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.

We address the task of zero-shot fine-grained video classification, where no video examples or temporal annotations are available for unseen action classes. While contrastive vision-language models such as SigLIP demonstrate strong open-set recognition via mean-pooled image-text similarity, they fail to capture the temporal structure critical for distinguishing fine-grained activities. We introduce ActAlign, a zero-shot framework that formulates video classification as sequence alignment. For each class, a large language model generates an ordered sub-action sequence, which is aligned with video frames using Dynamic Time Warping (DTW) in a shared embedding space. Without any video-text supervision or fine-tuning, ActAlign achieves 30.5% accuracy on the extremely challenging ActionAtlas benchmark, where human accuracy is only 61.6%. ActAlign outperforms billion-parameter video-language models while using approximately 8x less parameters. These results demonstrate that structured language priors, combined with classical alignment techniques, offer a scalable and general approach to unlocking the open-set recognition potential of vision-language models for fine-grained video understanding.

The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction, AF2's accuracy is significantly influenced by the depth of multiple sequence alignment (MSA), which requires extensive exploration of a large protein database for similar sequences. However, not all protein sequences possess abundant homologous families, and consequently, AF2's performance can degrade on such queries, at times failing to produce meaningful results. To address this, we introduce a novel generative language model, MSA-Augmenter, which leverages protein-specific attention mechanisms and large-scale MSAs to generate useful, novel protein sequences not currently found in databases. These sequences supplement shallow MSAs, enhancing the accuracy of structural property predictions. Our experiments on CASP14 demonstrate that MSA-Augmenter can generate de novo sequences that retain co-evolutionary information from inferior MSAs, thereby improving protein structure prediction quality on top of strong AF2.

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (Peptide Mass Deviation) and RMD (residual Mass Deviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

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.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

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.

We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm. To guarantee robust scalability, we establish a predictive scaling law and reveal the progressive emergence of structural understanding via loss perspective, culminating in a strong 1.7-billion model. Building on this foundation, we devise a multiple sequence alignment (MSA)-based in-context learning strategy to unify protein design into a general framework, where AMix-1 recognizes deep evolutionary signals among MSAs and consistently generates structurally and functionally coherent proteins. This framework enables the successful design of a dramatically improved AmeR variant with an up to 50times activity increase over its wild type. Pushing the boundaries of protein engineering, we further empower AMix-1 with an evolutionary test-time scaling algorithm for in silico directed evolution that delivers substantial, scalable performance gains as verification budgets are intensified, laying the groundwork for next-generation lab-in-the-loop protein design.

Advances in peptide identification are revolutionizing our ability to decipher protein functions and accelerate therapeutic discovery. We present PDeepPP, a deep learning framework that integrates pretrained protein language models with parallel transformer-CNN architectures, achieving state-of-the-art performance in peptide characterization tasks. The model's hybrid architecture demonstrates unique capabilities in capturing both local sequence motifs and global structural features, as evidenced by 29% improved cluster separation in UMAP visualizations compared to conventional approaches. Evaluated across 33 biological recognition tasks - including post-translational modification site prediction and bioactive peptide identification - PDeepPP outperformed existing methods in 25 tasks with average AUC improvements of 4.2%. Notably, it achieved 0.9726 accuracy with PR AUC 0.9977 in antimicrobial peptide detection while reducing false negatives by 37.5% in antimalarial recognition scenarios. This framework enables accurate large-scale peptide analysis, achieving 218* acceleration over sequence-alignment-based methods while maintaining 99.5% specificity in critical glycosylation site detection.PDeepPP establishes a new paradigm for computational peptide analysis through its synergistic architecture design, enabling rapid yet precise functional annotation that bridges molecular pattern recognition with translational biomedical applications.We have made our implementation, including code, data, and pretrained models, publicly available via GitHub (https://github.com/fondress/PDeepPP) and Hugging Face (https://huggingface.co/fondress/PDeppPP).

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.

This paper presents a novel approach to calculating the Levenshtein (edit) distance within the framework of Fully Homomorphic Encryption (FHE), specifically targeting third-generation schemes like TFHE. Edit distance computations are essential in applications across finance and genomics, such as DNA sequence alignment. We introduce an optimised algorithm that significantly reduces the cost of edit distance calculations called Leuvenshtein. This algorithm specifically reduces the number of programmable bootstraps (PBS) needed per cell of the calculation, lowering it from approximately 94 operations -- required by the conventional Wagner-Fisher algorithm -- to just 1. Additionally, we propose an efficient method for performing equality checks on characters, reducing ASCII character comparisons to only 2 PBS operations. Finally, we explore the potential for further performance improvements by utilising preprocessing when one of the input strings is unencrypted. Our Leuvenshtein achieves up to 278times faster performance compared to the best available TFHE implementation and up to 39times faster than an optimised implementation of the Wagner-Fisher algorithm. Moreover, when offline preprocessing is possible due to the presence of one unencrypted input on the server side, an additional 3times speedup can be achieved.

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.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families. To address this, we propose Protein Evolutionary Transformer (PoET), an autoregressive generative model of whole protein families that learns to generate sets of related proteins as sequences-of-sequences across tens of millions of natural protein sequence clusters. PoET can be used as a retrieval-augmented language model to generate and score arbitrary modifications conditioned on any protein family of interest, and can extrapolate from short context lengths to generalize well even for small families. This is enabled by a unique Transformer layer; we model tokens sequentially within sequences while attending between sequences order invariantly, allowing PoET to scale to context lengths beyond those used during training. In extensive experiments on deep mutational scanning datasets, we show that PoET outperforms existing protein language models and evolutionary sequence models for variant function prediction across proteins of all MSA depths. We also demonstrate PoET's ability to controllably generate new protein sequences.

