Daily Papers

Mixture of Experts (MoE) models enhance neural network scalability by dynamically selecting relevant experts per input token, enabling larger model sizes while maintaining manageable computation costs. However, efficient training of large-scale MoE models across thousands of GPUs presents significant challenges due to limitations in existing parallelism strategies. We introduce an end-to-end training framework for large-scale MoE models that utilizes five-dimensional hybrid parallelism: Tensor Parallelism, Expert Parallelism, Context Parallelism, Data Parallelism, and Pipeline Parallelism. Central to our approach is MoE Parallel Folding, a novel strategy that decouples the parallelization of attention and MoE layers in Transformer models, allowing each layer type to adopt optimal parallel configurations. Additionally, we develop a flexible token-level dispatcher that supports both token-dropping and token-dropless MoE training across all five dimensions of parallelism. This dispatcher accommodates dynamic tensor shapes and coordinates different parallelism schemes for Attention and MoE layers, facilitating complex parallelism implementations. Our experiments demonstrate significant improvements in training efficiency and scalability. We achieve up to 49.3% Model Flops Utilization (MFU) for the Mixtral 8x22B model and 39.0% MFU for the Qwen2-57B-A14B model on H100 GPUs, outperforming existing methods. The framework scales efficiently up to 1,024 GPUs and maintains high performance with sequence lengths up to 128K tokens, validating its effectiveness for large-scale MoE model training. The code is available in Megatron-Core.

Scaling Mixture-of-Experts (MoE) training introduces systems challenges absent in dense models. Because each token activates only a subset of experts, this sparsity allows total parameters to grow much faster than per-token computation, creating coupled constraints across memory, communication, and computation. Optimizing one dimension often shifts pressure to another, demanding co-design across the full system stack. We address these challenges for MoE training through integrated optimizations spanning memory (fine-grained recomputation, offloading, etc.), communication (optimized dispatchers, overlapping, etc.), and computation (Grouped GEMM, fusions, CUDA Graphs, etc.). The framework also provides Parallel Folding for flexible multi-dimensional parallelism, low-precision training support for FP8 and NVFP4, and efficient long-context training. On NVIDIA GB300 and GB200, it achieves 1,233/1,048 TFLOPS/GPU for DeepSeek-V3-685B and 974/919 TFLOPS/GPU for Qwen3-235B. As a performant, scalable, and production-ready open-source solution, it has been used across academia and industry for training MoE models ranging from billions to trillions of parameters on clusters scaling up to thousands of GPUs. This report explains how these techniques work, their trade-offs, and their interactions at the systems level, providing practical guidance for scaling MoE models with Megatron Core.

Understanding cellular machinery requires atomic-scale reconstruction of large biomolecular assemblies. However, predicting the structures of these systems has been constrained by hardware memory requirements of models like AlphaFold 3, imposing a practical ceiling of a few thousand residues that can be processed on a single GPU. Here we present NVIDIA BioNeMo Fold-CP, a context parallelism framework that overcomes this barrier by distributing the inference and training pipelines of co-folding models across multiple GPUs. We use the Boltz models as open source reference architectures and implement custom multidimensional primitives that efficiently parallelize both the dense triangular updates and the irregular, data-dependent pattern of window-batched local attention. Our approach achieves efficient memory scaling; for an N-token input distributed across P GPUs, per-device memory scales as O(N^2/P), enabling the structure prediction of assemblies exceeding 30,000 residues on 64 NVIDIA B300 GPUs. We demonstrate the scientific utility of this approach through successful developer use cases: Fold-CP enabled the scoring of over 90% of Comprehensive Resource of Mammalian protein complexes (CORUM) database, as well as folding of disease-relevant PI4KA lipid kinase complex bound to an intrinsically disordered region without cropping. By providing a scalable pathway for modeling massive systems with full global context, Fold-CP represents a significant step toward the realization of a virtual cell.

The ability to transform a flat sheet into a complex three-dimensional structure is a fundamental test of physical intelligence. Unlike cloth manipulation, origami is governed by strict geometric axioms and hard kinematic constraints, where a single invalid crease or collision can invalidate the entire folding sequence. As a result, origami demands long-horizon constructive reasoning that jointly satisfies precise physical laws and high-level semantic intent. Existing approaches fall into two disjoint paradigms: optimization-based methods enforce physical validity but require dense, precisely specified inputs, making them unsuitable for sparse natural language descriptions, while generative foundation models excel at semantic and perceptual synthesis yet fail to produce long-horizon, physics-consistent folding processes. Consequently, generating valid origami folding sequences directly from text remains an open challenge. To address this gap, we introduce Learn2Fold, a neuro-symbolic framework that formulates origami folding as conditional program induction over a crease-pattern graph. Our key insight is to decouple semantic proposal from physical verification. A large language model generates candidate folding programs from abstract text prompts, while a learned graph-structured world model serves as a differentiable surrogate simulator that predicts physical feasibility and failure modes before execution. Integrated within a lookahead planning loop, Learn2Fold enables robust generation of physically valid folding sequences for complex and out-of-distribution patterns, demonstrating that effective spatial intelligence arises from the synergy between symbolic reasoning and grounded physical simulation.

Highly accurate biomolecular structure prediction is a key component of developing biomolecular foundation models, and one of the most critical aspects of building foundation models is identifying the recipes for scaling the model. In this work, we present SeedFold, a folding model that successfully scales up the model capacity. Our contributions are threefold: first, we identify an effective width-scaling strategy for the Pairformer to increase representation capacity; second, we introduce a novel linear triangular attention that reduces computational complexity to enable efficient scaling; finally, we construct a large-scale distillation dataset to substantially enlarge the training set. Experiments on FoldBench show that SeedFold outperforms AlphaFold3 on most protein-related tasks.

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.

Origami metamaterials typically consist of folded sheets with periodic patterns, conferring them with remarkable mechanical properties. In the context of Continuum Mechanics, the majority of existing predictive methods are mechanism analogs which favor rigid folding and panel bending. While effective in predicting primary deformation modes, existing methods fall short in capturing the full spectrum of deformation of non-rigid foldable origami, such as the emergence of curvature along straight creases, local strain at vertices and warpage in panels. To fully capture the entire deformation spectrum and enhance the accuracy of existing methods, this paper introduces a homogenization framework for origami metamaterials where the faces are modeled as plate elements. Both asymptotic and energy-based homogenization methods are formulated and implemented. As a representative crease pattern, we examine the Miura origami sheet homogenized as an equivalent Kirchhoff-Love plate. The results reveal that certain effective elastic properties are nonlinearly related to both the initial fold angle and the crease stiffness. When benchmarked with results from fully resolved simulations, our framework yields errors up to 12.9\%, while existing models, including the bar-and-hinge model and the rigid-panel model, show up to 161\% error. The differences in errors are associated with the complex modes of crease and panel deformation in non-rigid origami, unexplored by the existing models. This work demonstrates a precise and efficient continuum framework for origami metamaterials as an effective strategy for predicting their elastic properties, understanding their mechanics, and designing their functionalities.

We present FoldingAgent, an agentic framework for inferring explicit parametric folding programs directly from origami demonstration videos. Our framework leverages the reasoning power of a pre-trained Vision-Language Model (VLM) equipped with a suite of specialized tools that enable the agent to simulate geometric transitions, verify physical plausibility, retrieve and compare visual content, and evaluate its own predictions. To translate visual content into folding programs, we define a parametric space that consists of the paper's geometry and a set of parametric folding actions. Unlike models that predict static crease patterns, our agent operates sequentially and possesses the ability to re-plan its actions, effectively mitigating the compounding errors inherent in multi-step folding. Our approach takes a step toward closing the gap between human origami knowledge, which is primarily shared through unstructured visual demonstrations, and computational methods, which typically rely on structured, parametric representations such as a crease pattern or an executable parametric plan. We evaluate our approach on PurelandFold, a newly curated benchmark of diverse Pureland origami videos with ground-truth geometry and action labels. Our results demonstrate that by combining VLM reasoning with a set of specialized tools and physical simulation, we can successfully transform unstructured visual demonstrations into executable, physically plausible folding procedures.

AlphaFold predicts protein structures from the amino acid sequence at or near experimental resolution, solving the 50-year-old protein folding challenge, leading to progress by transforming large-scale genomics data into protein structures. AlphaFold will also greatly change the scientific research model from low-throughput to high-throughput manner. The AlphaFold framework is a mixture of two types of workloads: MSA construction based on CPUs and model inference on GPUs. The first CPU stage dominates the overall runtime, taking hours for a single protein due to the large database sizes and I/O bottlenecks. However, GPUs in this CPU stage remain idle, resulting in low GPU utilization and restricting the capacity of large-scale structure predictions. Therefore, we proposed ParaFold, an open-source parallel version of AlphaFold for high throughput protein structure predictions. ParaFold separates the CPU and GPU parts to enable large-scale structure predictions. ParaFold also effectively reduces the CPU and GPU runtime with two optimizations without compromising the quality of prediction results: using multi-threaded parallelism on CPUs and using optimized JAX compilation on GPUs. We evaluated ParaFold with three datasets of different size and protein lengths. We evaluated the accuracy and efficiency of optimizations on CPUs and GPUs, and showed the large-scale prediction capability by running ParaFold inferences of 19,704 small proteins in five hours on one NVIDIA DGX-2. Using the JAX compile optimization, ParaFold attained a 13.8X average speedup over AlphaFold. ParaFold offers a rapid and effective approach for high-throughput structure predictions, leveraging the predictive power by running on supercomputers, with shorter time, and at a lower cost. The development of ParaFold will greatly speed up high-throughput studies and render the protein "structure-omics" feasible.

