Daily Papers

Event extraction is challenging due to the complex structure of event records and the semantic gap between text and event. Traditional methods usually extract event records by decomposing the complex structure prediction task into multiple subtasks. In this paper, we propose Text2Event, a sequence-to-structure generation paradigm that can directly extract events from the text in an end-to-end manner. Specifically, we design a sequence-to-structure network for unified event extraction, a constrained decoding algorithm for event knowledge injection during inference, and a curriculum learning algorithm for efficient model learning. Experimental results show that, by uniformly modeling all tasks in a single model and universally predicting different labels, our method can achieve competitive performance using only record-level annotations in both supervised learning and transfer learning settings.

Autoregressive transformers remain comparatively weak for protein sequence and structure generation. We study the role of target representation: amino acid tokens encode residue identities without explicit contextual semantics, while backbone coordinates require a discrete representation in our framework. We introduce two learned latent protein languages. Protein Latent Language (PLL) maps sequences to a 4,096-state contextual alphabet built on a frozen ESM-2 encoder, with one token per residue. Structure Latent Language (SLL) adapts GCP-VQVAE Lite with auxiliary sequence and confidence supervision while retaining decoding to backbone coordinates. We separately pretrain autoregressive transformer models on PLL and SLL tokens using next-token prediction, yielding PLLM and SLLM. Under matched downstream sequence training, PLLM has a fitted compute-scaling exponent of 0.038 versus 0.020 for the amino acid autoregressive model. In unconditional sequence generation, PLLM reduces the fraction of samples below a heuristic 1.5-bit residue-composition entropy threshold by 54% relative to the amino acid model across sampling temperatures. For sequence-to-structure prediction, replacing the original GCP-VQVAE Lite tokenizer with SLL reduces best validation perplexity by 34% under matched training. For long proteins, latent-token sampling is approximately 1,000 times faster than MSA-based AlphaFold2 in our measurements. In backbone generation, SLLM compares favorably with other generative models on diversity and novelty. We also observe early signs that using SLLM's internal token confidence for inference-time sampling can improve sequence-to-structure prediction quality beyond a single decoded sample. These results position learned latent protein languages as a promising substrate for autoregressive transformer scaling and inference-time sampling in protein generation.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

The task of Grammatical Error Correction (GEC) has received remarkable attention with wide applications in Natural Language Processing (NLP) in recent years. While one of the key principles of GEC is to keep the correct parts unchanged and avoid over-correction, previous sequence-to-sequence (seq2seq) models generate results from scratch, which are not guaranteed to follow the original sentence structure and may suffer from the over-correction problem. In the meantime, the recently proposed sequence tagging models can overcome the over-correction problem by only generating edit operations, but are conditioned on human designed language-specific tagging labels. In this paper, we combine the pros and alleviate the cons of both models by proposing a novel Sequence-to-Action~(S2A) module. The S2A module jointly takes the source and target sentences as input, and is able to automatically generate a token-level action sequence before predicting each token, where each action is generated from three choices named SKIP, COPY and GENerate. Then the actions are fused with the basic seq2seq framework to provide final predictions. We conduct experiments on the benchmark datasets of both English and Chinese GEC tasks. Our model consistently outperforms the seq2seq baselines, while being able to significantly alleviate the over-correction problem as well as holding better generality and diversity in the generation results compared to the sequence tagging models.

Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at https://github.com/Eurekashen/MolSpectLLM{https://github.com/Eurekashen/MolSpectLLM}.

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

Generative Recommendation (GR), powered by Large Language Models (LLMs), represents a promising new paradigm for industrial recommender systems. However, their practical application is severely hindered by high inference latency, which makes them infeasible for high-throughput, real-time services and limits their overall business impact. While Speculative Decoding (SD) has been proposed to accelerate the autoregressive generation process, existing implementations introduce new bottlenecks: they typically require separate draft models and model-based verifiers, requiring additional training and increasing the latency overhead. In this paper, we address these challenges with NEZHA, a novel architecture that achieves hyperspeed decoding for GR systems without sacrificing recommendation quality. Specifically, NEZHA integrates a nimble autoregressive draft head directly into the primary model, enabling efficient self-drafting. This design, combined with a specialized input prompt structure, preserves the integrity of sequence-to-sequence generation. Furthermore, to tackle the critical problem of hallucination, a major source of performance degradation, we introduce an efficient, model-free verifier based on a hash set. We demonstrate the effectiveness of NEZHA through extensive experiments on public datasets and have successfully deployed the system on Taobao since October 2025, driving the billion-level advertising revenue and serving hundreds of millions of daily active users.

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.

Diffusion and flow-based generative models produce strong images, yet their controllability remains largely endpoint-centric: users specify conditions and receive final outputs, while the intermediate generative dynamics remain hidden. Recent methods have begun to exploit generation order and process decomposition to improve sample quality, but still treat intermediate states as internal computation rather than objects for interaction. We propose Trajectory Forcing (TF), a trajectory-centric framework that makes the generation path explicit, semantic, and editable. TF organizes synthesis as a sequence of semantically structured stages, progressing from global layout to object-, part-, and detail-level representations. Each stage produces a decodable latent state that can be inspected, evaluated, and locally edited before the next stage begins. To instantiate this path, we derive coarse-to-fine teacher hierarchies by clustering pretrained visual representations such as DINOv2, and train a hierarchy-conditioned one-step flow-matching model at each level. We further introduce trajectory-aware metrics that measure structural consistency and local controllability beyond endpoint quality metrics such as FID. Experiments show that TF achieves competitive sample quality while exposing coherent intermediate states and supporting localized edits across semantic levels. By shifting the focus from final images to the generative path itself, TF opens a route toward controllable, trajectory-aware image synthesis.

We present TableSeq, an image-only, end-to-end framework for joint table structure recognition, content recognition, and cell localization. The model formulates these tasks as a single sequence-generation problem: one decoder produces an interleaved stream of HTML tags, cell text, and discretized coordinate tokens, thereby aligning logical structure, textual content, and cell geometry within a unified autoregressive sequence. This design avoids external OCR, auxiliary decoders, and complex multi-stage post-processing. TableSeq combines a lightweight high-resolution FCN-H16 encoder with a minimal structure-prior head and a single-layer transformer encoder, yielding a compact architecture that remains effective on challenging layouts. Across standard benchmarks, TableSeq achieves competitive or state-of-the-art results while preserving architectural simplicity. It reaches 95.23 TEDS / 96.83 S-TEDS on PubTabNet, 97.45 TEDS / 98.69 S-TEDS on FinTabNet, and 99.79 / 99.54 / 99.66 precision / recall / F1 on SciTSR under the CAR protocol, while remaining competitive on PubTables-1M under GriTS. Beyond TSR/TCR, the same sequence interface generalizes to index-based table querying without task-specific heads, achieving the best IRDR score and competitive ICDR/ICR performance. We also study multi-token prediction for faster blockwise decoding and show that it reduces inference latency with only limited accuracy degradation. Overall, TableSeq provides a practical and reproducible single-stream baseline for unified table recognition, and the source code will be made publicly available at https://github.com/hamdilaziz/TableSeq.

Generating human videos with consistent motion from text prompts remains a significant challenge, particularly for whole-body or long-range motion. Existing video generation models prioritize appearance fidelity, resulting in unrealistic or physically implausible human movements with poor structural coherence. Additionally, most existing human video datasets primarily focus on facial or upper-body motions, or consist of vertically oriented dance videos, limiting the scope of corresponding generation methods to simple movements. To overcome these challenges, we propose MoCo, which decouples the process of human video generation into two components: structure generation and appearance generation. Specifically, our method first employs an efficient 3D structure generator to produce a human motion sequence from a text prompt. The remaining video appearance is then synthesized under the guidance of the generated structural sequence. To improve fine-grained control over sparse human structures, we introduce Human-Aware Dynamic Control modules and integrate dense tracking constraints during training. Furthermore, recognizing the limitations of existing datasets, we construct a large-scale whole-body human video dataset featuring complex and diverse motions. Extensive experiments demonstrate that MoCo outperforms existing approaches in generating realistic and structurally coherent human videos.

Natively training joint video-audio generation models at higher resolutions empowers them to learn richer visual details and sharper motion dynamics. However, full attention incurs quadratic cost and, as resolution increases, spreads attention over increasingly redundant tokens, diluting learning signals for informative content and disrupting pretrained priors. Existing sparse attention methods either target training-free acceleration or overlook the unique structure of joint video-audio data, where cross-modal interactions are inherently concentrated around sound-producing regions. To address this, we propose Prism, a dynamic sparse attention framework for natively training joint video-audio generation models at 2K. In particular, Prism organizes the token sequence into spatiotemporal macro-zones, enabling the attention structure to adapt to local content. For each zone, it estimates local information structure via video feature variance along the channel and feature norms from the audio-to-video cross-attention, jointly capturing how visual content varies directionally and how strongly audio influences each visual region. Based on these signals, Prism dynamically assigns a tailored block shape to each zone, applying finer partitioning along axes of rapid visual content variation and strong audio-visual coupling. This encourages tokens within each block to remain semantically coherent, allowing block-level features to capture both visual content and joint video-audio interaction patterns. Prism further adopts a hybrid block selection strategy to dynamically determine per-query sparsity. Experiments show that Prism achieves 2.5times training speedup compared to full attention, while surpassing it in generation quality.

State-of-the-art text-to-image models excel at photorealistic rendering but often struggle to capture the layout and object relationships implied by complex prompts. Scene graphs provide a natural structural prior, yet previous graph-guided approaches have typically relied on heavy GAN or diffusion pipelines, which lag behind modern autoregressive architectures in both speed and fidelity. We introduce SATURN (Structured Arrangement of Triplets for Unified Rendering Networks), a lightweight extension to VAR-CLIP that translates a scene graph into a salience-ordered token sequence, enabling a frozen CLIP-VQ-VAE backbone to interpret graph structure while fine-tuning only the VAR transformer. On the Visual Genome dataset, SATURN reduces FID from 56.45% to 21.62% and increases the Inception Score from 16.03 to 24.78, outperforming prior methods such as SG2IM and SGDiff without requiring extra modules or multi-stage training. Qualitative results further confirm improvements in object count fidelity and spatial relation accuracy, showing that SATURN effectively combines structural awareness with state-of-the-art autoregressive fidelity.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Recent advances in large language models(LLMs) enable compelling story generation, but connecting narrative text to playable visual environments remains an open challenge in procedural content generation(PCG). We present a lightweight pipeline that transforms short narrative prompts into a sequence of 2D tile-based game scenes, reflecting the temporal structure of stories. Given an LLM-generated narrative, our system identifies three key time frames, extracts spatial predicates in the form of "Object-Relation-Object" triples, and retrieves visual assets using affordance-aware semantic embeddings from the GameTileNet dataset. A layered terrain is generated using Cellular Automata, and objects are placed using spatial rules grounded in the predicate structure. We evaluated our system in ten diverse stories, analyzing tile-object matching, affordance-layer alignment, and spatial constraint satisfaction across frames. This prototype offers a scalable approach to narrative-driven scene generation and lays the foundation for future work on multi-frame continuity, symbolic tracking, and multi-agent coordination in story-centered PCG.

