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Haoyuan Shi

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4 papers

2 author rows

AAAI Conference 2026 Conference Paper

Efficient Plug-and-Play Weight Refinement for Sparse Large Models

Jingcheng Xie
Yinda Chen
Xiaoyu Liu
Yinglong Li
Haoyuan Shi
Zhiwei Xiong

One-shot pruning efficiently compresses Large Language Models but produces coarse sparse weights, causing significant performance degradation. Traditional fine-tuning approaches to refine these weights are prohibitively expensive for large models. This highlights the need for a training-free weight refinement method that works seamlessly with one-shot pruning and can efficiently recover the lost performance. To tackle this problem, we propose Efficient Iterative Weight Refinement (EIWR), a lightweight, plug-and-play, and training-free method that refines pruned weights through layer-wise iterative optimization. EIWR achieves efficient weight refinement via three key components: a Global Soft Constraint that eliminates costly row-wise Hessian inversions and expands the solution space; a Historical Momentum Strategy that leverages one-shot pruning priors to accelerate convergence and enhance final performance; and Neumann Series Extrapolation that significantly speeds up per-iteration computation. As a result, EIWR enables effective weight refinement with minimal time and memory overhead. Extensive experiments on LLaMA2/3 and Qwen under different pruning strategies and sparsity levels demonstrate that our method can efficiently refine sparse weights and mitigate performance degradation. For example, on LLaMA2-7B under 70 percent sparsity, EIWR reduces perplexity by 15 percent compared with SparseGPT on the WikiText2 benchmark, with only 1.81 additional minutes of computation and 1GB of additional memory.

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AIIM Journal 2025 Journal Article

DRExplainer: Quantifiable interpretability in drug response prediction with directed graph convolutional network

Haoyuan Shi
Tao Xu
Xiaodi Li
Qian Gao
Zhiwei Xiong
Junfeng Xia
Zhenyu Yue

Predicting the response of a cancer cell line to a therapeutic drug is pivotal for personalized medicine. Despite numerous deep learning methods that have been developed for drug response prediction, integrating diverse information about biological entities and predicting the directional response remain major challenges. Here, we propose a novel interpretable predictive model, DRExplainer, which leverages a directed graph convolutional network to enhance the prediction in a directed bipartite network framework. DRExplainer constructs a directed bipartite network integrating multi-omics profiles of cell lines, the chemical structure of drugs and known drug response to achieve directed prediction. Then, DRExplainer identifies the most relevant subgraph to each prediction in this directed bipartite network by learning a mask, facilitating critical medical decision-making. Additionally, we introduce a quantifiable method for model interpretability that leverages a ground truth benchmark dataset curated from biological features. In computational experiments, DRExplainer outperforms state-of-the-art predictive methods and another graph-based explanation method under the same experimental setting. Finally, the case studies further validate the interpretability and the effectiveness of DRExplainer in predictive novel drug response. Our code is available at: https: //github. com/vshy-dream/DRExplainer.

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JBHI Journal 2025 Journal Article

Interpretable Dynamic Directed Graph Convolutional Network for Multi-Relational Prediction of Missense Mutation and Drug Response

Qian Gao
Tao Xu
Xiaodi Li
Wanling Gao
Haoyuan Shi
Youhua Zhang
Jie Chen
Zhenyu Yue

Tumor heterogeneity presents a significant challenge in predicting drug responses, especially as missense mutations within the same gene can lead to varied outcomes such as drug resistance, enhanced sensitivity, or therapeutic ineffectiveness. These complex relationships highlight the need for advanced analytical approaches in oncology. Due to their powerful ability to handle heterogeneous data, graph convolutional networks (GCNs) represent a promising approach for predicting drug responses. However, simple bipartite graphs cannot accurately capture the complex relationships involved in missense mutation and drug response. Furthermore, Deep learning models for drug response are often considered “black boxes”, and their interpretability remains a widely discussed issue. To address these challenges, we propose an Interpretable Dynamic Directed Graph Convolutional Network (IDDGCN) framework, which incorporates four key features: 1) the use of directed graphs to differentiate between sensitivity and resistance relationships, 2) the dynamic updating of node weights based on node-specific interactions, 3) the exploration of associations between different mutations within the same gene and drug response, and 4) the enhancement of interpretability models through the integration of a weighted mechanism that accounts for the biological significance, alongside a ground truth construction method to evaluate prediction transparency. The experimental results demonstrate that IDDGCN outperforms existing state-of-the-art models, exhibiting excellent predictive power. Both qualitative and quantitative evaluations of its interpretability further highlight its ability to explain predictions, offering a fresh perspective for precision oncology and targeted drug development.

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ICML Conference 2024 Conference Paper

VisionGraph: Leveraging Large Multimodal Models for Graph Theory Problems in Visual Context

Yunxin Li
Baotian Hu
Haoyuan Shi
Wei Wang 0164
Longyue Wang
Min Zhang 0005

Large Multimodal Models (LMMs) have achieved impressive success in visual reasoning, particularly in visual mathematics. However, problem-solving capabilities in graph theory remain less explored for LMMs, despite being a crucial aspect of mathematical reasoning that requires an accurate understanding of graphical structures and multi-step reasoning on visual graphs. To step forward in this direction, we are the first to design a benchmark named VisionGraph, used to explore the capabilities of advanced LMMs in solving multimodal graph theory problems. It encompasses eight complex graph problem tasks, from connectivity to shortest path problems. Subsequently, we present a Description-Program-Reasoning (DPR) chain to enhance the logical accuracy of reasoning processes through graphical structure description generation and algorithm-aware multi-step reasoning. Our extensive study shows that 1) GPT-4V outperforms Gemini Pro in multi-step graph reasoning; 2) All LMMs exhibit inferior perception accuracy for graphical structures, whether in zero/few-shot settings or with supervised fine-tuning (SFT), which further affects problem-solving performance; 3) DPR significantly improves the multi-step graph reasoning capabilities of LMMs and the GPT-4V (DPR) agent achieves SOTA performance.

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