Zhongming Yu

Haotian Tang, Shang Yang, Zhijian Liu et al. · mit

Sparse convolution plays a pivotal role in emerging workloads, including point cloud processing in AR/VR, autonomous driving, and graph understanding in recommendation systems. Since the computation pattern is sparse and irregular, specialized high-performance kernels are required. Existing GPU libraries offer two dataflow types for sparse convolution. The gather-GEMM-scatter dataflow is easy to implement but not optimal in performance, while the dataflows with overlapped computation and memory access (e.g.implicit GEMM) are highly performant but have very high engineering costs. In this paper, we introduce TorchSparse++, a new GPU library that achieves the best of both worlds. We create a highly efficient Sparse Kernel Generator that generates performant sparse convolution kernels at less than one-tenth of the engineering cost of the current state-of-the-art system. On top of this, we design the Sparse Autotuner, which extends the design space of existing sparse convolution libraries and searches for the best dataflow configurations for training and inference workloads. Consequently, TorchSparse++ achieves 2.9x, 3.3x, 2.2x and 1.7x measured end-to-end speedup on an NVIDIA A100 GPU over state-of-the-art MinkowskiEngine, SpConv 1.2, TorchSparse and SpConv v2 in inference; and is 1.2-1.3x faster than SpConv v2 in mixed precision training across seven representative autonomous driving benchmarks. It also seamlessly supports graph convolutions, achieving 2.6-7.6x faster inference speed compared with state-of-the-art graph deep learning libraries.

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.

Hejia Zhang, Zhongming Yu, Chia-Tung Ho et al.

Execution-aware LLM agents offer a promising paradigm for learning from tool feedback, but such feedback is often expensive and slow to obtain, making online reinforcement learning (RL) impractical. High-coverage hardware verification exemplifies this challenge due to its reliance on industrial simulators and non-differentiable execution signals. We propose LLM4Cov, an offline agent-learning framework that models verification as memoryless state transitions guided by deterministic evaluators. Building on this formulation, we introduce execution-validated data curation, policy-aware agentic data synthesis, and worst-state-prioritized sampling to enable scalable learning under execution constraints. We further curate a reality-aligned benchmark adapted from an existing verification suite through a revised evaluation protocol. Using the proposed pipeline, a compact 4B-parameter model achieves 69.2% coverage pass rate under agentic evaluation, outperforming its teacher by 5.3% and demonstrating competitive performance against models an order of magnitude larger.

Yuwei Hu, Jiajie Li, Zhongming Yu et al.

Graph neural networks (GNNs), which have emerged as an effective method for handling machine learning tasks on graphs, bring a new approach to building recommender systems, where the task of recommendation can be formulated as the link prediction problem on user-item bipartite graphs. Training GNN-based recommender systems (GNNRecSys) on large graphs incurs a large memory footprint, easily exceeding the DRAM capacity on a typical server. Existing solutions resort to distributed subgraph training, which is inefficient due to the high cost of dynamically constructing subgraphs and significant redundancy across subgraphs. The emerging persistent memory technologies provide a significantly larger memory capacity than DRAMs at an affordable cost, making single-machine GNNRecSys training feasible, which eliminates the inefficiencies in distributed training. One major concern of using persistent memory devices for GNNRecSys is their relatively low bandwidth compared with DRAMs. This limitation can be particularly detrimental to achieving high performance for GNNRecSys workloads since their dominant compute kernels are sparse and memory access intensive. To understand whether persistent memory is a good fit for GNNRecSys training, we perform an in-depth characterization of GNNRecSys workloads and a comprehensive analysis of their performance on a persistent memory device, namely, Intel Optane. Based on the analysis, we provide guidance on how to configure Optane for GNNRecSys workloads. Furthermore, we present techniques for large-batch training to fully realize the advantages of single-machine GNNRecSys training. Our experiment results show that with the tuned batch size and optimal system configuration, Optane-based single-machine GNNRecSys training outperforms distributed training by a large margin, especially when handling deep GNN models.

Yujie Zhao, Boqin Yuan, Junbo Huang et al.

Large Language Models (LLMs) are deployed as autonomous agents in increasingly complex applications, where enabling long-horizon memory is critical for achieving strong performance. However, a significant gap exists between practical applications and current evaluation standards for agent memory: existing benchmarks primarily focus on dialogue-centric, human-agent interactions. In reality, agent memory consists of a continuous stream of agent-environment interactions that are primarily composed of machine-generated representations. To bridge this gap, we introduce AMA-Bench (Agent Memory with Any length), which evaluates long-horizon memory for LLMs in real agentic applications. It features two key components: (1) a set of real-world agentic trajectories across representative agentic applications, paired with expert-curated QA, and (2) a set of synthetic agentic trajectories that scale to arbitrary horizons, paired with rule-based QA. Our comprehensive study shows that existing memory systems underperform on AMA-Bench primarily because they lack causality and objective information and are constrained by the lossy nature of similarity-based retrieval employed by many memory systems. To address these limitations, we propose AMA-Agent, an effective memory system featuring a causality graph and tool-augmented retrieval. Our results demonstrate that AMA-Agent achieves 57.22% average accuracy on AMA-Bench, surpassing the strongest memory system baselines by 11.16%.