Autoregressive models excel in modeling sequential dependencies by enforcing causal constraints, yet they struggle to capture complex bidirectional patterns due to their unidirectional nature. In contrast, mask-based models leverage bidirectional context, enabling richer dependency modeling. However, they often assume token independence during prediction, which undermines the modeling of sequential dependencies. Additionally, the corruption of sequences through masking or absorption can introduce unnatural distortions, complicating the learning process. To address these issues, we propose Bidirectional Autoregressive Diffusion (BAD), a novel approach that unifies the strengths of autoregressive and mask-based generative models. BAD utilizes a permutation-based corruption technique that preserves the natural sequence structure while enforcing causal dependencies through randomized ordering, enabling the effective capture of both sequential and bidirectional relationships. Comprehensive experiments show that BAD outperforms autoregressive and mask-based models in text-to-motion generation, suggesting a novel pre-training strategy for sequence modeling. The codebase for BAD is available on https://github.com/RohollahHS/BAD.

This paper presents DetailFlow, a coarse-to-fine 1D autoregressive (AR) image generation method that models images through a novel next-detail prediction strategy. By learning a resolution-aware token sequence supervised with progressively degraded images, DetailFlow enables the generation process to start from the global structure and incrementally refine details. This coarse-to-fine 1D token sequence aligns well with the autoregressive inference mechanism, providing a more natural and efficient way for the AR model to generate complex visual content. Our compact 1D AR model achieves high-quality image synthesis with significantly fewer tokens than previous approaches, i.e. VAR/VQGAN. We further propose a parallel inference mechanism with self-correction that accelerates generation speed by approximately 8x while reducing accumulation sampling error inherent in teacher-forcing supervision. On the ImageNet 256x256 benchmark, our method achieves 2.96 gFID with 128 tokens, outperforming VAR (3.3 FID) and FlexVAR (3.05 FID), which both require 680 tokens in their AR models. Moreover, due to the significantly reduced token count and parallel inference mechanism, our method runs nearly 2x faster inference speed compared to VAR and FlexVAR. Extensive experimental results demonstrate DetailFlow's superior generation quality and efficiency compared to existing state-of-the-art methods.

Recent text-to-CAD approaches have shown promising results by leveraging large language models, but they often struggle with maintaining structural consistency in complex designs and accurately grounding geometric parameters. To address these issues, we propose HierCAD, a hierarchical text-to-CAD framework that improves both structural reasoning and parameter prediction. HierCAD reformulates CAD generation as progressive reasoning by decomposing CAD construction trees into object-level procedural reasoning and part-level topology reasoning trajectories. To further improve generation fidelity, we introduce a unified Structure Alignment and Parameter Grounding (SAPG) learning strategy. Structure alignment aligns topology reasoning trajectories with their corresponding parametric CAD spans, while parameter grounding mitigates shortcut learning through structure-preserving parameter perturbations and ranking-based supervision. Experiments demonstrate that HierCAD outperforms prior state-of-the-art methods on both CAD sequence generation and reconstructed CAD model evaluation. Our code is available at https://github.com/Collab-Gen/HierCAD.

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

Human behavior is often assumed to be hierarchically structured, made up of abstract actions that can be decomposed into concrete actions. However, behavior is typically measured as a sequence of actions, which makes it difficult to infer its hierarchical structure. In this paper, we explore how people form hierarchically structured plans, using an experimental paradigm with observable hierarchical representations: participants create programs that produce sequences of actions in a language with explicit hierarchical structure. This task lets us test two well-established principles of human behavior: utility maximization (i.e. using fewer actions) and minimum description length (MDL; i.e. having a shorter program). We find that humans are sensitive to both metrics, but that both accounts fail to predict a qualitative feature of human-created programs, namely that people prefer programs with reuse over and above the predictions of MDL. We formalize this preference for reuse by extending the MDL account into a generative model over programs, modeling hierarchy choice as the induction of a grammar over actions. Our account can explain the preference for reuse and provides better predictions of human behavior, going beyond simple accounts of compressibility to highlight a principle that guides hierarchical planning.

We introduce QuadTok, a novel framework for visual tokenization and autoregressive image generation. Compared to traditional approaches using 2D grids or 1D token sequences, we propose a hierarchical quadtree structure, bridging the gap between 2D spatial binding and 1D sequence-level flexibility. The QuadTok tokenizer dynamically allocates representational capacity to visually intricate areas while leaving homogeneous regions at a coarse resolution. Compared with a fixed 256-token grid, our ImageNet-trained tokenizer saves approximately 10% of tokens on ImageNet and 9% when transferred zero-shot to the COCO dataset, while maintaining comparable reconstruction fidelity. Furthermore, the natural causality introduced by the tree structure seamlessly enables autoregressive image generation. Conditioned on a quadtree topology supplied before generation, our 947M GPT-style generative model achieves a 2.08 gFID on the ImageNet 256 times 256 benchmark. Additionally, leveraging the strong spatial correlation preserved by the quadtree structure, the QuadTok generator enables zero-shot spatially controlled image generation capabilities. Code: https://github.com/myc634/QuadTok.

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

While Diffusion Generative Models have achieved great success on image generation tasks, how to efficiently and effectively incorporate them into speech generation especially translation tasks remains a non-trivial problem. Specifically, due to the low information density of speech data, the transformed discrete speech unit sequence is much longer than the corresponding text transcription, posing significant challenges to existing auto-regressive models. Furthermore, it is not optimal to brutally apply discrete diffusion on the speech unit sequence while disregarding the continuous space structure, which will degrade the generation performance significantly. In this paper, we propose a novel diffusion model by applying the diffusion forward process in the continuous speech representation space, while employing the diffusion backward process in the discrete speech unit space. In this way, we preserve the semantic structure of the continuous speech representation space in the diffusion process and integrate the continuous and discrete diffusion models. We conduct extensive experiments on the textless direct speech-to-speech translation task, where the proposed method achieves comparable results to the computationally intensive auto-regressive baselines (500 steps on average) with significantly fewer decoding steps (50 steps).

Diffusion language models (DLMs) have recently emerged as a promising alternative to autoregressive models, primarily due to their ability to enable parallel decoding. Despite this advantage, most existing DLMs rely on a fixed generation length specified prior to decoding, which restricts their flexibility in real-world applications. While a few recent works attempt to support flexible-length generation, they typically suffer from notable limitations: some require costly retraining to accommodate variable-length outputs, while others depend solely on local confidence signals during decoding. Such local criteria fail to capture the evolving structure of the sequence, often resulting in suboptimal generation quality. In this paper, we propose a training-free, Bayesian structured decoding framework that formulates flexible-length generation as a dynamic structural inference problem. Our approach formulates flexible-length generation as a dynamic structural inference problem, jointly computing the expansion length, the block boundaries, and the decoding schedule. At each window expansion step, the method integrates local uncertainty with structural signals via a unified mechanism that supports dynamic structured generation, including both flexible block expansion and block organization, while maintaining coherence. Extensive experiments across multiple benchmarks demonstrate that our approach significantly improves generation quality and flexibility over existing fixed-length and flexible-length baselines. These results highlight the advantage of Bayesian structured decoding for diffusion language model, providing a principled and efficient solution for structured text generation.

Despite the recent advances in applying pre-trained language models to generate high-quality texts, generating long passages that maintain long-range coherence is yet challenging for these models. In this paper, we propose DiscoDVT, a discourse-aware discrete variational Transformer to tackle the incoherence issue. DiscoDVT learns a discrete variable sequence that summarizes the global structure of the text and then applies it to guide the generation process at each decoding step. To further embed discourse-aware information into the discrete latent representations, we introduce an auxiliary objective to model the discourse relations within the text. We conduct extensive experiments on two open story generation datasets and demonstrate that the latent codes learn meaningful correspondence to the discourse structures that guide the model to generate long texts with better long-range coherence.

In this paper, we present gfnx, a fast and scalable package for training and evaluating Generative Flow Networks (GFlowNets) written in JAX. gfnx provides an extensive set of environments and metrics for benchmarking, accompanied with single-file implementations of core objectives for training GFlowNets. We include synthetic hypergrids, multiple sequence generation environments with various editing regimes and particular reward designs for molecular generation, phylogenetic tree construction, Bayesian structure learning, and sampling from the Ising model energy. Across different tasks, gfnx achieves significant wall-clock speedups compared to Pytorch-based benchmarks (such as torchgfn library) and author implementations. For example, gfnx achieves up to 55 times speedup on CPU-based sequence generation environments, and up to 80 times speedup with the GPU-based Bayesian network structure learning setup. Our package provides a diverse set of benchmarks and aims to standardize empirical evaluation and accelerate research and applications of GFlowNets. The library is available on GitHub (https://github.com/d-tiapkin/gfnx) and on pypi (https://pypi.org/project/gfnx/). Documentation is available on https://gfnx.readthedocs.io.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Current instruction data synthesis methods primarily focus on single-turn instructions and often neglect cross-turn coherence, resulting in context drift and reduced task completion rates in extended conversations. To address this limitation, we propose Skeleton-Guided Multi-Turn Dialogue Generation, a framework that constrains multi-turn instruction synthesis by explicitly modeling human conversational intent. It operates in two stages: (1) Intent Modeling, which captures the global structure of human dialogues by assigning each conversation to one of nine well-defined intent trajectories, ensuring a coherent and goal-oriented information flow; and (2) Skeleton Generation, which constructs a structurally grounded sequence of user queries aligned with the modeled intent, thereby serving as a scaffold that constrains and guides the downstream instruction synthesis process. Based on this process, we construct ConsistentChat, a multi-turn instruction dataset with approximately 15,000 multi-turn conversations and 224,392 utterances. Experiments on the Light, Topdial, and MT-Eval benchmarks show that models fine-tuned on ConsistentChat achieve a 20-30% improvement in chat consistency and up to a 15% increase in task success rate, significantly outperforming models trained on existing single-turn and multi-turn instruction datasets.

