CODER: Knowledge infused cross-lingual medical term embedding for term normalization. - Zheng Yuan 002; Zhengyun Zhao; Sheng Yu 002 (CoRR, 2020)

Unsupervised multi-granular Chinese word segmentation and term discovery via graph partition. - Zheng Yuan 002; Yuanhao Liu; Qiuyang Yin; Boyao Li; Xiaobin Feng; Guoming Zhang; Sheng Yu 002 (J. Biomed. Informatics, 2020)

Improving Biomedical Pretrained Language Models with Knowledge. - Zheng Yuan 002; Yijia Liu; Chuanqi Tan; Songfang Huang; Fei Huang 002 (BioNLP@NAACL-HLT, 2021)

Alibaba DAMO Academy at TREC Clinical Trials 2021: ExploringEmbedding-based First-stage Retrieval with TrialMatcher. - Qiao Jin 001; Chuanqi Tan; Zhengyun Zhao; Zheng Yuan 002; Songfang Huang (TREC, 2021)

Biomedical Question Answering: A Comprehensive Review. - Qiao Jin 001; Zheng Yuan 002; Guangzhi Xiong; Qianlan Yu; Chuanqi Tan; Mosha Chen; Songfang Huang; Xiaozhong Liu; Sheng Yu 002 (CoRR, 2021)

CBLUE: A Chinese Biomedical Language Understanding Evaluation Benchmark. - Ningyu Zhang 001; Zhen Bi; Xiaozhuan Liang; Lei Li 040; Xiang Chen 016; Shumin Deng; Luoqiu Li; Hongbin Ye; Xin Shang; Kangping Yin; Chuanqi Tan; Jian Xu; et al. (CoRR, 2021)

Code Synonyms Do Matter: Multiple Synonyms Matching Network for Automatic ICD Coding. - Zheng Yuan 002; Chuanqi Tan; Songfang Huang (ACL (2), 2022)

Fusing Heterogeneous Factors with Triaffine Mechanism for Nested Named Entity Recognition. - Zheng Yuan 002; Chuanqi Tan; Songfang Huang; Fei Huang 002 (ACL (Findings), 2022)

CBLUE: A Chinese Biomedical Language Understanding Evaluation Benchmark. - Ningyu Zhang 001; Mosha Chen; Zhen Bi; Xiaozhuan Liang; Lei Li 040; Xin Shang; Kangping Yin; Chuanqi Tan; Jian Xu; Fei Huang 002; Luo Si; Yuan Ni; et al. (ACL (1), 2022)

BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model. - Hongyi Yuan; Zheng Yuan 002; Ruyi Gan; Jiaxing Zhang 001; Yutao Xie; Sheng Yu 002 (BioNLP@ACL, 2022)

Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations. - Sihang Zeng; Zheng Yuan 002; Sheng Yu 002 (BioNLP@ACL, 2022)

Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning. - Hongyi Yuan; Zheng Yuan 002; Sheng Yu 002 (NAACL-HLT, 2022)

BIOS: An Algorithmically Generated Biomedical Knowledge Graph. - Sheng Yu 002; Zheng Yuan 002; Jun Xia; Shengxuan Luo; Huaiyuan Ying; Sihang Zeng; Jingyi Ren; Hongyi Yuan; Zhengyun Zhao; Yucong Lin; Keming Lu; Jing Wang; et al. (CoRR, 2022)

SeqDiffuSeq: Text Diffusion with Encoder-Decoder Transformers. - Hongyi Yuan; Zheng Yuan 002; Chuanqi Tan; Fei Huang 002; Songfang Huang (CoRR, 2022)

CODER: Knowledge-infused cross-lingual medical term embedding for term normalization. - Zheng Yuan 002; Zhengyun Zhao; Haixia Sun; Jiao Li 001; Fei Wang 001; Sheng Yu 002 (J. Biomed. Informatics, 2022)

Prompt Discriminative Language Models for Domain Adaptation. - Keming Lu; Peter Potash; Xihui Lin; Yuwen Sun; Zihan Qian; Zheng Yuan 002; Tristan Naumann; Tianxi Cai; Junwei Lu (ClinicalNLP@ACL, 2023)

HyPe: Better Pre-trained Language Model Fine-tuning with Hidden Representation Perturbation. - Hongyi Yuan; Zheng Yuan 002; Chuanqi Tan; Fei Huang 002; Songfang Huang (ACL (1), 2023)

Exploring Partial Knowledge Base Inference in Biomedical Entity Linking. - Hongyi Yuan; Keming Lu; Zheng Yuan 002 (BioNLP@ACL, 2023)

Molecular Geometry-aware Transformer for accurate 3D Atomic System modeling. - Zheng Yuan 002; Yaoyun Zhang; Chuanqi Tan; Wei Wang 225; Fei Huang 002; Songfang Huang (CoRR, 2023)

RAMM: Retrieval-augmented Biomedical Visual Question Answering with Multi-modal Pre-training. - Zheng Yuan 002; Qiao Jin 001; Chuanqi Tan; Zhengyun Zhao; Hongyi Yuan; Fei Huang 002; Songfang Huang (CoRR, 2023)

