve good alignment. However, such parameter tuning is known to interfere with model performance on many tasks. Moreover, keeping up with shifting user preferences is tricky in such a situation. Decoding-time alignment with reward model guidance solves these issues at the cost of increased inference time. However, most of such methods fail to strike the right balance between exploration and exploitation of reward -- often due to the conflated formulation of these two aspects - to give well-aligned responses. To remedy this we decouple these two aspects and implement them in an evolutionary fashion: exploration is enforced by decoding from mutated instructions and exploitation is represented as the periodic replacement of poorly-rewarded generations with well-rewarded ones. Empirical evidences indicate that this strategy outperforms many preference optimization and decode-time alignment approaches on two widely accepted alignment benchmarks AlpacaEval 2 and MT-Bench. Our implementation will be available at: https://darwin-alignment.github.io.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

Cross-lingual alignment, the meaningful similarity of representations across languages in multilingual language models, has been an active field of research in recent years. We survey the literature of techniques to improve cross-lingual alignment, providing a taxonomy of methods and summarising insights from throughout the field. We present different understandings of cross-lingual alignment and their limitations. We provide a qualitative summary of results from a large number of surveyed papers. Finally, we discuss how these insights may be applied not only to encoder models, where this topic has been heavily studied, but also to encoder-decoder or even decoder-only models, and argue that an effective trade-off between language-neutral and language-specific information is key.

We introduce Baichuan Alignment, a detailed analysis of the alignment techniques employed in the Baichuan series of models. This represents the industry's first comprehensive account of alignment methodologies, offering valuable insights for advancing AI research. We investigate the critical components that enhance model performance during the alignment process, including optimization methods, data strategies, capability enhancements, and evaluation processes. The process spans three key stages: Prompt Augmentation System (PAS), Supervised Fine-Tuning (SFT), and Preference Alignment. The problems encountered, the solutions applied, and the improvements made are thoroughly recorded. Through comparisons across well-established benchmarks, we highlight the technological advancements enabled by Baichuan Alignment. Baichuan-Instruct is an internal model, while Qwen2-Nova-72B and Llama3-PBM-Nova-70B are instruct versions of the Qwen2-72B and Llama-3-70B base models, optimized through Baichuan Alignment. Baichuan-Instruct demonstrates significant improvements in core capabilities, with user experience gains ranging from 17% to 28%, and performs exceptionally well on specialized benchmarks. In open-source benchmark evaluations, both Qwen2-Nova-72B and Llama3-PBM-Nova-70B consistently outperform their respective official instruct versions across nearly all datasets. This report aims to clarify the key technologies behind the alignment process, fostering a deeper understanding within the community. Llama3-PBM-Nova-70B model is available at https://huggingface.co/PKU-Baichuan-MLSystemLab/Llama3-PBM-Nova-70B.

Large Language Models (LLMs) need to be aligned with human expectations to ensure their safety and utility in most applications. Alignment is challenging, costly, and needs to be repeated for every LLM and alignment criterion. We propose to decouple LLMs and alignment by training aligner models that can be used to align any LLM for a given criteria on an as-needed basis, thus also reducing the potential negative impacts of alignment on performance. Our recipe for training the aligner models solely relies on synthetic data generated with a (prompted) LLM and can be easily adjusted for a variety of alignment criteria. We illustrate our method by training an "ethical" aligner and verify its efficacy empirically.

The alignment problem in Large Language Models (LLMs) involves adapting them to the broad spectrum of human values. This requirement challenges existing alignment methods due to diversity of preferences and regulatory standards. This paper introduces a novel alignment paradigm, priority rule following, which defines rules as the primary control mechanism in each dialog, prioritizing them over user instructions. Our preliminary analysis reveals that even the advanced LLMs, such as GPT-4, exhibit shortcomings in understanding and prioritizing the rules. Therefore, we present PriorityDistill, a semi-automated approach for distilling priority following signals from LLM simulations to ensure robust rule integration and adherence. Our experiments show that this method not only effectively minimizes misalignments utilizing only one general rule but also adapts smoothly to various unseen rules, ensuring they are shielded from hijacking and that the model responds appropriately.

Connectionist Temporal Classification (CTC) is a widely used criterion for training supervised sequence-to-sequence (seq2seq) models. It enables learning the relations between input and output sequences, termed alignments, by marginalizing over perfect alignments (that yield the ground truth), at the expense of imperfect alignments. This binary differentiation of perfect and imperfect alignments falls short of capturing other essential alignment properties that hold significance in other real-world applications. Here we propose Align With Purpose, a general Plug-and-Play framework for enhancing a desired property in models trained with the CTC criterion. We do that by complementing the CTC with an additional loss term that prioritizes alignments according to a desired property. Our method does not require any intervention in the CTC loss function, enables easy optimization of a variety of properties, and allows differentiation between both perfect and imperfect alignments. We apply our framework in the domain of Automatic Speech Recognition (ASR) and show its generality in terms of property selection, architectural choice, and scale of training dataset (up to 280,000 hours). To demonstrate the effectiveness of our framework, we apply it to two unrelated properties: emission time and word error rate (WER). For the former, we report an improvement of up to 570ms in latency optimization with a minor reduction in WER, and for the latter, we report a relative improvement of 4.5% WER over the baseline models. To the best of our knowledge, these applications have never been demonstrated to work on a scale of data as large as ours. Notably, our method can be implemented using only a few lines of code, and can be extended to other alignment-free loss functions and to domains other than ASR.

Efforts to align Large Language Models (LLMs) are mainly conducted via Reinforcement Learning from Human Feedback (RLHF) methods. However, RLHF encounters major challenges including training reward models, actor-critic engineering, and importantly, it requires access to LLM parameters. Here we introduce Aligner, a new efficient alignment paradigm that bypasses the whole RLHF process by learning the correctional residuals between the aligned and the unaligned answers. Our Aligner offers several key advantages. Firstly, it is an autoregressive seq2seq model that is trained on the query-answer-correction dataset via supervised learning; this offers a parameter-efficient alignment solution with minimal resources. Secondly, the Aligner facilitates weak-to-strong generalization; finetuning large pretrained models by Aligner's supervisory signals demonstrates strong performance boost. Thirdly, Aligner functions as a model-agnostic plug-and-play module, allowing for its direct application on different open-source and API-based models. Remarkably, Aligner-7B improves 11 different LLMs by 21.9% in helpfulness and 23.8% in harmlessness on average (GPT-4 by 17.5% and 26.9%). When finetuning (strong) Llama2-70B with (weak) Aligner-13B's supervision, we can improve Llama2 by 8.2% in helpfulness and 61.6% in harmlessness. See our dataset and code at https://aligner2024.github.io

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Word alignment over parallel corpora has a wide variety of applications, including learning translation lexicons, cross-lingual transfer of language processing tools, and automatic evaluation or analysis of translation outputs. The great majority of past work on word alignment has worked by performing unsupervised learning on parallel texts. Recently, however, other work has demonstrated that pre-trained contextualized word embeddings derived from multilingually trained language models (LMs) prove an attractive alternative, achieving competitive results on the word alignment task even in the absence of explicit training on parallel data. In this paper, we examine methods to marry the two approaches: leveraging pre-trained LMs but fine-tuning them on parallel text with objectives designed to improve alignment quality, and proposing methods to effectively extract alignments from these fine-tuned models. We perform experiments on five language pairs and demonstrate that our model can consistently outperform previous state-of-the-art models of all varieties. In addition, we demonstrate that we are able to train multilingual word aligners that can obtain robust performance on different language pairs. Our aligner, AWESOME (Aligning Word Embedding Spaces of Multilingual Encoders), with pre-trained models is available at https://github.com/neulab/awesome-align

Aligning foundation models is essential for their safe and trustworthy deployment. However, traditional fine-tuning methods are computationally intensive and require updating billions of model parameters. A promising alternative, alignment via decoding, adjusts the response distribution directly without model updates to maximize a target reward r, thus providing a lightweight and adaptable framework for alignment. However, principled decoding methods rely on oracle access to an optimal Q-function (Q^*), which is often unavailable in practice. Hence, prior SoTA methods either approximate this Q^* using Q^{pi_{sft}} (derived from the reference SFT model) or rely on short-term rewards, resulting in sub-optimal decoding performance. In this work, we propose Transfer Q^*, which implicitly estimates the optimal value function for a target reward r through a baseline model rho_{BL} aligned with a baseline reward rho_{BL} (which can be different from the target reward r). Theoretical analyses of Transfer Q^* provide a rigorous characterization of its optimality, deriving an upper bound on the sub-optimality gap and identifying a hyperparameter to control the deviation from the pre-trained reference SFT model based on user needs. Our approach significantly reduces the sub-optimality gap observed in prior SoTA methods and demonstrates superior empirical performance across key metrics such as coherence, diversity, and quality in extensive tests on several synthetic and real datasets.

Language model alignment has become a critical step in training modern generative language models. The goal of alignment is to finetune a reference model such that the win rate of a sample from the aligned model over a sample from the reference model is high, subject to a KL divergence constraint. Today, we are increasingly using inference-time algorithms (e.g., Best-of-N, controlled decoding, tree search) to decode from language models rather than standard sampling. However, the alignment objective does not capture such inference-time decoding procedures. We show that the existing alignment framework is sub-optimal in view of such inference-time methods. We then modify the alignment objective and propose a framework for inference-aware alignment (IAPO). We prove that for any inference-time decoding algorithm, the optimal solution that optimizes the inference-time win rate of the aligned policy against the reference policy is the solution to the typical RLHF problem with a transformation of the reward. This motivates us to provide the KL-regularized calibrate-and-transform RL (CTRL) algorithm to solve this problem, which involves a reward calibration step and a KL-regularized reward maximization step with a transformation of the calibrated reward. We particularize our study to two important inference-time strategies: best-of-N sampling and best-of-N jailbreaking, where N responses are sampled from the model and the one with the highest or lowest reward is selected. We propose specific transformations for these strategies and demonstrate that our framework offers significant improvements over existing state-of-the-art methods for language model alignment. Empirically, we outperform baselines that are designed without taking inference-time decoding into consideration by 8-12% and 4-9% on inference-time win rates over the Anthropic helpfulness and harmlessness dialog benchmark datasets.

We study methods for efficiently aligning large language models (LLMs) with human preferences given budgeted online feedback. We first formulate the LLM alignment problem in the frame of contextual dueling bandits. This formulation, subsuming recent paradigms such as online RLHF and online DPO, inherently quests for sample-efficient algorithms that incorporate online active exploration. Leveraging insights from bandit theory, we introduce a unified algorithm based on Thompson sampling and highlight its applications in two distinct LLM alignment scenarios. The practical agent that efficiently implements this algorithm, named SEA (Sample-Efficient Alignment), is empirically validated through extensive experiments across three model scales (1B, 2.8B, 6.9B) and three preference learning algorithms (DPO, IPO, SLiC). The results demonstrate that SEA achieves highly sample-efficient alignment with oracle's preferences, outperforming recent active exploration methods for LLMs. Additionally, we release the implementation of SEA together with an efficient codebase designed for online alignment of LLMs, aiming to accelerate future research in this field.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Generative models, widely utilized in various applications, can often struggle with prompts corresponding to partial tokens. This struggle stems from tokenization, where partial tokens fall out of distribution during inference, leading to incorrect or nonsensical outputs. This paper examines a technique to alleviate the tokenization artifact on text completion in generative models, maintaining performance even in regular non-subword cases. The method, termed token alignment, involves backtracking to the last complete tokens and ensuring the model's generation aligns with the prompt. This approach showcases marked improvement across many partial token scenarios, including nuanced cases like space-prefix and partial indentation, with only a minor time increase. The technique and analysis detailed in this paper contribute to the continuous advancement of generative models in handling partial inputs, bearing relevance for applications like code completion and text autocompletion.

