Yingce Xia · Research

Publications

Work across Agentic Science, LLMs and agents, and AI for Science, followed by earlier research in learning, generation, and decision-making.

Latest Work

Preprints

6 works · 2025–2026

2026

Phenotype-Guided In Silico Molecular Generation Using Large Language Models

Qun Jiang, Xing Ye, Zekun Guo, Yingce Xia, Zequn Liu, Jiaying Xu, Peiran Jin, Fusong Ju, Huanhuan Xia, Haiguang Liu, Tao Qin, Pan Deng, Sida Shao

bioRxiv

2026

Deciphering Scientific Reasoning Steps from Outcome Data for Molecule Optimization

Zequn Liu, Kehan Wu, Shufang Xie, Zekun Guo, Wei Zhang, Tao Qin, Renhe Liu, Yingce Xia

arXiv / CoRR

2026

ForeSci: Evaluating LLM Agents for Forward-Looking AI Research Judgment

Qiuyu Tian, Haojie Yin, Yingce Xia, Youyong Kong, Yingce Xia, Zequn Liu

arXiv / CoRR

2026

VeriGeo: Controllable Geometry Question Generation with Numerical and Analytical Verification

Xiaoxian Duan, Zequn Liu, Yingce Xia

arXiv / CoRR

2025

NatureLM: Deciphering the Language of Nature for Scientific Discovery

Yingce Xia, Peiran Jin, Shufang Xie, Liang He, Chuan Cao, Renqian Luo, Guoqing Liu, Yue Wang, Zequn Liu, Yuan-Jyue Chen, Zekun Guo, Yeqi Bai, Pan Deng, Yaosen Min, Ziheng Lu, Hongxia Hao, Han Yang, Jielan Li, Chang Liu, Jia Zhang, Jianwei Zhu, Kehan Wu, Wei Zhang, Kaiyuan Gao, Qizhi Pei, Qian Wang, Xixian Liu, Yanting Li, Houtian Zhu, Yeqing Lu, Mingqian Ma, Zun Wang, Tian Xie, Krzysztof Maziarz, Marwin H. S. Segler, Zhao Yang, Zilong Chen, Yu Shi, Shuxin Zheng, Lijun Wu, Chen Hu, Peggy Dai, Tie-Yan Liu, Haiguang Liu, Tao Qin

arXiv / CoRR

2025

HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model

Mingqian Ma, Guoqing Liu, Chuan Cao, Pan Deng, Tri Dao, Albert Gu, Peiran Jin, Zhao Yang, Yingce Xia, Renqian Luo, Pipi Hu, Zun Wang, Yuan-Jyue Chen, Haiguang Liu, Tao Qin

arXiv / CoRR; MLGenX 2025 Workshop

2025

UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion

Gongbo Zhang, Yanting Li, Renqian Luo, Pipi Hu, Zeru Zhao, Lingbo Li, Guoqing Liu, Zun Wang, Ran Bi, Kaiyuan Gao, Liya Guo, Yu Xie, Chang Liu, Jia Zhang, Tian Xie, Robert Pinsler, Claudio Zeni, Ziheng Lu, Yingce Xia, Marwin H. S. Segler, Maik Riechert, Li Yuan, Lei Chen, Haiguang Liu, Tao Qin

arXiv / CoRR

2025

MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design

Wei Zhang, Zekun Guo, Yingce Xia, Peiran Jin, Shufang Xie, Tao Qin, Xiang-Yang Li

arXiv / CoRR

2022–2026

AI for Science Publications

22 works

2026

SciCustom: A Framework for Custom Evaluation of Scientific Capabilities in Large Language Models

Yiyang Gu, Junwei Yang, Junyu Luo, Ye Yuan, Bin Feng, Yingce Xia, Shufang Xie, Kaili Liu, Bohan Wu, Qi Shi, Haoran Li, Beier Xiao, Zhiping Xiao, Xiao Luo, Weizhi Zhang, Philip S. Yu, Zequn Liu, Ming Zhang

ACL 2026, Long Papers

2024

TamGen: Drug Design with Target-Aware Molecule Generation Through a Chemical Language Model

Kehan Wu, Yingce Xia, Pan Deng, Renhe Liu, Yuan Zhang, Han Guo, Yumeng Cui, Qizhi Pei, Lijun Wu, Shufang Xie, Si Chen, Xi Lu, Song Hu, Jinzhi Wu, Chi-Kin Chan, Shawn Chen, Liangliang Zhou, Nenghai Yu, Enhong Chen, Haiguang Liu, Jinjiang Guo, Tao Qin, Tie-Yan Liu