The rapid evolution of generative models has unlocked new potentials in protein binder design, a pivotal task in structural biology, by facilitating end-to-end generation via joint sequence-structure modeling or hallucination. However, existing approaches are predominantly implemented under a single-target, single-state assumption, limiting their ability to model multi-target or multi-state interactions required for advanced function-oriented protein design. Here, we introduce Chamaileon, which unifies multi-target and multi-state binder design by formulating the problem as cross-context binding landscape modeling. The framework is underpinned by a training paradigm termed In-Context Complex Co-Design (I3CD) for context-aware sequence-structure co-modeling. During inference, we employ Mixture-of-Paths Sampling (MoPS), a scalable strategy that optimizes a single sequence across contexts while alleviating the scarcity of high-quality multi-conformational paired data. Extensive evaluation on our newly constructed benchmark, CROSS, demonstrates that Chamaileon effectively generates sequences adaptable to diverse conformational landscapes and multi-target requirements. The code is available on https://github.com/caohengyuan/Chamaileon.

Synthesizing SQL queries from natural language is a long-standing open problem and has been attracting considerable interest recently. Toward solving the problem, the de facto approach is to employ a sequence-to-sequence-style model. Such an approach will necessarily require the SQL queries to be serialized. Since the same SQL query may have multiple equivalent serializations, training a sequence-to-sequence-style model is sensitive to the choice from one of them. This phenomenon is documented as the "order-matters" problem. Existing state-of-the-art approaches rely on reinforcement learning to reward the decoder when it generates any of the equivalent serializations. However, we observe that the improvement from reinforcement learning is limited. In this paper, we propose a novel approach, i.e., SQLNet, to fundamentally solve this problem by avoiding the sequence-to-sequence structure when the order does not matter. In particular, we employ a sketch-based approach where the sketch contains a dependency graph so that one prediction can be done by taking into consideration only the previous predictions that it depends on. In addition, we propose a sequence-to-set model as well as the column attention mechanism to synthesize the query based on the sketch. By combining all these novel techniques, we show that SQLNet can outperform the prior art by 9% to 13% on the WikiSQL task.

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (MFE) criterion under the Turner model. In this paper, we address this gap by first introducing mathematical theorems outlining sufficient conditions for recognizing undesignable structures, then proposing efficient algorithms, guided by these theorems, to verify the undesignability of RNA structures. Through the application of these theorems and algorithms to the Eterna100 puzzles, we demonstrate the ability to efficiently establish that 15 of the puzzles indeed fall within the category of undesignable structures. In addition, we provide specific insights from the study of undesignability, in the hope that it will enable more understanding of RNA folding and RNA design.

Large language models (LLMs) have demonstrated excellent capabilities in generating structured diagrams from natural language descriptions. In particular, they have shown great promise in generating sequence diagrams for software engineering, typically represented in a text-based syntax such as Mermaid. However, systematic evaluations in this space remain underdeveloped as there is a lack of existing benchmarks to assess the LLM's correctness in this task. To address this shortcoming, we introduce MermaidSeqBench, a human-verified and LLM-synthetically-extended benchmark for assessing an LLM's capabilities in generating Mermaid sequence diagrams from textual prompts. The benchmark consists of a core set of 132 samples, starting from a small set of manually crafted and verified flows. These were expanded via a hybrid methodology combining human annotation, in-context LLM prompting, and rule-based variation generation. Our benchmark uses an LLM-as-a-judge model to assess Mermaid sequence diagram generation across fine-grained metrics, including syntax correctness, activation handling, error handling, and practical usability. We perform initial evaluations on numerous state-of-the-art LLMs and utilize multiple LLM judge models to demonstrate the effectiveness and flexibility of our benchmark. Our results reveal significant capability gaps across models and evaluation modes. Our proposed benchmark provides a foundation for advancing research in structured diagram generation and for developing more rigorous, fine-grained evaluation methodologies.

Learning to generate fluent natural language from structured data with neural networks has become an common approach for NLG. This problem can be challenging when the form of the structured data varies between examples. This paper presents a survey of several extensions to sequence-to-sequence models to account for the latent content selection process, particularly variants of copy attention and coverage decoding. We further propose a training method based on diverse ensembling to encourage models to learn distinct sentence templates during training. An empirical evaluation of these techniques shows an increase in the quality of generated text across five automated metrics, as well as human evaluation.

Given the remarkable achievements in image generation through diffusion models, the research community has shown increasing interest in extending these models to video generation. Recent diffusion models for video generation have predominantly utilized attention layers to extract temporal features. However, attention layers are limited by their memory consumption, which increases quadratically with the length of the sequence. This limitation presents significant challenges when attempting to generate longer video sequences using diffusion models. To overcome this challenge, we propose leveraging state-space models (SSMs). SSMs have recently gained attention as viable alternatives due to their linear memory consumption relative to sequence length. In the experiments, we first evaluate our SSM-based model with UCF101, a standard benchmark of video generation. In addition, to investigate the potential of SSMs for longer video generation, we perform an experiment using the MineRL Navigate dataset, varying the number of frames to 64 and 150. In these settings, our SSM-based model can considerably save memory consumption for longer sequences, while maintaining competitive FVD scores to the attention-based models. Our codes are available at https://github.com/shim0114/SSM-Meets-Video-Diffusion-Models.

The increasing size of language models raises great research interests in parameter-efficient fine-tuning such as LoRA that freezes the pre-trained model, and injects small-scale trainable parameters for multiple downstream tasks (e.g., summarization, question answering and translation). To further enhance the efficiency of fine-tuning, we propose a framework that integrates LoRA and structured layer pruning. The integrated framework is validated on two created deidentified medical report summarization datasets based on MIMIC-IV-Note and two public medical dialogue datasets. By tuning 0.6% parameters of the original model and pruning over 30% Transformer-layers, our framework can reduce 50% of GPU memory usage and speed up 100% of the training phase, while preserving over 92% generation qualities on free-text sequence-to-sequence tasks.

Direct Preference Optimization is an offline post-SFT method for aligning language models from preference pairs, with strong results in instruction following and summarization. However, DPO's sequence-level implicit reward can be brittle for token-critical structured prediction settings such as medical annotation, which often exhibit (i) low-separation preference pairs, where chosen and rejected completions differ by minimal edit distance (often 1-3 tokens), and (ii) token-importance skew, where sparse semantic tokens (hierarchical labels and evidence Spans) carry disproportionate task importance relative to high-frequency structural tokens (JSON scaffolding). In this regime, standard DPO suffers from margin collapse (insufficient log-probability separation between near-identical preferences), likelihood squeezing (the margin objective shifts the absolute likelihoods of both completions together), and gradient dilution, where uniform sequence-level weighting diffuses learning signal across shared scaffolding while rare, confusable label tokens receive weak, noisy updates. We introduce Token-Adaptive Barrier Preference Optimization (TAB-PO), which augments DPO with token-weighted, reference-adjusted advantages that prioritize high-value semantic tokens, and a conditional token-level barrier that regularizes under-confident tokens balancing SFT-anchored likelihood and preference-driven separation in low-separation, importance-skewed regimes. We evaluate TAB-PO on medical communication annotation, a task requiring joint prediction of hierarchical labels and evidence Spans from patient-provider messages. TAB-PO achieves a ~ 4% relative improvement in micro-F1 over SFT and consistently outperforms recent preference-optimization baselines.

We propose KnowGL, a tool that allows converting text into structured relational data represented as a set of ABox assertions compliant with the TBox of a given Knowledge Graph (KG), such as Wikidata. We address this problem as a sequence generation task by leveraging pre-trained sequence-to-sequence language models, e.g. BART. Given a sentence, we fine-tune such models to detect pairs of entity mentions and jointly generate a set of facts consisting of the full set of semantic annotations for a KG, such as entity labels, entity types, and their relationships. To showcase the capabilities of our tool, we build a web application consisting of a set of UI widgets that help users to navigate through the semantic data extracted from a given input text. We make the KnowGL model available at https://huggingface.co/ibm/knowgl-large.

Large pre-trained video diffusion models excel in video frame interpolation but struggle to generate high fidelity frames due to reliance on intrinsic generative priors, limiting detail preservation from start and end frames. Existing methods often depend on motion control for temporal consistency, yet dense optical flow is error-prone, and sparse points lack structural context. In this paper, we propose FC-VFI for faithful and consistent video frame interpolation, supporting \(4\times\)x and \(8\times\) interpolation, boosting frame rates from 30 FPS to 120 and 240 FPS at \(2560\times 1440\)resolution while preserving visual fidelity and motion consistency. We introduce a temporal modeling strategy on the latent sequences to inherit fidelity cues from start and end frames and leverage semantic matching lines for structure-aware motion guidance, improving motion consistency. Furthermore, we propose a temporal difference loss to mitigate temporal inconsistencies. Extensive experiments show FC-VFI achieves high performance and structural integrity across diverse scenarios.

We introduce SPAFormer, an innovative model designed to overcome the combinatorial explosion challenge in the 3D Part Assembly (3D-PA) task. This task requires accurate prediction of each part's poses in sequential steps. As the number of parts increases, the possible assembly combinations increase exponentially, leading to a combinatorial explosion that severely hinders the efficacy of 3D-PA. SPAFormer addresses this problem by leveraging weak constraints from assembly sequences, effectively reducing the solution space's complexity. Since the sequence of parts conveys construction rules similar to sentences structured through words, our model explores both parallel and autoregressive generation. We further strengthen SPAFormer through knowledge enhancement strategies that utilize the attributes of parts and their sequence information, enabling it to capture the inherent assembly pattern and relationships among sequentially ordered parts. We also construct a more challenging benchmark named PartNet-Assembly covering 21 varied categories to more comprehensively validate the effectiveness of SPAFormer. Extensive experiments demonstrate the superior generalization capabilities of SPAFormer, particularly with multi-tasking and in scenarios requiring long-horizon assembly. Code is available at https://github.com/xuboshen/SPAFormer.