Large Language Models (LLMs) have achieved significant advancements, however, the common learning paradigm treats LLMs as passive information repositories, neglecting their potential for active learning and alignment. Some approaches train LLMs using their own generated synthetic data, exploring the possibility of active alignment. However, there is still a huge gap between these one-time alignment methods and the continuous automatic alignment of humans. In this paper, we introduce I-SHEEP, an Iterative Self-EnHancEmEnt Paradigm.This human-like paradigm enables LLMs to continuously self-align from scratch with nothing. Compared to the one-time alignment method Dromedary sun2023principledriven, which refers to the first iteration in this paper, I-SHEEP can significantly enhance capacities on both Qwen and Llama models. I-SHEEP achieves a maximum relative improvement of 78.2\% in the Alpaca Eval, 24.0\% in the MT Bench, and an absolute increase of 8.88\% in the IFEval accuracy over subsequent iterations in Qwen-1.5 72B model. Additionally, I-SHEEP surpasses the base model in various standard benchmark generation tasks, achieving an average improvement of 24.77\% in code generation tasks, 12.04\% in TrivialQA, and 20.29\% in SQuAD. We also provide new insights based on the experiment results. Our codes, datasets, and models are available at https://anonymous.4open.science/r/I-SHEEP.

The alignment tuning process of large language models (LLMs) typically involves instruction learning through supervised fine-tuning (SFT) and preference tuning via reinforcement learning from human feedback (RLHF). A recent study, LIMA (Zhou et al. 2023), shows that using merely 1K examples for SFT can achieve significant alignment performance as well, suggesting that the effect of alignment tuning might be "superficial." This raises questions about how exactly the alignment tuning transforms a base LLM. We analyze the effect of alignment tuning by examining the token distribution shift between base LLMs and their aligned counterpart. Our findings reveal that base LLMs and their alignment-tuned versions perform nearly identically in decoding on the majority of token positions. Most distribution shifts occur with stylistic tokens. These direct evidence strongly supports the Superficial Alignment Hypothesis suggested by LIMA. Based on these findings, we rethink the alignment of LLMs by posing the research question: how effectively can we align base LLMs without SFT or RLHF? To address this, we introduce a simple, tuning-free alignment method, URIAL. URIAL achieves effective alignment purely through in-context learning (ICL) with base LLMs, requiring as few as three constant stylistic examples and a system prompt. We conduct a fine-grained and interpretable evaluation on a diverse set of examples, named JUST-EVAL-INSTRUCT. Results demonstrate that base LLMs with URIAL can match or even surpass the performance of LLMs aligned with SFT or SFT+RLHF. We show that the gap between tuning-free and tuning-based alignment methods can be significantly reduced through strategic prompting and ICL. Our findings on the superficial nature of alignment tuning and results with URIAL suggest that deeper analysis and theoretical understanding of alignment is crucial to future LLM research.

Recent years have witnessed remarkable progress made in large language models (LLMs). Such advancements, while garnering significant attention, have concurrently elicited various concerns. The potential of these models is undeniably vast; however, they may yield texts that are imprecise, misleading, or even detrimental. Consequently, it becomes paramount to employ alignment techniques to ensure these models to exhibit behaviors consistent with human values. This survey endeavors to furnish an extensive exploration of alignment methodologies designed for LLMs, in conjunction with the extant capability research in this domain. Adopting the lens of AI alignment, we categorize the prevailing methods and emergent proposals for the alignment of LLMs into outer and inner alignment. We also probe into salient issues including the models' interpretability, and potential vulnerabilities to adversarial attacks. To assess LLM alignment, we present a wide variety of benchmarks and evaluation methodologies. After discussing the state of alignment research for LLMs, we finally cast a vision toward the future, contemplating the promising avenues of research that lie ahead. Our aspiration for this survey extends beyond merely spurring research interests in this realm. We also envision bridging the gap between the AI alignment research community and the researchers engrossed in the capability exploration of LLMs for both capable and safe LLMs.

Alignment, endowing a pre-trained Large language model (LLM) with the ability to follow instructions, is crucial for its real-world applications. Conventional supervised fine-tuning (SFT) methods formalize it as causal language modeling typically with a cross-entropy objective, requiring a large amount of high-quality instruction-response pairs. However, the quality of widely used SFT datasets can not be guaranteed due to the high cost and intensive labor for the creation and maintenance in practice. To overcome the limitations associated with the quality of SFT datasets, we introduce a novel preference-oriented supervised fine-tuning approach, namely PoFT. The intuition is to boost SFT by imposing a particular preference: favoring the target model over aligned LLMs on the same SFT data. This preference encourages the target model to predict a higher likelihood than that predicted by the aligned LLMs, incorporating assessment information on data quality (i.e., predicted likelihood by the aligned LLMs) into the training process. Extensive experiments are conducted, and the results validate the effectiveness of the proposed method. PoFT achieves stable and consistent improvements over the SFT baselines across different training datasets and base models. Moreover, we prove that PoFT can be integrated with existing SFT data filtering methods to achieve better performance, and further improved by following preference optimization procedures, such as DPO.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

We test similarity-based word alignment models (SimAlign and awesome-align) in combination with word embeddings from mBERT and XLM-R on parallel sentences in German and Romansh. Since Romansh is an unseen language, we are dealing with a zero-shot setting. Using embeddings from mBERT, both models reach an alignment error rate of 0.22, which outperforms fast_align, a statistical model, and is on par with similarity-based word alignment for seen languages. We interpret these results as evidence that mBERT contains information that can be meaningful and applicable to Romansh. To evaluate performance, we also present a new trilingual corpus, which we call the DERMIT (DE-RM-IT) corpus, containing press releases made by the Canton of Grisons in German, Romansh and Italian in the past 25 years. The corpus contains 4 547 parallel documents and approximately 100 000 sentence pairs in each language combination. We additionally present a gold standard for German-Romansh word alignment. The data is available at https://github.com/eyldlv/DERMIT-Corpus.

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.

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.

The Scielo database is an important source of scientific information in Latin America, containing articles from several research domains. A striking characteristic of Scielo is that many of its full-text contents are presented in more than one language, thus being a potential source of parallel corpora. In this article, we present the development of a parallel corpus from Scielo in three languages: English, Portuguese, and Spanish. Sentences were automatically aligned using the Hunalign algorithm for all language pairs, and for a subset of trilingual articles also. We demonstrate the capabilities of our corpus by training a Statistical Machine Translation system (Moses) for each language pair, which outperformed related works on scientific articles. Sentence alignment was also manually evaluated, presenting an average of 98.8% correctly aligned sentences across all languages. Our parallel corpus is freely available in the TMX format, with complementary information regarding article metadata.

Time-aligned lyrics can enrich the music listening experience by enabling karaoke, text-based song retrieval and intra-song navigation, and other applications. Compared to text-to-speech alignment, lyrics alignment remains highly challenging, despite many attempts to combine numerous sub-modules including vocal separation and detection in an effort to break down the problem. Furthermore, training required fine-grained annotations to be available in some form. Here, we present a novel system based on a modified Wave-U-Net architecture, which predicts character probabilities directly from raw audio using learnt multi-scale representations of the various signal components. There are no sub-modules whose interdependencies need to be optimized. Our training procedure is designed to work with weak, line-level annotations available in the real world. With a mean alignment error of 0.35s on a standard dataset our system outperforms the state-of-the-art by an order of magnitude.

Alignment is a standard procedure to fine-tune pre-trained large language models (LLMs) to follow natural language instructions and serve as helpful AI assistants. We have observed, however, that the conventional alignment process fails to enhance the factual accuracy of LLMs, and often leads to the generation of more false facts (i.e. hallucination). In this paper, we study how to make the LLM alignment process more factual, by first identifying factors that lead to hallucination in both alignment steps:\ supervised fine-tuning (SFT) and reinforcement learning (RL). In particular, we find that training the LLM on new knowledge or unfamiliar texts can encourage hallucination. This makes SFT less factual as it trains on human labeled data that may be novel to the LLM. Furthermore, reward functions used in standard RL can also encourage hallucination, because it guides the LLM to provide more helpful responses on a diverse set of instructions, often preferring longer and more detailed responses. Based on these observations, we propose factuality-aware alignment, comprised of factuality-aware SFT and factuality-aware RL through direct preference optimization. Experiments show that our proposed factuality-aware alignment guides LLMs to output more factual responses while maintaining instruction-following capability.

String similarity models are vital for record linkage, entity resolution, and search. In this work, we present STANCE --a learned model for computing the similarity of two strings. Our approach encodes the characters of each string, aligns the encodings using Sinkhorn Iteration (alignment is posed as an instance of optimal transport) and scores the alignment with a convolutional neural network. We evaluate STANCE's ability to detect whether two strings can refer to the same entity--a task we term alias detection. We construct five new alias detection datasets (and make them publicly available). We show that STANCE or one of its variants outperforms both state-of-the-art and classic, parameter-free similarity models on four of the five datasets. We also demonstrate STANCE's ability to improve downstream tasks by applying it to an instance of cross-document coreference and show that it leads to a 2.8 point improvement in B^3 F1 over the previous state-of-the-art approach.

This paper concerns the problem of aligning samples from large language models to human preferences using best-of-n sampling, where we draw n samples, rank them, and return the best one. We consider two fundamental problems. First: what is the relationship between best-of-n and approaches to alignment that train LLMs to output samples with a high expected reward (e.g., RLHF or DPO)? To answer this, we embed both the best-of-n distribution and the sampling distributions learned by alignment procedures in a common class of tiltings of the base LLM distribution. We then show that, within this class, best-of-n is essentially optimal in terms of the trade-off between win-rate against the base model vs KL distance from the base model. That is, best-of-n is the best choice of alignment distribution if the goal is to maximize win rate. However, best-of-n requires drawing n samples for each inference, a substantial cost. To avoid this, the second problem we consider is how to fine-tune a LLM to mimic the best-of-n sampling distribution. We derive BoNBoN Alignment to achieve this by exploiting the special structure of the best-of-n distribution. Experiments show that BoNBoN alignment yields substantial improvements in producing a model that is preferred to the base policy while minimally affecting off-target aspects.

Aligning large language models (LLMs) with human values is a vital task for LLM practitioners. Current alignment techniques have several limitations: (1) requiring a large amount of annotated data; (2) demanding heavy human involvement; (3) lacking a systematic mechanism to continuously improve. In this work, we study aligning LLMs to a new domain with limited samples (e.g. < 100). We propose an algorithm that can self-align LLMs iteratively without active human involvement. Unlike existing works, our algorithm relies on neither human-crafted instructions nor labeled rewards, significantly reducing human involvement. In addition, our algorithm can self-improve the alignment continuously. The key idea is to first retrieve high-quality samples related to the target domain and use them as In-context Learning examples to generate more samples. Then we use the self-generated samples to finetune the LLM iteratively. We show that our method can unlock the LLMs' self-generalization ability to perform alignment with near-zero human supervision. We test our algorithm on three benchmarks in safety, truthfulness, and instruction-following, and show good performance in alignment, domain adaptability, and scalability.

Sequence-to-sequence models are commonly trained via maximum likelihood estimation (MLE). However, standard MLE training considers a word-level objective, predicting the next word given the previous ground-truth partial sentence. This procedure focuses on modeling local syntactic patterns, and may fail to capture long-range semantic structure. We present a novel solution to alleviate these issues. Our approach imposes global sequence-level guidance via new supervision based on optimal transport, enabling the overall characterization and preservation of semantic features. We further show that this method can be understood as a Wasserstein gradient flow trying to match our model to the ground truth sequence distribution. Extensive experiments are conducted to validate the utility of the proposed approach, showing consistent improvements over a wide variety of NLP tasks, including machine translation, abstractive text summarization, and image captioning.