How well do Large Language Models perform in Arithmetic tasks? - Zheng Yuan 002; Hongyi Yuan; Chuanqi Tan; Wei Wang 225; Songfang Huang (CoRR, 2023)

RRHF: Rank Responses to Align Language Models with Human Feedback without tears. - Zheng Yuan 002; Hongyi Yuan; Chuanqi Tan; Wei Wang 225; Songfang Huang; Fei Huang 002 (CoRR, 2023)

DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins. - Lei Huang; Zheng Yuan 002; Huihui Yan; Rong Sheng; Linjing Liu; Fuzhou Wang; Weidun Xie; Nanjun Chen; Fei Huang 002; Songfang Huang; Ka-Chun Wong; Yaoyun Zhang (CoRR, 2023)

Hierarchical Pretraining for Biomedical Term Embeddings. - Bryan Cai; Sihang Zeng; Yucong Lin; Zheng Yuan 002; Doudou Zhou; Lu Tian (CoRR, 2023)

Scaling Relationship on Learning Mathematical Reasoning with Large Language Models. - Zheng Yuan 002; Hongyi Yuan; Chengpeng Li 001; Guanting Dong; Chuanqi Tan; Chang Zhou (CoRR, 2023)

Qwen Technical Report. - Jinze Bai; Shuai Bai; Yunfei Chu; Zeyu Cui; Kai Dang; Xiaodong Deng; Yang Fan; Wenbin Ge; Yu Han; Fei Huang 005; Binyuan Hui; Luo Ji; et al. (CoRR, 2023)

Query and Response Augmentation Cannot Help Out-of-domain Math Reasoning Generalization. - Chengpeng Li 001; Zheng Yuan 002; Hongyi Yuan; Guanting Dong; Keming Lu; Jiancan Wu; Chuanqi Tan; Xiang Wang 010; Chang Zhou (CoRR, 2023)

OccuQuest: Mitigating Occupational Bias for Inclusive Large Language Models. - Mingfeng Xue; Dayiheng Liu; Kexin Yang 002; Guanting Dong; Wenqiang Lei; Zheng Yuan 002; Chang Zhou; Jingren Zhou 001 (CoRR, 2023)

Biomedical Question Answering: A Survey of Approaches and Challenges. - Qiao Jin 001; Zheng Yuan 002; Guangzhi Xiong; Qianlan Yu; Huaiyuan Ying; Chuanqi Tan; Mosha Chen; Songfang Huang; Xiaozhong Liu; Sheng Yu 002 (ACM Comput. Surv., 2023)

A machine learning method for improving liver cancer staging. - Zhengyun Zhao; Yichen Tian; Zheng Yuan 002; Peng Zhao; Feng Xia 010; Sheng Yu 002 (J. Biomed. Informatics, 2023)

How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Composition. - Guanting Dong; Hongyi Yuan; Keming Lu; Chengpeng Li 001; Mingfeng Xue; Dayiheng Liu; Wei Wang 225; Zheng Yuan 002; Chang Zhou; Jingren Zhou 001 (ACL (1), 2024)

MuggleMath: Assessing the Impact of Query and Response Augmentation on Math Reasoning. - Chengpeng Li 001; Zheng Yuan 002; Hongyi Yuan; Guanting Dong; Keming Lu; Jiancan Wu; Chuanqi Tan; Xiang Wang 010; Chang Zhou (ACL (1), 2024)

Speculative Contrastive Decoding. - Hongyi Yuan; Keming Lu; Fei Huang 005; Zheng Yuan 002; Chang Zhou (ACL (Short Papers), 2024)

#InsTag: Instruction Tagging for Analyzing Supervised Fine-tuning of Large Language Models. - Keming Lu; Hongyi Yuan; Zheng Yuan 002; Runji Lin; Junyang Lin; Chuanqi Tan; Chang Zhou; Jingren Zhou 001 (ICLR, 2024)

Routing to the Expert: Efficient Reward-guided Ensemble of Large Language Models. - Keming Lu; Hongyi Yuan; Runji Lin; Junyang Lin; Zheng Yuan 002; Chang Zhou; Jingren Zhou 001 (NAACL-HLT, 2024)

A Unified Conditional Diffusion Framework for Dual Protein Targets-Based Bioactive Molecule Generation. - Lei Huang; Zheng Yuan 002; Huihui Yan; Rong Sheng; Linjing Liu; Fuzhou Wang; Weidun Xie; Nanjun Chen; Fei Huang 002; Songfang Huang; Ka-Chun Wong; Yaoyun Zhang (IEEE Trans. Artif. Intell., 2024)

TranSeis: A high precision multitask seismic waveform detector. - Yuxin Zhou; Huai Zhang; Shi Chen; Zheng Yuan 002; Chuanqi Tan; Fei Huang 002; Yicun Guo; Yaolin Shi (Comput. Geosci., 2025)