Autoregressive models (ARMs), which predict subsequent tokens one-by-one ``from left to right,'' have achieved significant success across a wide range of sequence generation tasks. However, they struggle to accurately represent sequences that require satisfying sophisticated constraints or whose sequential dependencies are better addressed by out-of-order generation. Masked Diffusion Models (MDMs) address some of these limitations, but the process of unmasking multiple tokens simultaneously in MDMs can introduce incoherences, and MDMs cannot handle arbitrary infilling constraints when the number of tokens to be filled in is not known in advance. In this work, we introduce Insertion Language Models (ILMs), which learn to insert tokens at arbitrary positions in a sequence -- that is, they select jointly both the position and the vocabulary element to be inserted. By inserting tokens one at a time, ILMs can represent strong dependencies between tokens, and their ability to generate sequences in arbitrary order allows them to accurately model sequences where token dependencies do not follow a left-to-right sequential structure. To train ILMs, we propose a tailored network parameterization and use a simple denoising objective. Our empirical evaluation demonstrates that ILMs outperform both ARMs and MDMs on common planning tasks. Furthermore, we show that ILMs outperform MDMs and perform on par with ARMs in an unconditional text generation task while offering greater flexibility than MDMs in arbitrary-length text infilling.

Speculative Decoding (SD) is a technique to accelerate the inference of Large Language Models (LLMs) by using a lower complexity draft model to propose candidate tokens verified by a larger target model. To further improve efficiency, Multi-Candidate Speculative Decoding (MCSD) improves upon this by sampling multiple candidate tokens from the draft model at each step and verifying them in parallel, thus increasing the chances of accepting a token and reducing generation time. Existing MCSD methods rely on the draft model to initialize the multi-candidate sequences and use static length and tree attention structure for draft generation. However, such an approach suffers from the draft and target model's output distribution differences, especially in dynamic generation context. In this work, we introduce an improved version of MCSD that includes a target model initialized multi-candidate process, dynamic sliced topology-aware causal mask for dynamic length adjustment, and decision models to optimize early stopping. Our framework improves the acceptance rate, defined as the ratio of the longest draft sequence length accepted by the target model over the maximum draft sequence length, by a maximum of 164% and gains a maximum of 75% generation speed up over the MCSD baseline. We also conduct an ablation study to evaluate the impact of the decision model.

Tokenization is a key component of autoregressive (AR) generative models, converting raw data into more manageable units for modeling. Commonly, tokens describe local information, such as regions of pixels in images or word pieces in text, and AR generation predicts these tokens in a fixed order. A worthwhile question is whether token structures affect the ability to steer the generation through test-time search, where multiple candidate generations are explored and evaluated by a verifier. Using image generation as our testbed, we hypothesize that recent 1D ordered tokenizers with coarse-to-fine structure can be more amenable to search than classical 2D grid structures. This is rooted in the fact that the intermediate states in coarse-to-fine sequences carry semantic meaning that verifiers can reliably evaluate, enabling effective steering during generation. Through controlled experiments, we find that AR models trained on coarse-to-fine ordered tokens exhibit improved test-time scaling behavior compared to grid-based counterparts. Moreover, we demonstrate that, thanks to the ordered structure, pure test-time search over token sequences (i.e., without training an AR model) can perform training-free text-to-image generation when guided by an image-text verifier. Beyond this, we systematically study how classical search algorithms (best-of-N, beam search, lookahead search) interact with different token structures, as well as the role of different verifiers and AR priors. Our results highlight the impact of token structure on inference-time scalability and provide practical guidance for test-time scaling in AR models.

We explore using T5 (Raffel et al. (2019)) to directly translate natural language questions into SQL statements. General purpose natural language that interfaces to information stored within databases requires flexibly translating natural language questions into database queries. The best performing text-to-SQL systems approach this task by first converting questions into an intermediate logical form (LF) (Lyu et al. (2020)). While LFs provide a convenient intermediate representation and simplify query generation, they introduce an additional layer of complexity and annotation requirements. However, weakly supervised modeling that directly converts questions to SQL statements has proven more difficult without the scaffolding provided by LFs (Min et al. (2019)). We approach direct conversion of questions to SQL statements using T5 (Raffel et al. (2019)), a pre-trained textto-text generation model, modified to support pointer-generator style decoding (See et al. (2017)). We explore using question augmentation with table schema information and the use of automatically generated silver training data. The resulting model achieves 90.5% execution accuracy on the WikiSQL (Zhong et al. (2017)) test data set, a new state-of-the-art on weakly supervised SQL generation. The performance improvement is 6.6% absolute over the prior state-of-the-art (Min et al. (2019)) and approaches the performance of state-ofthe-art systems making use of LFs.

We are creating multimedia contents everyday and everywhere. While automatic content generation has played a fundamental challenge to multimedia community for decades, recent advances of deep learning have made this problem feasible. For example, the Generative Adversarial Networks (GANs) is a rewarding approach to synthesize images. Nevertheless, it is not trivial when capitalizing on GANs to generate videos. The difficulty originates from the intrinsic structure where a video is a sequence of visually coherent and semantically dependent frames. This motivates us to explore semantic and temporal coherence in designing GANs to generate videos. In this paper, we present a novel Temporal GANs conditioning on Captions, namely TGANs-C, in which the input to the generator network is a concatenation of a latent noise vector and caption embedding, and then is transformed into a frame sequence with 3D spatio-temporal convolutions. Unlike the naive discriminator which only judges pairs as fake or real, our discriminator additionally notes whether the video matches the correct caption. In particular, the discriminator network consists of three discriminators: video discriminator classifying realistic videos from generated ones and optimizes video-caption matching, frame discriminator discriminating between real and fake frames and aligning frames with the conditioning caption, and motion discriminator emphasizing the philosophy that the adjacent frames in the generated videos should be smoothly connected as in real ones. We qualitatively demonstrate the capability of our TGANs-C to generate plausible videos conditioning on the given captions on two synthetic datasets (SBMG and TBMG) and one real-world dataset (MSVD). Moreover, quantitative experiments on MSVD are performed to validate our proposal via Generative Adversarial Metric and human study.

Recent advances in diffusion-based video generation have significantly improved visual quality and short-term temporal coherence. However, existing methods still struggle to produce videos with physically consistent and causally plausible dynamics, especially in scenarios involving long-horizon interactions. This limitation arises from the fact that video diffusion models primarily learn physical consistency implicitly, while vision-language models can directly model physical laws. Based on this idea, in this work, we propose CausalMotion, a training-free framework that injects explicit physical reasoning into video generation through structured intermediate representations. Our key idea is to decouple reasoning from generation by leveraging a vision-language model to decompose a text prompt into a sequence of causally consistent keyframes and object-centric motion trajectories. These representations are then aligned and integrated as soft constraints to guide a pretrained video diffusion model during inference. This design enables explicit modeling of object dynamics and causal transitions without requiring additional training or supervision. Extensive experiments show that our method consistently improves physical plausibility and temporal coherence, particularly in dynamics-intensive scenarios, while maintaining high perceptual video quality.

A hallmark of human intelligence is the ability to create complex artifacts through structured multi-step processes. Generating procedural tutorials with AI is a longstanding but challenging goal, facing three key obstacles: (1) scarcity of multi-task procedural datasets, (2) maintaining logical continuity and visual consistency between steps, and (3) generalizing across multiple domains. To address these challenges, we propose a multi-domain dataset covering 21 tasks with over 24,000 procedural sequences. Building upon this foundation, we introduce MakeAnything, a framework based on the diffusion transformer (DIT), which leverages fine-tuning to activate the in-context capabilities of DIT for generating consistent procedural sequences. We introduce asymmetric low-rank adaptation (LoRA) for image generation, which balances generalization capabilities and task-specific performance by freezing encoder parameters while adaptively tuning decoder layers. Additionally, our ReCraft model enables image-to-process generation through spatiotemporal consistency constraints, allowing static images to be decomposed into plausible creation sequences. Extensive experiments demonstrate that MakeAnything surpasses existing methods, setting new performance benchmarks for procedural generation tasks.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

Reconstructing a structured vector-graphics representation from a rasterized floorplan image is typically an important prerequisite for computational tasks involving floorplans such as automated understanding or CAD workflows. However, existing techniques struggle in faithfully generating the structure and semantics conveyed by complex floorplans that depict large indoor spaces with many rooms and a varying numbers of polygon corners. To this end, we propose Raster2Seq, framing floorplan reconstruction as a sequence-to-sequence task in which floorplan elements--such as rooms, windows, and doors--are represented as labeled polygon sequences that jointly encode geometry and semantics. Our approach introduces an autoregressive decoder that learns to predict the next corner conditioned on image features and previously generated corners using guidance from learnable anchors. These anchors represent spatial coordinates in image space, hence allowing for effectively directing the attention mechanism to focus on informative image regions. By embracing the autoregressive mechanism, our method offers flexibility in the output format, enabling for efficiently handling complex floorplans with numerous rooms and diverse polygon structures. Our method achieves state-of-the-art performance on standard benchmarks such as Structure3D, CubiCasa5K, and Raster2Graph, while also demonstrating strong generalization to more challenging datasets like WAFFLE, which contain diverse room structures and complex geometric variations.

Part-aware 3D object generation is essential for graphics applications such as controllable modeling, editing, and articulation, where objects are represented as coherent assemblies of semantic parts. However, existing part-aware generation methods, do not scale well to highly complex objects. As the number of parts increases, generating detailed geometry becomes prohibitively expensive in token length and memory. We introduce MegaParts, a scalable autoregressive 3D generation framework to address this challenge by combining structured sequence modeling with a token-efficient vector-quantized shape tokenizer. Our tokenizer learns discrete latent representations for part-level geometry by minimizing token usage subject to high-fidelity reconstruction, enabling adaptive-length tokenization based on geometric complexity. On top of this compact representation, we train a large language model to generate object bounding boxes, part bounding boxes, and part shape tokens within a unified structured sequence. Combined with efficient long-context training strategy, our token-efficient formulation scales to objects with up to 300 parts and sequence lengths up to 256k tokens. This substantially extends the scale of part-aware 3D generation while preserving compositional structure and enabling fine-grained part-level control. Our method achieves higher mesh quality than baseline autoregressive and diffusion models, showing that compressed discrete part tokens improve not only scalability but also the achievable fidelity of generated geometry. These results suggest that LLM native token-efficient autoregressive modeling is a compelling alternative to diffusion for large-scale part-aware 3D generation. The project page is available at https://expmaster.github.io/megaparts_webpage.

In this paper we propose a novel model for unconditional audio generation based on generating one audio sample at a time. We show that our model, which profits from combining memory-less modules, namely autoregressive multilayer perceptrons, and stateful recurrent neural networks in a hierarchical structure is able to capture underlying sources of variations in the temporal sequences over very long time spans, on three datasets of different nature. Human evaluation on the generated samples indicate that our model is preferred over competing models. We also show how each component of the model contributes to the exhibited performance.