Vector representations of natural language are ubiquitous in search applications. Recently, various methods based on contrastive learning have been proposed to learn textual representations from unlabelled data; by maximizing alignment between minimally-perturbed embeddings of the same text, and encouraging a uniform distribution of embeddings across a broader corpus. Differently, we propose maximizing alignment between texts and a composition of their phrasal constituents. We consider several realizations of this objective and elaborate the impact on representations in each case. Experimental results on semantic textual similarity tasks show improvements over baselines that are comparable with state-of-the-art approaches. Moreover, this work is the first to do so without incurring costs in auxiliary training objectives or additional network parameters.

Alignment has become a critical step for instruction-tuned Large Language Models (LLMs) to become helpful assistants. However, effective evaluation of alignment for emerging Chinese LLMs is still significantly lacking, calling for real-scenario grounded, open-ended, challenging and automatic evaluations tailored for alignment. To fill in this gap, we introduce AlignBench, a comprehensive multi-dimensional benchmark for evaluating LLMs' alignment in Chinese. Equipped with a human-in-the-loop data curation pipeline, our benchmark employs a rule-calibrated multi-dimensional LLM-as-Judge with Chain-of-Thought to generate explanations and final ratings as evaluations, ensuring high reliability and interpretability. Furthermore, we report AlignBench evaluated by CritiqueLLM, a dedicated Chinese evaluator LLM that recovers 95% of GPT-4's evaluation ability. We will provide public APIs for evaluating AlignBench with CritiqueLLM to facilitate the evaluation of LLMs' Chinese alignment. All evaluation codes, data, and LLM generations are available at https://github.com/THUDM/AlignBench.

We study unsupervised multilingual alignment, the problem of finding word-to-word translations between multiple languages without using any parallel data. One popular strategy is to reduce multilingual alignment to the much simplified bilingual setting, by picking one of the input languages as the pivot language that we transit through. However, it is well-known that transiting through a poorly chosen pivot language (such as English) may severely degrade the translation quality, since the assumed transitive relations among all pairs of languages may not be enforced in the training process. Instead of going through a rather arbitrarily chosen pivot language, we propose to use the Wasserstein barycenter as a more informative "mean" language: it encapsulates information from all languages and minimizes all pairwise transportation costs. We evaluate our method on standard benchmarks and demonstrate state-of-the-art performances.

Large Language Models (LLMs) are nowadays expected to generate content aligned with human preferences. Current work focuses on alignment at model training time, through techniques such as Reinforcement Learning with Human Feedback (RLHF). However, it is unclear if such methods are an effective choice to teach alignment objectives to the model. First, the inability to incorporate multiple, custom rewards and reliance on a model developer's view of universal and static principles are key limitations. Second, the residual gaps in model training and the reliability of such approaches are also questionable (e.g. susceptibility to jail-breaking even after safety training). To address these, we propose DeAL, a framework that allows the user to customize reward functions and enables Decoding-time Alignment of LLMs (DeAL). At its core, we view decoding as a heuristic-guided search process and facilitate the use of a wide variety of alignment objectives. Our experiments with programmatic constraints such as keyword and length constraints (studied widely in the pre-LLM era) and abstract objectives such as harmlessness and helpfulness (proposed in the post-LLM era) show that we can DeAL with fine-grained trade-offs, improve adherence to alignment objectives, and address residual gaps in LLMs. Lastly, while DeAL can be effectively paired with RLHF and prompting techniques, its generality makes decoding slower, an optimization we leave for future work.

One of the most important problems in machine translation (MT) evaluation is to evaluate the similarity between translation hypotheses with different surface forms from the reference, especially at the segment level. We propose to use word embeddings to perform word alignment for segment-level MT evaluation. We performed experiments with three types of alignment methods using word embeddings. We evaluated our proposed methods with various translation datasets. Experimental results show that our proposed methods outperform previous word embeddings-based methods.

Large language models are susceptible to jailbreak attacks, which can result in the generation of harmful content. While prior defenses mitigate these risks by perturbing or inspecting inputs, they ignore competing objectives, the underlying cause of alignment failures. In this paper, we propose Alignment-Enhanced Decoding (AED), a novel defense that employs adaptive decoding to address the root causes of jailbreak issues. We first define the Competitive Index to quantify alignment failures and utilize feedback from self-evaluation to compute post-alignment logits. Then, AED adaptively combines AED and post-alignment logits with the original logits to obtain harmless and helpful distributions. Consequently, our method enhances safety alignment while maintaining helpfulness. We conduct experiments across five models and four common jailbreaks, with the results validating the effectiveness of our approach. Code is available at https://github.com/GIGABaozi/AED.git.

We present a corpus of sentence-aligned triples of German audio, German text, and English translation, based on German audiobooks. The speech translation data consist of 110 hours of audio material aligned to over 50k parallel sentences. An even larger dataset comprising 547 hours of German speech aligned to German text is available for speech recognition. The audio data is read speech and thus low in disfluencies. The quality of audio and sentence alignments has been checked by a manual evaluation, showing that speech alignment quality is in general very high. The sentence alignment quality is comparable to well-used parallel translation data and can be adjusted by cutoffs on the automatic alignment score. To our knowledge, this corpus is to date the largest resource for German speech recognition and for end-to-end German-to-English speech translation.

Recent studies have demonstrated the cross-lingual alignment ability of multilingual pretrained language models. In this work, we found that the cross-lingual alignment can be further improved by training seq2seq models on sentence pairs mined using their own encoder outputs. We utilized these findings to develop a new approach -- cross-lingual retrieval for iterative self-supervised training (CRISS), where mining and training processes are applied iteratively, improving cross-lingual alignment and translation ability at the same time. Using this method, we achieved state-of-the-art unsupervised machine translation results on 9 language directions with an average improvement of 2.4 BLEU, and on the Tatoeba sentence retrieval task in the XTREME benchmark on 16 languages with an average improvement of 21.5% in absolute accuracy. Furthermore, CRISS also brings an additional 1.8 BLEU improvement on average compared to mBART, when finetuned on supervised machine translation downstream tasks.

Instruction tuning is a standard technique employed to align large language models to end tasks and user preferences after the initial pretraining phase. Recent research indicates the critical role of data engineering in instruction tuning -- when appropriately selected, only limited data is necessary to achieve superior performance. However, we still lack a principled understanding of what makes good instruction tuning data for alignment, and how we should select data automatically and effectively. In this work, we delve deeply into automatic data selection strategies for alignment. We start with controlled studies to measure data across three dimensions: complexity, quality, and diversity, along which we examine existing methods and introduce novel techniques for enhanced data measurement. Subsequently, we propose a simple strategy to select data samples based on the measurement. We present deita (short for Data-Efficient Instruction Tuning for Alignment), a series of models fine-tuned from LLaMA and Mistral models using data samples automatically selected with our proposed approach. Empirically, deita performs better or on par with the state-of-the-art open-source alignment models with only 6K SFT training data samples -- over 10x less than the data used in the baselines. When further trained with direct preference optimization (DPO), deita-Mistral-7B + DPO trained with 6K SFT and 10K DPO samples achieve 7.55 MT-Bench and 90.06% AlpacaEval scores. We anticipate this work to provide tools on automatic data selection, facilitating data-efficient alignment. We release our models as well as the selected datasets for future researches to effectively align models more efficiently.

Inference-time alignment provides an efficient alternative for aligning LLMs with humans. However, these approaches still face challenges, such as limited scalability due to policy-specific value functions and latency during the inference phase. In this paper, we propose a novel approach, Diffusion-styled Preference Optimization (\model), which provides an efficient and policy-agnostic solution for aligning LLMs with humans. By directly performing alignment at sentence level, \model~avoids the time latency associated with token-level generation. Designed as a plug-and-play module, \model~can be seamlessly integrated with various base models to enhance their alignment. Extensive experiments on AlpacaEval 2, MT-bench, and HH-RLHF demonstrate that \model~achieves superior alignment performance across various settings, achieving a favorable trade-off between alignment quality and inference-time latency. Furthermore, \model~demonstrates model-agnostic scalability, significantly improving the performance of large models such as Llama-3-70B.

The safe and effective deployment of Large Language Models (LLMs) involves a critical step called alignment, which ensures that the model's responses are in accordance with human preferences. Prevalent alignment techniques, such as DPO, PPO and their variants, align LLMs by changing the pre-trained model weights during a phase called post-training. While predominant, these post-training methods add substantial complexity before LLMs can be deployed. Inference-time alignment methods avoid the complex post-training step and instead bias the generation towards responses that are aligned with human preferences. The best-known inference-time alignment method, called Best-of-N, is as effective as the state-of-the-art post-training procedures. Unfortunately, Best-of-N requires vastly more resources at inference time than standard decoding strategies, which makes it computationally not viable. In this work, we introduce Speculative Rejection, a computationally-viable inference-time alignment algorithm. It generates high-scoring responses according to a given reward model, like Best-of-N does, while being between 16 to 32 times more computationally efficient.

Despite the remarkable advances in language modeling, current mainstream decoding methods still struggle to generate texts that align with human texts across different aspects. In particular, sampling-based methods produce less-repetitive texts which are often disjunctive in discourse, while search-based methods maintain topic coherence at the cost of increased repetition. Overall, these methods fall short in achieving holistic alignment across a broad range of aspects. In this work, we frame decoding from a language model as an optimization problem with the goal of strictly matching the expected performance with human texts measured by multiple metrics of desired aspects simultaneously. The resulting decoding distribution enjoys an analytical solution that scales the input language model distribution via a sequence-level energy function defined by these metrics. And most importantly, we prove that this induced distribution is guaranteed to improve the perplexity on human texts, which suggests a better approximation to the underlying distribution of human texts. To facilitate tractable sampling from this globally normalized distribution, we adopt the Sampling-Importance-Resampling technique. Experiments on various domains and model scales demonstrate the superiority of our method in metrics alignment with human texts and human evaluation over strong baselines.

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

High-quality data labeling from specific domains is costly and human time-consuming. In this work, we propose a self-supervised domain adaptation method, based upon an iterative pseudo-forced alignment algorithm. The produced alignments are employed to customize an end-to-end Automatic Speech Recognition (ASR) and iteratively refined. The algorithm is fed with frame-wise character posteriors produced by a seed ASR, trained with out-of-domain data, and optimized throughout a Connectionist Temporal Classification (CTC) loss. The alignments are computed iteratively upon a corpus of broadcast TV. The process is repeated by reducing the quantity of text to be aligned or expanding the alignment window until finding the best possible audio-text alignment. The starting timestamps, or temporal anchors, are produced uniquely based on the confidence score of the last aligned utterance. This score is computed with the paths of the CTC-alignment matrix. With this methodology, no human-revised text references are required. Alignments from long audio files with low-quality transcriptions, like TV captions, are filtered out by confidence score and ready for further ASR adaptation. The obtained results, on both the Spanish RTVE2022 and CommonVoice databases, underpin the feasibility of using CTC-based systems to perform: highly accurate audio-text alignments, domain adaptation and semi-supervised training of end-to-end ASR.

The alignment of large language models is usually done by model providers to add or control behaviors that are common or universally understood across use cases and contexts. In contrast, in this article, we present an approach and architecture that empowers application developers to tune a model to their particular values, social norms, laws and other regulations, and orchestrate between potentially conflicting requirements in context. We lay out three main components of such an Alignment Studio architecture: Framers, Instructors, and Auditors that work in concert to control the behavior of a language model. We illustrate this approach with a running example of aligning a company's internal-facing enterprise chatbot to its business conduct guidelines.

