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Oct 16

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation:Application in De Novo Peptide Sequencing

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

  • 8 authors
·
Oct 9, 2025

UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion

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.

  • 25 authors
·
Mar 9, 2025

Insertion Language Models: Sequence Generation with Arbitrary-Position Insertions

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.

  • 6 authors
·
May 8, 2025

How Many Heads Make an SSM? A Unified Framework for Attention and State Space Models

Sequence modeling has produced diverse architectures -- from classical recurrent neural networks to modern Transformers and state space models (SSMs) -- yet a unified theoretical understanding of expressivity and trainability trade-offs remains limited. We introduce a unified framework that represents a broad class of sequence maps via an input-dependent effective interaction operator W_{ij}(X), making explicit two recurring construction patterns: (i) the Unified Factorized Framework (Explicit) (attention-style mixing), in which W_{ij}(X) varies through scalar coefficients applied to shared value maps, and (ii) Structured Dynamics (Implicit) (state-space recurrences), in which W_{ij} is induced by a latent dynamical system. Using this framework, we derive three theoretical results. First, we establish the Interaction Rank Gap: models in the Unified Factorized Framework, such as single-head attention, are constrained to a low-dimensional operator span and cannot represent certain structured dynamical maps. Second, we prove an Equivalence (Head-Count) Theorem showing that, within our multi-head factorized class, representing a linear SSM whose lag operators span a k-dimensional subspace on length-n sequences requires and is achievable with H=k heads. Third, we prove a Gradient Highway Result, showing that attention layers admit inputs with distance-independent gradient paths, whereas stable linear dynamics exhibit distance-dependent gradient attenuation. Together, these results formalize a fundamental trade-off between algebraic expressivity (interaction/operator span) and long-range gradient propagation, providing theoretical grounding for modern sequence architecture design.

  • 1 authors
·
Dec 17, 2025

BERT4Rec: Sequential Recommendation with Bidirectional Encoder Representations from Transformer

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

  • 7 authors
·
Apr 14, 2019

TableSeq: Unified Generation of Structure, Content, and Layout

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.

  • 4 authors
·
Apr 16

Dual Triangle Attention: Effective Bidirectional Attention Without Positional Embeddings

Bidirectional transformers are the foundation of many sequence modeling tasks across natural, biological, and chemical language domains, but they are permutation-invariant without explicit positional embeddings. In contrast, unidirectional attention inherently encodes positional information through its triangular mask, enabling models to operate without positional embeddings altogether. Here, we introduce Dual Triangle Attention, a novel bidirectional attention mechanism that separates the query-key subspace of each attention head into two complementary triangular masks: one that attends to past-and-self positions and one that attends to future-and-self positions. This design provides bidirectional context while maintaining the causal mask's implicit positional inductive bias in both directions. Using PyTorch's flex_attention, Dual Triangle Attention is implemented as a single compiled kernel call with no additional parameters beyond standard multi-head attention. We evaluated Dual Triangle Attention across three settings: (1) a synthetic argmax position probe, (2) masked language modeling (MLM) on natural language, and (3) MLM on protein sequences. In the argmax task, both Dual Triangle Attention and causal attention learn positional information without explicit positional embeddings, whereas standard bidirectional attention cannot. In the MLM experiments, Dual Triangle Attention with Rotary Positional Embeddings (RoPE) achieved the best context extension performance and strong performance across the board. These findings suggest that Dual Triangle Attention is a viable attention mechanism for bidirectional transformers, with or without positional embeddings.

  • 2 authors
·
Apr 8

NFIG: Autoregressive Image Generation with Next-Frequency Prediction

Autoregressive models have achieved promising results in natural language processing. However, for image generation tasks, they encounter substantial challenges in effectively capturing long-range dependencies, managing computational costs, and most crucially, defining meaningful autoregressive sequences that reflect natural image hierarchies. To address these issues, we present Next-Frequency Image Generation (NFIG), a novel framework that decomposes the image generation process into multiple frequency-guided stages. Our approach first generates low-frequency components to establish global structure with fewer tokens, then progressively adds higher-frequency details, following the natural spectral hierarchy of images. This principled autoregressive sequence not only improves the quality of generated images by better capturing true causal relationships between image components, but also significantly reduces computational overhead during inference. Extensive experiments demonstrate that NFIG achieves state-of-the-art performance with fewer steps, offering a more efficient solution for image generation, with 1.25times speedup compared to VAR-d20 while achieving better performance (FID: 2.81) on the ImageNet-256 benchmark. We hope that our insight of incorporating frequency-domain knowledge to guide autoregressive sequence design will shed light on future research. We will make our code publicly available upon acceptance of the paper.