Protein family design emerges as a promising alternative by combining the advantages of de novo protein design and mutation-based directed evolution.In this paper, we propose ProfileBFN, the Profile Bayesian Flow Networks, for specifically generative modeling of protein families. ProfileBFN extends the discrete Bayesian Flow Network from an MSA profile perspective, which can be trained on single protein sequences by regarding it as a degenerate profile, thereby achieving efficient protein family design by avoiding large-scale MSA data construction and training. Empirical results show that ProfileBFN has a profound understanding of proteins. When generating diverse and novel family proteins, it can accurately capture the structural characteristics of the family. The enzyme produced by this method is more likely than the previous approach to have the corresponding function, offering better odds of generating diverse proteins with the desired functionality.

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 alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

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/.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

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.

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.

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.

We introduce Delayed Streams Modeling (DSM), a flexible formulation for streaming, multimodal sequence-to-sequence learning. Sequence-to-sequence generation is often cast in an offline manner, where the model consumes the complete input sequence before generating the first output timestep. Alternatively, streaming sequence-to-sequence rely on learning a policy for choosing when to advance on the input stream, or write to the output stream. DSM instead models already time-aligned streams with a decoder-only language model. By moving the alignment to a pre-processing step,and introducing appropriate delays between streams, DSM provides streaming inference of arbitrary output sequences, from any input combination, making it applicable to many sequence-to-sequence problems. In particular, given text and audio streams, automatic speech recognition (ASR) corresponds to the text stream being delayed, while the opposite gives a text-to-speech (TTS) model. We perform extensive experiments for these two major sequence-to-sequence tasks, showing that DSM provides state-of-the-art performance and latency while supporting arbitrary long sequences, being even competitive with offline baselines. Code, samples and demos are available at https://github.com/kyutai-labs/delayed-streams-modeling

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.

In this work, we propose a modular approach for the Vision-Language Navigation (VLN) task by decomposing the problem into four sub-modules that use state-of-the-art Large Language Models (LLMs) and Vision-Language Models (VLMs) in a zero-shot setting. Given navigation instruction in natural language, we first prompt LLM to extract the landmarks and the order in which they are visited. Assuming the known model of the environment, we retrieve the top-k locations of the last landmark and generate k path hypotheses from the starting location to the last landmark using the shortest path algorithm on the topological map of the environment. Each path hypothesis is represented by a sequence of panoramas. We then use dynamic programming to compute the alignment score between the sequence of panoramas and the sequence of landmark names, which match scores obtained from VLM. Finally, we compute the nDTW metric between the hypothesis that yields the highest alignment score to evaluate the path fidelity. We demonstrate superior performance compared to other approaches that use joint semantic maps like VLMaps vlmaps on the complex R2R-Habitat r2r instruction dataset and quantify in detail the effect of visual grounding on navigation performance.

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.

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.

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.

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.

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

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.

We present a new direction for increasing the interpretability of deep neural networks (DNNs) by promoting weight-input alignment during training. For this, we propose to replace the linear transforms in DNNs by our B-cos transform. As we show, a sequence (network) of such transforms induces a single linear transform that faithfully summarises the full model computations. Moreover, the B-cos transform introduces alignment pressure on the weights during optimisation. As a result, those induced linear transforms become highly interpretable and align with task-relevant features. Importantly, the B-cos transform is designed to be compatible with existing architectures and we show that it can easily be integrated into common models such as VGGs, ResNets, InceptionNets, and DenseNets, whilst maintaining similar performance on ImageNet. The resulting explanations are of high visual quality and perform well under quantitative metrics for interpretability. Code available at https://www.github.com/moboehle/B-cos.

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.

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/

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.

Despite recent advances in Large Video Language Models (LVLMs), they still struggle with fine-grained temporal understanding, hallucinate, and often make simple mistakes on even simple video question-answering tasks, all of which pose significant challenges to their safe and reliable deployment in real-world applications. To address these limitations, we propose a self-alignment framework that enables LVLMs to learn from their own errors. Our proposed framework first obtains a training set of preferred and non-preferred response pairs, where non-preferred responses are generated by incorporating common error patterns that often occur due to inadequate spatio-temporal understanding, spurious correlations between co-occurring concepts, and over-reliance on linguistic cues while neglecting the vision modality, among others. To facilitate self-alignment of LVLMs with the constructed preferred and non-preferred response pairs, we introduce Refined Regularized Preference Optimization (RRPO), a novel preference optimization method that utilizes sub-sequence-level refined rewards and token-wise KL regularization to address the limitations of Direct Preference Optimization (DPO). We demonstrate that RRPO achieves more precise alignment and more stable training compared to DPO. Our experiments and analysis validate the effectiveness of our approach across diverse video tasks, including video hallucination, short- and long-video understanding, and fine-grained temporal reasoning.

Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in cases where reward functions are non-differentiable. Some gradient-free guidance methods have been developed, but they often struggle to achieve optimal inference-time alignment. In this work, we newly frame inference-time alignment in diffusion as a search problem and propose Dynamic Search for Diffusion (DSearch), which subsamples from denoising processes and approximates intermediate node rewards. It also dynamically adjusts beam width and tree expansion to efficiently explore high-reward generations. To refine intermediate decisions, DSearch incorporates adaptive scheduling based on noise levels and a lookahead heuristic function. We validate DSearch across multiple domains, including biological sequence design, molecular optimization, and image generation, demonstrating superior reward optimization compared to existing approaches.

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.

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.

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.

We introduce SensorLLM, a two-stage framework that enables Large Language Models (LLMs) to perform human activity recognition (HAR) from wearable sensor data. While LLMs excel at reasoning and generalization, they struggle with time-series inputs due to limited semantic context, numerical complexity, and sequence variability. To address these challenges, we construct SensorQA, a question-answering dataset of human-intuitive sensor-text pairs spanning diverse HAR scenarios. It supervises the Sensor-Language Alignment stage, where the model aligns sensor inputs with trend descriptions. Special tokens are introduced to mark channel boundaries. This alignment enables LLMs to interpret numerical patterns, channel-specific signals, and variable-length inputs--without requiring human annotation. In the subsequent Task-Aware Tuning stage, we adapt the model for multivariate HAR classification, achieving performance that matches or exceeds state-of-the-art methods. Our results show that, guided by human-intuitive alignment, SensorLLM becomes an effective sensor learner, reasoner, and classifier--generalizing across varied HAR settings and paving the way for foundation model research in time-series analysis.

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.

The increasing sophistication of large vision-language models (LVLMs) has been accompanied by advances in safety alignment mechanisms designed to prevent harmful content generation. However, these defenses remain vulnerable to sophisticated adversarial attacks. Existing jailbreak methods typically rely on direct and semantically explicit prompts, overlooking subtle vulnerabilities in how LVLMs compose information over multiple reasoning steps. In this paper, we propose a novel and effective jailbreak framework inspired by Return-Oriented Programming (ROP) techniques from software security. Our approach decomposes a harmful instruction into a sequence of individually benign visual gadgets. A carefully engineered textual prompt directs the sequence of inputs, prompting the model to integrate the benign visual gadgets through its reasoning process to produce a coherent and harmful output. This makes the malicious intent emergent and difficult to detect from any single component. We validate our method through extensive experiments on established benchmarks including SafeBench and MM-SafetyBench, targeting popular LVLMs. Results show that our approach consistently and substantially outperforms existing baselines on state-of-the-art models, achieving near-perfect attack success rates (over 0.90 on SafeBench) and improving ASR by up to 0.39. Our findings reveal a critical and underexplored vulnerability that exploits the compositional reasoning abilities of LVLMs, highlighting the urgent need for defenses that secure the entire reasoning process.

Current multimodal large language models (MLLMs) face a critical challenge in modality alignment, often exhibiting a bias towards textual information at the expense of other modalities like vision. This paper conducts a systematic information-theoretic analysis of the widely used cross-entropy loss in MLLMs, uncovering its implicit alignment objective. Our theoretical investigation reveals that this implicit objective has inherent limitations, leading to a degradation of cross-modal alignment as text sequence length increases, thereby hindering effective multimodal information fusion. To overcome these drawbacks, we propose Vision-Text Alignment (VISTA), a novel approach guided by our theoretical insights. VISTA introduces an explicit alignment objective designed to maximize cross-modal mutual information, preventing the degradation of visual alignment. Notably, VISTA enhances the visual understanding capabilities of existing MLLMs without requiring any additional trainable modules or extra training data, making it both efficient and practical. Our method significantly outperforms baseline models across more than a dozen benchmark datasets, including VQAv2, MMStar, and MME, paving the way for new directions in MLLM modal alignment research.

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.

Training native 3D texture generative models remains a fundamental yet challenging problem, largely due to the limited availability of large-scale, high-quality 3D texture datasets. This scarcity hinders generalization to real-world scenarios. To address this, most existing methods finetune foundation image generative models to exploit their learned visual priors. However, these approaches typically generate only multi-view images and rely on post-processing to produce UV texture maps -- an essential representation in modern graphics pipelines. Such two-stage pipelines often suffer from error accumulation and spatial inconsistencies across the 3D surface. In this paper, we introduce SeqTex, a novel end-to-end framework that leverages the visual knowledge encoded in pretrained video foundation models to directly generate complete UV texture maps. Unlike previous methods that model the distribution of UV textures in isolation, SeqTex reformulates the task as a sequence generation problem, enabling the model to learn the joint distribution of multi-view renderings and UV textures. This design effectively transfers the consistent image-space priors from video foundation models into the UV domain. To further enhance performance, we propose several architectural innovations: a decoupled multi-view and UV branch design, geometry-informed attention to guide cross-domain feature alignment, and adaptive token resolution to preserve fine texture details while maintaining computational efficiency. Together, these components allow SeqTex to fully utilize pretrained video priors and synthesize high-fidelity UV texture maps without the need for post-processing. Extensive experiments show that SeqTex achieves state-of-the-art performance on both image-conditioned and text-conditioned 3D texture generation tasks, with superior 3D consistency, texture-geometry alignment, and real-world generalization.

