Xuanlei Zhao

Shenggan Cheng, Xuanlei Zhao, Guangyang Lu et al. · berkeley

Protein structure prediction helps to understand gene translation and protein function, which is of growing interest and importance in structural biology. The AlphaFold model, which used transformer architecture to achieve atomic-level accuracy in protein structure prediction, was a significant breakthrough. However, training and inference of the AlphaFold model are challenging due to its high computation and memory cost. In this work, we present FastFold, an efficient implementation of AlphaFold for both training and inference. We propose Dynamic Axial Parallelism and Duality Async Operations to improve the scaling efficiency of model parallelism. Besides, AutoChunk is proposed to reduce memory cost by over 80% during inference by automatically determining the chunk strategy. Experimental results show that FastFold reduces overall training time from 11 days to 67 hours and achieves 7.5X - 9.5X speedup for long-sequence inference. Furthermore, we scale FastFold to 512 GPUs and achieve an aggregate throughput of 6.02 PetaFLOP/s with 90.1% parallel efficiency.

Xuanlei Zhao, Xiaolong Jin, Kai Wang et al.

We present Pyramid Attention Broadcast (PAB), a real-time, high quality and training-free approach for DiT-based video generation. Our method is founded on the observation that attention difference in the diffusion process exhibits a U-shaped pattern, indicating significant redundancy. We mitigate this by broadcasting attention outputs to subsequent steps in a pyramid style. It applies different broadcast strategies to each attention based on their variance for best efficiency. We further introduce broadcast sequence parallel for more efficient distributed inference. PAB demonstrates up to 10.5x speedup across three models compared to baselines, achieving real-time generation for up to 720p videos. We anticipate that our simple yet effective method will serve as a robust baseline and facilitate future research and application for video generation.

Ziqiao Wang, Wangbo Zhao, Yuhao Zhou et al.

Diffusion Transformers (DiTs) deliver state-of-the-art image quality, yet their training remains notoriously slow. A recent remedy -- representation alignment (REPA) that matches DiT hidden features to those of a non-generative teacher (e.g. DINO) -- dramatically accelerates the early epochs but plateaus or even degrades performance later. We trace this failure to a capacity mismatch: once the generative student begins modelling the joint data distribution, the teacher's lower-dimensional embeddings and attention patterns become a straitjacket rather than a guide. We then introduce HASTE (Holistic Alignment with Stage-wise Termination for Efficient training), a two-phase schedule that keeps the help and drops the hindrance. Phase I applies a holistic alignment loss that simultaneously distills attention maps (relational priors) and feature projections (semantic anchors) from the teacher into mid-level layers of the DiT, yielding rapid convergence. Phase II then performs one-shot termination that deactivates the alignment loss, once a simple trigger such as a fixed iteration is hit, freeing the DiT to focus on denoising and exploit its generative capacity. HASTE speeds up training of diverse DiTs without architecture changes. On ImageNet 256X256, it reaches the vanilla SiT-XL/2 baseline FID in 50 epochs and matches REPA's best FID in 500 epochs, amounting to a 28X reduction in optimization steps. HASTE also improves text-to-image DiTs on MS-COCO, demonstrating to be a simple yet principled recipe for efficient diffusion training across various tasks. Our code is available at https://github.com/NUS-HPC-AI-Lab/HASTE .

Mengxuan Wu, Zekai Li, Zhiyuan Liang et al.

Mamba-based vision models have gained extensive attention as a result of being computationally more efficient than attention-based models. However, spatial redundancy still exists in these models, represented by token and block redundancy. For token redundancy, we analytically find that early token pruning methods will result in inconsistency between training and inference or introduce extra computation for inference. Therefore, we customize token pruning to fit the Mamba structure by rearranging the pruned sequence before feeding it into the next Mamba block. For block redundancy, we allow each image to select SSM blocks dynamically based on an empirical observation that the inference speed of Mamba-based vision models is largely affected by the number of SSM blocks. Our proposed method, Dynamic Vision Mamba (DyVM), effectively reduces FLOPs with minor performance drops. We achieve a reduction of 35.2\% FLOPs with only a loss of accuracy of 1.7\% on Vim-S. It also generalizes well across different Mamba vision model architectures and different vision tasks. Our code will be made public.

Geng Zhang, Shenggan Cheng, Xuanlei Zhao et al.