  • 6 authors
·
Mar 10, 2025

Efficiently Modeling Long Sequences with Structured State Spaces

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

  • 3 authors
·
Oct 30, 2021

Hydra: Bidirectional State Space Models Through Generalized Matrix Mixers

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

  • 4 authors
·
Jul 13, 2024

Towards Universal Sequence Representation Learning for Recommender Systems

In order to develop effective sequential recommenders, a series of sequence representation learning (SRL) methods are proposed to model historical user behaviors. Most existing SRL methods rely on explicit item IDs for developing the sequence models to better capture user preference. Though effective to some extent, these methods are difficult to be transferred to new recommendation scenarios, due to the limitation by explicitly modeling item IDs. To tackle this issue, we present a novel universal sequence representation learning approach, named UniSRec. The proposed approach utilizes the associated description text of items to learn transferable representations across different recommendation scenarios. For learning universal item representations, we design a lightweight item encoding architecture based on parametric whitening and mixture-of-experts enhanced adaptor. For learning universal sequence representations, we introduce two contrastive pre-training tasks by sampling multi-domain negatives. With the pre-trained universal sequence representation model, our approach can be effectively transferred to new recommendation domains or platforms in a parameter-efficient way, under either inductive or transductive settings. Extensive experiments conducted on real-world datasets demonstrate the effectiveness of the proposed approach. Especially, our approach also leads to a performance improvement in a cross-platform setting, showing the strong transferability of the proposed universal SRL method. The code and pre-trained model are available at: https://github.com/RUCAIBox/UniSRec.

  • 6 authors
·
Jun 12, 2022

Bidirectional Language Models Are Also Few-shot Learners

Large language models such as GPT-3 (Brown et al., 2020) can perform arbitrary tasks without undergoing fine-tuning after being prompted with only a few labeled examples. An arbitrary task can be reformulated as a natural language prompt, and a language model can be asked to generate the completion, indirectly performing the task in a paradigm known as prompt-based learning. To date, emergent prompt-based learning capabilities have mainly been demonstrated for unidirectional language models. However, bidirectional language models pre-trained on denoising objectives such as masked language modeling produce stronger learned representations for transfer learning. This motivates the possibility of prompting bidirectional models, but their pre-training objectives have made them largely incompatible with the existing prompting paradigm. We present SAP (Sequential Autoregressive Prompting), a technique that enables the prompting of bidirectional models. Utilizing the machine translation task as a case study, we prompt the bidirectional mT5 model (Xue et al., 2021) with SAP and demonstrate its few-shot and zero-shot translations outperform the few-shot translations of unidirectional models like GPT-3 and XGLM (Lin et al., 2021), despite mT5's approximately 50% fewer parameters. We further show SAP is effective on question answering and summarization. For the first time, our results demonstrate prompt-based learning is an emergent property of a broader class of language models, rather than only unidirectional models.

  • 6 authors
·
Sep 28, 2022

UniAnimate: Taming Unified Video Diffusion Models for Consistent Human Image Animation

Recent diffusion-based human image animation techniques have demonstrated impressive success in synthesizing videos that faithfully follow a given reference identity and a sequence of desired movement poses. Despite this, there are still two limitations: i) an extra reference model is required to align the identity image with the main video branch, which significantly increases the optimization burden and model parameters; ii) the generated video is usually short in time (e.g., 24 frames), hampering practical applications. To address these shortcomings, we present a UniAnimate framework to enable efficient and long-term human video generation. First, to reduce the optimization difficulty and ensure temporal coherence, we map the reference image along with the posture guidance and noise video into a common feature space by incorporating a unified video diffusion model. Second, we propose a unified noise input that supports random noised input as well as first frame conditioned input, which enhances the ability to generate long-term video. Finally, to further efficiently handle long sequences, we explore an alternative temporal modeling architecture based on state space model to replace the original computation-consuming temporal Transformer. Extensive experimental results indicate that UniAnimate achieves superior synthesis results over existing state-of-the-art counterparts in both quantitative and qualitative evaluations. Notably, UniAnimate can even generate highly consistent one-minute videos by iteratively employing the first frame conditioning strategy. Code and models will be publicly available. Project page: https://unianimate.github.io/.

  • 8 authors
·
Jun 3, 2024

UniRec: A Dual Enhancement of Uniformity and Frequency in Sequential Recommendations

Representation learning in sequential recommendation is critical for accurately modeling user interaction patterns and improving recommendation precision. However, existing approaches predominantly emphasize item-to-item transitions, often neglecting the time intervals between interactions, which are closely related to behavior pattern changes. Additionally, broader interaction attributes, such as item frequency, are frequently overlooked. We found that both sequences with more uniform time intervals and items with higher frequency yield better prediction performance. Conversely, non-uniform sequences exacerbate user interest drift and less-frequent items are difficult to model due to sparse sampling, presenting unique challenges inadequately addressed by current methods. In this paper, we propose UniRec, a novel bidirectional enhancement sequential recommendation method. UniRec leverages sequence uniformity and item frequency to enhance performance, particularly improving the representation of non-uniform sequences and less-frequent items. These two branches mutually reinforce each other, driving comprehensive performance optimization in complex sequential recommendation scenarios. Additionally, we present a multidimensional time module to further enhance adaptability. To the best of our knowledge, UniRec is the first method to utilize the characteristics of uniformity and frequency for feature augmentation. Comparing with eleven advanced models across four datasets, we demonstrate that UniRec outperforms SOTA models significantly. The code is available at https://github.com/Linxi000/UniRec.