This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible completions and evaluating these completions based on model confidence. By considering various paths in the search tree and scoring them according to the model's confidence in each completion, we can generate diverse and high-quality sequences. This research explores the implementation of this paradigm by using confidence as a proxy for response quality akin to beam search vijayakumar2016diverse. The primary goal of this paper is to outline the paradigm and demonstrate its potential, rather than focusing on achieving perfect results. The paper will outline the reasons why we believe this paradigm has the potential to improve LLMs in the following manners: 1) increase output quality, 2) decrease errors, 3) eliminate or reduce the compound error problems, 4) generate diverse and creative completions, 5) allow for iterative problem-solving, and 6) self-training. We expect this approach to yield a set of diverse and coherent sequences, offering insights into balancing exploration and exploitation in sequence generation. Potential applications include creative text generation tasks, such as storytelling and content creation, as well as other natural language processing domains, like machine translation and automated summarization. The goal is that the model will be far more effective as it will be able to consider many possible variations allowing it to find the ideal completion. This research aims to contribute to the understanding of effective search strategies in sequence generation and their impact on generating high-quality, varied textual outputs.

Aligning Large Language Models (LLMs) with human values and preferences is essential for making them helpful and safe. However, building efficient tools to perform alignment can be challenging, especially for the largest and most competent LLMs which often contain tens or hundreds of billions of parameters. We create NeMo-Aligner, a toolkit for model alignment that can efficiently scale to using hundreds of GPUs for training. NeMo-Aligner comes with highly optimized and scalable implementations for major paradigms of model alignment such as: Reinforcement Learning from Human Feedback (RLHF), Direct Preference Optimization (DPO), SteerLM, and Self-Play Fine-Tuning (SPIN). Additionally, our toolkit supports running most of the alignment techniques in a Parameter Efficient Fine-Tuning (PEFT) setting. NeMo-Aligner is designed for extensibility, allowing support for other alignment techniques with minimal effort. It is open-sourced with Apache 2.0 License and we invite community contributions at https://github.com/NVIDIA/NeMo-Aligner

With the release of ever more capable large language models (LLMs), researchers in NLP and related disciplines have started to explore the usability of LLMs for a wide variety of different annotation tasks. Very recently, a lot of this attention has shifted to tasks that are subjective in nature. Given that the latest generations of LLMs have digested and encoded extensive knowledge about different human subpopulations and individuals, the hope is that these models can be trained, tuned or prompted to align with a wide range of different human perspectives. While researchers already evaluate the success of this alignment via surveys and tests, there is a lack of resources to evaluate the alignment on what oftentimes matters the most in NLP; the actual downstream tasks. To fill this gap we present SubData, a Python library that offers researchers working on topics related to subjectivity in annotation tasks a convenient way of collecting, combining and using a range of suitable datasets.

Aligning Large Language Models (LLMs) to human preferences through preference optimization has been crucial but labor-intensive, necessitating for each prompt a comparison of both a chosen and a rejected text completion by evaluators. Recently, Kahneman-Tversky Optimization (KTO) has demonstrated that LLMs can be aligned using merely binary "thumbs-up" or "thumbs-down" signals on each prompt-completion pair. In this paper, we present theoretical foundations to explain the successful alignment achieved through these binary signals. Our analysis uncovers a new perspective: optimizing a binary classifier, whose logit is a reward, implicitly induces minimizing the Direct Preference Optimization (DPO) loss. In the process of this discovery, we identified two techniques for effective alignment: reward shift and underlying distribution matching. Consequently, we propose a new algorithm, Binary Classifier Optimization, that integrates the techniques. We validate our methodology in two settings: first, on a paired preference dataset, where our method performs on par with DPO and KTO; and second, on binary signal datasets simulating real-world conditions with divergent underlying distributions between thumbs-up and thumbs-down data. Our model consistently demonstrates effective and robust alignment across two base LLMs and three different binary signal datasets, showcasing the strength of our approach to learning from binary feedback.

Recent approaches to large language model (LLM) alignment typically require millions of human annotations or rely on external aligned models for synthetic data generation. This paper introduces ALMA: Alignment with Minimal Annotation, demonstrating that effective alignment can be achieved using only 9,000 labeled examples -- less than 1% of conventional approaches. ALMA generates large amounts of high-quality synthetic alignment data through new techniques: diverse prompt synthesis via few-shot learning, diverse response generation with multiple model checkpoints, and judge (reward model) enhancement through score aggregation and self-distillation. Using only a pretrained Llama3 base model, 5,000 SFT examples, and 4,000 judge annotations, ALMA achieves performance close to Llama3-Instruct across diverse alignment benchmarks (e.g., 0.1% difference on AlpacaEval 2.0 score). These results are achieved with a multi-round, self-bootstrapped data synthesis and training recipe that continues to improve for 10 rounds, surpassing the typical 3-round ceiling of previous methods. These results suggest that base models already possess sufficient knowledge for effective alignment, and that synthetic data generation methods can expose it.

Self-supervised representation learning of biological sequence embeddings alleviates computational resource constraints on downstream tasks while circumventing expensive experimental label acquisition. However, existing methods mostly borrow directly from large language models designed for NLP, rather than with bioinformatics philosophies in mind. Recently, contrastive mutual information maximization methods have achieved state-of-the-art representations for ImageNet. In this perspective piece, we discuss how viewing evolution as natural sequence augmentation and maximizing information across phylogenetic "noisy channels" is a biologically and theoretically desirable objective for pretraining encoders. We first provide a review of current contrastive learning literature, then provide an illustrative example where we show that contrastive learning using evolutionary augmentation can be used as a representation learning objective which maximizes the mutual information between biological sequences and their conserved function, and finally outline rationale for this approach.

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

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

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.

A key concern with the concept of "alignment" is the implicit question of "alignment to what?". AI systems are increasingly used across the world, yet safety alignment is often focused on homogeneous monolingual settings. Additionally, preference training and safety measures often overfit to harms common in Western-centric datasets. Here, we explore the viability of different alignment approaches when balancing dual objectives: addressing and optimizing for a non-homogeneous set of languages and cultural preferences while minimizing both global and local harms. We collect the first set of human annotated red-teaming prompts in different languages distinguishing between global and local harm, which serve as a laboratory for understanding the reliability of alignment techniques when faced with preference distributions that are non-stationary across geographies and languages. While this setting is seldom covered by the literature to date, which primarily centers on English harm mitigation, it captures real-world interactions with AI systems around the world. We establish a new precedent for state-of-the-art alignment techniques across 6 languages with minimal degradation in general performance. Our work provides important insights into cross-lingual transfer and novel optimization approaches to safeguard AI systems designed to serve global populations.

Although deep learning and end-to-end models have been widely used and shown superiority in automatic speech recognition (ASR) and text-to-speech (TTS) synthesis, state-of-the-art forced alignment (FA) models are still based on hidden Markov model (HMM). HMM has limited view of contextual information and is developed with long pipelines, leading to error accumulation and unsatisfactory performance. Inspired by the capability of attention mechanism in capturing long term contextual information and learning alignments in ASR and TTS, we propose a neural network based end-to-end forced aligner called NeuFA, in which a novel bidirectional attention mechanism plays an essential role. NeuFA integrates the alignment learning of both ASR and TTS tasks in a unified framework by learning bidirectional alignment information from a shared attention matrix in the proposed bidirectional attention mechanism. Alignments are extracted from the learnt attention weights and optimized by the ASR, TTS and FA tasks in a multi-task learning manner. Experimental results demonstrate the effectiveness of our proposed model, with mean absolute error on test set drops from 25.8 ms to 23.7 ms at word level, and from 17.0 ms to 15.7 ms at phoneme level compared with state-of-the-art HMM based model.

The success of AI assistants based on Language Models (LLMs) hinges on Reinforcement Learning from Human Feedback (RLHF) to comprehend and align with user intentions. However, traditional alignment algorithms, such as PPO, are hampered by complex annotation and training requirements. This reliance limits the applicability of RLHF and hinders the development of professional assistants tailored to diverse human preferences. In this work, we introduce Linear Alignment, a novel algorithm that aligns language models with human preferences in one single inference step, eliminating the reliance on data annotation and model training. Linear alignment incorporates a new parameterization for policy optimization under divergence constraints, which enables the extraction of optimal policy in a closed-form manner and facilitates the direct estimation of the aligned response. Extensive experiments on both general and personalized preference datasets demonstrate that linear alignment significantly enhances the performance and efficiency of LLM alignment across diverse scenarios. Our code and dataset will be published on https://github.com/Wizardcoast/Linear_Alignment.git.

Mining parallel document pairs poses a significant challenge because existing sentence embedding models often have limited context windows, preventing them from effectively capturing document-level information. Another overlooked issue is the lack of concrete evaluation benchmarks comprising high-quality parallel document pairs for assessing document-level mining approaches, particularly for Indic languages. In this study, we introduce Pralekha, a large-scale benchmark for document-level alignment evaluation. Pralekha includes over 2 million documents, with a 1:2 ratio of unaligned to aligned pairs, covering 11 Indic languages and English. Using Pralekha, we evaluate various document-level mining approaches across three dimensions: the embedding models, the granularity levels, and the alignment algorithm. To address the challenge of aligning documents using sentence and chunk-level alignments, we propose a novel scoring method, Document Alignment Coefficient (DAC). DAC demonstrates substantial improvements over baseline pooling approaches, particularly in noisy scenarios, achieving average gains of 20-30% in precision and 15-20% in F1 score. These results highlight DAC's effectiveness in parallel document mining for Indic languages.

High-quality instruction data is critical for aligning large language models (LLMs). Although some models, such as Llama-3-Instruct, have open weights, their alignment data remain private, which hinders the democratization of AI. High human labor costs and a limited, predefined scope for prompting prevent existing open-source data creation methods from scaling effectively, potentially limiting the diversity and quality of public alignment datasets. Is it possible to synthesize high-quality instruction data at scale by extracting it directly from an aligned LLM? We present a self-synthesis method for generating large-scale alignment data named Magpie. Our key observation is that aligned LLMs like Llama-3-Instruct can generate a user query when we input only the left-side templates up to the position reserved for user messages, thanks to their auto-regressive nature. We use this method to prompt Llama-3-Instruct and generate 4 million instructions along with their corresponding responses. We perform a comprehensive analysis of the extracted data and select 300K high-quality instances. To compare Magpie data with other public instruction datasets, we fine-tune Llama-3-8B-Base with each dataset and evaluate the performance of the fine-tuned models. Our results indicate that in some tasks, models fine-tuned with Magpie perform comparably to the official Llama-3-8B-Instruct, despite the latter being enhanced with 10 million data points through supervised fine-tuning (SFT) and subsequent feedback learning. We also show that using Magpie solely for SFT can surpass the performance of previous public datasets utilized for both SFT and preference optimization, such as direct preference optimization with UltraFeedback. This advantage is evident on alignment benchmarks such as AlpacaEval, ArenaHard, and WildBench.

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.

Since their inception, embeddings have become a primary ingredient in many flavours of Natural Language Processing (NLP) tasks supplanting earlier types of representation. Even though multilingual embeddings have been used for the increasing number of multilingual tasks, due to the scarcity of parallel training data, low-resource languages such as Sinhala, tend to focus more on monolingual embeddings. Then when it comes to the aforementioned multi-lingual tasks, it is challenging to utilize these monolingual embeddings given that even if the embedding spaces have a similar geometric arrangement due to an identical training process, the embeddings of the languages considered are not aligned. This is solved by the embedding alignment task. Even in this, high-resource language pairs are in the limelight while low-resource languages such as Sinhala which is in dire need of help seem to have fallen by the wayside. In this paper, we try to align Sinhala and English word embedding spaces based on available alignment techniques and introduce a benchmark for Sinhala language embedding alignment. In addition to that, to facilitate the supervised alignment, as an intermediate task, we also introduce Sinhala-English alignment datasets. These datasets serve as our anchor datasets for supervised word embedding alignment. Even though we do not obtain results comparable to the high-resource languages such as French, German, or Chinese, we believe our work lays the groundwork for more specialized alignment between English and Sinhala embeddings.