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

Evaluating image-text alignment while reflecting human preferences across multiple aspects is a significant issue for the development of reliable vision-language applications. It becomes especially crucial in real-world scenarios where multiple valid descriptions exist depending on contexts or user needs. However, research progress is hindered by the lack of comprehensive benchmarks and existing evaluation predictors lacking at least one of these key properties: (1) Alignment with human judgments, (2) Long-sequence processing, (3) Inference efficiency, and (4) Applicability to multi-objective scoring. To address these challenges, we propose a plug-and-play architecture to build a robust predictor, MULTI-TAP (Multi-Objective Task-Aware Predictor), capable of both multi and single-objective scoring. MULTI-TAP can produce a single overall score, utilizing a reward head built on top of a large vision-language model (LVLMs). We show that MULTI-TAP is robust in terms of application to different LVLM architectures, achieving significantly higher performance than existing metrics and even on par with the GPT-4o-based predictor, G-VEval, with a smaller size (7-8B). By training a lightweight ridge regression layer on the frozen hidden states of a pre-trained LVLM, MULTI-TAP can produce fine-grained scores for multiple human-interpretable objectives. MULTI-TAP performs better than VisionREWARD, a high-performing multi-objective reward model, in both performance and efficiency on multi-objective benchmarks and our newly released text-image-to-text dataset, EYE4ALL. Our new dataset, consisting of chosen/rejected human preferences (EYE4ALLPref) and human-annotated fine-grained scores across seven dimensions (EYE4ALLMulti), can serve as a foundation for developing more accessible AI systems by capturing the underlying preferences of users, including blind and low-vision (BLV) individuals.

Large Language Models (LLMs) have recently demonstrated impressive capabilities in natural language processing due to their strong generalization and sequence modeling capabilities. However, their direct application to time series forecasting remains challenging due to two fundamental issues: the inherent heterogeneity of temporal patterns and the modality gap between continuous numerical signals and discrete language representations. In this work, we propose TALON, a unified framework that enhances LLM-based forecasting by modeling temporal heterogeneity and enforcing semantic alignment. Specifically, we design a Heterogeneous Temporal Encoder that partitions multivariate time series into structurally coherent segments, enabling localized expert modeling across diverse temporal patterns. To bridge the modality gap, we introduce a Semantic Alignment Module that aligns temporal features with LLM-compatible representations, enabling effective integration of time series into language-based models while eliminating the need for handcrafted prompts during inference. Extensive experiments on seven real-world benchmarks demonstrate that TALON achieves superior performance across all datasets, with average MSE improvements of up to 11\% over recent state-of-the-art methods. These results underscore the effectiveness of incorporating both pattern-aware and semantic-aware designs when adapting LLMs for time series forecasting. The code is available at: https://github.com/syrGitHub/TALON.

Longitudinal multimodal data, including electronic health records (EHR) and sequential chest X-rays (CXRs), is critical for modeling disease progression, yet remains underutilized due to two key challenges: (1) redundancy in consecutive CXR sequences, where static anatomical regions dominate over clinically-meaningful dynamics, and (2) temporal misalignment between sparse, irregular imaging and continuous EHR data. We introduce DiPro, a novel framework that addresses these challenges through region-aware disentanglement and multi-timescale alignment. First, we disentangle static (anatomy) and dynamic (pathology progression) features in sequential CXRs, prioritizing disease-relevant changes. Second, we hierarchically align these static and dynamic CXR features with asynchronous EHR data via local (pairwise interval-level) and global (full-sequence) synchronization to model coherent progression pathways. Extensive experiments on the MIMIC dataset demonstrate that DiPro could effectively extract temporal clinical dynamics and achieve state-of-the-art performance on both disease progression identification and general ICU prediction tasks.

Large language models (LLMs) have achieved impressive performance in a variety of natural language processing (NLP) tasks. However, when applied to long-context scenarios, they face two challenges, i.e., low computational efficiency and much redundant information. This paper introduces GMSA, a context compression framework based on the encoder-decoder architecture, which addresses these challenges by reducing input sequence length and redundant information. Structurally, GMSA has two key components: Group Merging and Layer Semantic Alignment (LSA). Group merging is used to effectively and efficiently extract summary vectors from the original context. Layer semantic alignment, on the other hand, aligns the high-level summary vectors with the low-level primary input semantics, thus bridging the semantic gap between different layers. In the training process, GMSA first learns soft tokens that contain complete semantics through autoencoder training. To furtherly adapt GMSA to downstream tasks, we propose Knowledge Extraction Fine-tuning (KEFT) to extract knowledge from the soft tokens for downstream tasks. We train GMSA by randomly sampling the compression rate for each sample in the dataset. Under this condition, GMSA not only significantly outperforms the traditional compression paradigm in context restoration but also achieves stable and significantly faster convergence with only a few encoder layers. In downstream question-answering (QA) tasks, GMSA can achieve approximately a 2x speedup in end-to-end inference while outperforming both the original input prompts and various state-of-the-art (SOTA) methods by a large margin.

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.