  • 3 authors
·
Jun 26, 2024

ParaRNN: Unlocking Parallel Training of Nonlinear RNNs for Large Language Models

Recurrent Neural Networks (RNNs) laid the foundation for sequence modeling, but their intrinsic sequential nature restricts parallel computation, creating a fundamental barrier to scaling. This has led to the dominance of parallelizable architectures like Transformers and, more recently, State Space Models (SSMs). While SSMs achieve efficient parallelization through structured linear recurrences, this linearity constraint limits their expressive power and precludes modeling complex, nonlinear sequence-wise dependencies. To address this, we present ParaRNN, a framework that breaks the sequence-parallelization barrier for nonlinear RNNs. Building on prior work, we cast the sequence of nonlinear recurrence relationships as a single system of equations, which we solve in parallel using Newton's iterations combined with custom parallel reductions. Our implementation achieves speedups of up to 665x over naive sequential application, allowing training nonlinear RNNs at unprecedented scales. To showcase this, we apply ParaRNN to adaptations of LSTM and GRU architectures, successfully training models of 7B parameters that attain perplexity comparable to similarly-sized Transformers and Mamba2 architectures. To accelerate research in efficient sequence modeling, we release the ParaRNN codebase as an open-source framework for automatic training-parallelization of nonlinear RNNs, enabling researchers and practitioners to explore new nonlinear RNN models at scale.

  • 5 authors
·
Oct 24, 2025

LLM Tree Search

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.

  • 1 authors
·
Oct 24, 2024

DuoGen: Towards General Purpose Interleaved Multimodal Generation

Interleaved multimodal generation enables capabilities beyond unimodal generation models, such as step-by-step instructional guides, visual planning, and generating visual drafts for reasoning. However, the quality of existing interleaved generation models under general instructions remains limited by insufficient training data and base model capacity. We present DuoGen, a general-purpose interleaved generation framework that systematically addresses data curation, architecture design, and evaluation. On the data side, we build a large-scale, high-quality instruction-tuning dataset by combining multimodal conversations rewritten from curated raw websites, and diverse synthetic examples covering everyday scenarios. Architecturally, DuoGen leverages the strong visual understanding of a pretrained multimodal LLM and the visual generation capabilities of a diffusion transformer (DiT) pretrained on video generation, avoiding costly unimodal pretraining and enabling flexible base model selection. A two-stage decoupled strategy first instruction-tunes the MLLM, then aligns DiT with it using curated interleaved image-text sequences. Across public and newly proposed benchmarks, DuoGen outperforms prior open-source models in text quality, image fidelity, and image-context alignment, and also achieves state-of-the-art performance on text-to-image and image editing among unified generation models. Data and code will be released at https://research.nvidia.com/labs/dir/duogen/.

  • 16 authors
·
Jan 30

Diverse Beam Search: Decoding Diverse Solutions from Neural Sequence Models

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

  • 7 authors
·
Oct 7, 2016

Skywork UniPic 3.0: Unified Multi-Image Composition via Sequence Modeling

The recent surge in popularity of Nano-Banana and Seedream 4.0 underscores the community's strong interest in multi-image composition tasks. Compared to single-image editing, multi-image composition presents significantly greater challenges in terms of consistency and quality, yet existing models have not disclosed specific methodological details for achieving high-quality fusion. Through statistical analysis, we identify Human-Object Interaction (HOI) as the most sought-after category by the community. We therefore systematically analyze and implement a state-of-the-art solution for multi-image composition with a primary focus on HOI-centric tasks. We present Skywork UniPic 3.0, a unified multimodal framework that integrates single-image editing and multi-image composition. Our model supports an arbitrary (1~6) number and resolution of input images, as well as arbitrary output resolutions (within a total pixel budget of 1024x1024). To address the challenges of multi-image composition, we design a comprehensive data collection, filtering, and synthesis pipeline, achieving strong performance with only 700K high-quality training samples. Furthermore, we introduce a novel training paradigm that formulates multi-image composition as a sequence-modeling problem, transforming conditional generation into unified sequence synthesis. To accelerate inference, we integrate trajectory mapping and distribution matching into the post-training stage, enabling the model to produce high-fidelity samples in just 8 steps and achieve a 12.5x speedup over standard synthesis sampling. Skywork UniPic 3.0 achieves state-of-the-art performance on single-image editing benchmark and surpasses both Nano-Banana and Seedream 4.0 on multi-image composition benchmark, thereby validating the effectiveness of our data pipeline and training paradigm. Code, models and dataset are publicly available.