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

We propose a novel approach to image generation by decomposing an image into a structured sequence, where each element in the sequence shares the same spatial resolution but differs in the number of unique tokens used, capturing different level of visual granularity. Image generation is carried out through our newly introduced Next Visual Granularity (NVG) generation framework, which generates a visual granularity sequence beginning from an empty image and progressively refines it, from global layout to fine details, in a structured manner. This iterative process encodes a hierarchical, layered representation that offers fine-grained control over the generation process across multiple granularity levels. We train a series of NVG models for class-conditional image generation on the ImageNet dataset and observe clear scaling behavior. Compared to the VAR series, NVG consistently outperforms it in terms of FID scores (3.30 -> 3.03, 2.57 ->2.44, 2.09 -> 2.06). We also conduct extensive analysis to showcase the capability and potential of the NVG framework. Our code and models will be released.

Articulated 3D object generation is fundamental for creating realistic, functional, and interactable virtual assets which are not simply static. We introduce MeshArt, a hierarchical transformer-based approach to generate articulated 3D meshes with clean, compact geometry, reminiscent of human-crafted 3D models. We approach articulated mesh generation in a part-by-part fashion across two stages. First, we generate a high-level articulation-aware object structure; then, based on this structural information, we synthesize each part's mesh faces. Key to our approach is modeling both articulation structures and part meshes as sequences of quantized triangle embeddings, leading to a unified hierarchical framework with transformers for autoregressive generation. Object part structures are first generated as their bounding primitives and articulation modes; a second transformer, guided by these articulation structures, then generates each part's mesh triangles. To ensure coherency among generated parts, we introduce structure-guided conditioning that also incorporates local part mesh connectivity. MeshArt shows significant improvements over state of the art, with 57.1% improvement in structure coverage and a 209-point improvement in mesh generation FID.

Generative visual models fundamentally struggle with precise spatial control. This arises from a core disconnect: models can process textual descriptions of space but cannot directly map numerical coordinates onto the 2D image canvas. We introduce MetaPoint, a method that bridges this gap by representing a continuous 2D coordinate as a single, special token. Crucially, MetaPoint requires no new architectural components; it directly leverages the model's inherent positional encoding schemes to interpret these coordinates, treating our token as a virtual point on the canvas. This lightweight approach enables pixel-level control of an object's position with one token or its bounding box with two, all without requiring architectural changes or bespoke attention masking. The MetaPoint tokens are designed to be compositional, serving as spatial primitives. This allows a planner agent to decompose a high-level user request into a structured sequence of primitives for the generator. By providing a simple, precise, and scalable building block for spatial control, MetaPoint unlocks more powerful compositional generative agents and enables intuitive, interactive editing systems.

Current video generation models excel at generating short clips but still struggle with creating multi-shot, movie-like videos. Existing models trained on large-scale data on the back of rich computational resources are unsurprisingly inadequate for maintaining a logical storyline and visual consistency across multiple shots of a cohesive script since they are often trained with a single-shot objective. To this end, we propose VideoGen-of-Thought (VGoT), a collaborative and training-free architecture designed specifically for multi-shot video generation. VGoT is designed with three goals in mind as follows. Multi-Shot Video Generation: We divide the video generation process into a structured, modular sequence, including (1) Script Generation, which translates a curt story into detailed prompts for each shot; (2) Keyframe Generation, responsible for creating visually consistent keyframes faithful to character portrayals; and (3) Shot-Level Video Generation, which transforms information from scripts and keyframes into shots; (4) Smoothing Mechanism that ensures a consistent multi-shot output. Reasonable Narrative Design: Inspired by cinematic scriptwriting, our prompt generation approach spans five key domains, ensuring logical consistency, character development, and narrative flow across the entire video. Cross-Shot Consistency: We ensure temporal and identity consistency by leveraging identity-preserving (IP) embeddings across shots, which are automatically created from the narrative. Additionally, we incorporate a cross-shot smoothing mechanism, which integrates a reset boundary that effectively combines latent features from adjacent shots, resulting in smooth transitions and maintaining visual coherence throughout the video. Our experiments demonstrate that VGoT surpasses existing video generation methods in producing high-quality, coherent, multi-shot videos.

Recently, there is a growing interest in creating computer-aided design (CAD) models based on user intent, known as controllable CAD generation. Existing work offers limited controllability and needs separate models for different types of control, reducing efficiency and practicality. To achieve controllable generation across all CAD construction hierarchies, such as sketch-extrusion, extrusion, sketch, face, loop and curve, we propose FlexCAD, a unified model by fine-tuning large language models (LLMs). First, to enhance comprehension by LLMs, we represent a CAD model as a structured text by abstracting each hierarchy as a sequence of text tokens. Second, to address various controllable generation tasks in a unified model, we introduce a hierarchy-aware masking strategy. Specifically, during training, we mask a hierarchy-aware field in the CAD text with a mask token. This field, composed of a sequence of tokens, can be set flexibly to represent various hierarchies. Subsequently, we ask LLMs to predict this masked field. During inference, the user intent is converted into a CAD text with a mask token replacing the part the user wants to modify, which is then fed into FlexCAD to generate new CAD models. Comprehensive experiments on public dataset demonstrate the effectiveness of FlexCAD in both generation quality and controllability. Code will be available at https://github.com/microsoft/FlexCAD.

Modern large language models (LLMs) are inherently auto-regressive, requiring input to be serialized into flat sequences regardless of their structural dependencies. This serialization hinders the model's ability to leverage structural inductive biases, especially in tasks such as retrieval-augmented generation (RAG) and reasoning on data with native graph structures, where inter-segment dependencies are crucial. We introduce Graph-KV with the potential to overcome this limitation. Graph-KV leverages the KV-cache of text segments as condensed representations and governs their interaction through structural inductive biases. In this framework, 'target' segments selectively attend only to the KV-caches of their designated 'source' segments, rather than all preceding segments in a serialized sequence. This approach induces a graph-structured block mask, sparsifying attention and enabling a message-passing-like step within the LLM. Furthermore, strategically allocated positional encodings for source and target segments reduce positional bias and context window consumption. We evaluate Graph-KV across three scenarios: (1) seven RAG benchmarks spanning direct inference, multi-hop reasoning, and long-document understanding; (2) Arxiv-QA, a novel academic paper QA task with full-text scientific papers structured as citation ego-graphs; and (3) paper topic classification within a citation network. By effectively reducing positional bias and harnessing structural inductive biases, Graph-KV substantially outperforms baselines, including standard costly sequential encoding, across various settings. Code and the Graph-KV data are publicly available.

Efficient key-value (KV) cache compression is critical for scaling transformer-based Large Language Models (LLMs) in long sequences and resource-limited settings. Existing methods evict tokens based on their positions or importance scores, but position-based strategies can miss crucial information outside predefined regions, while those relying on global importance scores resulting in strong regional biases, limiting the KV cache's overall context retention and potentially impairing the performance of LLMs on complex tasks. Our wavelet analysis reveals that as tokens approach the end of sequence, their contributions to generation gradually increase and tends to diverge more from neighboring tokens, indicating a smooth transition with increasing complexity and variability from distant to nearby context. Motivated by this observation, we propose TreeKV, an intuitive, training-free method that employs a tree structure for smooth cache compression. TreeKV maintains a fixed cache size, allowing LLMs to deliver high-quality output even in long text scenarios. Unlike most compression methods, TreeKV is applicable to both the generation and prefilling stages. TreeKV consistently surpasses all baseline models in language modeling tasks on PG19 and OpenWebText2, allowing LLMs trained with short context window to generalize to longer window with a 16x cache reduction. On the Longbench benchmark, TreeKV achieves the best performance with only 6\% of the budget at optimal efficiency.

Speculative decoding (SPD) aims to accelerate the auto-regressive token generation process of a target Large Language Model (LLM). Some approaches employ a draft model with multiple heads to predict a sequence of future tokens, where each head handles a token in the sequence. The target LLM verifies the predicted sequence and accepts aligned tokens, enabling efficient multi-token generation. However, existing methods assume that all tokens within a sequence are equally important, employing identical head structures and relying on a single-generation paradigm, either serial or parallel. To this end, we theoretically demonstrate that initial tokens in the draft sequence are more important than later ones. Building on this insight, we propose Gumiho, a hybrid model combining serial and parallel heads. Specifically, given the critical importance of early tokens, we employ a sophisticated Transformer architecture for the early draft heads in a serial configuration to improve accuracy. For later tokens, we utilize multiple lightweight MLP heads operating in parallel to enhance efficiency. By allocating more advanced model structures and longer running times to the early heads, Gumiho achieves improved overall performance. The experimental results demonstrate that our method outperforms existing approaches, fully validating its effectiveness.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Constructing computer-aided design (CAD) models is labor-intensive but essential for engineering and manufacturing. Recent advances in Large Language Models (LLMs) have inspired the LLM-based CAD generation by representing CAD as command sequences. But these methods struggle in practical scenarios because command sequence representation does not support entity selection (e.g. faces or edges), limiting its ability to support complex editing operations such as chamfer or fillet. Further, the discretization of a continuous variable during sketch and extrude operations may result in topological errors. To address these limitations, we present Pointer-CAD, a novel LLM-based CAD generation framework that leverages a pointer-based command sequence representation to explicitly incorporate the geometric information of B-rep models into sequential modeling. In particular, Pointer-CAD decomposes CAD model generation into steps, conditioning the generation of each subsequent step on both the textual description and the B-rep generated from previous steps. Whenever an operation requires the selection of a specific geometric entity, the LLM predicts a Pointer that selects the most feature-consistent candidate from the available set. Such a selection operation also reduces the quantization error in the command sequence-based representation. To support the training of Pointer-CAD, we develop a data annotation pipeline that produces expert-level natural language descriptions and apply it to build a dataset of approximately 575K CAD models. Extensive experimental results demonstrate that Pointer-CAD effectively supports the generation of complex geometric structures and reduces segmentation error to an extremely low level, achieving a significant improvement over prior command sequence methods, thereby significantly mitigating the topological inaccuracies introduced by quantization error.

We study series-level cinematic remaking, a long-horizon video-to-video generation problem that localizes full episodes or films via stylization or actor replacement while strictly preserving narrative structure, motion choreography, and character identity across hundreds of shots. Existing video generation and editing pipelines often break down in this regime due to compounding identity drift, background mutation, and semantic erosion under large camera motions and viewpoint changes. We propose Soap2Soap, a multi-agent framework that enforces long-term language-visual consistency through a Dual-Bridge Consistency mechanism: a scene-aware JSON screenplay serving as a persistent semantic backbone, and dynamically allocated visual reference anchors at both scene and shot levels. To suppress drift before video synthesis, we introduce batch keyframe consistency, jointly generating multiple keyframes in a shared latent context via a grid-based formulation. A closed-loop verification agent further audits identity, stability, and alignment to trigger selective regeneration. Experiments on SoapBench demonstrate strong improvements over commercial video generation APIs in long-term consistency and narrative fidelity.