Transformers evaluated in a single, fixed-depth pass are provably limited in expressive power to the constant-depth circuit class TC0. Running a Transformer autoregressively removes that ceiling -- first in next-token prediction and, more recently, in chain-of-thought reasoning. Both regimes rely on feedback loops that decode internal states into tokens only to re-encode them in subsequent steps. While this "thinking aloud" mirrors human reasoning, biological brains iterate without externalising intermediate states as language. To boost the expressive power of encoder Transformers without resorting to token-level autoregression, we introduce the SELF-Transformer: an encoder layer that iteratively refines its own attention weights to a fixed point. Instead of producing -- in one pass -- the alignment matrix that remixes the input sequence, the SELF-Transformer iteratively updates that matrix internally, scaling test-time computation with input difficulty. This adaptivity yields up to 20\% accuracy gains on encoder-style benchmarks without increasing parameter count, demonstrating that input-adaptive alignment at test time offers substantial benefits for only a modest extra compute budget. Self-Transformers thus recover much of the expressive power of iterative reasoning while preserving the simplicity of pure encoder architectures.

The emergence of GPT-4o-like large multimodal models (LMMs) has raised the exploration of integrating text, vision, and speech modalities to support more flexible multimodal interaction. Existing LMMs typically concatenate representation of modalities along the sequence dimension and feed them into a large language model (LLM) backbone. While sequence-dimension concatenation is straightforward for modality integration, it often relies heavily on large-scale data to learn modality alignments. In this paper, we aim to model the relationships between modalities more purposefully, thereby achieving more efficient and flexible modality alignments. To this end, we propose Stream-Omni, a large language-vision-speech model with efficient modality alignments, which can simultaneously support interactions under various modality combinations. Stream-Omni employs LLM as the backbone and aligns the vision and speech to the text based on their relationships. For vision that is semantically complementary to text, Stream-Omni uses sequence-dimension concatenation to achieve vision-text alignment. For speech that is semantically consistent with text, Stream-Omni introduces a CTC-based layer-dimension mapping to achieve speech-text alignment. In this way, Stream-Omni can achieve modality alignments with less data (especially speech), enabling the transfer of text capabilities to other modalities. Experiments on various benchmarks demonstrate that Stream-Omni achieves strong performance on visual understanding, speech interaction, and vision-grounded speech interaction tasks. Owing to the layer-dimensional mapping, Stream-Omni can simultaneously provide intermediate text outputs (such as ASR transcriptions and model responses) during speech interaction, offering users a comprehensive multimodal experience.

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.

Unified multimodal large language models (MLLMs) have shown promise in jointly advancing multimodal understanding and generation, with visual codebooks discretizing images into tokens for autoregressive modeling. Existing codebook-based methods either rely on small vocabularies (~16K entries) that lack fine-grained semantics or naively scale up, resulting in low token utilization and unstable training. We propose UniCode^2, a cascaded codebook framework enabling large-scale, semantically aligned, and stable visual tokenization. By clustering millions of SigLIP sequence embeddings, we build a 500K-entry codebook that preserves vision-language alignment while expanding capacity. Stability is ensured via a cascaded design: a frozen codebook anchors the embedding space, and a trainable codebook refines task-specific semantics. This decoupling promotes high utilization and robust learning. Moreover, the alignment of our visual tokens with textual semantics enables seamless integration with pretrained diffusion decoders, supporting high-quality visual synthesis with minimal adaptation. UniCode^2 delivers strong performance across diverse benchmarks, demonstrating the viability of scaling visual token spaces without sacrificing stability, semantics, or modularity.

In this paper, we present a novel framework designed to reconstruct long-sequence 3D human motion in the world coordinates from in-the-wild videos with multiple shot transitions. Such long-sequence in-the-wild motions are highly valuable to applications such as motion generation and motion understanding, but are of great challenge to be recovered due to abrupt shot transitions, partial occlusions, and dynamic backgrounds presented in such videos. Existing methods primarily focus on single-shot videos, where continuity is maintained within a single camera view, or simplify multi-shot alignment in camera space only. In this work, we tackle the challenges by integrating an enhanced camera pose estimation with Human Motion Recovery (HMR) by incorporating a shot transition detector and a robust alignment module for accurate pose and orientation continuity across shots. By leveraging a custom motion integrator, we effectively mitigate the problem of foot sliding and ensure temporal consistency in human pose. Extensive evaluations on our created multi-shot dataset from public 3D human datasets demonstrate the robustness of our method in reconstructing realistic human motion in world coordinates.

Current LLM safety defenses fail under decomposition attacks, where a malicious goal is decomposed into benign subtasks that circumvent refusals. The challenge lies in the existing shallow safety alignment techniques: they only detect harm in the immediate prompt and do not reason about long-range intent, leaving them blind to malicious intent that emerges over a sequence of seemingly benign instructions. We therefore propose adding an external monitor that observes the conversation at a higher granularity. To facilitate our study of monitoring decomposition attacks, we curate the largest and most diverse dataset to date, including question-answering, text-to-image, and agentic tasks. We verify our datasets by testing them on frontier LLMs and show an 87% attack success rate on average on GPT-4o. This confirms that decomposition attack is broadly effective. Additionally, we find that random tasks can be injected into the decomposed subtasks to further obfuscate malicious intents. To defend in real time, we propose a lightweight sequential monitoring framework that cumulatively evaluates each subtask. We show that a carefully prompt engineered lightweight monitor achieves a 93% defense success rate, beating reasoning models like o3 mini as a monitor. Moreover, it remains robust against random task injection and cuts cost by 90% and latency by 50%. Our findings suggest that lightweight sequential monitors are highly effective in mitigating decomposition attacks and are viable in deployment.