  • 14 authors
·
Jan 22

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

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

  • 5 authors
·
Dec 5, 2024

Order Matters: Sequence to sequence for sets

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

  • 3 authors
·
Nov 19, 2015

PRISM: Streaming Human Motion Generation with Per-Joint Latent Decomposition

Text-to-motion generation has advanced rapidly, yet two challenges persist. First, existing motion autoencoders compress each frame into a single monolithic latent vector, entangling trajectory and per-joint rotations in an unstructured representation that downstream generators struggle to model faithfully. Second, text-to-motion, pose-conditioned generation, and long-horizon sequential synthesis typically require separate models or task-specific mechanisms, with autoregressive approaches suffering from severe error accumulation over extended rollouts. We present PRISM, addressing each challenge with a dedicated contribution. (1) A joint-factorized motion latent space: each body joint occupies its own token, forming a structured 2D grid (time joints) compressed by a causal VAE with forward-kinematics supervision. This simple change to the latent space -- without modifying the generator -- substantially improves generation quality, revealing that latent space design has been an underestimated bottleneck. (2) Noise-free condition injection: each latent token carries its own timestep embedding, allowing conditioning frames to be injected as clean tokens (timestep0) while the remaining tokens are denoised. This unifies text-to-motion and pose-conditioned generation in a single model, and directly enables autoregressive segment chaining for streaming synthesis. Self-forcing training further suppresses drift in long rollouts. With these two components, we train a single motion generation foundation model that seamlessly handles text-to-motion, pose-conditioned generation, autoregressive sequential generation, and narrative motion composition, achieving state-of-the-art on HumanML3D, MotionHub, BABEL, and a 50-scenario user study.

  • 6 authors
·
Mar 9

Associative-State Universal Transformers: Sparse Retrieval Meets Structured Recurrence

We study whether a structured recurrent state can serve as a compact associative backbone for language modeling while still supporting exact retrieval. We introduce UniMatrix, a Universal Transformer style family that reuses a shared recurrent block across depth and augments it with hybrid state updates, a ROSA-style residual path, and token-conditioned embedding modulation. We evaluate these models on byte-level WikiText-2, synthetic associative recall, throughput profiling on Apple MPS, and a corrected benchmark for triple-token interactions. At small scale, UniMatrix-Core and UniMatrix-ROSA slightly outperform a parameter-matched Transformer on WikiText-2 while using many fewer parameters, reaching 5.084 and 5.083 bits-per-byte versus 5.124. The main negative result is equally important: on associative recall, the original UniMatrix family remains near chance while the Transformer reaches 25.4 percent, showing that compressed recurrent state alone is not enough for exact lookup. A retrieval-oriented follow-up, UniMatrix-Assoc, helps only marginally. By contrast, UniMatrix-SparsePointer, which adds sparse slot routing and direct pointer-logit fusion, reaches 75.6 percent on the original pilot recipe and 99.2 percent on a no-dropout follow-up while using 53.8 percent fewer parameters than the Transformer baseline. Ablations show that the gain comes from sufficient slot capacity and exact pointer-level output routing. Overall, structured recurrent state is promising and parameter-efficient, but strong long-range behavior still requires explicit sparse retrieval and better kernels.

  • 1 authors
·
Mar 31

SequenceMatch: Imitation Learning for Autoregressive Sequence Modelling with Backtracking

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

  • 2 authors
·
Jun 8, 2023

AutoRegressive Generation with B-rep Holistic Token Sequence Representation

Previous representation and generation approaches for the B-rep relied on graph-based representations that disentangle geometric and topological features through decoupled computational pipelines, thereby precluding the application of sequence-based generative frameworks, such as transformer architectures that have demonstrated remarkable performance. In this paper, we propose BrepARG, the first attempt to encode B-rep's geometry and topology into a holistic token sequence representation, enabling sequence-based B-rep generation with an autoregressive architecture. Specifically, BrepARG encodes B-rep into 3 types of tokens: geometry and position tokens representing geometric features, and face index tokens representing topology. Then the holistic token sequence is constructed hierarchically, starting with constructing the geometry blocks (i.e., faces and edges) using the above tokens, followed by geometry block sequencing. Finally, we assemble the holistic sequence representation for the entire B-rep. We also construct a transformer-based autoregressive model that learns the distribution over holistic token sequences via next-token prediction, using a multi-layer decoder-only architecture with causal masking. Experiments demonstrate that BrepARG achieves state-of-the-art (SOTA) performance. BrepARG validates the feasibility of representing B-rep as holistic token sequences, opening new directions for B-rep generation.

  • 6 authors
·
Mar 29

It's Raw! Audio Generation with State-Space Models

Developing architectures suitable for modeling raw audio is a challenging problem due to the high sampling rates of audio waveforms. Standard sequence modeling approaches like RNNs and CNNs have previously been tailored to fit the demands of audio, but the resultant architectures make undesirable computational tradeoffs and struggle to model waveforms effectively. We propose SaShiMi, a new multi-scale architecture for waveform modeling built around the recently introduced S4 model for long sequence modeling. We identify that S4 can be unstable during autoregressive generation, and provide a simple improvement to its parameterization by drawing connections to Hurwitz matrices. SaShiMi yields state-of-the-art performance for unconditional waveform generation in the autoregressive setting. Additionally, SaShiMi improves non-autoregressive generation performance when used as the backbone architecture for a diffusion model. Compared to prior architectures in the autoregressive generation setting, SaShiMi generates piano and speech waveforms which humans find more musical and coherent respectively, e.g. 2x better mean opinion scores than WaveNet on an unconditional speech generation task. On a music generation task, SaShiMi outperforms WaveNet on density estimation and speed at both training and inference even when using 3x fewer parameters. Code can be found at https://github.com/HazyResearch/state-spaces and samples at https://hazyresearch.stanford.edu/sashimi-examples.