Recent findings suggest that consecutive layers of neural networks with the ReLU activation function fold the input space during the learning process. While many works hint at this phenomenon, an approach to quantify the folding was only recently proposed by means of a space folding measure based on Hamming distance in the ReLU activation space. We generalize this measure to a wider class of activation functions through introduction of equivalence classes of input data, analyse its mathematical and computational properties and come up with an efficient sampling strategy for its implementation. Moreover, it has been observed that space folding values increase with network depth when the generalization error is low, but decrease when the error increases. This underpins that learned symmetries in the data manifold (e.g., invariance under reflection) become visible in terms of space folds, contributing to the network's generalization capacity. Inspired by these findings, we outline a novel regularization scheme that encourages the network to seek solutions characterized by higher folding values.

We characterize the cut patterns that can be produced by "orthogonal fold & cut": folding an axis-aligned rectangular sheet of paper along horizontal and vertical creases, and then making a single straight cut (at any angle). Along the way, we solve a handful of related problems: orthogonal fold & punch, 1D fold & cut, signed 1D fold & cut, and 1D interval fold & cut.

Parallel thinking has emerged as a promising paradigm for reasoning, yet it imposes significant computational burdens. Existing efficiency methods primarily rely on local, per-trajectory signals and lack principled mechanisms to exploit global dynamics across parallel branches. We introduce 2D probing, an interface that exposes the width-depth dynamics of parallel thinking by periodically eliciting intermediate answers from all branches. Our analysis reveals three key insights: non-monotonic scaling across width-depth allocations, heterogeneous reasoning branch lengths, and early stabilization of global consensus. Guided by these insights, we introduce Parallel-Probe, a training-free controller designed to optimize online parallel thinking. Parallel-Probe employs consensus-based early stopping to regulate reasoning depth and deviation-based branch pruning to dynamically adjust width. Extensive experiments across three benchmarks and multiple models demonstrate that Parallel-Probe establishes a superior Pareto frontier for test-time scaling. Compared to standard majority voting, it reduces sequential tokens by up to 35.8% and total token cost by over 25.8% while maintaining competitive accuracy.

Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Nonetheless, given the success of generative models across different but related problems, it is natural to question whether these architectural designs are a necessary condition to build performant models. In this paper, we introduce SimpleFold, the first flow-matching based protein folding model that solely uses general purpose transformer blocks. Protein folding models typically employ computationally expensive modules involving triangular updates, explicit pair representations or multiple training objectives curated for this specific domain. Instead, SimpleFold employs standard transformer blocks with adaptive layers and is trained via a generative flow-matching objective with an additional structural term. We scale SimpleFold to 3B parameters and train it on approximately 9M distilled protein structures together with experimental PDB data. On standard folding benchmarks, SimpleFold-3B achieves competitive performance compared to state-of-the-art baselines, in addition SimpleFold demonstrates strong performance in ensemble prediction which is typically difficult for models trained via deterministic reconstruction objectives. Due to its general-purpose architecture, SimpleFold shows efficiency in deployment and inference on consumer-level hardware. SimpleFold challenges the reliance on complex domain-specific architectures designs in protein folding, opening up an alternative design space for future progress.

The transition from sequential to parallel computing is essential for modern high-performance applications but is hindered by the steep learning curve of concurrent programming. This challenge is magnified for irregular data structures (such as sparse graphs, unbalanced trees, and non-uniform meshes) where static scheduling fails and data dependencies are unpredictable. Current Large Language Models (LLMs) often fail catastrophically on these tasks, generating code plagued by subtle race conditions, deadlocks, and sub-optimal scaling. We bridge this gap with ParEVO, a framework designed to synthesize high-performance parallel algorithms for irregular data. Our contributions include: (1) The Parlay-Instruct Corpus, a curated dataset of 13,820 tasks synthesized via a "Critic-Refine" pipeline that explicitly filters for empirically performant algorithms that effectively utilize Work-Span parallel primitives; (2) specialized DeepSeek, Qwen, and Gemini models fine-tuned to align probabilistic generation with the rigorous semantics of the ParlayLib library; and (3) an Evolutionary Coding Agent (ECA) that improves the "last mile" of correctness by iteratively repairing code using feedback from compilers, dynamic race detectors, and performance profilers. On the ParEval benchmark, ParEVO achieves an average 106x speedup (with a maximum of 1103x) across the suite, and a robust 13.6x speedup specifically on complex irregular graph problems, outperforming state-of-the-art commercial models. Furthermore, our evolutionary approach matches state-of-the-art expert human baselines, achieving up to a 4.1x speedup on specific highly-irregular kernels. Source code and datasets are available at https://github.com/WildAlg/ParEVO.

It is commonly believed that scaling language models should commit a significant space or time cost, by increasing the parameters (parameter scaling) or output tokens (inference-time scaling). We introduce the third and more inference-efficient scaling paradigm: increasing the model's parallel computation during both training and inference time. We apply P diverse and learnable transformations to the input, execute forward passes of the model in parallel, and dynamically aggregate the P outputs. This method, namely parallel scaling (ParScale), scales parallel computation by reusing existing parameters and can be applied to any model structure, optimization procedure, data, or task. We theoretically propose a new scaling law and validate it through large-scale pre-training, which shows that a model with P parallel streams is similar to scaling the parameters by O(log P) while showing superior inference efficiency. For example, ParScale can use up to 22times less memory increase and 6times less latency increase compared to parameter scaling that achieves the same performance improvement. It can also recycle an off-the-shelf pre-trained model into a parallelly scaled one by post-training on a small amount of tokens, further reducing the training budget. The new scaling law we discovered potentially facilitates the deployment of more powerful models in low-resource scenarios, and provides an alternative perspective for the role of computation in machine learning.

Large language models rely heavily on human text, which often conveys surface answers rather than the spatial and structural logic behind them. Protein folding is a natural testbed, because one solved structure yields thousands of exactly checkable spatial and topological statements. We ask: can learning to fold proteins teach general models reusable reasoning capabilities? To answer this, we build FoldingCorpus, a protein-derived question-answer dataset, and Fold2Reason, a recipe that post-trains on it through two complementary signals: discrete structural answers predicted via the model's native language head, and continuous 3D geometry decoded from the same shared representations. On FoldBench, Fold2Reason achieves structure prediction scores 2.7 to 3.5 times those of Qwen3.5-9B. Beyond protein structure prediction, it improves performance on all 10 benchmarks spanning spatial, graph, scientific, and general reasoning, raising macro-average accuracy from 45.09% to 48.33% (+3.23 pp), with positive gains on all 10 benchmarks, while matched controls built from random, synthetic, and shuffled structure yield substantially smaller or negative gains. Our work shows that non-linguistic, structure-dense scientific data can systematically improve broad reasoning in language models, making a solved scientific problem a practical source of post-training supervision.

Garment folding is a common yet challenging task in robotic manipulation. The deformability of garments leads to a vast state space and complex dynamics, which complicates precise and fine-grained manipulation. Previous approaches often rely on predefined key points or demonstrations, limiting their generalization across diverse garment categories. This paper presents a framework, MetaFold, that disentangles task planning from action prediction, learning each independently to enhance model generalization. It employs language-guided point cloud trajectory generation for task planning and a low-level foundation model for action prediction. This structure facilitates multi-category learning, enabling the model to adapt flexibly to various user instructions and folding tasks. Experimental results demonstrate the superiority of our proposed framework. Supplementary materials are available on our website: https://meta-fold.github.io/.

Scientific LLM agents have shown promise in literature reasoning, tool use, and experiment planning, but it remains unclear whether they can autonomously improve large, tightly coupled scientific machine-learning systems through executable code changes and computationally expensive validation. We study this question in protein folding, where progress requires coordinated architectural modifications, multi-objective evaluation, and domain-aware interpretation. We present AgentFold, a multi-agent framework that formulates folding-model development as a closed-loop search over executable code variants. Starting from ESMFold, AgentFold proposes hypotheses, implements and debugs code-level modifications, evaluates model variants, analyzes experimental outcomes, and stores both successful and failed interventions in structured memory. An MCTS-style policy allocates computational resources across high-scoring search branches. On an engineering-scale protein-folding codebase comprising more than 2,000 lines of code, AgentFold explores approximately 80 model variants using approximately 5,000 GPU-hours and 170 million LLM tokens. Under a matched computational budget, AgentFold improves the best lDDT by 7.5% over independent Codex proposals and outperforms a random-search control. Beyond model improvement, the resulting intervention traces reveal recurring empirical design patterns: stable gains tend to arise from early, soft, learnable priors and gated refinement, whereas direct geometric perturbations and geometry-conditioned feedback often destabilize training. The code and experimental resources are publicly available at https://github.com/lmqfly/AgentFold.

Cloth folding is a complex task due to the inevitable self-occlusions of clothes, their complicated dynamics, and the disparate materials, geometries, and textures that garments can have. In this work, we learn folding actions conditioned on text commands. Translating high-level, abstract instructions into precise robotic actions requires sophisticated language understanding and manipulation capabilities. To do that, we leverage a pre-trained vision-language model and repurpose it to predict manipulation actions. Our model, BiFold, can take context into account and achieves state-of-the-art performance on an existing language-conditioned folding benchmark. Given the lack of annotated bimanual folding data, we devise a procedure to automatically parse actions of a simulated dataset and tag them with aligned text instructions. BiFold attains the best performance on our dataset and can transfer to new instructions, garments, and environments.

Discrete diffusion language models (dLLMs) accelerate text generation by unmasking multiple tokens in parallel. However, parallel decoding introduces a distributional mismatch: it approximates the joint conditional using a fully factorized product of per-token marginals, which degrades output quality when selected tokens are strongly dependent. We propose DEMASK (DEpendency-guided unMASKing), a lightweight dependency predictor that attaches to the final hidden states of a dLLM. In a single forward pass, it estimates pairwise conditional influences between masked positions. Using these predictions, a greedy selection algorithm identifies positions with bounded cumulative dependency for simultaneous unmasking. Under a sub-additivity assumption, we prove this bounds the total variation distance between our parallel sampling and the model's joint. Empirically, DEMASK achieves 1.7-2.2times speedup on Dream-7B while matching or improving accuracy compared to confidence-based and KL-based baselines.