Developing an interpretable system for generating reports in chest X-ray (CXR) analysis is becoming increasingly crucial in Computer-aided Diagnosis (CAD) systems, enabling radiologists to comprehend the decisions made by these systems. Despite the growth of diverse datasets and methods focusing on report generation, there remains a notable gap in how closely these models' generated reports align with the interpretations of real radiologists. In this study, we tackle this challenge by initially introducing Fine-Grained CXR (FG-CXR) dataset, which provides fine-grained paired information between the captions generated by radiologists and the corresponding gaze attention heatmaps for each anatomy. Unlike existing datasets that include a raw sequence of gaze alongside a report, with significant misalignment between gaze location and report content, our FG-CXR dataset offers a more grained alignment between gaze attention and diagnosis transcript. Furthermore, our analysis reveals that simply applying black-box image captioning methods to generate reports cannot adequately explain which information in CXR is utilized and how long needs to attend to accurately generate reports. Consequently, we propose a novel explainable radiologist's attention generator network (Gen-XAI) that mimics the diagnosis process of radiologists, explicitly constraining its output to closely align with both radiologist's gaze attention and transcript. Finally, we perform extensive experiments to illustrate the effectiveness of our method. Our datasets and checkpoint is available at https://github.com/UARK-AICV/FG-CXR.

Learning from long-horizon demonstrations with complex action sequences presents significant challenges for visual imitation learning, particularly in understanding temporal relationships of actions and spatial relationships between objects. In this paper, we propose a new agent framework that incorporates two dedicated reflection modules to enhance both plan and code generation. The plan generation module produces an initial action sequence, which is then verified by the plan reflection module to ensure temporal coherence and spatial alignment with the demonstration video. The code generation module translates the plan into executable code, while the code reflection module verifies and refines the generated code to ensure correctness and consistency with the generated plan. These two reflection modules jointly enable the agent to detect and correct errors in both the plan generation and code generation, improving performance in tasks with intricate temporal and spatial dependencies. To support systematic evaluation, we introduce LongVILBench, a benchmark comprising 300 human demonstrations with action sequences of up to 18 steps. LongVILBench emphasizes temporal and spatial complexity across multiple task types. Experimental results demonstrate that existing methods perform poorly on this benchmark, whereas our new framework establishes a strong baseline for long-horizon visual imitation learning.

Visual grounding is essential for precise perception and reasoning in multimodal large language models (MLLMs), especially in medical imaging domains. While existing medical visual grounding benchmarks primarily focus on single-image scenarios, real-world clinical applications often involve sequential images, where accurate lesion localization across different modalities and temporal tracking of disease progression (e.g., pre- vs. post-treatment comparison) require fine-grained cross-image semantic alignment and context-aware reasoning. To remedy the underrepresentation of image sequences in existing medical visual grounding benchmarks, we propose MedSG-Bench, the first benchmark tailored for Medical Image Sequences Grounding. It comprises eight VQA-style tasks, formulated into two paradigms of the grounding tasks, including 1) Image Difference Grounding, which focuses on detecting change regions across images, and 2) Image Consistency Grounding, which emphasizes detection of consistent or shared semantics across sequential images. MedSG-Bench covers 76 public datasets, 10 medical imaging modalities, and a wide spectrum of anatomical structures and diseases, totaling 9,630 question-answer pairs. We benchmark both general-purpose MLLMs (e.g., Qwen2.5-VL) and medical-domain specialized MLLMs (e.g., HuatuoGPT-vision), observing that even the advanced models exhibit substantial limitations in medical sequential grounding tasks. To advance this field, we construct MedSG-188K, a large-scale instruction-tuning dataset tailored for sequential visual grounding, and further develop MedSeq-Grounder, an MLLM designed to facilitate future research on fine-grained understanding across medical sequential images. The benchmark, dataset, and model are available at https://huggingface.co/MedSG-Bench

The increasing prevalence of lumbar spinal canal stenosis has resulted in a surge of MRI (Magnetic Resonance Imaging), leading to labor-intensive interpretation and significant inter-reader variability, even among expert radiologists. This paper introduces a novel and efficient deep-learning framework that fully automates the grading of lumbar spinal canal stenosis. We demonstrate state-of-the-art performance in grading spinal canal stenosis on a dataset of 1,975 unique studies, each containing three distinct types of 3D cross-sectional spine images: Axial T2, Sagittal T1, and Sagittal T2/STIR. Employing a distinctive training strategy, our proposed multistage approach effectively integrates sagittal and axial images. This strategy employs a multi-view model with a sequence-based architecture, optimizing feature extraction and cross-view alignment to achieve an AUROC (Area Under the Receiver Operating Characteristic Curve) of 0.971 in spinal canal stenosis grading surpassing other state-of-the-art methods.

Motion retrieval is crucial for motion acquisition, offering superior precision, realism, controllability, and editability compared to motion generation. Existing approaches leverage contrastive learning to construct a unified embedding space for motion retrieval from text or visual modality. However, these methods lack a more intuitive and user-friendly interaction mode and often overlook the sequential representation of most modalities for improved retrieval performance. To address these limitations, we propose a framework that aligns four modalities -- text, audio, video, and motion -- within a fine-grained joint embedding space, incorporating audio for the first time in motion retrieval to enhance user immersion and convenience. This fine-grained space is achieved through a sequence-level contrastive learning approach, which captures critical details across modalities for better alignment. To evaluate our framework, we augment existing text-motion datasets with synthetic but diverse audio recordings, creating two multi-modal motion retrieval datasets. Experimental results demonstrate superior performance over state-of-the-art methods across multiple sub-tasks, including an 10.16% improvement in R@10 for text-to-motion retrieval and a 25.43% improvement in R@1 for video-to-motion retrieval on the HumanML3D dataset. Furthermore, our results show that our 4-modal framework significantly outperforms its 3-modal counterpart, underscoring the potential of multi-modal motion retrieval for advancing motion acquisition.