A long-running goal of the clinical NLP community is the extraction of important variables trapped in clinical notes. However, roadblocks have included dataset shift from the general domain and a lack of public clinical corpora and annotations. In this work, we show that large language models, such as InstructGPT, perform well at zero- and few-shot information extraction from clinical text despite not being trained specifically for the clinical domain. Whereas text classification and generation performance have already been studied extensively in such models, here we additionally demonstrate how to leverage them to tackle a diverse set of NLP tasks which require more structured outputs, including span identification, token-level sequence classification, and relation extraction. Further, due to the dearth of available data to evaluate these systems, we introduce new datasets for benchmarking few-shot clinical information extraction based on a manual re-annotation of the CASI dataset for new tasks. On the clinical extraction tasks we studied, the GPT-3 systems significantly outperform existing zero- and few-shot baselines.

Exploration capacity shapes both inference-time performance and reinforcement learning (RL) training for large (vision-) language models, as stochastic sampling often yields redundant reasoning paths with little high-level diversity. This paper proposes Reasoning Palette, a novel latent-modulation framework that endows the model with a stochastic latent variable for strategic contextualization, guiding its internal planning prior to token generation. This latent context is inferred from the mean-pooled embedding of a question-answer pair via a variational autoencoder (VAE), where each sampled latent potentially encodes a distinct reasoning context. During inference, a sampled latent is decoded into learnable token prefixes and prepended to the input prompt, modulating the model's internal reasoning trajectory. In this way, the model performs internal sampling over reasoning strategies prior to output generation, which shapes the style and structure of the entire response sequence. A brief supervised fine-tuning (SFT) warm-up phase allows the model to adapt to this latent conditioning. Within RL optimization, Reasoning Palette facilitates structured exploration by enabling on-demand injection for diverse reasoning modes, significantly enhancing exploration efficiency and sustained learning capability. Experiments across multiple reasoning benchmarks demonstrate that our method enables interpretable and controllable control over the (vision-) language model's strategic behavior, thereby achieving consistent performance gains over standard RL methods.

A significant amount of the world's knowledge is stored in relational databases. However, the ability for users to retrieve facts from a database is limited due to a lack of understanding of query languages such as SQL. We propose Seq2SQL, a deep neural network for translating natural language questions to corresponding SQL queries. Our model leverages the structure of SQL queries to significantly reduce the output space of generated queries. Moreover, we use rewards from in-the-loop query execution over the database to learn a policy to generate unordered parts of the query, which we show are less suitable for optimization via cross entropy loss. In addition, we will publish WikiSQL, a dataset of 80654 hand-annotated examples of questions and SQL queries distributed across 24241 tables from Wikipedia. This dataset is required to train our model and is an order of magnitude larger than comparable datasets. By applying policy-based reinforcement learning with a query execution environment to WikiSQL, our model Seq2SQL outperforms attentional sequence to sequence models, improving execution accuracy from 35.9% to 59.4% and logical form accuracy from 23.4% to 48.3%.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Information in industry, research, and the public sector is widely stored as rendered documents (e.g., PDF files, scans). Hence, to enable downstream tasks, systems are needed that map rendered documents onto a structured hierarchical format. However, existing systems for this task are limited by heuristics and are not end-to-end trainable. In this work, we introduce the Document Structure Generator (DSG), a novel system for document parsing that is fully end-to-end trainable. DSG combines a deep neural network for parsing (i) entities in documents (e.g., figures, text blocks, headers, etc.) and (ii) relations that capture the sequence and nested structure between entities. Unlike existing systems that rely on heuristics, our DSG is trained end-to-end, making it effective and flexible for real-world applications. We further contribute a new, large-scale dataset called E-Periodica comprising real-world magazines with complex document structures for evaluation. Our results demonstrate that our DSG outperforms commercial OCR tools and, on top of that, achieves state-of-the-art performance. To the best of our knowledge, our DSG system is the first end-to-end trainable system for hierarchical document parsing.

Video-to-audio (V2A) generation leverages visual-only video features to render plausible sounds that match the scene. Importantly, the generated sound onsets should match the visual actions that are aligned with them, otherwise unnatural synchronization artifacts arise. Recent works have explored the progression of conditioning sound generators on still images and then video features, focusing on quality and semantic matching while ignoring synchronization, or by sacrificing some amount of quality to focus on improving synchronization only. In this work, we propose a V2A generative model, named MaskVAT, that interconnects a full-band high-quality general audio codec with a sequence-to-sequence masked generative model. This combination allows modeling both high audio quality, semantic matching, and temporal synchronicity at the same time. Our results show that, by combining a high-quality codec with the proper pre-trained audio-visual features and a sequence-to-sequence parallel structure, we are able to yield highly synchronized results on one hand, whilst being competitive with the state of the art of non-codec generative audio models. Sample videos and generated audios are available at https://maskvat.github.io .

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

High-resolution video generation faces a coupled bottleneck of optimization instability and prohibitive computational costs. The massive expansion of the token sequence not only biases optimization toward local textures at the expense of global coherence, leading to structural collapse, but also imposes prohibitive training costs and severe inference latency. To address this, we propose PixelWizard, a framework that hierarchically decouples global structure modeling from fine-grained detail synthesis. PixelWizard first establishes a compact spatiotemporal anchor to concentrate dense structural priors, which then guides fine-grained generation at high resolution. This mitigates the local optimization bias to ensure structural stability without compromising high-frequency details. Leveraging this structural stability, we introduce Noise-Span Aligned Shortcut Training to break the inference bottleneck. By explicitly modeling the step size, this mechanism allows the model to traverse the generation trajectory with large steps. Crucially, we incorporate Exponential Index-Biased Sampling and Adaptive Noise-Span Calibration to align optimization with the shifted noise schedules of high-resolution grids, ensuring robust few-step inference without incurring the heavy overhead of distillation. Extensive experiments demonstrate that PixelWizard achieves superior visual quality while accelerating the generative sampling of native 2K/4K videos by over 10x.

Video Diffusion Models (VDMs) have emerged as powerful generative tools, capable of synthesizing high-quality spatiotemporal content. Yet, their potential goes far beyond mere video generation. We argue that the training dynamics of VDMs, driven by the need to model coherent sequences, naturally pushes them to internalize structured representations and an implicit understanding of the visual world. To probe the extent of this internal knowledge, we introduce a few-shot fine-tuning framework that repurposes VDMs for new tasks using only a handful of examples. Our method transforms each task into a visual transition, enabling the training of LoRA weights on short input-output sequences without altering the generative interface of a frozen VDM. Despite minimal supervision, the model exhibits strong generalization across diverse tasks, from low-level vision (for example, segmentation and pose estimation) to high-level reasoning (for example, on ARC-AGI). These results reframe VDMs as more than generative engines. They are adaptable visual learners with the potential to serve as the backbone for future foundation models in vision.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

In this work, we present HieraTok, a novel multi-scale Vision Transformer (ViT)-based tokenizer that overcomes the inherent limitation of modeling single-scale representations. This is realized through two key designs: (1) multi-scale downsampling applied to the token map generated by the tokenizer encoder, producing a sequence of multi-scale tokens, and (2) a scale-causal attention mechanism that enables the progressive flow of information from low-resolution global semantic features to high-resolution structural details. Coupling these designs, HieraTok achieves significant improvements in both image reconstruction and generation tasks. Under identical settings, the multi-scale visual tokenizer outperforms its single-scale counterpart by a 27.2\% improvement in rFID (1.47 rightarrow 1.07). When integrated into downstream generation frameworks, it achieves a 1.38times faster convergence rate and an 18.9\% boost in gFID (16.4 rightarrow 13.3), which may be attributed to the smoother and more uniformly distributed latent space. Furthermore, by scaling up the tokenizer's training, we demonstrate its potential by a sota rFID of 0.45 and a gFID of 1.82 among ViT tokenizers. To the best of our knowledge, we are the first to introduce multi-scale ViT-based tokenizer in image reconstruction and image generation. We hope our findings and designs advance the ViT-based tokenizers in visual generation tasks.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

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

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.

Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring alignment between generated drugs and their pharmacological properties, remains a critical challenge. To address these challenges, we propose MolChord, which integrates two key techniques: (1) to align protein and molecule structures with their textual descriptions and sequential representations (e.g., FASTA for proteins and SMILES for molecules), we leverage NatureLM, an autoregressive model unifying text, small molecules, and proteins, as the molecule generator, alongside a diffusion-based structure encoder; and (2) to guide molecules toward desired properties, we curate a property-aware dataset by integrating preference data and refine the alignment process using Direct Preference Optimization (DPO). Experimental results on CrossDocked2020 demonstrate that our approach achieves state-of-the-art performance on key evaluation metrics, highlighting its potential as a practical tool for SBDD.

RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural constraints, known as the inverse folding problem. Computational approaches have emerged to address this problem based on secondary structures. However, designing RNA sequences directly from 3D structures is still challenging, due to the scarcity of data, the non-unique structure-sequence mapping, and the flexibility of RNA conformation. In this study, we propose RiboDiffusion, a generative diffusion model for RNA inverse folding that can learn the conditional distribution of RNA sequences given 3D backbone structures. Our model consists of a graph neural network-based structure module and a Transformer-based sequence module, which iteratively transforms random sequences into desired sequences. By tuning the sampling weight, our model allows for a trade-off between sequence recovery and diversity to explore more candidates. We split test sets based on RNA clustering with different cut-offs for sequence or structure similarity. Our model outperforms baselines in sequence recovery, with an average relative improvement of 11% for sequence similarity splits and 16% for structure similarity splits. Moreover, RiboDiffusion performs consistently well across various RNA length categories and RNA types. We also apply in-silico folding to validate whether the generated sequences can fold into the given 3D RNA backbones. Our method could be a powerful tool for RNA design that explores the vast sequence space and finds novel solutions to 3D structural constraints.