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

We propose procedures for evaluating and strengthening contextual embedding alignment and show that they are useful in analyzing and improving multilingual BERT. In particular, after our proposed alignment procedure, BERT exhibits significantly improved zero-shot performance on XNLI compared to the base model, remarkably matching pseudo-fully-supervised translate-train models for Bulgarian and Greek. Further, to measure the degree of alignment, we introduce a contextual version of word retrieval and show that it correlates well with downstream zero-shot transfer. Using this word retrieval task, we also analyze BERT and find that it exhibits systematic deficiencies, e.g. worse alignment for open-class parts-of-speech and word pairs written in different scripts, that are corrected by the alignment procedure. These results support contextual alignment as a useful concept for understanding large multilingual pre-trained models.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

Language model alignment is a cutting-edge technique in large language model training to align the model output to user's intent, e.g., being helpful and harmless. Recent alignment framework consists of two steps: supervised fine-tuning with demonstration data and preference learning with human preference data. Previous preference learning methods, such as RLHF and DPO, mainly focus on pair-wise preference data. However, in many real-world scenarios where human feedbacks are intrinsically point-wise, these methods will suffer from information loss or even fail. To fill this gap, in this paper, we first develop a preference learning method called point-wise DPO to tackle point-wise preference data. Further revelation on the connection between supervised fine-tuning and point-wise preference learning enables us to develop a unified framework for both human demonstration and point-wise preference data, which sheds new light on the construction of preference dataset. Extensive experiments on point-wise datasets with binary or continuous labels demonstrate the superior performance and efficiency of our proposed methods. A new dataset with high-quality demonstration samples on harmlessness is constructed and made publicly available.

With the proliferation of large language models (LLMs), the comprehensive alignment of such models across multiple tasks has emerged as a critical area of research. Existing alignment methodologies primarily address single task, such as multi-turn dialogue, coding, mathematical problem-solving, and tool usage. However, AI-driven products that leverage language models usually necessitate a fusion of these abilities to function effectively in real-world scenarios. Moreover, the considerable computational resources required for proper alignment of LLMs underscore the need for a more robust, efficient, and encompassing approach to multi-task alignment, ensuring improved generative performance. In response to these challenges, we introduce a novel technique termed Mixture-of-Instructions (MoI), which employs a strategy of instruction concatenation combined with diverse system prompts to boost the alignment efficiency of language models. We have also compiled a diverse set of seven benchmark datasets to rigorously evaluate the alignment efficacy of the MoI-enhanced language model. Our methodology was applied to the open-source Qwen-7B-chat model, culminating in the development of Qwen-SFT-MoI. This enhanced model demonstrates significant advancements in generative capabilities across coding, mathematics, and tool use tasks.

This article introduces contrastive alignment instructions (AlignInstruct) to address two challenges in machine translation (MT) on large language models (LLMs). One is the expansion of supported languages to previously unseen ones. The second relates to the lack of data in low-resource languages. Model fine-tuning through MT instructions (MTInstruct) is a straightforward approach to the first challenge. However, MTInstruct is limited by weak cross-lingual signals inherent in the second challenge. AlignInstruct emphasizes cross-lingual supervision via a cross-lingual discriminator built using statistical word alignments. Our results based on fine-tuning the BLOOMZ models (1b1, 3b, and 7b1) in up to 24 unseen languages showed that: (1) LLMs can effectively translate unseen languages using MTInstruct; (2) AlignInstruct led to consistent improvements in translation quality across 48 translation directions involving English; (3) Discriminator-based instructions outperformed their generative counterparts as cross-lingual instructions; (4) AlignInstruct improved performance in 30 zero-shot directions.

With the rapid development of large language models (LLMs), they are not only used as general-purpose AI assistants but are also customized through further fine-tuning to meet the requirements of different applications. A pivotal factor in the success of current LLMs is the alignment process. Current alignment methods, such as supervised fine-tuning (SFT) and reinforcement learning from human feedback (RLHF), focus on training-time alignment and are often complex and cumbersome to implement. Therefore, we develop InferAligner, a novel inference-time alignment method that utilizes cross-model guidance for harmlessness alignment. InferAligner utilizes safety steering vectors extracted from safety-aligned model to modify the activations of the target model when responding to harmful inputs, thereby guiding the target model to provide harmless responses. Experimental results show that our method can be very effectively applied to domain-specific models in finance, medicine, and mathematics, as well as to multimodal large language models (MLLMs) such as LLaVA. It significantly diminishes the Attack Success Rate (ASR) of both harmful instructions and jailbreak attacks, while maintaining almost unchanged performance in downstream tasks.

Due to the limited availability of high quality datasets for training sentence embeddings in Turkish, we propose a training methodology and a regimen to develop a sentence embedding model. The central idea is simple but effective : is to fine-tune a pretrained encoder-decoder model in two consecutive stages, where the first stage involves aligning the embedding space with translation pairs. Thanks to this alignment, the prowess of the main model can be better projected onto the target language in a sentence embedding setting where it can be fine-tuned with high accuracy in short duration with limited target language dataset.

Reordering is a preprocessing stage for Statistical Machine Translation (SMT) system where the words of the source sentence are reordered as per the syntax of the target language. We are proposing a rich set of rules for better reordering. The idea is to facilitate the training process by better alignments and parallel phrase extraction for a phrase-based SMT system. Reordering also helps the decoding process and hence improving the machine translation quality. We have observed significant improvements in the translation quality by using our approach over the baseline SMT. We have used BLEU, NIST, multi-reference word error rate, multi-reference position independent error rate for judging the improvements. We have exploited open source SMT toolkit MOSES to develop the system.

This paper delves into the continuous post-training optimization methods for small language models, and proposes a continuous post-training alignment data construction method for small language models. The core of this method is based on the data guidance of large models, optimizing the diversity and accuracy of alignment data. In addition, to verify the effectiveness of the methods in this paper, we used Qwen2-0.5B-Instruct model as the baseline model for small language models, using the alignment dataset constructed by our proposed method, we trained and compared several groups of experiments, including SFT (Supervised Fine Tuning) post-training experiment and KTO (Kahneman Tversky optimization) post-training experiment, as well as SFT-KTO two-stage post-training experiment and model weight fusion experiment. Finally, we evaluated and analyzed the performance of post-training models, and confirmed that the continuous post-training optimization method proposed by us can significantly improve the performance of small language models.

As large language models rapidly evolve to support longer context, there is a notable disparity in their capability to generate output at greater lengths. Recent study suggests that the primary cause for this imbalance may arise from the lack of data with long-output during alignment training. In light of this observation, attempts are made to re-align foundation models with data that fills the gap, which result in models capable of generating lengthy output when instructed. In this paper, we explore the impact of data-quality in tuning a model for long output, and the possibility of doing so from the starting points of human-aligned (instruct or chat) models. With careful data curation, we show that it possible to achieve similar performance improvement in our tuned models, with only a small fraction of training data instances and compute. In addition, we assess the generalizability of such approaches by applying our tuning-recipes to several models. our findings suggest that, while capacities for generating long output vary across different models out-of-the-box, our approach to tune them with high-quality data using lite compute, consistently yields notable improvement across all models we experimented on. We have made public our curated dataset for tuning long-writing capability, the implementations of model tuning and evaluation, as well as the fine-tuned models, all of which can be openly-accessed.

Neural sequence-to-sequence models provide a competitive approach to the task of mapping a question in natural language to an SQL query, also referred to as text-to-SQL generation. The Byte-Pair Encoding algorithm (BPE) has previously been used to improve machine translation (MT) between natural languages. In this work, we adapt BPE for text-to-SQL generation. As the datasets for this task are rather small compared to MT, we present a novel stopping criterion that prevents overfitting the BPE encoding to the training set. Additionally, we present AST BPE, which is a version of BPE that uses the Abstract Syntax Tree (AST) of the SQL statement to guide BPE merges and therefore produce BPE encodings that generalize better. We improved the accuracy of a strong attentive seq2seq baseline on five out of six English text-to-SQL tasks while reducing training time by more than 50% on four of them due to the shortened targets. Finally, on two of these tasks we exceeded previously reported accuracies.

Creating an abridged version of a text involves shortening it while maintaining its linguistic qualities. In this paper, we examine this task from an NLP perspective for the first time. We present a new resource, AbLit, which is derived from abridged versions of English literature books. The dataset captures passage-level alignments between the original and abridged texts. We characterize the linguistic relations of these alignments, and create automated models to predict these relations as well as to generate abridgements for new texts. Our findings establish abridgement as a challenging task, motivating future resources and research. The dataset is available at github.com/roemmele/AbLit.

Multilingual generative models obtain remarkable cross-lingual capabilities through pre-training on large-scale corpora. However, they still exhibit a performance bias toward high-resource languages, and learn isolated distributions of sentence representations across languages. To bridge this gap, we propose a simple yet effective alignment framework exploiting pairs of translation sentences. It aligns the internal sentence representations across different languages via multilingual contrastive learning and aligns model outputs by answering prompts in different languages. Experimental results demonstrate that even with less than 0.1 {\textperthousand} of pre-training tokens, our alignment framework significantly boosts the cross-lingual abilities of generative models and mitigates the performance gap. Further analysis reveals that it results in a better internal multilingual representation distribution of multilingual models.

Aligning sentences in a reference summary with their counterparts in source documents was shown as a useful auxiliary summarization task, notably for generating training data for salience detection. Despite its assessed utility, the alignment step was mostly approached with heuristic unsupervised methods, typically ROUGE-based, and was never independently optimized or evaluated. In this paper, we propose establishing summary-source alignment as an explicit task, while introducing two major novelties: (1) applying it at the more accurate proposition span level, and (2) approaching it as a supervised classification task. To that end, we created a novel training dataset for proposition-level alignment, derived automatically from available summarization evaluation data. In addition, we crowdsourced dev and test datasets, enabling model development and proper evaluation. Utilizing these data, we present a supervised proposition alignment baseline model, showing improved alignment-quality over the unsupervised approach.

As development of large language models (LLM) progresses, aligning them with human preferences has become increasingly important. We propose stepwise DPO (sDPO), an extension of the recently popularized direct preference optimization (DPO) for alignment tuning. This approach involves dividing the available preference datasets and utilizing them in a stepwise manner, rather than employing it all at once. We demonstrate that this method facilitates the use of more precisely aligned reference models within the DPO training framework. Furthermore, sDPO trains the final model to be more performant, even outperforming other popular LLMs with more parameters.

Large language models demonstrate reasonable multilingual abilities, despite predominantly English-centric pretraining. However, the spontaneous multilingual alignment in these models is shown to be weak, leading to unsatisfactory cross-lingual transfer and knowledge sharing. Previous works attempt to address this issue by explicitly injecting multilingual alignment information during or after pretraining. Thus for the early stage in pretraining, the alignment is weak for sharing information or knowledge across languages. In this paper, we propose PreAlign, a framework that establishes multilingual alignment prior to language model pretraining. PreAlign injects multilingual alignment by initializing the model to generate similar representations of aligned words and preserves this alignment using a code-switching strategy during pretraining. Extensive experiments in a synthetic English to English-Clone setting demonstrate that PreAlign significantly outperforms standard multilingual joint training in language modeling, zero-shot cross-lingual transfer, and cross-lingual knowledge application. Further experiments in real-world scenarios further validate PreAlign's effectiveness across various model sizes.

The success of a text simplification system heavily depends on the quality and quantity of complex-simple sentence pairs in the training corpus, which are extracted by aligning sentences between parallel articles. To evaluate and improve sentence alignment quality, we create two manually annotated sentence-aligned datasets from two commonly used text simplification corpora, Newsela and Wikipedia. We propose a novel neural CRF alignment model which not only leverages the sequential nature of sentences in parallel documents but also utilizes a neural sentence pair model to capture semantic similarity. Experiments demonstrate that our proposed approach outperforms all the previous work on monolingual sentence alignment task by more than 5 points in F1. We apply our CRF aligner to construct two new text simplification datasets, Newsela-Auto and Wiki-Auto, which are much larger and of better quality compared to the existing datasets. A Transformer-based seq2seq model trained on our datasets establishes a new state-of-the-art for text simplification in both automatic and human evaluation.