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.

Parallel speculative drafting generates multiple candidates in one backbone pass, but independent token selection can produce inconsistent continuations that shorten the accepted prefix. Existing methods mostly leave conditional decoding to a lightweight module after the backbone, which limits the flow of predecessor information to successors. Our analysis of DFlash shows that early positions already form recoverable predictions in shallow layers, and that accurate adjacent predecessors help successors more when they enter earlier. We therefore propose DSpine, a drafter with causal conditioning injection throughout the backbone: at every layer, gated adjacent injection writes each predecessor's predicted feature into its successor, so the causal conditioning chain unfolds over network depth while all positions update in parallel. A unified transfer space built from the target model's output embeddings unifies layer-wise injection with predecessor-conditioned decoding, and layer-wise output-embedding supervision promotes the formation of predicted features in shallow layers. Fused kernels and a transition cache execute both efficiently in parallel within SGLang. Across seven math, code, and chat benchmarks, DSpine achieves the longest acceptance length at both temperatures on Qwen3-4B and Qwen3-8B. At temperature zero on Qwen3-8B, it raises the seven-benchmark mean from DFlash's 3.77 to 4.82 (+27.8%); in SGLang serving tests, it delivers 23.3% higher throughput than DFlash on average.

Given two images depicting a person and a garment worn by another person, our goal is to generate a visualization of how the garment might look on the input person. A key challenge is to synthesize a photorealistic detail-preserving visualization of the garment, while warping the garment to accommodate a significant body pose and shape change across the subjects. Previous methods either focus on garment detail preservation without effective pose and shape variation, or allow try-on with the desired shape and pose but lack garment details. In this paper, we propose a diffusion-based architecture that unifies two UNets (referred to as Parallel-UNet), which allows us to preserve garment details and warp the garment for significant pose and body change in a single network. The key ideas behind Parallel-UNet include: 1) garment is warped implicitly via a cross attention mechanism, 2) garment warp and person blend happen as part of a unified process as opposed to a sequence of two separate tasks. Experimental results indicate that TryOnDiffusion achieves state-of-the-art performance both qualitatively and quantitatively.

Building AI systems that can plan, act, and create in the physical world requires more than pattern recognition. Such systems must understand the causal mechanisms and constraints governing physical processes in order to guide sequential decisions. This capability relies on internal representations, analogous to an internal language model, that relate observations, actions, and resulting environmental changes. However, many existing benchmarks treat visual perception and programmatic reasoning as separate problems, focusing either on visual recognition or on symbolic tasks. The domain of origami provides a natural testbed that integrates these modalities. Constructing shapes through folding operations requires visual perception, reasoning about geometric and physical constraints, and sequential planning, while remaining sufficiently structured for systematic evaluation. We introduce OrigamiBench, an interactive benchmark in which models iteratively propose folds and receive feedback on physical validity and similarity to a target configuration. Experiments with modern vision-language models show that scaling model size alone does not reliably produce causal reasoning about physical transformations. Models fail to generate coherent multi-step folding strategies, suggesting that visual and language representations remain weakly integrated.

How can we design protein sequences folding into the desired structures effectively and efficiently? AI methods for structure-based protein design have attracted increasing attention in recent years; however, few methods can simultaneously improve the accuracy and efficiency due to the lack of expressive features and autoregressive sequence decoder. To address these issues, we propose PiFold, which contains a novel residue featurizer and PiGNN layers to generate protein sequences in a one-shot way with improved recovery. Experiments show that PiFold could achieve 51.66\% recovery on CATH 4.2, while the inference speed is 70 times faster than the autoregressive competitors. In addition, PiFold achieves 58.72\% and 60.42\% recovery scores on TS50 and TS500, respectively. We conduct comprehensive ablation studies to reveal the role of different types of protein features and model designs, inspiring further simplification and improvement. The PyTorch code is available at https://github.com/A4Bio/PiFold{GitHub}.

Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has entered a new phase, and many methods are proposed based on the component of AlphaFold2. The importance of a unified research framework in protein folding contains implementations and benchmarks to consistently and fairly compare various approaches. To achieve this, we present Solvent, an protein folding framework that supports significant components of state-of-th-arts models in the manner of off-the-shelf interface Solvent contains different models implemented in a unified codebase and supports training and evaluation for defined models on the same dataset. We benchmark well-known algorithms and their components and provide experiments that give helpful insights into the protein structure modeling field. We hope that Solvent will increase the reliability and consistency of proposed models and gives efficiency in both speed and costs, resulting in acceleration on protein folding modeling research. The code is available at https://github.com/kakaobrain/solvent, and the project will continue to be developed.

We study low-precision computation of C=AB with both factors quantized. We derive an exact finite-dimensional identity for the expected squared product error under independent, zero-mean entrywise errors with known variance fields; it holds exactly for non-overloading subtractive dither and for independent stochastic rounding, and we empirically assess deterministic round-to-nearest (RTN). Using the product-preserving equivalence AB=(AT)(T^{-1}B), we formulate contraction-gauge preconditioning: jointly choosing a factor representation and its sharing pattern before quantization. Preconditioning can reduce product error but may require extra transformed, quantized copies of the opposite operand: a shared transform needs one copy, a block-specific transform up to one per block. Within the bounded family of positive diagonal gauges (folds), a geometric program computes a globally optimal shared fold and a linear program decides whether the identity fold is already optimal. For other families we derive computable selection statistics -- tail index for scaling, profile spread for partitioning, coherence and weighted-Gram energy for rotations, slice-energy covariance for hierarchy depth -- with upper bounds for ranking heuristic candidates. Across twelve linear products from a trained three-block image classifier, median within-product rank correlations between dither-model predictions and deterministic-RTN errors are 0.937 at 8 bits and 0.918 at 4 bits. The GP fold cuts held-out product error over the identity fold by 18.0% (8-bit) and 20.5% (4-bit) in geometric mean, beats a SmoothQuant-style grid baseline at both precisions and on ten of twelve products, and lowers composed logit MSE by 15.4% and 26.4%. We thus provide exact stochastic product-error accounting, certified selection within the diagonal family, and a common objective for evaluating reusable transform candidates under RTN.

Multi-vector vision-language retrievers enable fine-grained Visual Document Retrieval (VDR) through late interaction, but storing and scoring hundreds of visual patch embeddings per page incurs substantial overhead. Existing training-free methods rely on pruning or merging: pruning degrades sharply under aggressive compression, whereas merging does not explicitly prioritize important regions when forming representatives. We introduce AnchorFold, a training-free focus-then-fold framework for document-side index compression. AnchorFold applies Recursive Attention Propagation over visual self-attention graphs, performing multi-step propagation within each attention head and integrating scores across heads and layers. The focus stage selects the highest-centrality tokens as anchors. The fold stage assigns remaining tokens to their most similar anchors in the normalized retrieval space and summarizes each anchor-centered group through centrality-weighted aggregation. This preserves non-anchor contributions while concentrating capacity on structurally important tokens. Across ViDoRe v1/v2 and REAL-MM-RAG with three diverse retrieval backbones, AnchorFold consistently outperforms all evaluated training-free baselines at γleq 0.20. On ViDoRe v1/v2, it retains 98.3% of full-index NDCG@5 on average at 5times compression, achieving near-lossless compression, and 92.4% at 20times compression.

Protein inverse folding, the design of an amino acid sequence based on a target 3D structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external knowledge or relying on protein language models (PLMs). The former omits the evolutionary information stored in protein databases, while the latter is parameter-inefficient and inflexible to adapt to ever-growing protein data. To overcome the above drawbacks, in this paper we propose a novel method, called retrieval-augmented denoising diffusion (RadDiff), for protein inverse folding. Given the target protein backbone, RadDiff uses a hierarchical search strategy to efficiently retrieve structurally similar proteins from large protein databases. The retrieved structures are then aligned residue-by-residue to the target to construct a position-specific amino acid profile, which serves as an evolutionary-informed prior that conditions the denoising process. A lightweight integration module is further designed to incorporate this prior effectively. Experimental results on the CATH, PDB, and TS50 datasets show that RadDiff consistently outperforms existing methods, improving sequence recovery rate by up to 19%. Experimental results also demonstrate that RadDiff generates highly foldable sequences and scales effectively with database size.

Generative machine learning models are increasingly being used to design novel proteins for therapeutic and biotechnological applications. However, the current methods mostly focus on the design of proteins with a fixed backbone structure, which leads to their limited ability to account for protein flexibility, one of the crucial properties for protein function. Learning to engineer protein flexibility is problematic because the available data are scarce, heterogeneous, and costly to obtain using computational as well as experimental methods. Our contributions to address this problem are three-fold. First, we comprehensively compare methods for quantifying protein flexibility and identify data relevant to learning. Second, we design and train flexibility predictors utilizing sequential or both sequential and structural information on the input. We overcome the data scarcity issue by leveraging a pre-trained protein language model. Third, we introduce a method for fine-tuning a protein inverse folding model to steer it toward desired flexibility in specified regions. We demonstrate that our method Flexpert-Design enables guidance of inverse folding models toward increased flexibility. This opens up new possibilities for protein flexibility engineering and the development of proteins with enhanced biological activities.

Recent findings suggest that the consecutive layers of ReLU neural networks can be understood geometrically as space folding transformations of the input space, revealing patterns of self-similarity. In this paper, we present the first quantitative analysis of this space folding phenomenon in ReLU neural networks. Our approach focuses on examining how straight paths in the Euclidean input space are mapped to their counterparts in the Hamming activation space. In this process, the convexity of straight lines is generally lost, giving rise to non-convex folding behavior. To quantify this effect, we introduce a novel measure based on range metrics, similar to those used in the study of random walks, and provide the proof for the equivalence of convexity notions between the input and activation spaces. Furthermore, we provide empirical analysis on a geometrical analysis benchmark (CantorNet) as well as an image classification benchmark (MNIST). Our work advances the understanding of the activation space in ReLU neural networks by leveraging the phenomena of geometric folding, providing valuable insights on how these models process input information.

Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes when it folds. Understanding protein kinetics is essential as a protein needs to fold correctly for it to perform its biological functions optimally, and a misfolded protein can sometimes be contorted into shapes that are not ideal for a cellular environment giving rise to many degenerative, neuro-degenerative disorders and amyloid diseases. Monitoring at-risk individuals and detecting protein discrepancies in a protein's folding kinetics at the early stages could majorly result in public health benefits, as preventive measures can be taken. This research proposes an efficient pipeline for predicting protein folding kinetics with high accuracy and low memory footprint. The deployed machine learning (ML) model outperformed the state-of-the-art ML models by 4.8% in terms of accuracy while consuming 327x lesser memory and being 7.3% faster.

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

Parallel diffusion decoding can accelerate diffusion language model inference by unmasking multiple tokens per step, but aggressive parallelism often harms quality. Revocable decoding mitigates this by rechecking earlier tokens, yet we observe that existing verification schemes frequently trigger flip-flop oscillations, where tokens are remasked and later restored unchanged. This behaviour slows inference in two ways: remasking verified positions weakens the conditioning context for parallel drafting, and repeated remask cycles consume the revision budget with little net progress. We propose COVER (Cache Override Verification for Efficient Revision), which performs leave-one-out verification and stable drafting within a single forward pass. COVER constructs two attention views via KV cache override: selected seeds are masked for verification, while their cached key value states are injected for all other queries to preserve contextual information, with a closed form diagonal correction preventing self leakage at the seed positions. COVER further prioritises seeds using a stability aware score that balances uncertainty, downstream influence, and cache drift, and it adapts the number of verified seeds per step. Across benchmarks, COVER markedly reduces unnecessary revisions and yields faster decoding while preserving output quality.

Multimodal large language models (MLLMs) are proficient in perception and instruction-following, but they still struggle with spatial reasoning: the ability to mentally track and manipulate objects across multiple views and over time. Spatial reasoning is a key component of human intelligence, but most existing benchmarks focus on static images or final outputs, failing to account for the sequential and viewpoint-dependent nature of this skill. To close this gap, we introduce GamiBench, a benchmark designed to evaluate spatial reasoning and 2D-to-3D planning in MLLMs through origami-inspired folding tasks. GamiBench includes 186 regular and 186 impossible 2D crease patterns paired with their corresponding 3D folded shapes, produced from six distinct viewpoints across three visual question-answering (VQA) tasks: predicting 3D fold configurations, distinguishing valid viewpoints, and detecting impossible patterns. Unlike previous benchmarks that assess only final predictions, GamiBench holistically evaluates the entire reasoning process--measuring cross-view consistency, physical feasibility through impossible-fold detection, and interpretation of intermediate folding steps. It further introduces new diagnostic metrics--viewpoint consistency (VC) and impossible fold selection rate (IFSR)--to measure how well models handle folds of varying complexity. Our experiments show that even leading models such as GPT-5 and Gemini-2.5-Pro struggle on single-step spatial understanding. These contributions establish a standardized framework for evaluating geometric understanding and spatial reasoning in MLLMs. Dataset and code: https://github.com/stvngo/GamiBench.

Parallel coding agents can independently produce locally valid changes while still interfering at integration time, expanding beyond planned scope, or relying on premises invalidated by concurrent work. Existing responses emphasize communication, isolated workspaces, late merge-time repair, continuous supervision, or post-hoc runtime recovery. This paper presents Claim Plane, a model-agnostic coordination architecture that treats concurrent software change as a pre-write admission problem. Before implementation, each worker declares a versioned ChangeIntent containing an exact base commit, typed resources, dependencies, and operations marked as committed or contingent. A deterministic control plane atomically admits compatible intents, constrains same-file parallelism to declared regions, serializes unresolved overlap, tracks dependency invalidation, and fails closed on ambiguous authority. During execution, a contingent mutation does not reserve write ownership initially; the first attempted mutation triggers atomic scope promotion and re-admission against the current active set. Brokered execution binds capabilities to intent versions, leases, OS-level worktree locks, monotonic fencing tokens, and Git-tree provenance, while integration verifies immutable patches and evidence. A preliminary six-pair CooperBench mechanism check is reported only as feasibility evidence: static Claim Plane achieved 6/6 pair passes with full serialization, while dynamic scope retained parallel admission on half of the pairs, performed seven successful scope promotions, and failed closed on two undeclared mutations. The sample is intentionally too small for comparative claims. We argue that separating probabilistic planning from deterministic authority provides a foundation for a future learned semantic-dependency model and frontier-model escalation only on unresolved cases.

Diffusion models have emerged as a powerful class of generative models across various modalities, including image, video, and audio synthesis. However, their deployment is often limited by significant inference latency, primarily due to the inherently sequential nature of the denoising process. While existing parallelization strategies attempt to accelerate inference by distributing computation across multiple devices, they typically incur high communication overhead, hindering deployment on commercial hardware. To address this challenge, we propose ParaStep, a novel parallelization method based on a reuse-then-predict mechanism that parallelizes diffusion inference by exploiting similarity between adjacent denoising steps. Unlike prior approaches that rely on layer-wise or stage-wise communication, ParaStep employs lightweight, step-wise communication, substantially reducing overhead. ParaStep achieves end-to-end speedups of up to 3.88times on SVD, 2.43times on CogVideoX-2b, and 6.56times on AudioLDM2-large, while maintaining generation quality. These results highlight ParaStep as a scalable and communication-efficient solution for accelerating diffusion inference, particularly in bandwidth-constrained environments.

Diffusion models are pivotal for generating high-quality images and videos. Inspired by the success of OpenAI's Sora, the backbone of diffusion models is evolving from U-Net to Transformer, known as Diffusion Transformers (DiTs). However, generating high-quality content necessitates longer sequence lengths, exponentially increasing the computation required for the attention mechanism, and escalating DiTs inference latency. Parallel inference is essential for real-time DiTs deployments, but relying on a single parallel method is impractical due to poor scalability at large scales. This paper introduces xDiT, a comprehensive parallel inference engine for DiTs. After thoroughly investigating existing DiTs parallel approaches, xDiT chooses Sequence Parallel (SP) and PipeFusion, a novel Patch-level Pipeline Parallel method, as intra-image parallel strategies, alongside CFG parallel for inter-image parallelism. xDiT can flexibly combine these parallel approaches in a hybrid manner, offering a robust and scalable solution. Experimental results on two 8xL40 GPUs (PCIe) nodes interconnected by Ethernet and an 8xA100 (NVLink) node showcase xDiT's exceptional scalability across five state-of-the-art DiTs. Notably, we are the first to demonstrate DiTs scalability on Ethernet-connected GPU clusters. xDiT is available at https://github.com/xdit-project/xDiT.

Variance reduction (VR) techniques have contributed significantly to accelerating learning with massive datasets in the smooth and strongly convex setting (Schmidt et al., 2017; Johnson & Zhang, 2013; Roux et al., 2012). However, such techniques have not yet met the same success in the realm of large-scale deep learning due to various factors such as the use of data augmentation or regularization methods like dropout (Defazio & Bottou, 2019). This challenge has recently motivated the design of novel variance reduction techniques tailored explicitly for deep learning (Arnold et al., 2019; Ma & Yarats, 2018). This work is an additional step in this direction. In particular, we exploit the ubiquitous clustering structure of rich datasets used in deep learning to design a family of scalable variance reduced optimization procedures by combining existing optimizers (e.g., SGD+Momentum, Quasi Hyperbolic Momentum, Implicit Gradient Transport) with a multi-momentum strategy (Yuan et al., 2019). Our proposal leads to faster convergence than vanilla methods on standard benchmark datasets (e.g., CIFAR and ImageNet). It is robust to label noise and amenable to distributed optimization. We provide a parallel implementation in JAX.

We present a novel Learning from Demonstration (LfD) method, Deformable Manipulation from Demonstrations (DMfD), to solve deformable manipulation tasks using states or images as inputs, given expert demonstrations. Our method uses demonstrations in three different ways, and balances the trade-off between exploring the environment online and using guidance from experts to explore high dimensional spaces effectively. We test DMfD on a set of representative manipulation tasks for a 1-dimensional rope and a 2-dimensional cloth from the SoftGym suite of tasks, each with state and image observations. Our method exceeds baseline performance by up to 12.9% for state-based tasks and up to 33.44% on image-based tasks, with comparable or better robustness to randomness. Additionally, we create two challenging environments for folding a 2D cloth using image-based observations, and set a performance benchmark for them. We deploy DMfD on a real robot with a minimal loss in normalized performance during real-world execution compared to simulation (~6%). Source code is on github.com/uscresl/dmfd

AlphaFold has transformed protein structure prediction, but emerging applications such as virtual ligand screening, proteome-wide folding, and de novo binder design demand predictions at a massive scale, where runtime and memory costs become prohibitive. A major bottleneck lies in the Pairformer backbone of AlphaFold3-style models, which relies on computationally expensive triangular primitives-especially triangle attention-for pairwise reasoning. We introduce Pairmixer, a streamlined alternative that eliminates triangle attention while preserving higher-order geometric reasoning capabilities that are critical for structure prediction. Pairmixer substantially improves computational efficiency, matching state-of-the-art structure predictors across folding and docking benchmarks, delivering up to 4x faster inference on long sequences while reducing training cost by 34%. Its efficiency alleviates the computational burden of downstream applications such as modeling large protein complexes, high-throughput ligand and binder screening, and hallucination-based design. Within BoltzDesign, for example, Pairmixer delivers over 2x faster sampling and scales to sequences ~30% longer than the memory limits of Pairformer.