Gangda Deng, Zhaoling Chen, Zhongming Yu et al.

With AI agents increasingly deployed as long-running systems, it becomes essential to autonomously construct and continuously evolve customized software to enable interaction within dynamic environments. Yet, existing benchmarks evaluate agents on isolated, one-off coding tasks, neglecting the temporal dependencies and technical debt inherent in real-world software evolution. To bridge this gap, we introduce DeepCommit, an agentic pipeline that reconstructs verifiable Milestone DAGs from noisy commit logs, where milestones are defined as semantically cohesive development goals. These executable sequences enable EvoClaw, a novel benchmark that requires agents to sustain system integrity and limit error accumulation, dimensions of long-term software evolution largely missing from current benchmarks. Our evaluation of 12 frontier models across 4 agent frameworks reveals a critical vulnerability: overall performance scores drop significantly from $>$80% on isolated tasks to at most 38% in continuous settings, exposing agents' profound struggle with long-term maintenance and error propagation.

Zhongming Yu, Hejia Zhang, Yujie Zhao et al.

Recent developments in Large Language Model (LLM) agents are revolutionizing Autonomous Software Engineering (ASE), enabling automated coding, problem fixes, and feature improvements. However, localization -- precisely identifying software problems by navigating to relevant code sections -- remains a significant challenge. Current approaches often yield suboptimal results due to a lack of effective integration between LLM agents and precise code search mechanisms. This paper introduces OrcaLoca, an LLM agent framework that improves accuracy for software issue localization by integrating priority-based scheduling for LLM-guided action, action decomposition with relevance scoring, and distance-aware context pruning. Experimental results demonstrate that OrcaLoca becomes the new open-source state-of-the-art (SOTA) in function match rate (65.33%) on SWE-bench Lite. It also improves the final resolved rate of an open-source framework by 6.33 percentage points through its patch generation integration.

Zhongming Yu, Naicheng Yu, Hejia Zhang et al.

As LLM agents evolve into collaborative multi-agent systems, their memory requirements grow rapidly in complexity. This position paper frames multi-agent memory as a computer architecture problem. We distinguish shared and distributed memory paradigms, propose a three-layer memory hierarchy (I/O, cache, and memory), and identify two critical protocol gaps: cache sharing across agents and structured memory access control. We argue that the most pressing open challenge is multi-agent memory consistency. Our architectural framing provides a foundation for building reliable, scalable multi-agent systems.

Yujie Zhao, Hejia Zhang, Hanxian Huang et al.

The automatic generation of RTL code (e.g., Verilog) through natural language instructions has emerged as a promising direction with the advancement of large language models (LLMs). However, producing RTL code that is both syntactically and functionally correct remains a significant challenge. Existing single-LLM-agent approaches face substantial limitations because they must navigate between various programming languages and handle intricate generation, verification, and modification tasks. To address these challenges, this paper introduces MAGE, the first open-source multi-agent AI system designed for robust and accurate Verilog RTL code generation. We propose a novel high-temperature RTL candidate sampling and debugging system that effectively explores the space of code candidates and significantly improves the quality of the candidates. Furthermore, we design a novel Verilog-state checkpoint checking mechanism that enables early detection of functional errors and delivers precise feedback for targeted fixes, significantly enhancing the functional correctness of the generated RTL code. MAGE achieves a 95.7% rate of syntactic and functional correctness code generation on VerilogEval-Human 2 benchmark, surpassing the state-of-the-art Claude-3.5-sonnet by 23.3 %, demonstrating a robust and reliable approach for AI-driven RTL design workflows.

Wentao Ni, Kangqi Zhang, Zhongming Yu et al.

As long-context inference becomes central to large language models (LLMs), attention over growing key-value caches emerges as a dominant decoding bottleneck, motivating sparse attention for scalable inference. Fixed-budget top-k sparse attention cannot adapt to heterogeneous attention distributions across heads and layers, whereas top-p sparse attention directly preserves attention mass and provides stronger accuracy guarantees. Existing top-p methods, however, fail to jointly optimize top-p accuracy, selection overhead, and sparse attention cost, which limits their overall efficiency. We present Double-P, a hierarchical sparse attention framework that optimizes all three stages. Double-P first performs coarse-grained top-p estimation at the cluster level using size-weighted centroids, then adaptively refines computation through a second top-p stage that allocates token-level attention only when needed. Across long-context benchmarks, Double-P consistently achieves near-zero accuracy drop, reducing attention computation overhead by up to 1.8x and delivers up to 1.3x end-to-end decoding speedup over state-of-the-art fixed-budget sparse attention methods.