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

Aligning with personalized preferences, which vary significantly across cultural, educational, and political differences, poses a significant challenge due to the computational costs and data demands of traditional alignment methods. In response, this paper presents Personalized Alignment at Decoding-time (PAD), a novel framework designed to align LLM outputs with diverse personalized preferences during the inference phase, eliminating the need for additional training. By introducing a unique personalized reward modeling strategy, this framework decouples the text generation process from personalized preferences, facilitating the generation of generalizable token-level personalized rewards. The PAD algorithm leverages these rewards to guide the decoding process, dynamically tailoring the base model's predictions to personalized preferences. Extensive experimental results demonstrate that PAD not only outperforms existing training-based alignment methods in terms of aligning with diverse preferences but also shows significant generalizability to preferences unseen during training and scalability across different base models. This work advances the capability of LLMs to meet user needs in real-time applications, presenting a substantial step forward in personalized LLM alignment.

Multimodal Large Language Models (MLLMs) are widely regarded as crucial in the exploration of Artificial General Intelligence (AGI). The core of MLLMs lies in their capability to achieve cross-modal alignment. To attain this goal, current MLLMs typically follow a two-phase training paradigm: the pre-training phase and the instruction-tuning phase. Despite their success, there are shortcomings in the modeling of alignment capabilities within these models. Firstly, during the pre-training phase, the model usually assumes that all image-text pairs are uniformly aligned, but in fact the degree of alignment between different image-text pairs is inconsistent. Secondly, the instructions currently used for finetuning incorporate a variety of tasks, different tasks's instructions usually require different levels of alignment capabilities, but previous MLLMs overlook these differentiated alignment needs. To tackle these issues, we propose a new multimodal large language model AlignGPT. In the pre-training stage, instead of treating all image-text pairs equally, we assign different levels of alignment capabilities to different image-text pairs. Then, in the instruction-tuning phase, we adaptively combine these different levels of alignment capabilities to meet the dynamic alignment needs of different instructions. Extensive experimental results show that our model achieves competitive performance on 12 benchmarks.

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

The RNN transducer is a promising end-to-end model candidate. We compare the original training criterion with the full marginalization over all alignments, to the commonly used maximum approximation, which simplifies, improves and speeds up our training. We also generalize from the original neural network model and study more powerful models, made possible due to the maximum approximation. We further generalize the output label topology to cover RNN-T, RNA and CTC. We perform several studies among all these aspects, including a study on the effect of external alignments. We find that the transducer model generalizes much better on longer sequences than the attention model. Our final transducer model outperforms our attention model on Switchboard 300h by over 6% relative WER.

In this paper, we aim to align large language models with the ever-changing, complex, and diverse human values (e.g., social norms) across time and locations. This presents a challenge to existing alignment techniques, such as supervised fine-tuning, which internalize values within model parameters. To overcome this, we propose an On-the-fly Preference Optimization (OPO) method, which is a real-time alignment that works in a streaming way. It employs an external memory to store established rules for alignment, which can constrain LLMs' behaviors without further training, allowing for convenient updates and customization of human values. We also introduce a scalable evaluation to assess the proposed method more effectively. Experimental results on both human-annotated and auto-generated questions from legal and moral domains indicate the effectiveness of the proposed OPO method. Our code and data are released at https://github.com/GAIR-NLP/OPO.

Forced alignment (FA) plays a key role in speech research through the automatic time alignment of speech signals with corresponding text transcriptions. Despite the move towards end-to-end architectures for speech technology, FA is still dominantly achieved through a classic GMM-HMM acoustic model. This work directly compares alignment performance from leading automatic speech recognition (ASR) methods, WhisperX and Massively Multilingual Speech Recognition (MMS), against a Kaldi-based GMM-HMM system, the Montreal Forced Aligner (MFA). Performance was assessed on the manually aligned TIMIT and Buckeye datasets, with comparisons conducted only on words correctly recognized by WhisperX and MMS. The MFA outperformed both WhisperX and MMS, revealing a shortcoming of modern ASR systems. These findings highlight the need for advancements in forced alignment and emphasize the importance of integrating traditional expertise with modern innovation to foster progress. Index Terms: forced alignment, phoneme alignment, word alignment

We present a novel supervised word alignment method based on cross-language span prediction. We first formalize a word alignment problem as a collection of independent predictions from a token in the source sentence to a span in the target sentence. As this is equivalent to a SQuAD v2.0 style question answering task, we then solve this problem by using multilingual BERT, which is fine-tuned on a manually created gold word alignment data. We greatly improved the word alignment accuracy by adding the context of the token to the question. In the experiments using five word alignment datasets among Chinese, Japanese, German, Romanian, French, and English, we show that the proposed method significantly outperformed previous supervised and unsupervised word alignment methods without using any bitexts for pretraining. For example, we achieved an F1 score of 86.7 for the Chinese-English data, which is 13.3 points higher than the previous state-of-the-art supervised methods.

Automated alignment develops alignment systems with minimal human intervention. The key to automated alignment lies in providing learnable and accurate preference signals for preference learning without human annotation. In this paper, we introduce Self-Steering Optimization (SSO), an algorithm that autonomously generates high-quality preference signals based on predefined principles during iterative training, eliminating the need for manual annotation. SSO maintains the accuracy of signals by ensuring a consistent gap between chosen and rejected responses while keeping them both on-policy to suit the current policy model's learning capacity. SSO can benefit the online and offline training of the policy model, as well as enhance the training of reward models. We validate the effectiveness of SSO with two foundation models, Qwen2 and Llama3.1, indicating that it provides accurate, on-policy preference signals throughout iterative training. Without any manual annotation or external models, SSO leads to significant performance improvements across six subjective or objective benchmarks. Besides, the preference data generated by SSO significantly enhanced the performance of the reward model on Rewardbench. Our work presents a scalable approach to preference optimization, paving the way for more efficient and effective automated alignment.

A popular natural language processing task decades ago, word alignment has been dominated until recently by GIZA++, a statistical method based on the 30-year-old IBM models. New methods that outperform GIZA++ primarily rely on large machine translation models, massively multilingual language models, or supervision from GIZA++ alignments itself. We introduce Embedding-Enhanced GIZA++, and outperform GIZA++ without any of the aforementioned factors. Taking advantage of monolingual embedding spaces of source and target language only, we exceed GIZA++'s performance in every tested scenario for three languages pairs. In the lowest-resource setting, we outperform GIZA++ by 8.5, 10.9, and 12 AER for Ro-En, De-En, and En-Fr, respectively. We release our code at https://github.com/kellymarchisio/ee-giza.

This paper revisits recent code similarity evaluation metrics, particularly focusing on the application of Abstract Syntax Tree (AST) editing distance in diverse programming languages. In particular, we explore the usefulness of these metrics and compare them to traditional sequence similarity metrics. Our experiments showcase the effectiveness of AST editing distance in capturing intricate code structures, revealing a high correlation with established metrics. Furthermore, we explore the strengths and weaknesses of AST editing distance and prompt-based GPT similarity scores in comparison to BLEU score, execution match, and Jaccard Similarity. We propose, optimize, and publish an adaptable metric that demonstrates effectiveness across all tested languages, representing an enhanced version of Tree Similarity of Edit Distance (TSED).

Aligning large language models (LLMs) with human objectives is crucial for real-world applications. However, fine-tuning LLMs for alignment often suffers from unstable training and requires substantial computing resources. Test-time alignment techniques, such as prompting and guided decoding, do not modify the underlying model, and their performance remains dependent on the original model's capabilities. To address these challenges, we propose aligning LLMs through representation editing. The core of our method is to view a pre-trained autoregressive LLM as a discrete-time stochastic dynamical system. To achieve alignment for specific objectives, we introduce external control signals into the state space of this language dynamical system. We train a value function directly on the hidden states according to the Bellman equation, enabling gradient-based optimization to obtain the optimal control signals at test time. Our experiments demonstrate that our method outperforms existing test-time alignment techniques while requiring significantly fewer resources compared to fine-tuning methods.

In this paper, we present Neural Phrase-based Machine Translation (NPMT). Our method explicitly models the phrase structures in output sequences using Sleep-WAke Networks (SWAN), a recently proposed segmentation-based sequence modeling method. To mitigate the monotonic alignment requirement of SWAN, we introduce a new layer to perform (soft) local reordering of input sequences. Different from existing neural machine translation (NMT) approaches, NPMT does not use attention-based decoding mechanisms. Instead, it directly outputs phrases in a sequential order and can decode in linear time. Our experiments show that NPMT achieves superior performances on IWSLT 2014 German-English/English-German and IWSLT 2015 English-Vietnamese machine translation tasks compared with strong NMT baselines. We also observe that our method produces meaningful phrases in output languages.

Self-alignment is an effective way to reduce the cost of human annotation while ensuring promising model capability. However, most current methods complete the data collection and training steps in a single round, which may overlook the continuously improving ability of self-aligned models. This gives rise to a key query: What if we do multi-time bootstrapping self-alignment? Does this strategy enhance model performance or lead to rapid degradation? In this paper, our pioneering exploration delves into the impact of bootstrapping self-alignment on large language models. Our findings reveal that bootstrapping self-alignment markedly surpasses the single-round approach, by guaranteeing data diversity from in-context learning. To further exploit the capabilities of bootstrapping, we investigate and adjust the training order of data, which yields improved performance of the model. Drawing on these findings, we propose Step-On-Feet Tuning (SOFT) which leverages model's continuously enhanced few-shot ability to boost zero or one-shot performance. Based on easy-to-hard training recipe, we propose SOFT+ which further boost self-alignment's performance. Our experiments demonstrate the efficiency of SOFT (SOFT+) across various classification and generation tasks, highlighting the potential of bootstrapping self-alignment on continually enhancing model alignment performance.

The evolution of Neural Machine Translation (NMT) has been significantly influenced by six core challenges (Koehn and Knowles, 2017), which have acted as benchmarks for progress in this field. This study revisits these challenges, offering insights into their ongoing relevance in the context of advanced Large Language Models (LLMs): domain mismatch, amount of parallel data, rare word prediction, translation of long sentences, attention model as word alignment, and sub-optimal beam search. Our empirical findings indicate that LLMs effectively lessen the reliance on parallel data for major languages in the pretraining phase. Additionally, the LLM-based translation system significantly enhances the translation of long sentences that contain approximately 80 words and shows the capability to translate documents of up to 512 words. However, despite these significant improvements, the challenges of domain mismatch and prediction of rare words persist. While the challenges of word alignment and beam search, specifically associated with NMT, may not apply to LLMs, we identify three new challenges for LLMs in translation tasks: inference efficiency, translation of low-resource languages in the pretraining phase, and human-aligned evaluation. The datasets and models are released at https://github.com/pangjh3/LLM4MT.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

In Brazil, the governmental body responsible for overseeing and coordinating post-graduate programs, CAPES, keeps records of all theses and dissertations presented in the country. Information regarding such documents can be accessed online in the Theses and Dissertations Catalog (TDC), which contains abstracts in Portuguese and English, and additional metadata. Thus, this database can be a potential source of parallel corpora for the Portuguese and English languages. In this article, we present the development of a parallel corpus from TDC, which is made available by CAPES under the open data initiative. Approximately 240,000 documents were collected and aligned using the Hunalign tool. We demonstrate the capability of our developed corpus by training Statistical Machine Translation (SMT) and Neural Machine Translation (NMT) models for both language directions, followed by a comparison with Google Translate (GT). Both translation models presented better BLEU scores than GT, with NMT system being the most accurate one. Sentence alignment was also manually evaluated, presenting an average of 82.30% correctly aligned sentences. Our parallel corpus is freely available in TMX format, with complementary information regarding document metadata