  • 4 authors
·
Feb 19, 2022

InterleaveThinker: Reinforcing Agentic Interleaved Generation

Recent image generators have demonstrated impressive photorealism and instruction-following capabilities in single-image generation and editing. However, constrained by their architectures, they cannot achieve interleaved generation (text-image sequence), which has crucial applications in visual narratives, guidance, and embodied manipulation. Even the latest open-source Unified Multimodal Models (UMMs) exhibit limited performance in this regard. In this paper, we introduce InterleaveThinker, the first multi-agent pipeline designed to endow any existing image generator with interleaved generation capabilities. Specifically, we employ a planner agent to organize the image-text input sequence, instructing the image generator on the required execution at each step. Subsequently, we introduce a critic agent to evaluate the generator's outputs, identify samples that deviate from the planned instructions, and refine the instructions for regeneration. To implement this pipeline, we construct the Interleave-Planner-SFT-80k and Interleave-Critic-SFT-112k to perform a format cold-start. Then we develop Interleave-Critic-RL-13k to reinforce the step-wise instruction correction capability within a generation trajectory using GRPO. Since a single interleaved generation trajectory may involve over 25 generator calls, optimizing the entire trajectory is computationally impractical. Therefore, we propose accuracy reward and step-wise reward, allowing single-step RL to effectively guide the entire generation trajectory. The results show that InterleaveThinker improves performance across various image generators. On interleaved generation benchmarks, it achieves performance comparable to Nano Banana and GPT-5. Surprisingly, it also significantly enhances the base model on reasoning-based benchmarks; for example, on 4-step FLUX.2-klein, we observe substantial gains on WISE and RISE.

  • 7 authors
·
Jun 10 3

Data-Centric and Heterogeneity-Adaptive Sequence Parallelism for Efficient LLM Training

Extending the context length (i.e., the maximum supported sequence length) of LLMs is of paramount significance. To facilitate long context training of LLMs, sequence parallelism has emerged as an essential technique, which scatters each input sequence across multiple devices and necessitates communication to process the sequence. In essence, existing sequence parallelism methods assume homogeneous sequence lengths (i.e., all input sequences are equal in length) and therefore leverages a single, static scattering strategy for all input sequences. However, in reality, the sequence lengths in LLM training corpora exhibit substantial variability, often following a long-tail distribution, which leads to workload heterogeneity. In this paper, we show that employing a single, static strategy results in inefficiency and resource under-utilization, highlighting the need for adaptive approaches to handle the heterogeneous workloads across sequences. To address this, we propose a heterogeneity-adaptive sequence parallelism method. For each training step, our approach captures the variability in sequence lengths and assigns the optimal combination of scattering strategies based on workload characteristics. We model this problem as a linear programming optimization and design an efficient and effective solver to find the optimal solution. Furthermore, we implement our method in a high-performance system that supports adaptive parallelization in distributed LLM training. Experimental results demonstrate that our system outperforms state-of-the-art training frameworks by up to 1.98x.

  • 10 authors
·
Dec 2, 2024

ViD-GPT: Introducing GPT-style Autoregressive Generation in Video Diffusion Models

With the advance of diffusion models, today's video generation has achieved impressive quality. But generating temporal consistent long videos is still challenging. A majority of video diffusion models (VDMs) generate long videos in an autoregressive manner, i.e., generating subsequent clips conditioned on last frames of previous clip. However, existing approaches all involve bidirectional computations, which restricts the receptive context of each autoregression step, and results in the model lacking long-term dependencies. Inspired from the huge success of large language models (LLMs) and following GPT (generative pre-trained transformer), we bring causal (i.e., unidirectional) generation into VDMs, and use past frames as prompt to generate future frames. For Causal Generation, we introduce causal temporal attention into VDM, which forces each generated frame to depend on its previous frames. For Frame as Prompt, we inject the conditional frames by concatenating them with noisy frames (frames to be generated) along the temporal axis. Consequently, we present Video Diffusion GPT (ViD-GPT). Based on the two key designs, in each autoregression step, it is able to acquire long-term context from prompting frames concatenated by all previously generated frames. Additionally, we bring the kv-cache mechanism to VDMs, which eliminates the redundant computation from overlapped frames, significantly boosting the inference speed. Extensive experiments demonstrate that our ViD-GPT achieves state-of-the-art performance both quantitatively and qualitatively on long video generation. Code will be available at https://github.com/Dawn-LX/Causal-VideoGen.