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.

In this paper, we propose a novel soft and monotonic alignment mechanism used for sequence transduction. It is inspired by the integrate-and-fire model in spiking neural networks and employed in the encoder-decoder framework consists of continuous functions, thus being named as: Continuous Integrate-and-Fire (CIF). Applied to the ASR task, CIF not only shows a concise calculation, but also supports online recognition and acoustic boundary positioning, thus suitable for various ASR scenarios. Several support strategies are also proposed to alleviate the unique problems of CIF-based model. With the joint action of these methods, the CIF-based model shows competitive performance. Notably, it achieves a word error rate (WER) of 2.86% on the test-clean of Librispeech and creates new state-of-the-art result on Mandarin telephone ASR benchmark.

Recurrent neural network (RNN) and connectionist temporal classification (CTC) have showed successes in many sequence labeling tasks with the strong ability of dealing with the problems where the alignment between the inputs and the target labels is unknown. Residual network is a new structure of convolutional neural network and works well in various computer vision tasks. In this paper, we take advantage of the architectures mentioned above to create a new network for handwritten digit string recognition. First we design a residual network to extract features from input images, then we employ a RNN to model the contextual information within feature sequences and predict recognition results. At the top of this network, a standard CTC is applied to calculate the loss and yield the final results. These three parts compose an end-to-end trainable network. The proposed new architecture achieves the highest performances on ORAND-CAR-A and ORAND-CAR-B with recognition rates 89.75% and 91.14%, respectively. In addition, the experiments on a generated captcha dataset which has much longer string length show the potential of the proposed network to handle long strings.

Mean Opinion Score (MOS) prediction for text to music systems requires evaluating both overall musical quality and text prompt alignment. This paper introduces WhisQ, a multimodal architecture that addresses this dual-assessment challenge through sequence level co-attention and optimal transport regularization. WhisQ employs the Whisper Base pretrained model for temporal audio encoding and Qwen 3, a 0.6B Small Language Model (SLM), for text encoding, with both maintaining sequence structure for fine grained cross-modal modeling. The architecture features specialized prediction pathways: OMQ is predicted from pooled audio embeddings, while TA leverages bidirectional sequence co-attention between audio and text. Sinkhorn optimal transport loss further enforce semantic alignment in the shared embedding space. On the MusicEval Track-1 dataset, WhisQ achieves substantial improvements over the baseline: 7% improvement in Spearman correlation for OMQ and 14% for TA. Ablation studies reveal that optimal transport regularization provides the largest performance gain (10% SRCC improvement), demonstrating the importance of explicit cross-modal alignment for text-to-music evaluation.

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.

Sign Language Translation (SLT) is a challenging task that aims to translate sign videos into spoken language. Inspired by the strong translation capabilities of large language models (LLMs) that are trained on extensive multilingual text corpora, we aim to harness off-the-shelf LLMs to handle SLT. In this paper, we regularize the sign videos to embody linguistic characteristics of spoken language, and propose a novel SignLLM framework to transform sign videos into a language-like representation for improved readability by off-the-shelf LLMs. SignLLM comprises two key modules: (1) The Vector-Quantized Visual Sign module converts sign videos into a sequence of discrete character-level sign tokens, and (2) the Codebook Reconstruction and Alignment module converts these character-level tokens into word-level sign representations using an optimal transport formulation. A sign-text alignment loss further bridges the gap between sign and text tokens, enhancing semantic compatibility. We achieve state-of-the-art gloss-free results on two widely-used SLT benchmarks.

In recent years, while natural language processing and multimodal learning have seen rapid advancements, the field of de novo protein design has also experienced significant growth. However, most current methods rely on proprietary datasets and evaluation rubrics, making fair comparisons between different approaches challenging. Moreover, these methods often employ evaluation metrics that capture only a subset of the desired properties of designed proteins, lacking a comprehensive assessment framework. To address these, we introduce PDFBench, the first comprehensive benchmark for evaluating de novo protein design from function. PDFBench supports two tasks: description-guided design and keyword-guided design. To ensure fair and multifaceted evaluation, we compile 22 metrics covering sequence plausibility, structural fidelity, and language-protein alignment, along with measures of novelty and diversity. We evaluate five state-of-the-art baselines, revealing their respective strengths and weaknesses across tasks. Finally, we analyze inter-metric correlations, exploring the relationships between four categories of metrics, and offering guidelines for metric selection. PDFBench establishes a unified framework to drive future advances in function-driven de novo protein design.

