Publications

Persistent Activation Steering Disrupts Language-Model Termination: A Failure Mode Distinct from Quality Degradation

Under review.

Emergent Steering Beyond Endpoint Alignment in Chemical Reaction Models

Under review.

Driving Reaction Trajectories via Latent Flow Matching

Yili Shen, Xiangliang Zhang

KDD 2026.

Paper · Code · Slides

AgentTrap: Measuring Runtime Trust Failures in Third-Party Agent Skills

Haomin Zhuang, Hanwen Xing, Yujun Zhou, Yuchen Ma, Yue Huang, Yili Shen, Yufei Han, Xiangliang Zhang

arXiv preprint.

arXiv

SenseMath: Do LLMs Have Number Sense? Evaluating Shortcut Use, Judgment, and Generation

Haomin Zhuang, Xiangqi Wang, Yili Shen, Ying Cheng, Xiangliang Zhang

arXiv preprint.

arXiv

Reward Transport: Property Control in Flow Matching via Noise-Space Alignment

Kehan Guo, Yili Shen, Yujun Zhou, Yue Huang, Chujie Gao, Shiyi Du, Xiangliang Zhang

arXiv preprint.

arXiv

Transferable FB-GNN-MBE Framework for Potential Energy Surfaces: Data-Adaptive Transfer Learning in Deep Learned Many-Body Expansion Theory

Siqi Chen, Zhiqiang Wang, Yili Shen, Xianqi Deng, Xi Cheng, Cheng-Wei Ju, Jun Yi, Guo Ling, Dieaa Alhmoud, Hui Guan, Zhou Lin

The Journal of Chemical Physics, 2026.

arXiv

Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms

Nitesh V. Chawla, Gisela A. González-Montiel, Kehan Guo, Taicheng Guo, Ting Hua, Xiaobao Huang, Eric Inae, Meng Jiang, Khiem Le, Gang Liu, J. Charlie Maier, Nuno Moniz, Brenda Nogueira, Deng Pan, Bryan V. Piguave, Brett M. Savoie, Andrew B. Schofield, Yili Shen, Alexander Taylor, Xiangliang Zhang, Yihan Zhu, Olaf Wiest

Chemical Reviews, 126(13), 7587–7635, 2026.

DOI

From VAEs to Diffusion and LLMs: Modern Generative Models for Molecular Discovery

Kehan Guo, Yili Shen, Jeeyhun Hwang, Yue Huang, Chijie Gao, Olexandr Isayev, Olaf Wiest, Wei Wang, Xiangliang Zhang

KDD 2026 Tutorial.

KDD

Towards Few-shot Chemical Reaction Outcome Prediction

Yili Shen, Yijun Tian, Cheng-Wei Ju, Olaf Wiest, Xiangliang Zhang

CIKM 2025, 2599–2609.

DOI

Artificial Intelligence in Spectroscopy: Advancing Chemistry from Prediction to Generation and Beyond

Kehan Guo, Yili Shen, Gisela Abigail González-Montiel, Yue Huang, Yujun Zhou, Mihir Surve, Zhichun Guo, Payel Das, Nitesh V. Chawla, Olaf Wiest, Xiangliang Zhang

IJCAI 2025 Survey Track, 10445–10454.

DOI

Accurate Electronic and Optical Properties of Organic Doublet Radicals Using Machine Learned Range-Separated Functionals

Cheng-Wei Ju, Yili Shen, Ethan J. French, Jun Yi, Hongshan Bi, Aaron Tian, Zhou Lin

The Journal of Physical Chemistry A, 128(12), 2457–2471, 2024.

DOI

Integrating Graph Neural Networks and Many-Body Expansion Theory for Potential Energy Surfaces

Siqi Chen, Zhiqiang Wang, Xianqi Deng, Yili Shen, Cheng-Wei Ju, Jun Yi, Lin Xiong, Guo Ling, Dieaa Alhmoud, Hui Guan, Zhou Lin

NeurIPS 2024 AI4Mat Spotlight.

OpenReview

Improving Subgraph Representation Learning via Multi-View Augmentation

Yili Shen, Jiaxu Yan, Cheng-Wei Ju, Jun Yi, Zhou Lin, Hui Guan

ICML 2022 AI4Science.

OpenReview

TCR: A Transformer-Based Deep Network for Predicting Cancer Drug Response

Jie Gao, Jing Hu, Wanqing Sun, Yili Shen, Xiaonan Zhang, Xiaomin Fang, Fan Wang, Guodong Zhao

arXiv preprint.

arXiv

Accelerating Many-Body Expansion Theory Through Graph Convolutional Networks

Yili Shen, Cheng-Wei Ju, Jun Yi, Zhou Lin, Hui Guan

75th International Symposium on Molecular Spectroscopy, 2022.

Abstract book

Quality Prediction of Discrete Manufacturing Process Based on CGAN & CatBoost Hybrid Model

Peng Xu, Zhichen Ren, Yili Shen, Wendi Yu, Lianghua He

Journal of Physics: Conference Series, 1757(1), 012072, 2021.

DOI