  • 5 authors
·
Jun 16, 2024

Verification of the Implicit World Model in a Generative Model via Adversarial Sequences

Generative sequence models are typically trained on sample sequences from natural or formal languages. It is a crucial question whether -- or to what extent -- sample-based training is able to capture the true structure of these languages, often referred to as the ``world model''. Theoretical results indicate that we can hope for soundness at best, that is, generating valid sequences, but not necessarily all of them. However, it is still important to have practical tools that are able to verify whether a given sequence model is sound. In this study, we focus on chess, as it is a domain that provides enough complexity while having a simple rule-based world model. We propose adversarial sequence generation for verifying the soundness of the sequence model. Our adversaries generate valid sequences so as to force the sequence model to generate an invalid next move prediction. Apart from the falsification of soundness, this method is also suitable for a more fine-grained analysis of the failure modes and the effects of different choices during training. To demonstrate this, we propose a number of methods for adversarial sequence generation and evaluate the approach on a large set of chess models. We train models on random as well as high-quality chess games, using several training recipes. We find that none of the models are sound, but some training techniques and dataset choices are able to improve soundness remarkably. We also investigate the potential application of board state probes in both our training and attack methods. Our findings indicate that the extracted board states have no causal role in next token prediction in most of the models.

  • 2 authors
·
Feb 5

Free Draft-and-Verification: Toward Lossless Parallel Decoding for Diffusion Large Language Models

Diffusion Large Language Models (DLLMs) have emerged as a new paradigm of language modeling beyond autoregressive next-token prediction. Thanks to their bidirectional attention mechanism, DLLMs are more capable of capturing the connection of context, and thus show unique advantages in challenges like the famous "reversal curse" or learning under data-constrained scenarios. In addition, taking advantage of their inherent modeling foundations, DLLMs have the great potential of efficient inference with parallel decoding algorithms, which enable multi-token prediction per step. However, the high generation quality often requires the number of decoding steps equal to the sequence length, which performs a one-token-per-step decoding, and existing parallel decoding algorithms, which yield suboptimal decoding paths, bring inference speedup at the cost of non-negligible performance degradation. To overcome this challenge, we introduce Free Draft-and-Verification (FreeDave), a novel fast decoding algorithm tailored for DLLMs that achieves lossless parallel decoding without any model modification or extra modules. Specifically, we propose an algorithm of parallel-decoded candidate generation and verification, which is theoretically guaranteed to use the fewest model forward calls to reproduce the same sequence generated by static decoding when enough computation and memory budget is provided. By extensive evaluations on math reasoning and code generation benchmarks across different DLLMs, FreeDave is proven to boost the inference throughput up to 3.78times without performance degradation.

  • 2 authors
·
Sep 30, 2025

Simplifying and Understanding State Space Models with Diagonal Linear RNNs

Sequence models based on linear state spaces (SSMs) have recently emerged as a promising choice of architecture for modeling long range dependencies across various modalities. However, they invariably rely on discretization of a continuous state space, which complicates their presentation and understanding. In this work, we dispose of the discretization step, and propose a model based on vanilla Diagonal Linear RNNs (DLR). We empirically show that, despite being conceptually much simpler, DLR is as performant as previously-proposed SSMs on a variety of tasks and benchmarks including Long Range Arena and raw speech classification. Moreover, we characterize the expressivity of SSMs (including DLR) and attention-based models via a suite of 13 synthetic sequence-to-sequence tasks involving interactions over tens of thousands of tokens, ranging from simple operations, such as shifting an input sequence, to detecting co-dependent visual features over long spatial ranges in flattened images. We find that while SSMs report near-perfect performance on tasks that can be modeled via few convolutional kernels, they struggle on tasks requiring many such kernels and especially when the desired sequence manipulation is context-dependent. Despite these limitations, DLR reaches high performance on two higher-order reasoning tasks ListOpsSubTrees and PathfinderSegmentation-256 with input lengths 8K and 65K respectively, and gives encouraging performance on PathfinderSegmentation-512 with input length 262K for which attention is not a viable choice.

  • 3 authors
·
Nov 13, 2023

UniGRPO: Unified Policy Optimization for Reasoning-Driven Visual Generation

Unified models capable of interleaved generation have emerged as a promising paradigm, with the community increasingly converging on autoregressive modeling for text and flow matching for image generation. To advance this direction, we propose a unified reinforcement learning framework tailored for interleaved generation. We validate our approach on its fundamental unit: a single round of reasoning-driven image generation, where the model first expands the user prompt through reasoning, followed by image synthesis. Formulating this multimodal generation process as a Markov Decision Process with sparse terminal rewards, we introduce UniGRPO to jointly optimize text and image generation policies using GRPO. Adopting a minimalist methodology to avoid over-design, we leverage established training recipes for both modalities by seamlessly integrating standard GRPO for reasoning and FlowGRPO for visual synthesis. To ensure scalability to multi-round interleaved generation, we introduce two critical modifications to the original FlowGRPO: (1) eliminating classifier-free guidance to maintain linear, unbranched rollouts, which is essential for scaling to complex scenarios involving multi-turn interactions and multi-condition generation (e.g., editing); and (2) replacing the standard latent KL penalty with an MSE penalty directly on the velocity fields, providing a more robust and direct regularization signal to mitigate reward hacking effectively. Our experiments demonstrate that this unified training recipe significantly enhances image generation quality through reasoning, providing a robust and scalable baseline for the future post-training of fully interleaved models.