Yujie Zhao, Zhijing Wu, Hejia Zhang et al.

LLM-assisted hardware verification is gaining substantial attention due to its potential to significantly reduce the cost and effort of crafting effective testbenches. It also serves as a critical enabler for LLM-aided end-to-end hardware language design. However, existing current LLMs often struggle with Register Transfer Level (RTL) code generation, resulting in testbenches that exhibit functional errors in Hardware Description Languages (HDL) logic. Motivated by the strong performance of LLMs in Python code generation under inference-time sampling strategies, and their promising capabilities as judge agents, we propose PRO-V a fully program generation multi-agent system for robust RTL verification. Pro-V incorporates an efficient best-of-n iterative sampling strategy to enhance the correctness of generated testbenches. Moreover, it introduces an LLM-as-a-judge aid validation framework featuring an automated prompt generation pipeline. By converting rule-based static analysis from the compiler into natural language through in-context learning, this pipeline enables LLMs to assist the compiler in determining whether verification failures stem from errors in the RTL design or the testbench. PRO-V attains a verification accuracy of 87.17% on golden RTL implementations and 76.28% on RTL mutants. Our code is open-sourced at https://github.com/stable-lab/Pro-V.

Zhongming Yu, Genghan Zhang, Hanxian Huang et al.

In recent years, Graph Neural Networks (GNNs) have ignited a surge of innovation, significantly enhancing the processing of geometric data structures such as graphs, point clouds, and meshes. As the domain continues to evolve, a series of frameworks and libraries are being developed to push GNN efficiency to new heights. While graph-centric libraries have achieved success in the past, the advent of efficient tensor compilers has highlighted the urgent need for tensor-centric libraries. Yet, efficient tensor-centric frameworks for GNNs remain scarce due to unique challenges and limitations encountered when implementing segment reduction in GNN contexts. We introduce GeoT, a cutting-edge tensor-centric library designed specifically for GNNs via efficient segment reduction. GeoT debuts innovative parallel algorithms that not only introduce new design principles but also expand the available design space. Importantly, GeoT is engineered for straightforward fusion within a computation graph, ensuring compatibility with contemporary tensor-centric machine learning frameworks and compilers. Setting a new performance benchmark, GeoT marks a considerable advancement by showcasing an average operator speedup of 1.80x and an end-to-end speedup of 1.68x.

Hengrui Zhang, Zhongming Yu, Guohao Dai et al.

Graph Neural Networks (GNNs) have been widely used in various domains, and GNNs with sophisticated computational graph lead to higher latency and larger memory consumption. Optimizing the GNN computational graph suffers from: (1) Redundant neural operator computation. The same data are propagated through the graph structure to perform the same neural operation multiple times in GNNs, leading to redundant computation which accounts for 92.4% of total operators. (2) Inconsistent thread mapping. Efficient thread mapping schemes for vertex-centric and edge-centric operators are different. This inconsistency prohibits operator fusion to reduce memory IO. (3) Excessive intermediate data. For GNN training which is usually performed concurrently with inference, intermediate data must be stored for the backward pass, consuming 91.9% of the total memory requirement. To tackle these challenges, we propose following designs to optimize the GNN computational graph from a novel coordinated computation, IO, and memory perspective: (1) Propagation-postponed operator reorganization. We reorganize operators to perform neural operations before the propagation, thus the redundant computation is eliminated. (2) Unified thread mapping for fusion. We propose a unified thread mapping scheme for both vertex- and edge-centric operators to enable fusion and reduce IO. (3) Intermediate data recomputation. Intermediate data are recomputed during the backward pass to reduce the total memory consumption. Extensive experimental results on three typical GNN models show that, we achieve up to 2.75x end-to-end speedup, 6.89x less memory IO, and 7.73x less memory consumption over state-of-the-art frameworks.

Yukuo Cen, Zhenyu Hou, Yan Wang et al.

Graph neural networks (GNNs) have attracted tremendous attention from the graph learning community in recent years. It has been widely adopted in various real-world applications from diverse domains, such as social networks and biological graphs. The research and applications of graph deep learning present new challenges, including the sparse nature of graph data, complicated training of GNNs, and non-standard evaluation of graph tasks. To tackle the issues, we present CogDL, a comprehensive library for graph deep learning that allows researchers and practitioners to conduct experiments, compare methods, and build applications with ease and efficiency. In CogDL, we propose a unified design for the training and evaluation of GNN models for various graph tasks, making it unique among existing graph learning libraries. By utilizing this unified trainer, CogDL can optimize the GNN training loop with several training techniques, such as mixed precision training. Moreover, we develop efficient sparse operators for CogDL, enabling it to become the most competitive graph library for efficiency. Another important CogDL feature is its focus on ease of use with the aim of facilitating open and reproducible research of graph learning. We leverage CogDL to report and maintain benchmark results on fundamental graph tasks, which can be reproduced and directly used by the community.