As transformer sequence lengths grow, existing pipeline parallelisms incur suboptimal performance due to the quadratic attention computation and the substantial memory overhead. To relieve these challenges, we propose HelixPipe, a novel pipeline parallelism for long sequence transformer training. First, HelixPipe introduces attention parallel partition, which schedules attention computations of different micro batches across different pipeline stages in parallel, reducing pipeline bubbles. Second, it employs a two-fold first-in-last-out micro batch schedule to balance memory usage and overlap communication with computation. Additionally, HelixPipe utilizes recomputation without attention and chunked MLP to mitigate fragmentation and enable longer sequences. Experiments demonstrate that HelixPipe gains increasing advantages with longer sequence lengths, and outperforms existing methods in throughput and scalability across varying pipeline sizes, model sizes, and cluster configurations. Notably, it achieves a 26\% speedup over baseline methods when training a 7B model with 128k sequence length on 64 H20 GPUs. Code is available at https://github.com/code-tunnel/Megatron-LM/tree/dev.

Xuanlei Zhao, Shenggan Cheng, Chang Chen et al.

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.

Zekai Li, Xinhao Zhong, Samir Khaki et al.

In recent years, dataset distillation has provided a reliable solution for data compression, where models trained on the resulting smaller synthetic datasets achieve performance comparable to those trained on the original datasets. To further improve the performance of synthetic datasets, various training pipelines and optimization objectives have been proposed, greatly advancing the field of dataset distillation. Recent decoupled dataset distillation methods introduce soft labels and stronger data augmentation during the post-evaluation phase and scale dataset distillation up to larger datasets (e.g., ImageNet-1K). However, this raises a question: Is accuracy still a reliable metric to fairly evaluate dataset distillation methods? Our empirical findings suggest that the performance improvements of these methods often stem from additional techniques rather than the inherent quality of the images themselves, with even randomly sampled images achieving superior results. Such misaligned evaluation settings severely hinder the development of DD. Therefore, we propose DD-Ranking, a unified evaluation framework, along with new general evaluation metrics to uncover the true performance improvements achieved by different methods. By refocusing on the actual information enhancement of distilled datasets, DD-Ranking provides a more comprehensive and fair evaluation standard for future research advancements.

Zhiyuan Liang, Dongwen Tang, Yuhao Zhou et al.

Modern Parameter-Efficient Fine-Tuning (PEFT) methods such as low-rank adaptation (LoRA) reduce the cost of customizing large language models (LLMs), yet still require a separate optimization run for every downstream dataset. We introduce \textbf{Drag-and-Drop LLMs (\textit{DnD})}, a prompt-conditioned parameter generator that eliminates per-task training by mapping a handful of unlabeled task prompts directly to LoRA weight updates. A lightweight text encoder distills each prompt batch into condition embeddings, which are then transformed by a cascaded hyper-convolutional decoder into the full set of LoRA matrices. Once trained in a diverse collection of prompt-checkpoint pairs, DnD produces task-specific parameters in seconds, yielding i) up to \textbf{12,000$\times$} lower overhead than full fine-tuning, ii) average gains up to \textbf{30\%} in performance over the strongest training LoRAs on unseen common-sense reasoning, math, coding, and multimodal benchmarks, and iii) robust cross-domain generalization despite never seeing the target data or labels. Our results demonstrate that prompt-conditioned parameter generation is a viable alternative to gradient-based adaptation for rapidly specializing LLMs. Our project is available at \href{https://jerryliang24.github.io/DnD}{https://jerryliang24.github.io/DnD}.

Yang Luo, Xuanlei Zhao, Mengzhao Chen et al.

DiT-based video generation has achieved remarkable results, but research into enhancing existing models remains relatively unexplored. In this work, we introduce a training-free approach to enhance the coherence and quality of DiT-based generated videos, named Enhance-A-Video. The core idea is enhancing the cross-frame correlations based on non-diagonal temporal attention distributions. Thanks to its simple design, our approach can be easily applied to most DiT-based video generation frameworks without any retraining or fine-tuning. Across various DiT-based video generation models, our approach demonstrates promising improvements in both temporal consistency and visual quality. We hope this research can inspire future explorations in video generation enhancement.

Mingjia Shi, Yuhao Zhou, Ruiji Yu et al.