AlphaFold2 has been hailed as a breakthrough in protein folding. It can rapidly predict protein structures with lab-grade accuracy. However, its implementation does not include the necessary training code. OpenFold is the first trainable public reimplementation of AlphaFold. AlphaFold training procedure is prohibitively time-consuming, and gets diminishing benefits from scaling to more compute resources. In this work, we conducted a comprehensive analysis on the AlphaFold training procedure based on Openfold, identified that inefficient communications and overhead-dominated computations were the key factors that prevented the AlphaFold training from effective scaling. We introduced ScaleFold, a systematic training method that incorporated optimizations specifically for these factors. ScaleFold successfully scaled the AlphaFold training to 2080 NVIDIA H100 GPUs with high resource utilization. In the MLPerf HPC v3.0 benchmark, ScaleFold finished the OpenFold benchmark in 7.51 minutes, shown over 6times speedup than the baseline. For training the AlphaFold model from scratch, ScaleFold completed the pretraining in 10 hours, a significant improvement over the seven days required by the original AlphaFold pretraining baseline.

Scaling the size of language models to tens of billions of parameters has led to impressive performance on a wide range of tasks. At generation, these models are used auto-regressively, requiring a forward pass for each generated token, and thus reading the full set of parameters from memory. This memory access forms the primary bottleneck for generation and it worsens as the model size increases. Moreover, executing a forward pass for multiple tokens in parallel often takes nearly the same time as it does for just one token. These two observations lead to the development of speculative sampling, where a second smaller model is used to draft a few tokens, that are then validated or rejected using a single forward pass of the large model. Unfortunately, this method requires two models that share the same tokenizer and thus limits its adoption. As an alternative, we propose to use parallel decoding as a way to draft multiple tokens from a single model with no computational cost, nor the need for a second model. Our approach only requires an additional input token that marks the words that will be generated simultaneously. We show promising performance (up to 30% speed-up) while requiring only as few as O(d_{emb}) additional parameters.

Large Language Models (LLMs) have demonstrated the ability to tackle increasingly complex tasks through advanced reasoning, long-form content generation, and tool use. Solving these tasks often involves long inference-time computations. In human problem solving, a common strategy to expedite work is collaboration: by dividing the problem into sub-tasks, exploring different strategies concurrently, etc. Recent research has shown that LLMs can also operate in parallel by implementing explicit cooperation frameworks, such as voting mechanisms or the explicit creation of independent sub-tasks that can be executed in parallel. However, each of these frameworks may not be suitable for all types of tasks, which can hinder their applicability. In this work, we propose a different design approach: we run LLM "workers" in parallel , allowing them to synchronize via a concurrently-updated attention cache and prompt these workers to decide how best to collaborate. Our approach allows the instances to come up with their own collaboration strategy for the problem at hand, all the while "seeing" each other's partial progress in the concurrent cache. We implement this approach via Hogwild! Inference: a parallel LLM inference engine where multiple instances of the same LLM run in parallel with the same attention cache, with "instant" access to each other's generated tokens. Hogwild! inference takes advantage of Rotary Position Embeddings (RoPE) to avoid recomputation while improving parallel hardware utilization. We find that modern reasoning-capable LLMs can perform inference with shared Key-Value cache out of the box, without additional fine-tuning.

Speculative decoding (SD) has emerged as a promising technique to accelerate LLM inference by employing a small draft model to propose draft tokens in advance, and validating them in parallel with the large target model. However, the existing SD methods still remain constrained by their serialized execution, which causes the mutual waiting bubbles between the draft and target models. To address this challenge, we draw inspiration from branch prediction in modern processors and propose a novel framework SpecBranch to unlock branch parallelism in SD. Specifically, we first take an in-depth analysis of the potential of branch parallelism in SD, and recognize that the key challenge lies in the trade-offs between parallelization and token rollback. Based on the analysis, we introduce parallel speculative branches to preemptively hedge against likely rejections. Meanwhile, to enhance parallelism, we jointly orchestrate adaptive draft lengths with a hybrid combination of the implicit draft model confidence and explicit reusing of target model features. Extensive experiments across various models and benchmarks show that SpecBranch achieves over 1.8times sim 4.5times speedups against the auto-regressive decoding and reduces rollback tokens by 50\% for poorly aligned models, while maintaining an identical sampling distribution.

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.

Long-horizon reinforcement learning (RL) for large language models faces critical scalability challenges from unbounded context growth, leading to context folding methods that compress interaction history during task execution. However, existing approaches treat summary actions as standard actions, overlooking that summaries fundamentally modify the agent's future observation space, creating a policy-dependent, non-stationary observation distribution that violates core RL assumptions. This introduces three fundamental challenges: (1) gradient dilution where summary tokens receive insufficient training signal, (2) self-conditioning where policy updates change summary distributions, creating a vicious cycle of training collapse, and (3) computational cost from processing unique contexts at each turn. We introduce FoldActhttps://github.com/SHAO-Jiaqi757/FoldAct, a framework that explicitly addresses these challenges through three key innovations: separated loss computation for independent gradient signals on summary and action tokens, full context consistency loss to reduce distribution shift, and selective segment training to reduce computational cost. Our method enables stable training of long-horizon search agents with context folding, addressing the non-stationary observation problem while improving training efficiency with 5.19times speedup.

We consider the problem of antibody sequence design given 3D structural information. Building on previous work, we propose a fine-tuned inverse folding model that is specifically optimised for antibody structures and outperforms generic protein models on sequence recovery and structure robustness when applied on antibodies, with notable improvement on the hypervariable CDR-H3 loop. We study the canonical conformations of complementarity-determining regions and find improved encoding of these loops into known clusters. Finally, we consider the applications of our model to drug discovery and binder design and evaluate the quality of proposed sequences using physics-based methods.

Parallel thinking expands exploration breadth, complementing the deep exploration of information-seeking (IS) agents to further enhance problem-solving capability. However, conventional parallel thinking faces two key challenges in this setting: inefficiency from repeatedly rolling out from scratch, and difficulty in integrating long-horizon reasoning trajectories during answer generation, as limited context capacity prevents full consideration of the reasoning process. To address these issues, we propose ParallelMuse, a two-stage paradigm designed for deep IS agents. The first stage, Functionality-Specified Partial Rollout, partitions generated sequences into functional regions and performs uncertainty-guided path reuse and branching to enhance exploration efficiency. The second stage, Compressed Reasoning Aggregation, exploits reasoning redundancy to losslessly compress information relevant to answer derivation and synthesize a coherent final answer. Experiments across multiple open-source agents and benchmarks demonstrate up to 62% performance improvement with a 10--30% reduction in exploratory token consumption.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

Reasoning LLMs produce longer outputs, requiring speculative decoding drafters trained on extended sequences. Parallel drafting - predicting multiple tokens per forward pass - offers latency benefits over sequential generation, but training complexity scales quadratically with the product of sequence length and parallel positions, rendering long-context training impractical. We present P(arallel)-EAGLE, which transforms EAGLE from autoregressive to parallel multi-token prediction via a learnable shared hidden state. To scale training to long contexts, we develop a framework featuring attention mask pre-computation and sequence partitioning techniques, enabling gradient accumulation within individual sequences for parallel-prediction training. We implement P-EAGLE in vLLM and demonstrate speedups of 1.10-1.36x over autoregressive EAGLE-3 across GPT-OSS 120B, 20B, and Qwen3-Coder 30B.

Fully Sharded Data Parallel (FSDP), also known as ZeRO, is widely used for training large-scale models, featuring its flexibility and minimal intrusion on model code. However, current FSDP systems struggle with structure-aware training methods (e.g., block-wise quantized training) and with non-element-wise optimizers (e.g., Shampoo and Muon) used in cutting-edge models (e.g., Gemini, Kimi K2). FSDP's fixed element- or row-wise sharding formats conflict with the block-structured computations. In addition, today's implementations fall short in communication and memory efficiency, limiting scaling to tens of thousands of GPUs. We introduce veScale-FSDP, a redesigned FSDP system that couples a flexible sharding format, RaggedShard, with a structure-aware planning algorithm to deliver both flexibility and performance at scale. veScale-FSDP natively supports efficient data placement required by FSDP, empowering block-wise quantization and non-element-wise optimizers. As a result, veScale-FSDP achieves 5~66% higher throughput and 16~30% lower memory usage than existing FSDP systems, while scaling efficiently to tens of thousands of GPUs.

The demand for deploying large language models(LLMs) on mobile devices continues to increase, driven by escalating data security concerns and cloud costs. However, network bandwidth and memory limitations pose challenges for deploying billion-level models on mobile devices. In this study, we investigate the outputs of different layers across various scales of LLMs and found that the outputs of most layers exhibit significant similarity. Moreover, this similarity becomes more pronounced as the model size increases, indicating substantial redundancy in the depth direction of the LLMs. Based on this observation, we propose an efficient model volume compression strategy, termed FoldGPT, which combines block removal and block parameter sharing.This strategy consists of three parts: (1) Based on the learnable gating parameters, we determine the block importance ranking while modeling the coupling effect between blocks. Then we delete some redundant layers based on the given removal rate. (2) For the retained blocks, we apply a specially designed group parameter sharing strategy, where blocks within the same group share identical weights, significantly compressing the number of parameters and slightly reducing latency overhead. (3) After sharing these Blocks, we "cure" the mismatch caused by sparsity with a minor amount of fine-tuning and introduce a tail-layer distillation strategy to improve the performance. Experiments demonstrate that FoldGPT outperforms previous state-of-the-art(SOTA) methods in efficient model compression, demonstrating the feasibility of achieving model lightweighting through straightforward block removal and parameter sharing.

