Publications
See also: Google Scholar
Selected
-
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
NeurIPS, 2026 · Under Review
-
Deep Scientific Reasoning under Physical Constraints: Structure-Aware Spectrum Prediction for Electronic Density of States
Yingheng Wang, Tao Yu, Shufeng Kong, Francesco Ricci, John M. Gregoire, Carla P. Gomes
ICML, 2026
-
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
ICLR, 2026
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
ICLR, 2026 · 🏆 TMLR Featured Certificate
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
Paper -
ModuLoRA: Finetuning 2-Bit LLMs on Consumer GPUs by Integrating with Modular Quantizers
Junjie Yin, Jiahao Dong, Yingheng Wang, Christopher De Sa, Volodymyr Kuleshov
ICLR, 2025 · 🏆 TMLR Featured Certificate
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 Parathyroid Hormone-Related Peptide Testing Across Multiple Clinical Centers
He S. Yang*, Weishen Pan*, Yingheng Wang*, Mark A. Zaydman, Nicholas C. Spies, Zhen Zhao, Theresa A. Guise, Qing H. Meng, Fei Wang*
Clinical Chemistry, 2023 · 🏅 The winning solution of the ML challenge (PTHrP Result Prediction) at AACC 2022 (* marks core team members)
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
The Web Conf (WWW), 2021 · 🏆 Best Paper Award at AAAI GraphDL 2021
Paper · Code
Others
-
A benchmark of expert-level academic questions to assess AI capabilities
Center for AI Safety, Scale AI, HLE Contributors Consortium (including Yingheng Wang)
Nature, 2026
Paper · Website -
Toward Honest Language Models for Deductive Reasoning
Jiarui Liu, Kaustubh Dhole, Yingheng Wang, Haoyang Wen, Sarah Zhang, Haitao Mao, Gaotang Li, Neeraj Varshney, Jingguo Liu, Xiaoman Pan
COLM, 2026 · Under Review
Paper -
AtomWorld: A Benchmark For Evaluating Spatial Reasoning In Large Language Models On Crystalline Materials
Taoyuze Lv, Alexander Chen, Fengyu Xie, Jeffrey Meng, Yingheng Wang, Bram Hoex, Zhicheng Zhong, Tong Xie
ICML, 2026
Paper -
MTCMB: A Multi-Task Benchmark for Evaluating LLMs on Knowledge, Reasoning, and Safety in Traditional Chinese Medicine
S. Kong, X. Yang, Y. Wei, Z. Wang, S. Huang, H. Tang, J. Qin, S. Lan, Yingheng Wang, J. Bai, Z. Chen, Z. Zheng, C. Liu, L. Hao
Nature npj Digital Medicine, 2026 · In Submission
Paper -
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 -
MIRNet: Intergrating Constrained Graph-Based Reasoning with Pre-training for Diagnostic Medical Imaging
S. Kong, Z. Wang, N. Cui, T. Hao, Y. Meng, Y. Wei, C. Fan, Yingheng Wang, Z. Cai, Y. Wang, Y. Zhang, Y. Li, Z. Zheng, C. Liu, L. Hao
AAAI, 2026
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 -
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 -
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, 2025 · Under Review
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 -
Molecular Graph Contrastive Learning with Parameterized Explainable Augmentations
Yingheng Wang, Yaosen Min, Erzhuo Shao, Ji Wu
BIBM, 2021
Paper -
MolCloze: A Unified Self-supervised Molecular Structure Pre-training Model for Chemical Property Prediction
Yingheng Wang, Xin Chen, Yaosen Min, Ji Wu
BIBM, 2021
Paper -
One-shot Transfer Learning for Population Mapping
Erzhuo Shao*, Jie Feng*, Yingheng Wang, Tong Xia, Yong Li
CIKM, 2021
Paper -
STELLAR: Spatio-Temporal Environmental Learning with Latent Alignment and Refinement for Long-Tailed Species Distribution Modeling
S. Kong, T. Yu, Y. Wei, C. Liu, J. Bai, Yingheng Wang, M. Grimson, D. Fink, C. P. Gomes
IJCAI, 2026
Paper -
Machine Learning Methods for Studying Latent Neural Activity Dynamics
S. Kong, F. Deng, X. Dong, C. Liu, W. Chen, Yingheng Wang, D. Cao, A. Oliva, A. Fernandez-Ruiz, C. P. Gomes
IJCAI, 2026
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