Exact Regular-Constrained Variable-Order Markov Generation via Sparse Context-State Belief Propagation

Variable-order Markov models generate sequences over a finite alphabet by conditioning each symbol on the longest available suffix of the generated history. Regular constraints, by contrast, describe finite-horizon control requirements by an automaton: fixed positions, forced endings, metrical patterns, and forbidden copied fragments are all special cases. Existing exact methods already handle regular constraints with belief propagation for first-order Markov chains. The contribution here is the variable-order extension: identifying the state space on which the existing BP-regular machinery must be run when the generator is a variable-order/backoff model. A first-order constraint layer can enforce useful support conditions, but it computes future mass after merging histories that a variable-order generator deliberately keeps distinct. We formalize this mismatch and give the sparse construction obtained by replacing the first-order Markov state with the observed context state, then taking the standard product with the regular constraint automaton. For a fixed trained context graph and automaton, inference is linear in the sequence horizon; in general it is polynomial in the number of reachable product edges. This gives the correct variable-order distribution conditioned on regular constraints without expanding to all K-tuples. The same finite-source interface supports reversible data augmentation by inverse count lookup, matching materialized transposition augmentation without storing transformed corpora. We also separate exact BP inference from generation-time backoff policies, such as singleton avoidance, whose stochastic semantics must be made explicit if exactness is claimed.

  • 1 authors
·
May 7

Dystruct: Dynamically Structured Diffusion Language Model Decoding via Bayesian Inference

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.

  • 4 authors
·
May 9 1

Uni-Instruct: One-step Diffusion Model through Unified Diffusion Divergence Instruction

In this paper, we unify more than 10 existing one-step diffusion distillation approaches, such as Diff-Instruct, DMD, SIM, SiD, f-distill, etc, inside a theory-driven framework which we name the \emph{Uni-Instruct}. Uni-Instruct is motivated by our proposed diffusion expansion theory of the f-divergence family. Then we introduce key theories that overcome the intractability issue of the original expanded f-divergence, resulting in an equivalent yet tractable loss that effectively trains one-step diffusion models by minimizing the expanded f-divergence family. The novel unification introduced by Uni-Instruct not only offers new theoretical contributions that help understand existing approaches from a high-level perspective but also leads to state-of-the-art one-step diffusion generation performances. On the CIFAR10 generation benchmark, Uni-Instruct achieves record-breaking Frechet Inception Distance (FID) values of \emph{1.46} for unconditional generation and \emph{1.38} for conditional generation. On the ImageNet-64times 64 generation benchmark, Uni-Instruct achieves a new SoTA one-step generation FID of \emph{1.02}, which outperforms its 79-step teacher diffusion with a significant improvement margin of 1.33 (1.02 vs 2.35). We also apply Uni-Instruct on broader tasks like text-to-3D generation. For text-to-3D generation, Uni-Instruct gives decent results, which slightly outperforms previous methods, such as SDS and VSD, in terms of both generation quality and diversity. Both the solid theoretical and empirical contributions of Uni-Instruct will potentially help future studies on one-step diffusion distillation and knowledge transferring of diffusion models.

  • 6 authors
·
May 27, 2025 2

OctGPT: Octree-based Multiscale Autoregressive Models for 3D Shape Generation

Autoregressive models have achieved remarkable success across various domains, yet their performance in 3D shape generation lags significantly behind that of diffusion models. In this paper, we introduce OctGPT, a novel multiscale autoregressive model for 3D shape generation that dramatically improves the efficiency and performance of prior 3D autoregressive approaches, while rivaling or surpassing state-of-the-art diffusion models. Our method employs a serialized octree representation to efficiently capture the hierarchical and spatial structures of 3D shapes. Coarse geometry is encoded via octree structures, while fine-grained details are represented by binary tokens generated using a vector quantized variational autoencoder (VQVAE), transforming 3D shapes into compact multiscale binary sequences suitable for autoregressive prediction. To address the computational challenges of handling long sequences, we incorporate octree-based transformers enhanced with 3D rotary positional encodings, scale-specific embeddings, and token-parallel generation schemes. These innovations reduce training time by 13 folds and generation time by 69 folds, enabling the efficient training of high-resolution 3D shapes, e.g.,1024^3, on just four NVIDIA 4090 GPUs only within days. OctGPT showcases exceptional versatility across various tasks, including text-, sketch-, and image-conditioned generation, as well as scene-level synthesis involving multiple objects. Extensive experiments demonstrate that OctGPT accelerates convergence and improves generation quality over prior autoregressive methods, offering a new paradigm for high-quality, scalable 3D content creation.