Pixel-space continuous-token autoregressive (AR) generation directly models images as sequences of raw pixel patches, avoiding discrete tokenization or a separately pretrained tokenizer. However, it faces coupled challenges: high-dimensional patch generation causes large single-step errors, and teacher-forced training creates a train--inference gap that makes these errors accumulate across AR steps. Existing fixes such as x-prediction and input noise injection only partially mitigate these issues. Exact rollout training better matches inference-time conditions, but is impractical due to prohibitively slow sequential sampling. We propose Parallel Rollout Approximation (PRA), a scalable framework that addresses both challenges jointly. PRA generates low-dimensional intermediate states instead of high-dimensional pixel patches, then maps them back to pixel-space tokens with a pixel decoder, preserving a pixel-in, pixel-out AR interface. It also constructs inference-like pixel inputs through the same intermediate-state-to-pixel path used at inference, independently across positions, approximating the pixel-feedback interface encountered during inference-time rollout while retaining parallel teacher-forced training. On class-conditional ImageNet-1K generation at 256times256 resolution, PRA-S with 135M parameters achieves an FID of 2.58, surpassing the previous billion-scale pixel-space AR result of 3.60. Scaling to PRA-L with 511M parameters further improves FID to 1.94, establishing a new state of the art among pixel-space AR models. Beyond generation, PRA achieves higher ImageNet classification probing accuracy than other AR and diffusion baselines, suggesting its potential for unified pixel-space image generation and understanding.

Vision-language models (VLMs) enable embodied agents to reason and act from visual observations and language instructions. Reinforcement learning (RL) post-training enhances these capabilities using task feedback, but current on-policy RL runtimes execute rollout, reference scoring, and actor training in strict serial phases. While effective for text-only RL, this phase-granular execution is wasteful for VLMs, where processing dense video inputs and prompt prefixes occupies a large fraction of each phase. Because prefix processing is independent of the generated response, it can be run alongside rollout decoding, which leaves GPU compute capacity underutilized, without breaking synchronous on-policy semantics. We present Rollplex, a runtime that decomposes the reference and training phase and moves the prefix computation into the rollout decode window. Realizing this schedule requires more than concurrent kernel launches: naive colocation of Qwen2.5-VL-32\,B requires roughly 165\,GiB per GPU, while rollout and training prefer different tensor-parallel (TP) degrees and weight layouts. Rollplex addresses these constraints with two mechanisms. Phase-aware memory management controls HBM residency according to producer--consumer lifetimes. Parallelism-aware weight sharing uses the same physical storage for layout-compatible tensors across distinct TP degrees and reconstructs only incompatible tensors, avoiding a complete second actor copy. On 32 H800 GPUs, Rollplex achieves 1.23times--1.30times speedup over serial colocation and 1.57times--2.24times over disaggregation under the same GPU budget, while preserving the synchronous RL update.

Mixture-of-Experts (MoE) models scale capacity for strong quality while keeping per-token compute bounded through sparse expert activation. Yet low-latency MoE serving is increasingly challenging, because it spans two inference phases with fundamentally different bottlenecks: prefill is dominated by token-wise expert computation, whereas decode is constrained by memory traffic from the batch-wise activated expert set. However, existing training-free acceleration methods optimize only a single resource proxy, either the experts each token executes or the experts a batch activates, and either discard the excluded experts' contribution or leave it only implicitly approximated. In this paper, we propose ExFold, a unified training-free expert-folding framework for jointly accelerating MoE prefill and decode. ExFold casts both prefill and decode as one budgeted output-approximation problem: execute only a phase-specific constrained expert set while projecting the contribution of budget-excluded experts onto retained experts using calibrated scalar projectors. Motivated by the observation that many expert outputs are directionally aligned but differ in magnitude, ExFold calibrates a pairwise scalar-projector matrix on unlabeled data and uses it at inference time to fold excluded expert contributions into retained experts. Under this view, prefill acceleration becomes token-level Top-K folding, and decode acceleration becomes batch-level expert-pool folding. The two phases differ only in how retained experts are selected, while excluded contributions are recovered by one shared folding mechanism. We implement ExFold as a plug-and-play plugin in vLLM, with a lightweight expert-folding CUDA kernel, delivering up to 1.41x TTFT and 2.45x TPOT speedups while retaining about 99% of the original average quality.

Recent advances in large language models (LLMs) have accelerated progress toward artificial general intelligence, with inference-time scaling emerging as a key technique. Contemporary approaches leverage either sequential reasoning (iteratively extending chains of thought) or parallel reasoning (generating multiple solutions simultaneously) to scale inference. However, both paradigms face fundamental limitations: sequential scaling typically relies on arbitrary token budgets for termination, leading to inefficiency or premature cutoff; while parallel scaling often lacks coordination among parallel branches and requires intrusive fine-tuning to perform effectively. In light of these challenges, we aim to design a flexible test-time collaborative inference framework that exploits the complementary strengths of both sequential and parallel reasoning paradigms. Towards this goal, the core challenge lies in developing an efficient and accurate intrinsic quality metric to assess model responses during collaborative inference, enabling dynamic control and early termination of the reasoning trace. To address this challenge, we introduce semantic entropy (SE), which quantifies the semantic diversity of parallel model responses and serves as a robust indicator of reasoning quality due to its strong negative correlation with accuracy...

Autoregressive decoding in Large Language Models (LLMs) is inherently sequential, creating a latency bottleneck that scales linearly with output length. While ``Decomposition-and-Fill'' methods like Skeleton-of-Thought attempt to parallelize generation via external orchestration, they suffer from coherence drift due to the lack of cross-stream communication. In this work, we introduce the Parallel Decoder Transformer (PDT), a parameter-efficient architecture that embeds coordination primitives directly into the inference process of a frozen pre-trained model. Instead of retraining the base model, PDT injects lightweight Speculative Note Conditioning (SNC) adapters that allow parallel decoding streams to synchronize via a shared, dynamic latent space. We formulate coordination as a speculative consensus problem, where sibling streams broadcast semantic ``notes'' to a global bus, gated by a learned verification head. We validate our approach on a 50,000-step curriculum using a frozen 20B-parameter backbone. Our results demonstrate that PDT achieves effective self-correction, reaching 77.8\% precision in coverage prediction and recovering approximate serial semantics without modifying the trunk weights. This establishes PDT as a scalable, efficient alternative to full model fine-tuning for structured parallel generation.

Scientific poster construction compresses a long multimodal paper into a readable, editable canvas. Existing systems hide request-level failures by scoring only completed outputs; direct image generation is not element-editable, while coding-agent workflows are costly. PosterMELD is a template-conditioned multi-agent pipeline: capacity-aware slots guide writing before rendering, and deterministic gates plus vision-language model (VLM) review route failures to bounded repair. Each accepted request exports editable PowerPoint (PPTX) and Portable Network Graphics (PNG) artifacts; explicit design controls yield same-paper variants. Across 621 papers, Print-Ready Rate (PRR) counts requests passing geometric, readability, asset-integrity, and obvious-factual-error checks, with native editability reported separately. A frozen VLM assigns conditional Craftsmanship-Harmony-Expressiveness (CHE) scores to print-ready outputs. PosterMELD attains 81.3% PRR, 3.4 times P2P's rate and 5.2 times PosterGen's, and the highest conditional CHE among generated methods with multiple print-ready outputs. Native editability and explicit design controls are retained at a mean cost of USD 0.38 per request, 3.5% of Codex+Skill's. Code and resources are available at https://github.com/Shannon4Science/PosterMELD.

Training large language models (LLMs) with increasingly long and varying sequence lengths introduces severe load imbalance challenges in large-scale data-parallel training. Recent frameworks attempt to mitigate these issues through data reorganization or hybrid parallel strategies. However, they often overlook how computational and communication costs scale with sequence length, resulting in suboptimal performance. We identify three critical challenges: (1) varying computation-to-communication ratios across sequences of different lengths in distributed attention, (2) mismatch between static NIC-GPU affinity and dynamic parallel workloads, and (3) distinct optimal partitioning strategies required for quadratic attention versus linear components. To address these challenges, we present Zeppelin, a novel training system that integrates three key techniques: (1) a hierarchical sequence partitioning method for the attention module that reduces communication overhead and balances computation, supported by an efficient attention engine that applies divergent parallel strategies; (2) a routing layer that orchestrates inter-node transfers to fully utilize NIC bandwidth; and (3) a remapping layer that transforms sequence layouts between attention and linear modules, ensuring high computational efficiency across both. Comprehensive evaluations across diverse configurations show that Zeppelin delivers an average 2.80x speedup over state-of-the-art methods.

Autoregressive models (ARMs) are hindered by slow sequential inference. While masked diffusion models (MDMs) offer a parallel alternative, they suffer from critical drawbacks: high computational overhead from precluding Key-Value (KV) caching, and incoherent generation arising from learning dependencies over an intractable space of token combinations. To address these limitations, we introduce ReFusion, a novel masked diffusion model that achieves superior performance and efficiency by elevating parallel decoding from the token level to a higher slot level, where each slot is a fixed-length, contiguous sub-sequence. This is achieved through an iterative ``plan-and-infill'' decoding process: a diffusion-based planning step first identifies a set of weakly dependent slots, and an autoregressive infilling step then decodes these selected slots in parallel. The slot-based design simultaneously unlocks full KV cache reuse with a unified causal framework and reduces the learning complexity from the token combination space to a manageable slot-level permutation space. Extensive experiments on seven diverse benchmarks show that ReFusion not only overwhelmingly surpasses prior MDMs with 34% performance gains and an over 18times speedup on average, but also bridges the performance gap to strong ARMs while maintaining a 2.33times average speedup.