Multilingual semantic search is the task of retrieving relevant contents to a query expressed in different language combinations. This requires a better semantic understanding of the user's intent and its contextual meaning. Multilingual semantic search is less explored and more challenging than its monolingual or bilingual counterparts, due to the lack of multilingual parallel resources for this task and the need to circumvent "language bias". In this work, we propose an alignment approach: MAML-Align, specifically for low-resource scenarios. Our approach leverages meta-distillation learning based on MAML, an optimization-based Model-Agnostic Meta-Learner. MAML-Align distills knowledge from a Teacher meta-transfer model T-MAML, specialized in transferring from monolingual to bilingual semantic search, to a Student model S-MAML, which meta-transfers from bilingual to multilingual semantic search. To the best of our knowledge, we are the first to extend meta-distillation to a multilingual search application. Our empirical results show that on top of a strong baseline based on sentence transformers, our meta-distillation approach boosts the gains provided by MAML and significantly outperforms naive fine-tuning methods. Furthermore, multilingual meta-distillation learning improves generalization even to unseen languages.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

Alignment of the language model with human preferences is a common approach to making a language model useful to end users. However, most alignment work is done in English, and human preference datasets are dominated by English, reflecting only the preferences of English-speaking annotators. Nevertheless, it is common practice to use the English preference data, either directly or by translating it into the target language, when aligning a multilingual language model. The question is whether such an alignment strategy marginalizes the preference of non-English speaking users. To this end, we investigate the effect of aligning Japanese language models with (mostly) English resources. In particular, we focus on evaluating whether the commonsense morality of the resulting fine-tuned models is aligned with Japanese culture using the JCommonsenseMorality (JCM) and ETHICS datasets. The experimental results show that the fine-tuned model outperforms the SFT model. However, it does not demonstrate the same level of improvement as a model fine-tuned using the JCM, suggesting that while some aspects of commonsense morality are transferable, others may not be.

Entity alignment is to find identical entities in different knowledge graphs (KGs) that refer to the same real-world object. Embedding-based entity alignment techniques have been drawing a lot of attention recently because they can help solve the issue of symbolic heterogeneity in different KGs. However, in this paper, we show that the progress made in the past was due to biased and unchallenging evaluation. We highlight two major flaws in existing datasets that favor embedding-based entity alignment techniques, i.e., the isomorphic graph structures in relation triples and the weak heterogeneity in attribute triples. Towards a critical evaluation of embedding-based entity alignment methods, we construct a new dataset with heterogeneous relations and attributes based on event-centric KGs. We conduct extensive experiments to evaluate existing popular methods, and find that they fail to achieve promising performance. As a new approach to this difficult problem, we propose a time-aware literal encoder for entity alignment. The dataset and source code are publicly available to foster future research. Our work calls for more effective and practical embedding-based solutions to entity alignment.

Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent neural networks such as the long short term memory (LSTM) model on the other hand are designed to handle sequences. In this study we demonstrate that LSTM networks predict the subcellular location of proteins given only the protein sequence with high accuracy (0.902) outperforming current state of the art algorithms. We further improve the performance by introducing convolutional filters and experiment with an attention mechanism which lets the LSTM focus on specific parts of the protein. Lastly we introduce new visualizations of both the convolutional filters and the attention mechanisms and show how they can be used to extract biological relevant knowledge from the LSTM networks.

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

In this paper, we consider the problem of temporally aligning the video and texts from instructional videos, specifically, given a long-term video, and associated text sentences, our goal is to determine their corresponding timestamps in the video. To this end, we establish a simple, yet strong model that adopts a Transformer-based architecture with all texts as queries, iteratively attending to the visual features, to infer the optimal timestamp. We conduct thorough experiments to investigate: (i) the effect of upgrading ASR systems to reduce errors from speech recognition, (ii) the effect of various visual-textual backbones, ranging from CLIP to S3D, to the more recent InternVideo, (iii) the effect of transforming noisy ASR transcripts into descriptive steps by prompting a large language model (LLM), to summarize the core activities within the ASR transcript as a new training dataset. As a result, our proposed simple model demonstrates superior performance on both narration alignment and procedural step grounding tasks, surpassing existing state-of-the-art methods by a significant margin on three public benchmarks, namely, 9.3% on HT-Step, 3.4% on HTM-Align and 4.7% on CrossTask. We believe the proposed model and dataset with descriptive steps can be treated as a strong baseline for future research in temporal video-text alignment. All codes, models, and the resulting dataset will be publicly released to the research community.

Recent significant improvements in speech and language technologies come both from self-supervised approaches over raw language data as well as various types of explicit supervision. To ensure high-quality processing of spoken data, the most useful type of explicit supervision is still the alignment between the speech signal and its corresponding text transcript, which is a data type that is not available for many languages. In this paper, we present our approach to building large and open speech-and-text-aligned datasets of less-resourced languages based on transcripts of parliamentary proceedings and their recordings. Our starting point are the ParlaMint comparable corpora of transcripts of parliamentary proceedings of 26 national European parliaments. In the pilot run on expanding the ParlaMint corpora with aligned publicly available recordings, we focus on three Slavic languages, namely Croatian, Polish, and Serbian. The main challenge of our approach is the lack of any global alignment between the ParlaMint texts and the available recordings, as well as the sometimes varying data order in each of the modalities, which requires a novel approach in aligning long sequences of text and audio in a large search space. The results of this pilot run are three high-quality datasets that span more than 5,000 hours of speech and accompanying text transcripts. Although these datasets already make a huge difference in the availability of spoken and textual data for the three languages, we want to emphasize the potential of the presented approach in building similar datasets for many more languages.

Alignment with human preference prevents large language models (LLMs) from generating misleading or toxic content while requiring high-cost human feedback. Assuming resources of human annotation are limited, there are two different ways of allocating considered: more diverse PROMPTS or more diverse RESPONSES to be labeled. Nonetheless, a straightforward comparison between their impact is absent. In this work, we first control the diversity of both sides according to the number of samples for fine-tuning, which can directly reflect their influence. We find that instead of numerous prompts, more responses but fewer prompts better trigger LLMs for human alignment. Additionally, the concept of diversity for prompts can be more complex than responses that are typically quantified by single digits. Consequently, a new formulation of prompt diversity is proposed, further implying a linear correlation with the final performance of LLMs after fine-tuning. We also leverage it on data augmentation and conduct experiments to show its effect on different algorithms.

Lyrics alignment gained considerable attention in recent years. State-of-the-art systems either re-use established speech recognition toolkits, or design end-to-end solutions involving a Connectionist Temporal Classification (CTC) loss. However, both approaches suffer from specific weaknesses: toolkits are known for their complexity, and CTC systems use a loss designed for transcription which can limit alignment accuracy. In this paper, we use instead a contrastive learning procedure that derives cross-modal embeddings linking the audio and text domains. This way, we obtain a novel system that is simple to train end-to-end, can make use of weakly annotated training data, jointly learns a powerful text model, and is tailored to alignment. The system is not only the first to yield an average absolute error below 0.2 seconds on the standard Jamendo dataset but it is also robust to other languages, even when trained on English data only. Finally, we release word-level alignments for the JamendoLyrics Multi-Lang dataset.

During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models(LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2 evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus variants. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools for combating virus threats

Image captioning is one of the straightforward tasks that can take advantage of large-scale web-crawled data which provides rich knowledge about the visual world for a captioning model. However, since web-crawled data contains image-text pairs that are aligned at different levels, the inherent noises (e.g., misaligned pairs) make it difficult to learn a precise captioning model. While the filtering strategy can effectively remove noisy data, however, it leads to a decrease in learnable knowledge and sometimes brings about a new problem of data deficiency. To take the best of both worlds, we propose a noise-aware learning framework, which learns rich knowledge from the whole web-crawled data while being less affected by the noises. This is achieved by the proposed quality controllable model, which is learned using alignment levels of the image-text pairs as an additional control signal during training. The alignment-conditioned training allows the model to generate high-quality captions of well-aligned by simply setting the control signal to desired alignment level at inference time. Through in-depth analysis, we show that our controllable captioning model is effective in handling noise. In addition, with two tasks of zero-shot captioning and text-to-image retrieval using generated captions (i.e., self-retrieval), we also demonstrate our model can produce high-quality captions in terms of descriptiveness and distinctiveness. Code is available at https://github.com/kakaobrain/noc.

We study lossless acceleration for seq2seq generation with a novel decoding algorithm -- Aggressive Decoding. Unlike the previous efforts (e.g., non-autoregressive decoding) speeding up seq2seq generation at the cost of quality loss, our approach aims to yield the identical (or better) generation compared with autoregressive decoding but in a significant speedup, achieved by innovative cooperation of aggressive decoding and verification that are both efficient due to parallel computing. We propose two Aggressive Decoding paradigms for 2 kinds of seq2seq tasks: 1) For the seq2seq tasks whose inputs and outputs are highly similar (e.g., Grammatical Error Correction), we propose Input-guided Aggressive Decoding (IAD) that aggressively copies from the input sentence as drafted decoded tokens to verify in parallel; 2) For other general seq2seq tasks (e.g., Machine Translation), we propose Generalized Aggressive Decoding (GAD) that first employs an additional non-autoregressive decoding model for aggressive decoding and then verifies in parallel in the autoregressive manner. We test Aggressive Decoding on the most popular 6-layer Transformer model on GPU in multiple seq2seq tasks: 1) For IAD, we show that it can introduce a 7x-9x speedup for the Transformer in Grammatical Error Correction and Text Simplification tasks with the identical results as greedy decoding; 2) For GAD, we observe a 3x-5x speedup with the identical or even better quality in two important seq2seq tasks: Machine Translation and Abstractive Summarization. Moreover, Aggressive Decoding can benefit even more from stronger computing devices that are better at parallel computing. Given the lossless quality as well as significant and promising speedup, we believe Aggressive Decoding may potentially evolve into a de facto standard for efficient and lossless seq2seq generation in the near future.

Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological analysis and AI development. Facebook's ESM2, the most advanced protein language model to date, leverages a masked prediction task for unsupervised learning, crafting amino acid representations with notable biochemical accuracy. Yet, it lacks in delivering functional protein insights, signaling an opportunity for enhancing representation quality.Our study addresses this gap by incorporating protein family classification into ESM2's training.This approach, augmented with Community Propagation-Based Clustering Algorithm, improves global protein representations, while a contextual prediction task fine-tunes local amino acid accuracy. Significantly, our model achieved state-of-the-art results in several downstream experiments, demonstrating the power of combining global and local methodologies to substantially boost protein representation quality.

For tasks like code synthesis from natural language, code retrieval, and code summarization, data-driven models have shown great promise. However, creating these models require parallel data between natural language (NL) and code with fine-grained alignments. Stack Overflow (SO) is a promising source to create such a data set: the questions are diverse and most of them have corresponding answers with high-quality code snippets. However, existing heuristic methods (e.g., pairing the title of a post with the code in the accepted answer) are limited both in their coverage and the correctness of the NL-code pairs obtained. In this paper, we propose a novel method to mine high-quality aligned data from SO using two sets of features: hand-crafted features considering the structure of the extracted snippets, and correspondence features obtained by training a probabilistic model to capture the correlation between NL and code using neural networks. These features are fed into a classifier that determines the quality of mined NL-code pairs. Experiments using Python and Java as test beds show that the proposed method greatly expands coverage and accuracy over existing mining methods, even when using only a small number of labeled examples. Further, we find that reasonable results are achieved even when training the classifier on one language and testing on another, showing promise for scaling NL-code mining to a wide variety of programming languages beyond those for which we are able to annotate data.

