CV

Education

• Ph.D in Chemistry(Theoretical & Computational Chemistry), New York University, 2023-2028 (expected)
• M.S. in Medical Informatics, Peking Union Medical College & Chinese Academy of Medical Sciences, 2020-2023
• B.S. in Medical Experimental Technology, Peking University, 2016-2020

Work experience

• 2022 Sep-2023 Jan: Research Scientist Intern
  • SILEXON
  • Compound-protein Interactin Prediction, Molecular Propertry Prediction.
  • Supervisor: Jianyang Zeng
• 2020 Nov-2021 Sep: Research Scientist Intern
  • Xtalpi AI Research Center
  • ADMET prediction, Molecular GNN
  • Supervisor: Bowen Zhang

Academic Service

• PC member: IEEE BIBM (23, 24)
• Conference reviewer: NeurIPS (24), AMIA (23, 24), BIBM (23, 24)

• Journal reviewr:

  • ML Journals: Information Fusion, Advanced Engineering Informatics, Expert Systems with Applications, Knowledge-based systems, Patterns, Neural Networks, Neurocomputing.

  • Bioinfo Journals: iMeta, SmartMat, Computers in Biology and Medicine, Briefings in Bioinformatics, Artificial Intelligence in Medicine, Journal of Medical Internet Research.

  • Biomed Journals: Frontiers in Endocrinology, Heliyon, Infectious Disease Modeling, JMIR Formative Research.

Skills

• ML package: Pytorch, PyG, DGL
• Comput Chem tool: AMBER, GROMACS, Gaussian, ChimeraX, PyMol, RDkit, Graphein

Publications

Developing a Personalized Meal Recommendation System for Chinese Older Adults: Observational Cohort Study

Zidu Xu, Yaowen Gu, Xiaowei Xu, Maxim Topaz, Zhen Guo, Hongyu Kang, Lianglong Sun, Jiao Li, "Developing a Personalized Meal Recommendation System for Chinese Older Adults: Observational Cohort Study." JMIR Formative Research, 2024.

Study on tumour cell-derived hybrid exosomes as dasatinib nanocarriers for pancreatic cancer therapy

Xiaofei Zhou, Yuetang Zhuang, Xiaohong Liu, Yaowen Gu, Junting Wang, Yuchen Shi, Li Zhang, Rui Li, Yelin Zhao, Hebing Chen, "Study on tumour cell-derived hybrid exosomes as dasatinib nanocarriers for pancreatic cancer therapy." Artificial Cells, Nanomedicine, and Biotechnology, 2023.

Prediction of medical disputes between health care workers and patients in terms of hospital legal construction using machine learning techniques: externally validated cross-sectional study

Min Yi, Yuebin Cao, Lin Wang, Yaowen Gu, Xueqian Zheng, Jiangjun Wang, Wei Chen, Liangyu Wei, Yujin Zhou, Chenyi Shi, "Prediction of medical disputes between health care workers and patients in terms of hospital legal construction using machine learning techniques: externally validated cross-sectional study." Journal of Medical Internet Research, 2023.

MGREL: A multi-graph representation learning-based ensemble learning method for gene-disease association prediction

Ziyang Wang, Yaowen Gu, Si Zheng, Lin Yang, Jiao Li, "MGREL: A multi-graph representation learning-based ensemble learning method for gene-disease association prediction." Computers in Biology and Medicine, 2023.

GNN-MTB: An Anti-Mycobacterium Drug Virtual Screening Model Based on Graph Neural Network

Gu Yaowen, Zheng Si, Yang Fengchun, Li Jiao, "GNN-MTB: An Anti-Mycobacterium Drug Virtual Screening Model Based on Graph Neural Network." Data Analysis and Knowledge Discovery, 2023.

Employing Molecular Conformations for Ligand-Based Virtual Screening with Equivariant Graph Neural Network and Deep Multiple Instance Learning

Yaowen Gu, Jiao Li, Hongyu Kang, Bowen Zhang, Si Zheng, "Employing Molecular Conformations for Ligand-Based Virtual Screening with Equivariant Graph Neural Network and Deep Multiple Instance Learning." Molecules, 2023.

Drug–disease association prediction with literature based multi-feature fusion

Hongyu Kang, Li Hou, Yaowen Gu, Xiao Lu, Jiao Li, Qin Li, "Drug–disease association prediction with literature based multi-feature fusion." Frontiers in Pharmacology, 2023.

Characteristics and Admission Preferences of Pediatric Emergency Patients and Their Waiting Time Prediction Using Electronic Medical Record Data: Retrospective Comparative Analysis

Lin Guo, Lin Guo, Jiao Li, Yao Gu, Jia Wang, Ying Cui, Qing Qian, Ting Chen, Rui Jiang, Si Zheng, "Characteristics and Admission Preferences of Pediatric Emergency Patients and Their Waiting Time Prediction Using Electronic Medical Record Data: Retrospective Comparative Analysis." Journal of Medical Internet Research, 2023.

REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction

Yaowen Gu, Si Zheng, Qijin Yin, Rui Jiang, Jiao Li, "REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction." Computers in biology and medicine, 2022.

Prediction of post-stroke urinary tract infection risk in immobile patients using machine learning: an observational cohort study

C Zhu, Z Xu, Y Gu, S Zheng, X Sun, J Cao, B Song, J Jin, Y Liu, X Wen, "Prediction of post-stroke urinary tract infection risk in immobile patients using machine learning: an observational cohort study." Journal of Hospital Infection, 2022.

Comparison of mortality predictive models of sepsis patients based on machine learning

Ziyang Wang, Yushan Lan, Zidu Xu, Yaowen Gu, Jiao Li, "Comparison of mortality predictive models of sepsis patients based on machine learning." Chinese Medical Sciences Journal, 2022.

An efficient curriculum learning-based strategy for molecular graph learning

Yaowen Gu, Si Zheng, Zidu Xu, Qijin Yin, Liang Li, Jiao Li, "An efficient curriculum learning-based strategy for molecular graph learning." Briefings in bioinformatics, 2022.

Predicting drug admet properties based on graph attention network

Gu Yaowen, Zhang Bowen, Zheng Si, Yang Fengchun, Li Jiao, "Predicting drug admet properties based on graph attention network." Data Analysis and Knowledge Discovery, 2021.

Teaching

General Chemistry I