Scaling inference-time computation has enabled Large Language Models (LLMs) to achieve strong reasoning performance, but inherently sequential decoding leads to substantial latency, especially on complex tasks. Recent work on adaptive parallel reasoning aims to improve inference efficiency by decomposing the problem-solving process into concurrent reasoning threads when beneficial. However, existing methods on realistic tasks are either limited to supervised behavior cloning or exhibit significant accuracy drops compared to widely-used sequential long chain-of-thought (CoT) baselines. Moreover, many require customized inference engines, complicating deployment. We introduce ThreadWeaver, a framework for adaptive parallel reasoning that achieves accuracy on par with popular sequential reasoning models of comparable size while significantly reducing inference latency. ThreadWeaver's performance stems from three key innovations: 1) a two-stage parallel trajectory generator that produces large-scale, high-quality CoT data with parallel annotations for supervised fine-tuning; 2) a trie-based training-inference co-design that enables parallel reasoning on any off-the-shelf autoregressive inference engine without modifying position embeddings or KV caches; and 3) a parallelization-aware reinforcement learning framework that teaches the model to balance accuracy with effective parallelization. Across six challenging mathematical reasoning benchmarks, ThreadWeaver trained atop Qwen3-8B achieves accuracy comparable to cutting-edge sequential reasoning models (71.9% on average and 79.9% on AIME24) while delivering up to 1.53x average speedup in token latency, establishing a new Pareto frontier between accuracy and efficiency.

Diffusion language models enable flexible arbitrary-order generation, but existing sampling methods are mostly designed for early masked diffusion models (MDMs). In this work, we study sampling for recent block diffusion language models (BDLMs). We show empirically and analytically that these models are naturally more aligned with left-to-right decoding than MDMs. Based on this observation, we propose Parallel Autoregressive Decoding (PARD), a simple training-free sampling method that preserves left-to-right unmasking structure while allowing parallel token commitment. Extensive experiments show that PARD consistently outperforms existing parallel samplers in generation quality, while achieving substantial speedups over pure AR decoding with only a small quality gap.

Voronoi diagrams are essential geometrical structures with numerous applications, particularly astrophysics-driven finite volume methods. While serial algorithms for constructing these entities are well-established, parallel construction remains challenging. This is especially true in distributed memory systems, where each host manages only a subset of the input points. This process requires redistributing points across hosts and accurately computing the corresponding Voronoi cells. In this paper, we introduce a new distributed construction algorithm, which is implemented in our open-source C++ 3-dimensional Voronoi construction framework. Our approach leverages Delaunay triangulation as an intermediate step, which is then transformed into a Voronoi diagram. We introduce the algorithms we implemented for the precise construction and our load-balancing approach and compare the running time with other state-of-the-art frameworks. MadVoro is a versatile tool that can be applied in various scientific domains, such as mesh decomposition, computational physics, chemistry, and machine learning.

Speculative decoding mitigates the latency of sequential generation in autoregressive Large Language Models (LLMs) by interleaving draft generation with target verification. However, existing parallel drafting backends often suffer from rapid accuracy degradation over long horizons, leading to high rejection rates during verification and suboptimal wall-clock speedups. We observe that drafting errors are not uniformly distributed but typically stem from localized high-uncertainty tokens that destabilize downstream generation trajectories. Motivated by this token error pattern, we propose CURE, a budget-aware dynamic repair tree designed to repair errors at uncertainty focal points without incurring prohibitive tree-verification overheads. Specifically, our method uses predictive confidence margins to dynamically locate candidate error tokens within a block-parallel draft, expands bounded repair paths only at these fragile nodes, and employs a novel repair resynchronization mechanism to realign draft states post-verification. Evaluations on code-generation benchmarks (HumanEval, MBPP, and LiveCodeBench-lite) and mathematical reasoning benchmark (GSM8K) demonstrate that CURE increases the average accepted length by 4.2-7.5% over parallel baselines without repair, translating to an end-to-end speedup of 2.66-3.49times over target-only decoding. Furthermore, we provide a plug-and-play repair module compatible with standard parallel drafting frameworks. We also characterize the trade-off between draft compute and verification efficiency.

Diffusion large language models (dLLMs) have recently drawn considerable attention within the research community as a promising alternative to autoregressive generation, offering parallel token prediction and lower inference latency. Yet, their parallel decoding potential remains largely underexplored, as existing open-source models still require nearly token-length decoding steps to ensure performance. To address this, we introduce dParallel, a simple and effective method that unlocks the inherent parallelism of dLLMs for fast sampling. We identify that the key bottleneck to parallel decoding arises from the sequential certainty convergence for masked tokens. Building on this insight, we introduce the core of our approach: certainty-forcing distillation, a novel training strategy that distills the model to follow its original sampling trajectories while enforcing it to achieve high certainty on masked tokens more rapidly and in parallel. Extensive experiments across various benchmarks demonstrate that our method can dramatically reduce the number of decoding steps while maintaining performance. When applied to the LLaDA-8B-Instruct model, dParallel reduces decoding steps from 256 to 30 on GSM8K, achieving an 8.5x speedup without performance degradation. On the MBPP benchmark, it cuts decoding steps from 256 to 24, resulting in a 10.5x speedup while maintaining accuracy. Our code is available at https://github.com/czg1225/dParallel

The advent of test-time scaling in large language models (LLMs), exemplified by OpenAI's o1 series, has advanced reasoning capabilities by scaling computational resource allocation during inference. While successors like QwQ, Deepseek-R1 (R1) and LIMO replicate these advancements, whether these models truly possess test-time scaling capabilities remains underexplored. This study found that longer CoTs of these o1-like models do not consistently enhance accuracy; in fact, correct solutions are often shorter than incorrect ones for the same questions. Further investigation shows this phenomenon is closely related to models' self-revision capabilities - longer CoTs contain more self-revisions, which often lead to performance degradation. We then compare sequential and parallel scaling strategies on QwQ, R1 and LIMO, finding that parallel scaling achieves better coverage and scalability. Based on these insights, we propose Shortest Majority Vote, a method that combines parallel scaling strategies with CoT length characteristics, significantly improving models' test-time scalability compared to conventional majority voting approaches.

RNA design aims to identify sequences that fold into specified secondary structures. Existing methods formulate the task as target-specific search or conditional generation. However, natural RNA evolution proceeds through sequence variation and selection, with compensatory substitutions, whereas these methods do not explicitly model this process. To address this limitation, we propose a two-stage framework comprising RNA Inverse-Folding Flow (RNA-IFlow) and RNA-IFlow-RL. RNA-IFlow uses structure-conditioned Dirichlet Flow Matching to model coordinated variation across the sequence, while RNA-IFlow-RL maps the learned flow to a pairing-preserving finite policy and refines it with thermodynamic feedback. Our framework achieves leading performance on multiple benchmarks, reaching 85.19% Pass@1 on Rfam-27. Further analyses reveal thermodynamic gains, policy dynamics, and robustness across settings. Our work couples coordinated variation with thermodynamic selection, offering a novel paradigm for RNA design.

While thinking-aware generation aims to improve performance on complex tasks, we identify a critical failure mode where existing sequential, autoregressive approaches can paradoxically degrade performance due to error propagation. To systematically analyze this issue, we propose ParaBench, a new benchmark designed to evaluate both text and image output modalities. Our analysis using ParaBench reveals that this performance degradation is strongly correlated with poor alignment between the generated reasoning and the final image. To resolve this, we propose a parallel multimodal diffusion framework, MMaDA-Parallel, that enables continuous, bidirectional interaction between text and images throughout the entire denoising trajectory. MMaDA-Parallel is trained with supervised finetuning and then further optimized by Parallel Reinforcement Learning (ParaRL), a novel strategy that applies semantic rewards along the trajectory to enforce cross-modal consistency. Experiments validate that our model significantly improves cross-modal alignment and semantic consistency, achieving a 6.9\% improvement in Output Alignment on ParaBench compared to the state-of-the-art model, Bagel, establishing a more robust paradigm for thinking-aware image synthesis. Our code is open-sourced at https://github.com/tyfeld/MMaDA-Parallel

Reasoning training incentivizes LLMs to produce long chains of thought (long CoT), which among other things, allows them to explore solution strategies with self-checking. This results in higher accuracy, but inflates context length, token/compute cost, and answer latency. We ask: Can current models leverage their metacognition to provide other combinations on this Pareto frontier, e.g., better accuracy with lower context length and/or latency? Abstractly, we view the model as an improvement operator on its own "thoughts" with a continuum of possible strategies. We identify an interesting inference family Parallel-Distill-Refine (PDR), which performs the following: (i) generate diverse drafts in parallel; (ii) distill them into a bounded, textual workspace; and (iii) refine conditioned on this workspace, producing an output that seeds the next round. Importantly, context length (hence compute cost) is controllable via degree of parallelism, and is no longer conflated with the total number of generated tokens. We report PDR instantiations of current models that give better accuracy than long CoT while incurring lower latency. Setting degree of parallelism to 1 yields an interesting subcase, Sequential Refinement (SR) (iteratively improve a single candidate answer) which provides performance superior to long CoT. Success of such model orchestrations raises the question whether further training could shift the Pareto frontier. To this end, we train an 8B thinking model with Reinforcement Learning (RL) to make it consistent with PDR as the inference method. On math tasks with verifiable answers, iterative pipelines surpass single-pass baselines at matched sequential budgets, with PDR delivering the largest gains (e.g., +11% on AIME 2024 and +9% on AIME 2025).

Scaling multi-dimensional transformers to long sequences is indispensable across various domains. However, the challenges of large memory requirements and slow speeds of such sequences necessitate sequence parallelism. All existing approaches fall under the category of embedded sequence parallelism, which are limited to shard along a single sequence dimension, thereby introducing significant communication overhead. However, the nature of multi-dimensional transformers involves independent calculations across multiple sequence dimensions. To this end, we propose Dynamic Sequence Parallelism (DSP) as a novel abstraction of sequence parallelism. DSP dynamically switches the parallel dimension among all sequences according to the computation stage with efficient resharding strategy. DSP offers significant reductions in communication costs, adaptability across modules, and ease of implementation with minimal constraints. Experimental evaluations demonstrate DSP's superiority over state-of-the-art embedded sequence parallelism methods by remarkable throughput improvements ranging from 32.2% to 10x, with less than 25% communication volume.

