Publications

Selected

Physics-informed Density of States Prediction with Structure-Aware Sequence Decoding and Mass-Conserving Refinement
Yingheng Wang, Francesco Ricci, Tao Yu, Junwen Bai, Shufeng Kong, John M. Gregoire, Carla P. Gomes
Nature Computational Science, 2026
Paper · Code
Iterative Multi-Objective Policy Optimization for Antibody Sequence Design
Yingheng Wang, Can Chen, Karla-Luise Herpoldt, Sukanya Sasmal, Tommi Jaakkola, Marcus D. Collins, Shang Shang
ICLR, 2026 · Under Review
Paper · Code
Unsupervised Combinatorial Probabilistic Reasoning: Probabilistic Coin Change Problem
Zhongdi Qu, Yingheng Wang, Utku Umur Acikalin, Aaron M. Ferber, Goncalo J. Gouveia, Brandon Bills, Guohui Li, Joshua Kline, Sunandini Yedla, Xiao Wang, Frank C. Schroeder, Carla P. Gomes
AAAI, 2026
Paper · Code
HeuriGym: An Agentic Benchmark for LLM-Crafted Heuristics in Combinatorial Optimization
Hongzheng Chen*, Yingheng Wang*, Yaohui Cai*, Hins Hu*, Jiajie Li*, Shirley Huang, Chenhui Deng, Rongjian Liang, Shufeng Kong, Haoxing Ren, Samitha Samaranayake, Carla P. Gomes, Zhiru Zhang
NeurIPS, 2025 · MATH-AI
Paper · Code
LC-PLM: Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers
Yingheng Wang, Zichen Wang, Gil Sadeh, Luca Zancato, Alessandro Achille, George Karypis, Huzefa Rangwala
TMLR, 2025 · 🏆 Featured Certification Award
Paper · Code
Diffusion Variational Inference: Diffusion Models as Expressive Variational Posteriors
Yingheng Wang*, Top Wasu Piriyakulkij*, Volodymyr Kuleshov
AAAI, 2025
Paper · Code
Conformal Crystal Graph Transformer with Robust Encoding of Periodic Invariance
Yingheng Wang, Shufeng Kong, John M. Gregoire, Carla P. Gomes
AAAI, 2024
ModuLoRA: Finetuning 2-Bit LLMs on Consumer GPUs by Integrating with Modular Quantizers
Junjie Yin, Jiahao Dong, Yingheng Wang, Christopher De Sa, Volodymyr Kuleshov
TMLR, 2024 · 🏆 Featured Certification Award
Paper · Code
InfoDiffusion: Representation Learning Using Information Maximizing Diffusion Models
Yingheng Wang, Yair Schiff, Aaron Gokaslan, Weishen Pan, Fei Wang, Christopher De Sa, Volodymyr Kuleshov
ICML, 2023
Paper · Code
M²Hub: Unlocking the Potential of Machine Learning for Materials Discovery
Yuanqi Du*, Yingheng Wang*, Yining Huang, Jianan Canal Li, Yanqiao Zhu, Tian Xie, Chenru Duan, John M. Gregoire, Carla P. Gomes
NeurIPS, 2023
Paper · Code
Generalizability of a Machine Learning Model for Improving Utilization of PTHrP Testing
He S. Yang*, Weishen Pan*, Yingheng Wang*, et al.
Clinical Chemistry, 2023 · 🏆 AACC 2022 ML Challenge Winner
Paper · Code
Going Deeper into Permutation-Sensitive Graph Neural Networks
Zhongyu Huang*, Yingheng Wang*, Chaozhuo Li, Huiguang He
ICML, 2022
Paper · Code
Multi-view Graph Contrastive Representation Learning for Drug-Drug Interaction Prediction
Yingheng Wang, Yaosen Min, Xin Chen, Ji Wu
WWW, 2021 · 🏆 Best Paper Award (AAAI GraphDL 2021)
Paper · Code
Molecular Graph Contrastive Learning with Parameterized Explainable Augmentations
Yingheng Wang, Yaosen Min, Erzhuo Shao, Ji Wu
BIBM, 2021
Paper · Code
MolCloze: A Unified Self-supervised Molecular Structure Pre-training Model
Yingheng Wang, Xin Chen, Yaosen Min, Ji Wu
BIBM, 2021
Paper · Code