Generative Recommenders (GRs), exemplified by the Hierarchical Sequential Transduction Unit (HSTU), have emerged as a powerful paradigm for modeling long user interaction sequences. However, we observe that their "flat-sequence" assumption overlooks the rich, intrinsic structure of user behavior. This leads to two key limitations: a failure to capture the temporal hierarchy of session-based engagement, and computational inefficiency, as dense attention introduces significant noise that obscures true preference signals within semantically sparse histories, which deteriorates the quality of the learned representations. To this end, we propose a novel framework named HPGR (Hierarchical and Preference-aware Generative Recommender), built upon a two-stage paradigm that injects these crucial structural priors into the model to handle the drawback. Specifically, HPGR comprises two synergistic stages. First, a structure-aware pre-training stage employs a session-based Masked Item Modeling (MIM) objective to learn a hierarchically-informed and semantically rich item representation space. Second, a preference-aware fine-tuning stage leverages these powerful representations to implement a Preference-Guided Sparse Attention mechanism, which dynamically constrains computation to only the most relevant historical items, enhancing both efficiency and signal-to-noise ratio. Empirical experiments on a large-scale proprietary industrial dataset from APPGallery and an online A/B test verify that HPGR achieves state-of-the-art performance over multiple strong baselines, including HSTU and MTGR.

This paper shows how Long Short-term Memory recurrent neural networks can be used to generate complex sequences with long-range structure, simply by predicting one data point at a time. The approach is demonstrated for text (where the data are discrete) and online handwriting (where the data are real-valued). It is then extended to handwriting synthesis by allowing the network to condition its predictions on a text sequence. The resulting system is able to generate highly realistic cursive handwriting in a wide variety of styles.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

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

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

Recent multimodal large language models have achieved strong performance in unified text and image understanding and generation, yet extending such native capability to 3D remains challenging due to limited data. Compared to abundant 2D imagery, high-quality 3D assets are scarce, making 3D synthesis under-constrained. Existing methods often rely on indirect pipelines that edit in 2D and lift results into 3D via optimization, sacrificing geometric consistency. We present Omni123, a 3D-native foundation model that unifies text-to-2D and text-to-3D generation within a single autoregressive framework. Our key insight is that cross-modal consistency between images and 3D can serve as an implicit structural constraint. By representing text, images, and 3D as discrete tokens in a shared sequence space, the model leverages abundant 2D data as a geometric prior to improve 3D representations. We introduce an interleaved X-to-X training paradigm that coordinates diverse cross-modal tasks over heterogeneous paired datasets without requiring fully aligned text-image-3D triplets. By traversing semantic-visual-geometric cycles (e.g., text to image to 3D to image) within autoregressive sequences, the model jointly enforces semantic alignment, appearance fidelity, and multi-view geometric consistency. Experiments show that Omni123 significantly improves text-guided 3D generation and editing, demonstrating a scalable path toward multimodal 3D world models.

Spatial perception and reasoning from visual observations require recovering geometric structure, establishing correspondences, and understanding spatial relations. Existing approaches typically address these capabilities separately using task-specific architectures or external geometric modules, limiting knowledge transfer among complementary representations of the same physical scene. We introduce SPARGen, a unified multimodal framework that casts 3D reconstruction, dense correspondence, and spatial reasoning as instruction-conditioned generation tasks. SPARGen serializes compact structured and linguistic outputs as token sequences while generating dense geometric fields in image-aligned forms, enabling spatial supervision to jointly shape shared representations within a native multimodal generative model. Experiments across benchmarks for 3D reconstruction, correspondence, and spatial reasoning show that SPARGen achieves competitive performance across heterogeneous spatial tasks within a single native multimodal generative framework.

Spider silks are remarkable materials characterized by superb mechanical properties such as strength, extensibility and lightweightedness. Yet, to date, limited models are available to fully explore sequence-property relationships for analysis and design. Here we propose a custom generative large-language model to enable design of novel spider silk protein sequences to meet complex combinations of target mechanical properties. The model, pretrained on a large set of protein sequences, is fine-tuned on ~1,000 major ampullate spidroin (MaSp) sequences for which associated fiber-level mechanical properties exist, to yield an end-to-end forward and inverse generative strategy. Performance is assessed through: (1), a novelty analysis and protein type classification for generated spidroin sequences through BLAST searches, (2) property evaluation and comparison with similar sequences, (3) comparison of molecular structures, as well as, and (4) a detailed sequence motif analyses. We generate silk sequences with property combinations that do not exist in nature, and develop a deep understanding the mechanistic roles of sequence patterns in achieving overarching key mechanical properties (elastic modulus, strength, toughness, failure strain). The model provides an efficient approach to expand the silkome dataset, facilitating further sequence-structure analyses of silks, and establishes a foundation for synthetic silk design and optimization.

The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repetitive regions of the proteins that constitute the fiber, the major ampullate spidroins (MaSps). However, establishing correlations between mechanical characteristics and repeat sequences is challenging due to the intricate sequence-structure-function relationships of MaSps and the limited availability of annotated datasets. In this study, we present a novel computational framework for designing MaSp repeat sequences with customizable mechanical properties. To achieve this, we developed a lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein language model. The distilled model was subjected to multilevel fine-tuning using curated subsets of the Spider Silkome dataset. Specifically, we adapt the model for MaSp repeat generation using 6,000 MaSp repeat sequences and further refine it with 572 repeats associated with experimentally determined fiber-level mechanical properties. Our model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties while also predicting those properties for given sequences. Validation includes sequence-level analysis, assessing physicochemical attributes and expected distribution of key motifs as well as secondary structure compositions. A correlation study using BLAST on the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the rational design of spider silk-inspired biomaterials, offering a versatile tool for engineering protein sequences with tailored mechanical attributes.

Autoregressive transformers have revolutionized high-fidelity image generation. One crucial ingredient lies in the tokenizer, which compresses high-resolution image patches into manageable discrete tokens with a scanning or hierarchical order suitable for large language models. Extending these tokenizers to 3D generation, however, presents a significant challenge: unlike image patches that naturally exhibit spatial sequence and multi-scale relationships, 3D data lacks an inherent order, making it difficult to compress into fewer tokens while preserving structural details. To address this, we introduce the Variational Tokenizer (VAT), which transforms unordered 3D data into compact latent tokens with an implicit hierarchy, suited for efficient and high-fidelity coarse-to-fine autoregressive modeling. VAT begins with an in-context transformer, which compress numerous unordered 3D features into a reduced token set with minimal information loss. This latent space is then mapped to a Gaussian distribution for residual quantization, with token counts progressively increasing across scales. In this way, tokens at different scales naturally establish the interconnections by allocating themselves into different subspaces within the same Gaussian distribution, facilitating discrete modeling of token relationships across scales. During the decoding phase, a high-resolution triplane is utilized to convert these compact latent tokens into detailed 3D shapes. Extensive experiments demonstrate that VAT enables scalable and efficient 3D generation, outperforming existing methods in quality, efficiency, and generalization. Remarkably, VAT achieves up to a 250x compression, reducing a 1MB mesh to just 3.9KB with a 96% F-score, and can further compress to 256 int8 tokens, achieving a 2000x reduction while maintaining a 92% F-score.

We present HOI-PAGE, a new approach that prioritizes part-level affordance reasoning to generate high-fidelity 4D human-object interactions (HOIs) from text prompts in a zero-shot fashion. In contrast to prior works that focus on global, whole body-object motion synthesis, our approach explicitly reasons about the underlying part-level mechanics of interactions using large language models (LLMs). We capture this reasoning in a structured part affordance graph (PAG) representation, serving as a high-level interaction scaffolding to guide a three-stage synthesis: first, decomposing input 3D objects into semantic parts; then, generating reference HOI videos from text prompts to extract part-based motion constraints; and finally, optimizing for 4D HOI motion sequences that mimic the reference dynamics while satisfying part-level contact constraints. Extensive experiments show that our approach is flexible and capable of generating complex multi-object or multi-person interaction sequences, with significantly improved realism and text alignment for zero-shot 4D HOI generation.

Recently, Large Language Models (LLMs) have achieved significant success, prompting increased interest in expanding their generative capabilities beyond general text into domain-specific areas. This study investigates the generation of parametric sequences for computer-aided design (CAD) models using LLMs. This endeavor represents an initial step towards creating parametric 3D shapes with LLMs, as CAD model parameters directly correlate with shapes in three-dimensional space. Despite the formidable generative capacities of LLMs, this task remains challenging, as these models neither encounter parametric sequences during their pretraining phase nor possess direct awareness of 3D structures. To address this, we present CAD-Llama, a framework designed to enhance pretrained LLMs for generating parametric 3D CAD models. Specifically, we develop a hierarchical annotation pipeline and a code-like format to translate parametric 3D CAD command sequences into Structured Parametric CAD Code (SPCC), incorporating hierarchical semantic descriptions. Furthermore, we propose an adaptive pretraining approach utilizing SPCC, followed by an instruction tuning process aligned with CAD-specific guidelines. This methodology aims to equip LLMs with the spatial knowledge inherent in parametric sequences. Experimental results demonstrate that our framework significantly outperforms prior autoregressive methods and existing LLM baselines.

Recent advances in large language models (LLMs) have demonstrated significant potential in hardware design automation, particularly in using natural language to synthesize Register-Transfer Level (RTL) code. Despite this progress, a gap remains between model capability and the demands of real-world RTL design, including syntax errors, functional hallucinations, and weak alignment to designer intent. Reinforcement Learning with Verifiable Rewards (RLVR) offers a promising approach to bridge this gap, as hardware provides executable and formally checkable signals that can be used to further align model outputs with design intent. However, in long, structured RTL code sequences, not all tokens contribute equally to functional correctness, and naïvely spreading gradients across all tokens dilutes learning signals. A key insight from our entropy analysis in RTL generation is that only a small fraction of tokens (e.g., always, if, assign, posedge) exhibit high uncertainty and largely influence control flow and module structure. To address these challenges, we present EARL, an Entropy-Aware Reinforcement Learning framework for Verilog generation. EARL performs policy optimization using verifiable reward signals and introduces entropy-guided selective updates that gate policy gradients to high-entropy tokens. This approach preserves training stability and concentrates gradient updates on functionally important regions of code. Our experiments on VerilogEval and RTLLM show that EARL improves functional pass rates over prior LLM baselines by up to 14.7%, while reducing unnecessary updates and improving training stability. These results indicate that focusing RL on critical, high-uncertainty tokens enables more reliable and targeted policy improvement for structured RTL code generation.

