About

I am a CS Ph.D student at CAIRI@Westlake University. I obtained my B.S. degree in Solid State Physics from Sichuan University. My research interests focus on generative models and their applications in AI4Science, including small molecule and protein generation. Additionally, I have worked on modeling continuous flow fields and extreme events.

Education

Ph.D.           Sep. 2021 - Present
                     - Westlake University & Zhejiang University, Hangzhou, China
                     - Ph.D. student in Computer Science;
                     - Under the supervision of Stan Z. Li

News

Three papers (CBGBench, EVA, SimDDG) are accepted by ICLR 2025, with CBGBench as spotlight presentation.
One paper (EDTPP) is finally accepted by IEEE TKDE after 3 years of review process from my first year of Ph.D. T^T
One paper (DiffBP) is accepted by Chemical Science.
One paper on Lead Optimization is accepted by Journal of the American Chemical Society.
Four papers (PPFlow; GeoAB; Prompt-DDG; Re-Dock) are accepted by ICML 2024, with Re-Dock as spotlight presentation.
One paper (MAPE-PPI) is accepted by ICLR 2024, as spotlight presentation.
Two papers (PSC-CPI; SAO) are accepted by AAAI 2024.
One paper (D3FG) is accepted by NeurIPS 2023.

Experiences

Jun. 2024 - Present - DP Technology, Beijing, China - Research Intern, working on Biomolecule Generation; - Under the guidance of Zhifeng Gao and Guolin Ke

Jul. 2019 - Aug. 2019 - CBICR, Tsinghua University, Beijing, China - Visiting Student, working on Neural Science with ML; - Supervisor: Quan Wen

Selected Publications

Drug Design:

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph

Lin, H., Zhao, G., Zhang, O., Huang, Y., Wu, L., Tan, C., Liu, Z., Gao, Z., Li, SZ.

International Conference on Learning Representations, 2024 (Spotlight, Top 2.0%)

[Paper] [Code]

DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding

Lin, H., Huang, Y., Zhang, O., Ma, S., Liu, M., Li, X., Wu, L., Ji, S., Hou, T., Li, SZ.

Chemical Science, Royal Society of Chemistry, 2024

[Paper] [Code]

Deep Lead Optimization: Leveraging Generative AI for Structural Modification

Zhang, O.*, Lin, H.* , Zhang, H., Zhao, H., Huang, Y., Hsieh, C. Y., Pan, P., Hou, T.

Journal of the American Chemical Society, 2024

[Paper]

Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration

Lin, H., Huang, Y., Zhang, O., Liu, Y., Wu, L., Li, S., Chen, Z., Li, SZ.

Neural Information Processing Systems, 2023

[Paper] [Code]

Protein&Peptide Design:

GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation

Lin, H., Wu, L., Huang, Y., Liu, Y., Zhang, O., Zhou, Y., Sun, R., Li, SZ.

International Conference on Machine Learning, 2024

[Paper] [Code]

Target-Aware Peptide Design with Torsional Flow Matching

Lin, H., Zhang, O., Zhao, H., Jiang, D., Wu, L., Liu, Z., Huang, Y., Li, SZ.

International Conference on Machine Learning, 2024

[Paper] [Code]

Continuous Flow & Extreme Events:

An Empirical Study: Extensive Deep Temporal Point Process

Lin, H., Tan, C., Wu, L., Liu, Z., Zhao, G., Li, SZ.

IEEE Transaction on Knowledge and Data Engineering, 2024

[Paper] [Code]

Exploring Generative Neural Temporal Point Process

Lin, H., Wu, L., Zhao, G., Liu, P., Li, SZ.

Transaction on Machine Learning Research, 2022

[Paper] [Code]

Conditional Local Convolution for Spatio-temporal Meteorological Forecasting

Lin, H., Gao, Z., Xu, Y., Wu, L., Li, L., Li, SZ.

AAAI Conference on Artificial Intelligence, 2022

[Paper] [Code]

Selected Honors & Awards

National Scholarship, 2016
National Scholarship, 2017

Miscellaneous

I enjoy cooking, brewing coffee, and spending time with my family and my cats (Edamame the Bicolor Garfield and Pinenut the British Golden Longhair).