Large language models have shown remarkable performance across a wide range of language tasks, owing to their exceptional capabilities in context modeling. The most commonly used method of context modeling is full self-attention, as seen in standard decoder-only Transformers. Although powerful, this method can be inefficient for long sequences and may overlook inherent input structures. To address these problems, an alternative approach is parallel context encoding, which splits the context into sub-pieces and encodes them parallelly. Because parallel patterns are not encountered during training, naively applying parallel encoding leads to performance degradation. However, the underlying reasons and potential mitigations are unclear. In this work, we provide a detailed analysis of this issue and identify that unusually high attention entropy can be a key factor. Furthermore, we adopt two straightforward methods to reduce attention entropy by incorporating attention sinks and selective mechanisms. Experiments on various tasks reveal that these methods effectively lower irregular attention entropy and narrow performance gaps. We hope this study can illuminate ways to enhance context modeling mechanisms.

Training-free high-resolution (HR) image generation has garnered significant attention due to the high costs of training large diffusion models. Most existing methods begin by reconstructing the overall structure and then proceed to refine the local details. Despite their advancements, they still face issues with repetitive patterns in HR image generation. Besides, HR generation with diffusion models incurs significant computational costs. Thus, parallel generation is essential for interactive applications. To solve the above limitations, we introduce a novel method named ASGDiffusion for parallel HR generation with Asynchronous Structure Guidance (ASG) using pre-trained diffusion models. To solve the pattern repetition problem of HR image generation, ASGDiffusion leverages the low-resolution (LR) noise weighted by the attention mask as the structure guidance for the denoising step to ensure semantic consistency. The proposed structure guidance can significantly alleviate the pattern repetition problem. To enable parallel generation, we further propose a parallelism strategy, which calculates the patch noises and structure guidance asynchronously. By leveraging multi-GPU parallel acceleration, we significantly accelerate generation speed and reduce memory usage per GPU. Extensive experiments demonstrate that our method effectively and efficiently addresses common issues like pattern repetition and achieves state-of-the-art HR generation.

Context-augmented generation (CAG) techniques, including RAG and ICL, require the efficient combination of multiple contexts to generate responses to user queries. Directly inputting these contexts as a sequence introduces a considerable computational burden by re-encoding the combined selection of contexts for every request. To address this, we explore the promising potential of parallel encoding to independently pre-compute and cache each context's KV states. This approach enables the direct loading of cached states during inference while accommodating more contexts through position reuse across contexts. However, due to misalignments in attention distribution, directly applying parallel encoding results in a significant performance drop. To enable effective and efficient CAG, we propose Adaptive Parallel Encoding (APE), which brings shared prefix, attention temperature, and scaling factor to align the distribution of parallel encoding with sequential encoding. Results on RAG and ICL tasks demonstrate that APE can preserve 98% and 93% sequential encoding performance using the same inputs while outperforming parallel encoding by 3.6% and 7.9%, respectively. It also scales to many-shot CAG, effectively encoding hundreds of contexts in parallel. Efficiency evaluation shows that APE can achieve an end-to-end 4.5times speedup by reducing 28times prefilling time for a 128K-length context.

Diffusion models have achieved great success in synthesizing high-quality images. However, generating high-resolution images with diffusion models is still challenging due to the enormous computational costs, resulting in a prohibitive latency for interactive applications. In this paper, we propose DistriFusion to tackle this problem by leveraging parallelism across multiple GPUs. Our method splits the model input into multiple patches and assigns each patch to a GPU. However, na\"{\i}vely implementing such an algorithm breaks the interaction between patches and loses fidelity, while incorporating such an interaction will incur tremendous communication overhead. To overcome this dilemma, we observe the high similarity between the input from adjacent diffusion steps and propose displaced patch parallelism, which takes advantage of the sequential nature of the diffusion process by reusing the pre-computed feature maps from the previous timestep to provide context for the current step. Therefore, our method supports asynchronous communication, which can be pipelined by computation. Extensive experiments show that our method can be applied to recent Stable Diffusion XL with no quality degradation and achieve up to a 6.1times speedup on eight NVIDIA A100s compared to one. Our code is publicly available at https://github.com/mit-han-lab/distrifuser.

Parallel thinking has emerged as a new paradigm for large reasoning models (LRMs) in tackling complex problems. Recent methods leverage Reinforcement Learning (RL) to enhance parallel thinking, aiming to address the limitations in computational resources and effectiveness encountered with supervised fine-tuning. However, most existing studies primarily focus on optimizing the aggregation phase, with limited attention to the path exploration stage. In this paper, we theoretically analyze the optimization of parallel thinking under the Reinforcement Learning with Verifiable Rewards (RLVR) setting, and identify that the mutual information bottleneck among exploration paths fundamentally restricts overall performance. To address this, we propose Outline-Guided Path Exploration (OPE), which explicitly partitions the solution space by generating diverse reasoning outlines prior to parallel path reasoning, thereby reducing information redundancy and improving the diversity of information captured across exploration paths. We implement OPE with an iterative RL strategy that optimizes outline planning and outline-guided reasoning independently. Extensive experiments across multiple challenging mathematical benchmarks demonstrate that OPE effectively improves reasoning performance in different aggregation strategies, enabling LRMs to more reliably discover correct solutions.

Parallel thinking has emerged as a novel approach for enhancing the reasoning capabilities of large language models (LLMs) by exploring multiple reasoning paths concurrently. However, activating such capabilities through training remains challenging, as existing methods predominantly rely on supervised fine-tuning (SFT) over synthetic data, which encourages teacher-forced imitation rather than exploration and generalization. Different from them, we propose Parallel-R1, the first reinforcement learning (RL) framework that enables parallel thinking behaviors for complex real-world reasoning tasks. Our framework employs a progressive curriculum that explicitly addresses the cold-start problem in training parallel thinking with RL. We first use SFT on prompt-generated trajectories from easier tasks to instill the parallel thinking ability, then transition to RL to explore and generalize this skill on harder problems. Experiments on various math benchmarks, including MATH, AMC23, and AIME, show that Parallel-R1 successfully instills parallel thinking, leading to 8.4% accuracy improvements over the sequential thinking model trained directly on challenging tasks with RL. Further analysis reveals a clear shift in the model's thinking behavior: at an early stage, it uses parallel thinking as an exploration strategy, while in a later stage, it uses the same capability for multi-perspective verification. Most significantly, we validate parallel thinking as a mid-training exploration scaffold, where this temporary exploratory phase unlocks a higher performance ceiling after RL, yielding a 42.9% improvement over the baseline on AIME25. Our model, data, and code will be open-source at https://github.com/zhengkid/Parallel-R1.

Test-Time Scaling (TTS) enhances the reasoning capabilities of large language models by allocating additional inference compute to explore the solution space. However, existing parallel TTS methods typically keep branches isolated during search: intermediate discoveries remain branch-private and cannot guide other branches in time. This information isolation causes substantial redundant exploration, as branches repeatedly rediscover information already found elsewhere and require more search steps to collect complete decision information needed to reach correct answers. To bridge this gap, we propose Collaborative Parallel Thinking (CPT), a training-free inference framework that enables search-time information sharing across parallel branches. CPT extracts compact intermediate information from ongoing branches, maintains a deduplicated query-level information pool, and broadcasts pool entries through the input context, allowing each branch in subsequent search steps to reuse discoveries made by other branches rather than rediscover the same information. Empirically, experiments on HMMT and AIME benchmarks show that CPT establishes a stronger accuracy--latency Pareto frontier than strong baselines across rollout budgets and model scales, highlighting search-time collaboration as an effective direction for efficient parallel TTS.

Efficient teamwork typically combines global coordination with parallel execution, a principle not yet fully reflected in unified Vision-Language Model (VLM)-based document parsers. Existing unified parsers process an entire page jointly but generate its output through a single token-by-token autoregressive trajectory, creating a sequential bottleneck that grows with document length. Such full-page sequential generation overlooks a key property of document parsing: layout must be analyzed globally, whereas block content can be parsed in parallel. Based on this observation, we introduce HPD-Parsing, which replaces full-page autoregressive generation with a Hierarchical Parallel Decoding paradigm. A main layout branch organizes the overall document structure and dynamically assigns block-level content decoding to concurrent branches, while progressive multi-token prediction (P-MTP) further reduces the decoding steps within each branch. Experiments on public benchmarks show that HPD-Parsing achieves 4,752 tokens per second, delivering 2.62times the throughput of the fastest existing document parsing model and 3.06times that of the vanilla autoregressive baseline, while maintaining competitive parsing accuracy. These results establish hierarchical parallel decoding as an effective alternative to full-page autoregressive generation, opening a new direction for efficient unified document parsing.

Multi-turn LLM serving accumulates dialogue history whose Key-Value (KV) cache grows with every turn and every user, quickly exceeding the model weights themselves and making memory -- not compute -- the binding constraint on throughput. Non-uniform KV compression, which allocates heterogeneous budgets across attention heads, preserves accuracy far better than uniform schemes, yet remains impractical: modern serving stacks assume identical KV lengths across heads, so heterogeneity traps freed memory as page fragmentation, spends up to 25% of prefill time reclaiming scattered pages, and skews GPU workloads that inflate decode latency by up to 1.7times or burn 15--20% of each decode step on re-planning. We observe that this heterogeneity need not be discovered at runtime: head-wise retention follows a two-level structural regularity -- an input-invariant head ranking with narrowly bounded per-head ratios -- that can be calibrated offline from as few as 50 samples. Building on this insight, we present Tangram, a serving framework that statically resolves what prior systems handle dynamically: Budget Reservation fixes each head's post-compression footprint at scheduling time, eliminating page reclamation; Ragged Paging clusters similar-budget heads into independent page tables, turning fragmentation into reclaimable memory; and Ahead-of-Time Load Balancing precomputes balanced GPU partitions with zero runtime planning. Implemented on vLLM, Tangram serves as a drop-in substrate for existing non-uniform compression methods, matching their accuracy while improving end-to-end throughput by up to 2.6times over the full-KV baseline. Our implementation is publicly available at https://github.com/aiha-lab/TANGRAM.