The development of powerful natural language models have increased the ability to learn meaningful representations of protein sequences. In addition, advances in high-throughput mutagenesis, directed evolution, and next-generation sequencing have allowed for the accumulation of large amounts of labeled fitness data. Leveraging these two trends, we introduce Regularized Latent Space Optimization (ReLSO), a deep transformer-based autoencoder which features a highly structured latent space that is trained to jointly generate sequences as well as predict fitness. Through regularized prediction heads, ReLSO introduces a powerful protein sequence encoder and novel approach for efficient fitness landscape traversal. Using ReLSO, we explicitly model the sequence-function landscape of large labeled datasets and generate new molecules by optimizing within the latent space using gradient-based methods. We evaluate this approach on several publicly-available protein datasets, including variant sets of anti-ranibizumab and GFP. We observe a greater sequence optimization efficiency (increase in fitness per optimization step) by ReLSO compared to other approaches, where ReLSO more robustly generates high-fitness sequences. Furthermore, the attention-based relationships learned by the jointly-trained ReLSO models provides a potential avenue towards sequence-level fitness attribution information.

In this paper, we present JADE, a targeted linguistic fuzzing platform which strengthens the linguistic complexity of seed questions to simultaneously and consistently break a wide range of widely-used LLMs categorized in three groups: eight open-sourced Chinese, six commercial Chinese and four commercial English LLMs. JADE generates three safety benchmarks for the three groups of LLMs, which contain unsafe questions that are highly threatening: the questions simultaneously trigger harmful generation of multiple LLMs, with an average unsafe generation ratio of 70% (please see the table below), while are still natural questions, fluent and preserving the core unsafe semantics. We release the benchmark demos generated for commercial English LLMs and open-sourced English LLMs in the following link: https://github.com/whitzard-ai/jade-db. For readers who are interested in evaluating on more questions generated by JADE, please contact us. JADE is based on Noam Chomsky's seminal theory of transformational-generative grammar. Given a seed question with unsafe intention, JADE invokes a sequence of generative and transformational rules to increment the complexity of the syntactic structure of the original question, until the safety guardrail is broken. Our key insight is: Due to the complexity of human language, most of the current best LLMs can hardly recognize the invariant evil from the infinite number of different syntactic structures which form an unbound example space that can never be fully covered. Technically, the generative/transformative rules are constructed by native speakers of the languages, and, once developed, can be used to automatically grow and transform the parse tree of a given question, until the guardrail is broken. For more evaluation results and demo, please check our website: https://whitzard-ai.github.io/jade.html.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance. Code is released at https://github.com/bytedance/dplm.

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

Sequential dependencies present a fundamental bottleneck in deploying large-scale autoregressive models, particularly for real-time applications. While traditional optimization approaches like pruning and quantization often compromise model quality, recent advances in generation-refinement frameworks demonstrate that this trade-off can be significantly mitigated. This survey presents a comprehensive taxonomy of generation-refinement frameworks, analyzing methods across autoregressive sequence tasks. We categorize methods based on their generation strategies (from simple n-gram prediction to sophisticated draft models) and refinement mechanisms (including single-pass verification and iterative approaches). Through systematic analysis of both algorithmic innovations and system-level implementations, we examine deployment strategies across computing environments and explore applications spanning text, images, and speech generation. This systematic examination of both theoretical frameworks and practical implementations provides a foundation for future research in efficient autoregressive decoding.

We present significant extensions to diffusion-based sequence generation models, blurring the line with autoregressive language models. We introduce hyperschedules, which assign distinct noise schedules to individual token positions, generalizing both autoregressive models (e.g., GPT) and conventional diffusion models (e.g., SEDD, MDLM) as special cases. Second, we propose two hybrid token-wise noising processes that interpolate between absorbing and uniform processes, enabling the model to fix past mistakes, and we introduce a novel inference algorithm that leverages this new feature in a simplified context inspired from MDLM. To support efficient training and inference, we design attention masks compatible with KV-caching. Our methods achieve state-of-the-art perplexity and generate diverse, high-quality sequences across standard benchmarks, suggesting a promising path for autoregressive diffusion-based sequence generation.

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pairs, impairing generative model performance. We leverage ProteinMPNN, whose sequences are experimentally favorable as well as amenable to folding, together with structure prediction models to align high-quality synthetic structures with recoverable synthetic sequences. In that way, we create a new dataset designed specifically for training expressive, fully atomistic protein generators. By retraining La-Proteina, which models discrete residue type and side chain structure in a continuous latent space, on this dataset, we achieve new state-of-the-art results, with improvements of +54% in structural diversity and +27% in co-designability. To validate the broad utility of our approach, we further introduce Proteina Atomistica, a unified flow-based framework that jointly learns the distribution of protein backbone structure, discrete sequences, and atomistic side chains without latent variables. We again find that training on our new sequence-structure data dramatically boosts benchmark performance, improving \method's structural diversity by +73% and co-designability by +5%. Our work highlights the critical importance of aligned sequence-structure data for training high-performance de novo protein design models. Our new dataset https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/resources/proteina-atomistica_data/files?version=release , the Consistency Distilled Synthetic Protein Database, is made available as an open-source resource.

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

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

Modern recurrent architectures, such as xLSTM and Mamba, have recently challenged the Transformer in language modeling. However, their structure constrains their applicability to sequences only or requires processing multi-dimensional data structures, such as images or molecular graphs, in a pre-defined sequential order. In contrast, Multi-Dimensional RNNs (MDRNNs) are well suited for data with a higher level structure, like 2D grids, trees, and directed acyclic graphs (DAGs). In this work, we extend the notion of multi-dimensionality to linear RNNs. We introduce parallelizable Linear Source Transition Mark networks (pLSTMs) using Source, Transition, and Mark gates that act on the line graph of a general DAG. This enables parallelization in analogy to parallel associative scans and the chunkwise-recurrent form of sequential linear RNNs, but for DAGs. For regular grids (1D and 2D), like images, this scheme can be efficiently implemented using einsum operations, concatenations, and padding in logarithmic time. pLSTMs tackle the vanishing/exploding activation/gradient problem for long distances in DAGs via two distinct modes: a directed propagation mode (P-mode) and a diffusive distribution mode (D-mode). To showcase the long-range capabilities of pLSTM, we introduce arrow-pointing extrapolation as a synthetic computer vision task that contains long-distance directional information. We demonstrate that pLSTMs generalize well to larger image sizes, whereas Transformers struggle to extrapolate. On established molecular graph and computer vision benchmarks, pLSTMs also show strong performance. Code and Datasets are available at: https://github.com/ml-jku/plstm_experiments.

In text-to-SQL task, seq-to-seq models often lead to sub-optimal performance due to limitations in their architecture. In this paper, we present a simple yet effective approach that adapts transformer-based seq-to-seq model to robust text-to-SQL generation. Instead of inducing constraint to decoder or reformat the task as slot-filling, we propose to train seq-to-seq model with Schema aware Denoising (SeaD), which consists of two denoising objectives that train model to either recover input or predict output from two novel erosion and shuffle noises. These denoising objectives acts as the auxiliary tasks for better modeling the structural data in S2S generation. In addition, we improve and propose a clause-sensitive execution guided (EG) decoding strategy to overcome the limitation of EG decoding for generative model. The experiments show that the proposed method improves the performance of seq-to-seq model in both schema linking and grammar correctness and establishes new state-of-the-art on WikiSQL benchmark. The results indicate that the capacity of vanilla seq-to-seq architecture for text-to-SQL may have been under-estimated.

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

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

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond conventional function annotation. We propose TriProRep, a structure-aware pretraining method that jointly models three aligned residue-level views: amino-acid identity, backbone geometry, and local full-atom geometry, discretely encoded via VQ-VAE tokenizers. By pretraining to recover original tokens from generator-corrupted views, TriProRep learns to distinguish plausible but incorrect cross-view augmentations from the original protein. We further introduce RepSP, a benchmark for evaluating protein representations in structure-predictive settings. RepSP tests three uses of representations: homodimer co-folding from apo-chain representations, residue-level prediction of homodimer-derived interaction properties, and representation-aligned monomer structure prediction. Across these tasks, TriProRep improves over sequence-only and prior structure-aware representation models, while maintaining competitive performance on conventional benchmarks.

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

We present a comprehensive evaluation of structured decoding for text-to-table generation with large language models (LLMs). While previous work has primarily focused on unconstrained generation of tables, the impact of enforcing structural constraints during generation remains underexplored. We systematically compare schema-guided (structured) decoding to standard one-shot prompting across three diverse benchmarks - E2E, Rotowire, and Livesum - using open-source LLMs of up to 32B parameters, assessing the performance of table generation approaches in resource-constrained settings. Our experiments cover a wide range of evaluation metrics at cell, row, and table levels. Results demonstrate that structured decoding significantly enhances the validity and alignment of generated tables, particularly in scenarios demanding precise numerical alignment (Rotowire), but may degrade performance in contexts involving densely packed textual information (E2E) or extensive aggregation over lengthy texts (Livesum). We further analyze the suitability of different evaluation metrics and discuss the influence of model size.

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.

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

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

Sequence modeling has demonstrated state-of-the-art performance on natural language and document understanding tasks. However, it is challenging to correctly serialize tokens in form-like documents in practice due to their variety of layout patterns. We propose FormNet, a structure-aware sequence model to mitigate the suboptimal serialization of forms. First, we design Rich Attention that leverages the spatial relationship between tokens in a form for more precise attention score calculation. Second, we construct Super-Tokens for each word by embedding representations from their neighboring tokens through graph convolutions. FormNet therefore explicitly recovers local syntactic information that may have been lost during serialization. In experiments, FormNet outperforms existing methods with a more compact model size and less pre-training data, establishing new state-of-the-art performance on CORD, FUNSD and Payment benchmarks.

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

Sequence generative models are transforming protein engineering. However, no principled framework exists for conditioning these models on auxiliary information, such as experimental data, without additional training of a generative model. Herein, we present ProteinGuide, a method for such "on-the-fly" conditioning, amenable to a broad class of protein generative models including Masked Language Models (e.g. ESM3), any-order auto-regressive models (e.g. ProteinMPNN) as well as diffusion and flow matching models (e.g. MultiFlow). ProteinGuide stems from our unifying view of these model classes under a single statistical framework. As proof of principle, we perform several in silico experiments. We first guide pre-trained generative models to design proteins with user-specified properties, such as higher stability or activity. Next, we design for optimizing two desired properties that are in tension with each other. Finally, we apply our method in the wet lab, using ProteinGuide to increase the editing activity of an adenine base editor in vivo with data from only a single pooled library of 2,000 variants. We find that a single round of ProteinGuide achieves a higher editing efficiency than was previously achieved using seven rounds of directed evolution.

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