Others

Stabilizing Reinforcement Learning for Honesty Alignment in Language Models on Deductive Reasoning
Jiarui Liu, Kaustubh Dhole, Yingheng Wang, Haoyang Wen, Sarah Zhang, Haitao Mao, Gaotang Li, Neeraj Varshney, Jingguo Liu, Xiaoman Pan
ICLR, 2026 · Under Review
Graffe: Graph Representation Learning Enabled via Diffusion Probabilistic Models
Dingshuo Chen, Shuchen Xue, Liuji Chen, Yingheng Wang, Qiang Liu, Shu Wu, Zhi-Ming Ma, Liang Wang
TKDE, 2026 · Under Review
MTCMB: A Multi-Task Benchmark for Evaluating LLMs on Knowledge, Reasoning, and Safety in Traditional Chinese Medicine
Shufeng Kong, Xingru Yang, Yuanyuan Wei, Zijie Wang, Sidie Huang, Hao Tang, Jiuqi Qin, Shuting Lan, Yingheng WangMe, Junwen Bai, Zhuangbin Chen, Zibin Zheng, Caihua Liu, Liang Hao
npj Digital Medicine, 2026 · Under Review
MIRNet: Intergrating Constrained Graph-Based Reasoning with Pre-training for Diagnostic Medical Imaging
Shufeng Kong, Zijie Wang, Nuan Cui, Tang Hao, Meng Yihan, Yuan Yuan Wei, Chenfei Fan, Yingheng Wang, Zhuo Cai, Yaonan Wang, Yulong Zhang, Yuzheng Li, Zibin Zheng, Caihua Liu, Liang Hao
AAAI, 2026
Paper
Benchmarking LLMs for atomic-level geometric manipulation in crystals
Taoyuze Lv, Alexander Chen, Fengyu Xie, Jeffrey Meng, Yingheng Wang, Bram Hoex, Zhicheng Zhong, Tong Xie
NeurIPS AI4Mat, 2025
Paper
Improving Electron Ptychography with a Generative Prior
Christian K. Belardi, Chia-Hao Lee, Yingheng Wang, Justin Lovelace, Kilian Q. Weinberger, David A. Muller, Carla P. Gomes
ICCV, 2025
Paper
Humanity's last exam
Long Phan*, Alice Gatti*, Ziwen Han*, Nathaniel Li*, ..., Yingheng Wang, et al.
arXiv, 2025
Paper
3D Ptychographic Inverse Imaging with Generative Diffusion Models
Chia-Hao Lee, Christian K. Belardi, Yingheng Wang, Justin Lovelace, Kilian Q. Weinberger, David A. Muller, Carla P. Gomes
Microscopy and Microanalysis, 2025
Paper
MatFusion: A Multi-Modal Framework Bridging LLMs and Structural Embeddings for Experimental Materials Property Prediction
Yuwei Wan, Yuqi An, Dongzhan Zhou, Jiahao Dong, Chunyu Kit, Wenjie Zhang, Bram Hoex, Tong Xie†, Yingheng Wang†
ICLR AI4Mat, 2025
Paper
Machine learning-aided generative molecular design
Yuanqi Du*, Arian R Jamasb*, Jeff Guo*, Tianfan Fu, Charles Harris, Yingheng Wang, Chenru Duan, Pietro Liò, Philippe Schwaller, Tom L Blundell
Nature Machine Intelligence, 2024
Paper
GEM-RAG: Graphical Eigen Memories For Retrieval Augmented Generation
Brendan H. Rappazzo, Yingheng Wang, Aaron M. Ferber, Carla P. Gomes
arXiv, 2024
Paper
Growing Like a Tree: Finding Trunks From Graph Skeleton Trees
Zhongyu Huang, Yingheng Wang, Chaozhuo Li, Huiguang He
IEEE TPAMI, 2024
Paper · Code
Graph Data Augmentation for Graph Machine Learning: A Survey
Tong Zhao, Wei Jin, Yozen Liu, Yingheng Wang, Gang Liu, Stephan Gunnemann, Neil Shah, Meng Jiang
IEEE Data Engineering Bulletin, 2023
Paper
Information-Aware Time Series Meta-Contrastive Learning
Dongsheng Luo, Wei Cheng, Yingheng Wang, Dongkuan Xu, Jingchao Ni, Wenchao Yu, Haifeng Chen, Xiang Zhang
AAAI, 2023
Paper · Code
Graph-Enhanced Emotion Neural Decoding
Zhongyu Huang, Changde Du, Yingheng Wang, Huiguang He
IEEE TMI, 2023
Paper
Xtal2DoS: Attention-based Crystal to Sequence Learning for Density of States Prediction
Junwen Bai, Yuanqi Du, Yingheng Wang, Shufeng Kong, John M. Gregoire, Carla P. Gomes
NeurIPS AI4Science, 2022
Paper · Code
Graph Emotion Decoding from Visually Evoked Neural Responses
Zhongyu Huang, Changde Du, Yingheng Wang, Huiguang He
MICCAI, 2022
Paper
One-shot Transfer Learning for Population Mapping
Erzhuo Shao*, Jie Feng*, Yingheng Wang, Tong Xia, Yong Li
CIKM, 2021
Paper
From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph‐Based Deep Learning
Y. Min, Y. Wei, P. Wang, N. Wu, S. Bauer, S. Zheng, Y. Shi, Yingheng Wang, X. Wang, D. Zhao, J. Wu, J. Zeng
Advanced Science, 2024
Paper
CAT Bridge: An Efficient Toolkit for Compound-Transcript Association Mining from Multi-Omics Data
B. Yang, T. Meng, X. Wang, J. Li, S. Zhao, Yingheng Wang, S. Yi, Y. Zhou, Y. Zhang, L. Li, L. Guo
GigaScience, 2024
Paper
Pipeline Image Haze Removal System Using Dark Channel Prior on Cloud Processing Platform
C. Li, T. He, Yingheng Wang, et al.
International Journal of Computational Science and Engineering, 2020
Paper
Mathematical Modeling and Simulation on the Stimulation Interactions in Coalbed Methane Thermal Recovery
T. Teng, Yingheng Wang, et al.
Processes, 2019
Paper