Vision Mamba has shown close to state of the art performance on computer vision tasks, drawing much interest in increasing it's efficiency. A promising approach is token reduction (that has been successfully implemented in ViTs). Pruning informative tokens in Mamba leads to a high loss of key knowledge and degraded performance. An alternative, of merging tokens preserves more information than pruning, also suffers for large compression ratios. Our key insight is that a quick round of retraining after token merging yeilds robust results across various compression ratios. Empirically, pruned Vims only drop up to 0.9% accuracy on ImageNet-1K, recovered by our proposed framework R-MeeTo in our main evaluation. We show how simple and effective the fast recovery can be achieved at minute-level, in particular, a 35.9% accuracy spike over 3 epochs of training on Vim-Ti. Moreover, Vim-Ti/S/B are re-trained within 5/7/17 minutes, and Vim-S only drops 1.3% with 1.2x (up to 1.5x) speed up in inference.

Yang Luo, Xuanlei Zhao, Baijiong Lin et al.

Recent progress in generative video models, such as Veo-3, has shown surprising zero-shot reasoning abilities, creating a growing need for systematic and reliable evaluation. We introduce V-ReasonBench, a benchmark designed to assess video reasoning across four key dimensions: structured problem-solving, spatial cognition, pattern-based inference, and physical dynamics. The benchmark is built from both synthetic and real-world image sequences and provides a diverse set of answer-verifiable tasks that are reproducible, scalable, and unambiguous. Evaluations of six state-of-the-art video models reveal clear dimension-wise differences, with strong variation in structured, spatial, pattern-based, and physical reasoning. We further compare video models with strong image models, analyze common hallucination behaviors, and study how video duration affects Chain-of-Frames reasoning. Overall, V-ReasonBench offers a unified and reproducible framework for measuring video reasoning and aims to support the development of models with more reliable, human-aligned reasoning skills.

Penghao Wang, Yuhao Zhou, Mengxuan Wu et al.

As large language models (LLMs) advance, the ultimate vision for their role in science is emerging: we could build an AI collaborator to effectively assist human beings throughout the entire scientific research process. We refer to this envisioned system as ResearchGPT. Given that scientific research progresses through multiple interdependent phases, achieving this vision requires rigorous benchmarks that evaluate the end-to-end workflow rather than isolated sub-tasks. To this end, we contribute CS-54k, a high-quality corpus of scientific Q&A pairs in computer science, built from 14k CC-licensed papers. It is constructed through a scalable, paper-grounded pipeline that combines retrieval-augmented generation (RAG) with multi-stage quality control to ensure factual grounding. From this unified corpus, we derive two complementary subsets: CS-4k, a carefully curated benchmark for evaluating AI's ability to assist scientific research, and CS-50k, a large-scale training dataset. Extensive experiments demonstrate that CS-4k stratifies state-of-the-art LLMs into distinct capability tiers. Open models trained on CS-50k with supervised training and reinforcement learning demonstrate substantial improvements. Even 7B-scale models, when properly trained, outperform many larger proprietary systems, such as GPT-4.1, GPT-4o, and Gemini 2.5 Pro. This indicates that making AI models better research assistants relies more on domain-aligned training with high-quality data than on pretraining scale or general benchmark performance. We release CS-4k and CS-50k in the hope of fostering AI systems as reliable collaborators in CS research.

Xuanlei Zhao, Shenggan Cheng, Guangyang Lu et al.

Large deep learning models have achieved impressive performance across a range of applications. However, their large memory requirements, including parameter memory and activation memory, have become a significant challenge for their practical serving. While existing methods mainly address parameter memory, the importance of activation memory has been overlooked. Especially for long input sequences, activation memory is expected to experience a significant exponential growth as the length of sequences increases. In this approach, we propose AutoChunk, an automatic and adaptive compiler system that efficiently reduces activation memory for long sequence inference by chunk strategies. The proposed system generates chunk plans by optimizing through multiple stages. In each stage, the chunk search pass explores all possible chunk candidates and the chunk selection pass identifies the optimal one. At runtime, AutoChunk employs code generation to automatically apply chunk strategies. The experiments demonstrate that AutoChunk can reduce over 80\% of activation memory while maintaining speed loss within 10%, extend max sequence length by 3.2x to 11.7x, and outperform state-of-the-art methods by a large margin.