Siyuan Chen

Ping Guo, Chenyu Zhu, Siyuan Chen et al.

CUDA kernel optimization has become a critical bottleneck for AI performance, as deep learning training and inference efficiency directly depends on highly optimized GPU kernels. Despite the promise of Large Language Models (LLMs) for automating kernel optimization, this field suffers from a fragmented ecosystem of isolated and incomparable approaches with unclear problem formulations. Furthermore, general-purpose LLM code evolution methods cannot meet strict correctness requirements of CUDA kernel optimization. We address these fundamental challenges by first formalizing CUDA kernel optimization as a code optimization task with a clear objective, constraints, and evaluation metrics. We then establish the first systematic LLM-based code evolution framework, EvoEngineer, that provides guidance for designing and adapting optimization strategies to achieve a balance between performance and correctness. Finally, we implement a kernel optimization system based on this framework and conduct extensive experiments on 91 real-world CUDA kernels. Our results demonstrate that EvoEngineer achieves a principled balance between performance and correctness, with the highest averaged median speedup of \textbf{2.72}$\times$ over baseline CUDA kernels and a code validity rate of \textbf{69.8}\%, outperforming existing methods on both dimensions. Our method achieves a maximum speedup of \textbf{36.75}$\times$ among all operations over PyTorch kernels and delivers the highest speedup on \textbf{28} (\textbf{56.0\%}) of 50 operations that achieve over \textbf{2$\times$} acceleration.

Siyuan Chen, Zhichao Lu, Qingfu Zhang

Automated kernel design is critical for overcoming software ecosystem barriers in emerging hardware platforms like RISC-V. While large language models (LLMs) have shown promise for automated kernel optimization, demonstrating success in CUDA domains with comprehensive technical documents and mature codebases, their effectiveness remains unproven for reference-scarce domains like RISC-V. We present Evolution of Kernels (EoK), a novel LLM-based evolutionary program search framework that automates kernel design for domains with limited reference material. EoK mitigates reference scarcity by mining and formalizing reusable optimization ideas (general design principles + actionable thoughts) from established kernel libraries' development histories; it then guides parallel LLM explorations using these ideas, enriched via Retrieval-Augmented Generation (RAG) with RISC-V-specific context, prioritizing historically effective techniques. Empirically, EoK achieves a median 1.27x speedup, surpassing human experts on all 80 evaluated kernel design tasks and improving upon prior LLM-based automated kernel design methods by 20%. These results underscore the viability of incorporating human experience into emerging domains and highlight the immense potential of LLM-based automated kernel optimization.

Junkang Wei, Siyuan Chen, Licheng Zong et al.

Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially the lack of protein structure data, most of the existing computational methods rely heavily on the sequence data, with only a small portion of the methods utilizing the structural information. Recently, AlphaFold has revolutionized the entire protein and biology field. Foreseeably, the protein-RNA interaction prediction will also be promoted significantly in the upcoming years. In this work, we give a thorough review of this field, surveying both the binding site and binding preference prediction problems and covering the commonly used datasets, features, and models. We also point out the potential challenges and opportunities in this field. This survey summarizes the development of the RBP-RNA interaction field in the past and foresees its future development in the post-AlphaFold era.