Nature Communications 15, 9360

2024

Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors

Qizhi Pei, Lijun Wu, Zhenyu He, Jinhua Zhu, Yingce Xia, Shufang Xie, Rui Yan

CIKM 2024

2023

R2-DDI: Relation-Aware Feature Refinement for Drug-Drug Interaction Prediction

Jiacheng Lin, Lijun Wu, Jinhua Zhu, Xiaobo Liang, Yingce Xia, Shufang Xie, Tao Qin, Tie-Yan Liu

Briefings in Bioinformatics 24(1)

2023

Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Qizhi Pei, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Haiguang Liu, Tie-Yan Liu, Rui Yan

Briefings in Bioinformatics 24(6)

2023

Retrosynthesis Prediction with Local Template Retrieval

Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, Tao Qin

AAAI 2023

2023

MolXPT: Wrapping Molecules with Text for Generative Pre-training

Zequn Liu, Wei Zhang, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Ming Zhang, Tie-Yan Liu

ACL 2023, Short Papers

2023

Revisiting Machine-Learning Based Drug Repurposing: Drug Indications Are Not a Right Prediction Target

Siun Kim, Jung-Hyun Won, David Seung U. Lee, Renqian Luo, Lijun Wu, Yingce Xia, Tao Qin, Howard Lee

CHIL 2023

2023

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations

Qizhi Pei, Wei Zhang, Jinhua Zhu, Kehan Wu, Kaiyuan Gao, Lijun Wu, Yingce Xia, Rui Yan

EMNLP 2023

2023

De Novo Molecular Generation via Connection-Aware Motif Mining

Zijie Geng, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Jie Wang, Yongdong Zhang, Feng Wu, Tie-Yan Liu

ICLR 2023

2023

O-GNN: Incorporating Ring Priors into Molecular Modeling

Jinhua Zhu, Kehan Wu, Bohan Wang, Yingce Xia, Shufang Xie, Qi Meng, Lijun Wu, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

ICLR 2023

2023

Retrosynthetic Planning with Dual Value Networks

Guoqing Liu, Di Xue, Shufang Xie, Yingce Xia, Austin Tripp, Krzysztof Maziarz, Marwin H. S. Segler, Tao Qin, Zongzhang Zhang, Tie-Yan Liu

ICML 2023

2023

Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design

Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Tianbo Peng, Yingce Xia, Liang He, Shufang Xie, Tao Qin, Haiguang Liu, Kun He, Tie-Yan Liu

KDD 2023

2023

Dual-view Molecular Pre-training

Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Wengang Zhou, Tao Qin, Houqiang Li, Tie-Yan Liu

KDD 2023

2023

FABind: Fast and Accurate Protein-Ligand Binding

Qizhi Pei, Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Kun He, Tie-Yan Liu, Rui Yan

NeurIPS 2023

2022

BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining

Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon, Tie-Yan Liu

Briefings in Bioinformatics 23(6)

2022

SPRoBERTa: Protein Embedding Learning with Local Fragment Modeling

Lijun Wu, Chengcan Yin, Jinhua Zhu, Zhen Wu, Liang He, Yingce Xia, Shufang Xie, Tao Qin, Tie-Yan Liu

Briefings in Bioinformatics 23(6)

2022

Back Translation for Molecule Generation

Yang Fan, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Tao Qin

Bioinformatics 38(5), 1244–1251

2022

Discovering Drug-Target Interaction Knowledge from Biomedical Literature

Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Tao Qin, Tie-Yan Liu

Bioinformatics 38(22), 5100–5107

2022

Direct Molecular Conformation Generation

Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Yusong Wang, Tong Wang, Tao Qin, Wengang Zhou, Houqiang Li, Haiguang Liu, Tie-Yan Liu

Transactions on Machine Learning Research (TMLR)

2022

RetroGraph: Retrosynthetic Planning with Graph Search

Shufang Xie, Rui Yan, Peng Han, Yingce Xia, Lijun Wu, Chenjuan Guo, Bin Yang, Tao Qin

KDD 2022

2022

Unified 2D and 3D Pre-Training of Molecular Representations

Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

KDD 2022

Emerging Direction

LLMs & Agents

1 work

2026

CoPA: Benchmarking Personalized Question Answering with Data-Informed Cognitive Factors

Hang Su, Zequn Liu, Chen, Hu, Xuesong Lu, Yingce Xia, Zhen Liu

ACL 2026 Findings

2015–2020

Earlier Work: Learning, Generation & Decision-Making

13 selected works

Earlier research spanning dual learning, neural machine translation, sequence generation, computer vision, and decision-making under uncertainty.