Model fusion combines multiple Large Language Models (LLMs) with different strengths into a more powerful, integrated model through lightweight training methods. Existing works on model fusion focus primarily on supervised fine-tuning (SFT), leaving preference alignment (PA) --a critical phase for enhancing LLM performance--largely unexplored. The current few fusion methods on PA phase, like WRPO, simplify the process by utilizing only response outputs from source models while discarding their probability information. To address this limitation, we propose InfiFPO, a preference optimization method for implicit model fusion. InfiFPO replaces the reference model in Direct Preference Optimization (DPO) with a fused source model that synthesizes multi-source probabilities at the sequence level, circumventing complex vocabulary alignment challenges in previous works and meanwhile maintaining the probability information. By introducing probability clipping and max-margin fusion strategies, InfiFPO enables the pivot model to align with human preferences while effectively distilling knowledge from source models. Comprehensive experiments on 11 widely-used benchmarks demonstrate that InfiFPO consistently outperforms existing model fusion and preference optimization methods. When using Phi-4 as the pivot model, InfiFPO improve its average performance from 79.95 to 83.33 on 11 benchmarks, significantly improving its capabilities in mathematics, coding, and reasoning tasks.

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.

Large-scale pretrained foundation models have been an emerging paradigm for building artificial intelligence (AI) systems, which can be quickly adapted to a wide range of downstream tasks. This paper presents mPLUG, a new vision-language foundation model for both cross-modal understanding and generation. Most existing pre-trained models suffer from the problems of low computational efficiency and information asymmetry brought by the long visual sequence in cross-modal alignment. To address these problems, mPLUG introduces an effective and efficient vision-language architecture with novel cross-modal skip-connections, which creates inter-layer shortcuts that skip a certain number of layers for time-consuming full self-attention on the vision side. mPLUG is pre-trained end-to-end on large-scale image-text pairs with both discriminative and generative objectives. It achieves state-of-the-art results on a wide range of vision-language downstream tasks, such as image captioning, image-text retrieval, visual grounding and visual question answering. mPLUG also demonstrates strong zero-shot transferability when directly transferred to multiple video-language tasks.

Despite their remarkable reasoning capabilities across diverse domains, large language models (LLMs) face fundamental challenges in natively functioning as generative reasoning recommendation models (GRRMs), where the intrinsic modeling gap between textual semantics and collaborative filtering signals, combined with the sparsity and stochasticity of user feedback, presents significant obstacles. This work explores how to build GRRMs by adapting pre-trained LLMs, which achieves a unified understanding-reasoning-prediction manner for recommendation tasks. We propose GREAM, an end-to-end framework that integrates three components: (i) Collaborative-Semantic Alignment, which fuses heterogeneous textual evidence to construct semantically consistent, discrete item indices and auxiliary alignment tasks that ground linguistic representations in interaction semantics; (ii) Reasoning Curriculum Activation, which builds a synthetic dataset with explicit Chain-of-Thought supervision and a curriculum that progresses through behavioral evidence extraction, latent preference modeling, intent inference, recommendation formulation, and denoised sequence rewriting; and (iii) Sparse-Regularized Group Policy Optimization (SRPO), which stabilizes post-training via Residual-Sensitive Verifiable Reward and Bonus-Calibrated Group Advantage Estimation, enabling end-to-end optimization under verifiable signals despite sparse successes. GREAM natively supports two complementary inference modes: Direct Sequence Recommendation for high-throughput, low-latency deployment, and Sequential Reasoning Recommendation that first emits an interpretable reasoning chain for causal transparency. Experiments on three datasets demonstrate consistent gains over strong baselines, providing a practical path toward verifiable-RL-driven LLM recommenders.

Multimodal large language models (MLLMs) extend the success of language models to visual understanding, and recent efforts have sought to build unified MLLMs that support both understanding and generation. However, constructing such models remains challenging: hybrid approaches combine continuous embeddings with diffusion or flow-based objectives, producing high-quality images but breaking the autoregressive paradigm, while pure autoregressive approaches unify text and image prediction over discrete visual tokens but often face trade-offs between semantic alignment and pixel-level fidelity. In this work, we present Bridge, a pure autoregressive unified MLLM that augments pre-trained visual understanding models with generative ability through a Mixture-of-Transformers architecture, enabling both image understanding and generation within a single next-token prediction framework. To further improve visual generation fidelity, we propose a semantic-to-pixel discrete representation that integrates compact semantic tokens with fine-grained pixel tokens, achieving strong language alignment and precise description of visual details with only a 7.9% increase in sequence length. Extensive experiments across diverse multimodal benchmarks demonstrate that Bridge achieves competitive or superior results in both understanding and generation benchmarks, while requiring less training data and reduced training time compared to prior unified MLLMs.

Current methods of building LLMs with voice interaction capabilities rely heavily on explicit text autoregressive generation before or during speech response generation to maintain content quality, which unfortunately brings computational overhead and increases latency in multi-turn interactions. To address this, we introduce IntrinsicVoic,e an LLM designed with intrinsic real-time voice interaction capabilities. IntrinsicVoice aims to facilitate the transfer of textual capabilities of pre-trained LLMs to the speech modality by mitigating the modality gap between text and speech. Our novelty architecture, GroupFormer, can reduce speech sequences to lengths comparable to text sequences while generating high-quality audio, significantly reducing the length difference between speech and text, speeding up inference, and alleviating long-text modeling issues. Additionally, we construct a multi-turn speech-to-speech dialogue dataset named \method-500k which includes nearly 500k turns of speech-to-speech dialogues, and a cross-modality training strategy to enhance the semantic alignment between speech and text. Experimental results demonstrate that IntrinsicVoice can generate high-quality speech response with latency lower than 100ms in multi-turn dialogue scenarios. Demos are available at https://instrinsicvoice.github.io/.

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.