  • 5 authors
·
Apr 14, 2025

Toward a Theory of Tokenization in LLMs

While there has been a large body of research attempting to circumvent tokenization for language modeling (Clark et al., 2022; Xue et al., 2022), the current consensus is that it is a necessary initial step for designing state-of-the-art performant language models. In this paper, we investigate tokenization from a theoretical point of view by studying the behavior of transformers on simple data generating processes. When trained on data drawn from certain simple k^{th}-order Markov processes for k > 1, transformers exhibit a surprising phenomenon - in the absence of tokenization, they empirically fail to learn the right distribution and predict characters according to a unigram model (Makkuva et al., 2024). With the addition of tokenization, however, we empirically observe that transformers break through this barrier and are able to model the probabilities of sequences drawn from the source near-optimally, achieving small cross-entropy loss. With this observation as starting point, we study the end-to-end cross-entropy loss achieved by transformers with and without tokenization. With the appropriate tokenization, we show that even the simplest unigram models (over tokens) learnt by transformers are able to model the probability of sequences drawn from k^{th}-order Markov sources near optimally. Our analysis provides a justification for the use of tokenization in practice through studying the behavior of transformers on Markovian data.

  • 3 authors
·
Apr 12, 2024 1

D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation

Early DNA foundation models adopted BERT-style training, achieving good performance on DNA understanding tasks but lacking generative capabilities. Recent autoregressive models enable DNA generation, but employ left-to-right causal modeling that is suboptimal for DNA where regulatory relationships are inherently bidirectional. We present D3LM (Discrete DNA Diffusion Language Model), which unifies bidirectional representation learning and DNA generation through masked diffusion. D3LM directly adopts the Nucleotide Transformer (NT) v2 architecture but reformulates the training objective as masked diffusion in discrete DNA space, enabling both bidirectional understanding and generation capabilities within a single model. Compared to NT v2 of the same size, D3LM achieves improved performance on understanding tasks. Notably, on regulatory element generation, D3LM achieves an SFID of 10.92, closely approaching real DNA sequences (7.85) and substantially outperforming the previous best result of 29.16 from autoregressive models. Our work suggests diffusion language models as a promising paradigm for unified DNA foundation models. We further present the first systematic study of masked diffusion models in the DNA domain, investigating practical design choices such as tokenization schemes and sampling strategies, thereby providing empirical insights and a solid foundation for future research. D3LM has been released at https://huggingface.co/collections/Hengchang-Liu/d3lm.

  • 4 authors
·
Mar 2

Distilled Continuous Diffusion Language Models Can Write Code in Few Steps---or One

Language generation is almost universally treated as a sequential process: autoregressive models emit one token at a time, while diffusion language models replace token-level seriality with a long trajectory of iterative refinement. In this work, we introduce PlaidQ, a 0.7B continuous diffusion language model for code generation, and show that its trajectory can be aggressively distilled into only a few denoising steps---or even one, enabling efficient code generation. PlaidQ repurposes a pretrained autoregressive model as a bidirectional denoiser over continuous token embeddings. We distill PlaidQ with distribution matching for few-step generation and paired-trajectory supervision for one-step generation. At matched model scale, PlaidQ is competitive with discrete diffusion language models on code generation. Distillation then shifts the quality--compute frontier: a 16-step student reaches 31.78 and 40.49 pass@10 on HumanEval and MBPP+, surpassing the same PlaidQ teacher sampled for 512 steps. At the extreme, paired-trajectory distillation achieves 7.07 pass@1 on HumanEval with a single denoising step, producing functionally correct programs. Together, these results establish continuous diffusion as a viable path to few-step and one-step code generation. Broadly, continuous diffusion is not merely another representation for language: it provides an interface through which language models can inherit the acceleration and distillation machinery of continuous diffusion modeling. Training and inference code and model checkpoints are available at https://github.com/pengzhangzhi/plaidq.

  • 3 authors
·
Sep 9

Beyond Confidence: Adaptive and Coherent Decoding for Diffusion Language Models

Diffusion Language Models (DLMs) have recently achieved significant success due to their any-order generation capabilities. However, existing inference methods typically rely on local, immediate-step metrics such as confidence or entropy which inherently lack a more reliable perspective. This limitation frequently leads to inconsistent sampling trajectories and suboptimal generation quality. To address this, we propose Coherent Contextual Decoding (CCD), a novel inference framework built upon two core innovations. First, CCD employs a trajectory rectification mechanism that leverages historical context to enhance sequence coherence, enabling the early rejection of suboptimal paths. We demonstrate that this mechanism is theoretically equivalent to modeling the consistency of historical steps via the conditional mutual information between context and token predictions. Building on this theoretical insight, we further address the inefficiency of conventional uniform decoding budgets. Instead of rigid allocations based on diffusion steps, we introduce an adaptive sampling strategy that dynamically adjusts the unmasking budget for each step according to our consistency metric. Consequently, our method significantly improves the quality of generation trajectories while accelerating the sampling process. Empirically, our method achieves a simultaneous enhancement in both inference speed and performance across diverse benchmarks on Dream and LLaDA, delivering up to 3.48x speedup alongside 3.91% performance improvement.

  • 10 authors
·
Nov 26, 2025