Large language models (LLMs) have shown impressive success in various applications. However, these models are often not well aligned with human intents, which calls for additional treatments on them, that is, the alignment problem. To make LLMs better follow user instructions, existing alignment methods mostly focus on further training them. However, the extra training of LLMs are usually expensive in terms of GPU compute; worse still, LLMs of interest are oftentimes not accessible for user-demanded training, such as GPTs. In this work, we take a different perspective -- Black-Box Prompt Optimization (BPO) -- to perform alignments. The idea is to optimize user prompts to suit LLMs' input understanding, so as to best realize users' intents without updating LLMs' parameters. BPO is model-agnostic and the empirical results demonstrate that the BPO-aligned ChatGPT yields a 22% increase in the win rate against its original version, and 10% for GPT-4. Importantly, the BPO-aligned LLMs can outperform the same models aligned by PPO and DPO, and it also brings additional performance gains when combining BPO with PPO or DPO. Code and datasets are released at https://github.com/thu-coai/BPO.

Most existing sequence generation models produce outputs in one pass, usually left-to-right. However, this is in contrast with a more natural approach that humans use in generating content; iterative refinement and editing. Recent work has introduced edit-based models for various tasks (such as neural machine translation and text style transfer), but these generally model a single edit step. In this work, we propose modeling editing processes, modeling the whole process of iteratively generating sequences. We form a conceptual framework to describe the likelihood of multi-step edits, and describe neural models that can learn a generative model of sequences based on these multistep edits. We introduce baseline results and metrics on this task, finding that modeling editing processes improves performance on a variety of axes on both our proposed task and related downstream tasks compared to previous single-step models of edits.

Extending large language models to effectively handle long contexts requires instruction fine-tuning on input sequences of similar length. To address this, we present LongAlign -- a recipe of the instruction data, training, and evaluation for long context alignment. First, we construct a long instruction-following dataset using Self-Instruct. To ensure the data diversity, it covers a broad range of tasks from various long context sources. Second, we adopt the packing and sorted batching strategies to speed up supervised fine-tuning on data with varied length distributions. Additionally, we develop a loss weighting method to balance the contribution to the loss across different sequences during packing training. Third, we introduce the LongBench-Chat benchmark for evaluating instruction-following capabilities on queries of 10k-100k in length. Experiments show that LongAlign outperforms existing recipes for LLMs in long context tasks by up to 30\%, while also maintaining their proficiency in handling short, generic tasks. The code, data, and long-aligned models are open-sourced at https://github.com/THUDM/LongAlign.

From the perspective of content safety issues, alignment has shown to limit large language models' (LLMs) harmful content generation. This intentional method of reinforcing models to not respond to certain user inputs seem to be present in many modern open-source instruction tuning datasets such as OpenAssistant or Guanaco. We introduce a novel insight to an instruction-tuned model's performance affected by the presence of alignment in supervised fine-tuning dataset. To be specific, we noticed that alignment acts as if it is poisoning the instruction dataset. Experimentally, we demonstrate that aligned answers significantly worsen the performance of the resulting fine-tuned model's on various reasoning benchmarks such as Big Bench (BBH), Massive Multitask Language Understanding (MMLU), Human Eval, and Discrete Reasoning Over Paragraphs (DROP), performing worse than the counterpart tuned without alignment by 4-33%.

We propose Diffusion-Sharpening, a fine-tuning approach that enhances downstream alignment by optimizing sampling trajectories. Existing RL-based fine-tuning methods focus on single training timesteps and neglect trajectory-level alignment, while recent sampling trajectory optimization methods incur significant inference NFE costs. Diffusion-Sharpening overcomes this by using a path integral framework to select optimal trajectories during training, leveraging reward feedback, and amortizing inference costs. Our method demonstrates superior training efficiency with faster convergence, and best inference efficiency without requiring additional NFEs. Extensive experiments show that Diffusion-Sharpening outperforms RL-based fine-tuning methods (e.g., Diffusion-DPO) and sampling trajectory optimization methods (e.g., Inference Scaling) across diverse metrics including text alignment, compositional capabilities, and human preferences, offering a scalable and efficient solution for future diffusion model fine-tuning. Code: https://github.com/Gen-Verse/Diffusion-Sharpening

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

Story video-text alignment, a core task in computational story understanding, aims to align video clips with corresponding sentences in their descriptions. However, progress on the task has been held back by the scarcity of manually annotated video-text correspondence and the heavy concentration on English narrations of Hollywood movies. To address these issues, in this paper, we construct a large-scale multilingual video story dataset named Multilingual Synopses of Movie Narratives (M-SYMON), containing 13,166 movie summary videos from 7 languages, as well as manual annotation of fine-grained video-text correspondences for 101.5 hours of video. Training on the human annotated data from SyMoN outperforms the SOTA methods by 15.7 and 16.2 percentage points on Clip Accuracy and Sentence IoU scores, respectively, demonstrating the effectiveness of the annotations. As benchmarks for future research, we create 6 baseline approaches with different multilingual training strategies, compare their performance in both intra-lingual and cross-lingual setups, exemplifying the challenges of multilingual video-text alignment. The dataset is released at: https://github.com/insundaycathy/M-SyMoN

To ensure safe usage, Large Language Models (LLMs) typically undergo alignment with human-defined values. However, this alignment often relies on primarily English data and is biased towards Western-centric values, limiting its effectiveness in low-resource language settings. In this paper, we describe our approach for aligning SEA-Lion-v2.1-Instruct (a Llama3-8B variant) to minimize toxicity in Singlish, an English creole specific to Singapore. We find that supervised fine-tuning and Kahneman-Tversky Optimization (KTO) on paired and unpaired preferences is more sample efficient and yields significantly better results than Direct Preference Optimization (DPO). Our analysis reveals that DPO implicitly enforces a weaker safety objective than KTO, and that SFT complements KTO by improving training stability. Finally, we introduce a simple but novel modification to KTO, KTO-S, which improves training stability through better gradient exploitation. Overall, we present a general approach for safety alignment conducive to low-resource English languages, successfully reducing toxicity by 99\% on our Singlish benchmark, with gains generalizing to the broader TOXIGEN dataset while maintaining strong performance across standard LLM benchmarks.

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

Antibodies are proteins produced by the immune system that can identify and neutralise a wide variety of antigens with high specificity and affinity, and constitute the most successful class of biotherapeutics. With the advent of next-generation sequencing, billions of antibody sequences have been collected in recent years, though their application in the design of better therapeutics has been constrained by the sheer volume and complexity of the data. To address this challenge, we present IgBert and IgT5, the best performing antibody-specific language models developed to date which can consistently handle both paired and unpaired variable region sequences as input. These models are trained comprehensively using the more than two billion unpaired sequences and two million paired sequences of light and heavy chains present in the Observed Antibody Space dataset. We show that our models outperform existing antibody and protein language models on a diverse range of design and regression tasks relevant to antibody engineering. This advancement marks a significant leap forward in leveraging machine learning, large scale data sets and high-performance computing for enhancing antibody design for therapeutic development.

Recent works have demonstrated the effectiveness of self-alignment in which a large language model is, by itself, aligned to follow general instructions through the automatic generation of instructional data using a handful of human-written seeds. Instead of general alignment, in this work, we focus on self-alignment for expert domain specialization (e.g., biomedicine), discovering it to be very effective for improving zero-shot and few-shot performance in target domains of interest. As a preliminary, we first present the benchmark results of existing aligned models within a specialized domain, which reveals the marginal effect that "generic" instruction-following training has on downstream expert domains' performance. To remedy this, we explore self-specialization that leverages domain-specific unlabelled data and a few labeled seeds for the self-alignment process. When augmented with retrieval to reduce hallucination and enhance concurrency of the alignment, self-specialization offers an effective (and efficient) way of "carving out" an expert model out of a "generalist", pre-trained LLM where different domains of expertise are originally combined in a form of "superposition". Our experimental results on a biomedical domain show that our self-specialized model (30B) outperforms its base model, MPT-30B by a large margin and even surpasses larger popular models based on LLaMA-65B, highlighting its potential and practicality for specialization, especially considering its efficiency in terms of data and parameters.

Text-to-image generation has advanced rapidly, yet aligning complex textual prompts with generated visuals remains challenging, especially with intricate object relationships and fine-grained details. This paper introduces Fast Prompt Alignment (FPA), a prompt optimization framework that leverages a one-pass approach, enhancing text-to-image alignment efficiency without the iterative overhead typical of current methods like OPT2I. FPA uses large language models (LLMs) for single-iteration prompt paraphrasing, followed by fine-tuning or in-context learning with optimized prompts to enable real-time inference, reducing computational demands while preserving alignment fidelity. Extensive evaluations on the COCO Captions and PartiPrompts datasets demonstrate that FPA achieves competitive text-image alignment scores at a fraction of the processing time, as validated through both automated metrics (TIFA, VQA) and human evaluation. A human study with expert annotators further reveals a strong correlation between human alignment judgments and automated scores, underscoring the robustness of FPA's improvements. The proposed method showcases a scalable, efficient alternative to iterative prompt optimization, enabling broader applicability in real-time, high-demand settings. The codebase is provided to facilitate further research: https://github.com/tiktok/fast_prompt_alignment

Effectively handling instructions with extremely long context remains a challenge for Large Language Models (LLMs), typically necessitating high-quality long data and substantial computational resources. This paper introduces Step-Skipping Alignment (SkipAlign), a new technique designed to enhance the long-context capabilities of LLMs in the phase of alignment without the need for additional efforts beyond training with original data length. SkipAlign is developed on the premise that long-range dependencies are fundamental to enhancing an LLM's capacity of long context. Departing from merely expanding the length of input samples, SkipAlign synthesizes long-range dependencies from the aspect of positions indices. This is achieved by the strategic insertion of skipped positions within instruction-following samples, which utilizes the semantic structure of the data to effectively expand the context. Through extensive experiments on base models with a variety of context window sizes, SkipAlign demonstrates its effectiveness across a spectrum of long-context tasks. Particularly noteworthy is that with a careful selection of the base model and alignment datasets, SkipAlign with only 6B parameters achieves it's best performance and comparable with strong baselines like GPT-3.5-Turbo-16K on LongBench.

Large language models (LLMs) have shown remarkable abilities in diverse natural language processing (NLP) tasks. The LLMs generally undergo supervised fine-tuning (SFT) followed by preference alignment to be usable in downstream applications. However, this sequential training pipeline leads to alignment tax that degrades the LLM performance. This paper introduces PAFT, a new PArallel training paradigm for effective LLM Fine-Tuning, which independently performs SFT and preference alignment (e.g., DPO and ORPO, etc.) with the same pre-trained model on respective datasets. The model produced by SFT and the model from preference alignment are then merged into a final model by parameter fusing for use in downstream applications. This work reveals important findings that preference alignment like DPO naturally results in a sparse model while SFT leads to a natural dense model which needs to be sparsified for effective model merging. This paper introduces an effective interference resolution which reduces the redundancy by sparsifying the delta parameters. The LLM resulted from the new training paradigm achieved Rank #1 on the HuggingFace Open LLM Leaderboard. Comprehensive evaluation shows the effectiveness of the parallel training paradigm.

Machine Translation (MT) has been predominantly designed for sentence-level translation using transformer-based architectures. While next-token prediction based Large Language Models (LLMs) demonstrate strong capabilities in long-text translation, non-extensive language models often suffer from omissions and semantic inconsistencies when processing paragraphs. Existing preference alignment methods improve sentence-level translation but fail to ensure coherence over extended contexts due to the myopic nature of next-token generation. We introduce Plan2Align, a test-time alignment framework that treats translation as a predictive planning problem, adapting Model Predictive Control to iteratively refine translation outputs. Experiments on WMT24 Discourse-Level Literary Translation show that Plan2Align significantly improves paragraph-level translation, achieving performance surpassing or on par with the existing training-time and test-time alignment methods on LLaMA-3.1 8B.