2020

Incorporating BERT into Neural Machine Translation

Jinhua Zhu, Yingce Xia, Lijun Wu, Di He, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

ICLR 2020

2020

Searching Better Architectures for Neural Machine Translation

Yang Fan, Fei Tian, Yingce Xia, Tao Qin, Xiangyang Li, Tie-Yan Liu

IEEE/ACM Transactions on Audio, Speech, and Language Processing, 2020

2019

Multi-Agent Dual Learning

Yiren Wang, Yingce Xia, Tianyu He, Fei Tian, Tao Qin, ChengXiang Zhai, Tie-Yan Liu

ICLR 2019

2019

Microsoft Research Asia's Systems for WMT19

Yingce Xia, Xu Tan, Fei Tian, Fei Gao, Di He, Weicong Chen, Yang Fan, Linyuan Gong, Yichong Leng, Renqian Luo, Yiren Wang, Lijun Wu, Jinhua Zhu, Tao Qin, Tie-Yan Liu

WMT 2019

2018

Model-Level Dual Learning

Yingce Xia, Xu Tan, Fei Tian, Tao Qin, Nenghai Yu, Tie-Yan Liu

ICML 2018

2018

Dual Transfer Learning for Neural Machine Translation with Marginal Distribution Regularization

Yijun Wang, Yingce Xia, Li Zhao, Jiang Bian, Tao Qin, Guiquan Liu, Tie-Yan Liu

AAAI 2018

2018

Conditional Image-to-Image Translation

Jianxin Lin, Yingce Xia, Tao Qin, Zhibo Chen, Tie-Yan Liu

CVPR 2018

2017

Dual Supervised Learning

Yingce Xia, Tao Qin, Wei Chen, Jiang Bian, Nenghai Yu, Tie-Yan Liu

ICML 2017

2017

Dual Inference for Machine Learning

Yingce Xia, Jiang Bian, Tao Qin, Nenghai Yu, Tie-Yan Liu

IJCAI 2017

2017

Deliberation Networks: Sequence Generation Beyond One-Pass Decoding

Yingce Xia, Fei Tian, Lijun Wu, Jianxin Lin, Tao Qin, Nenghai Yu, Tie-Yan Liu

NeurIPS 2017

2016

Dual Learning for Machine Translation

Di He, Yingce Xia, Tao Qin, Liwei Wang, Nenghai Yu, Tie-Yan Liu, Wei-Ying Ma

NeurIPS 2016

2016

Budgeted Multi-Armed Bandits with Multiple Plays

Yingce Xia, Tao Qin, Weidong Ma, Nenghai Yu, Tie-Yan Liu

IJCAI 2016

2015

Thompson Sampling for Budgeted Multi-Armed Bandits

Yingce Xia, Haifang Li, Tao Qin, Nenghai Yu, Tie-Yan Liu

IJCAI

Publications

Preprints

Phenotype-Guided In Silico Molecular Generation Using Large Language Models

Deciphering Scientific Reasoning Steps from Outcome Data for Molecule Optimization

ForeSci: Evaluating LLM Agents for Forward-Looking AI Research Judgment

VeriGeo: Controllable Geometry Question Generation with Numerical and Analytical Verification

NatureLM: Deciphering the Language of Nature for Scientific Discovery

HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model

UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion

MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design

AI for Science Publications

SciCustom: A Framework for Custom Evaluation of Scientific Capabilities in Large Language Models

TamGen: Drug Design with Target-Aware Molecule Generation Through a Chemical Language Model

Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors

R2-DDI: Relation-Aware Feature Refinement for Drug-Drug Interaction Prediction

Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Retrosynthesis Prediction with Local Template Retrieval

MolXPT: Wrapping Molecules with Text for Generative Pre-training

Revisiting Machine-Learning Based Drug Repurposing: Drug Indications Are Not a Right Prediction Target

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations

De Novo Molecular Generation via Connection-Aware Motif Mining

O-GNN: Incorporating Ring Priors into Molecular Modeling

Retrosynthetic Planning with Dual Value Networks

Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design

Dual-view Molecular Pre-training

FABind: Fast and Accurate Protein-Ligand Binding

BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining

SPRoBERTa: Protein Embedding Learning with Local Fragment Modeling

Back Translation for Molecule Generation

Discovering Drug-Target Interaction Knowledge from Biomedical Literature

Direct Molecular Conformation Generation

RetroGraph: Retrosynthetic Planning with Graph Search

Unified 2D and 3D Pre-Training of Molecular Representations

LLMs & Agents

CoPA: Benchmarking Personalized Question Answering with Data-Informed Cognitive Factors

Earlier Work: Learning, Generation & Decision-Making

Incorporating BERT into Neural Machine Translation

Searching Better Architectures for Neural Machine Translation

Multi-Agent Dual Learning

Microsoft Research Asia's Systems for WMT19

Model-Level Dual Learning

Dual Transfer Learning for Neural Machine Translation with Marginal Distribution Regularization

Conditional Image-to-Image Translation

Dual Supervised Learning

Dual Inference for Machine Learning

Deliberation Networks: Sequence Generation Beyond One-Pass Decoding

Dual Learning for Machine Translation

Budgeted Multi-Armed Bandits with Multiple Plays

Thompson Sampling for Budgeted Multi-Armed Bandits

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