CV

Master of Science

Carnegie Mellon University

Computer Science

Bachelor of Engineering

Shanghai Jiao Tong University

Artificial Intelligence

Learning Interactions of Intrinsically Disordered Proteins (IDPs) with DNA

First Author | Advisor: Prof. Jian Ma | Ma Lab, CMU

• Developed the first deep learning approach to explore protein-DNA interactions for multiple IDPs.
• Achieved 0.84 Pearson correlation in efficiently predicting 20 kb base-resolution binding profiles using U-Net.
• Generalized across cell types with accuracy comparable to experimental reproducibility.
• Identified IDP-binding motifs and their spatial distribution, cooperative interactions, and binding preferences.
• Submitted a paper to RECOMB 2025.

Accelerating Molecular Dynamics Simulations of RNAs with a Graph Neural Network

Bachelor’s Thesis | Advisor: Prof. Jinjin Li | AIMS Lab, SJTU

• Developed a graph neural network (GNN) to predict molecular force fields for RNAs, achieving 8% relative loss.
• Integrated the GNN with a simulation tool to replace potential energy surface models for >1000× speedups.
• Improved the GNN's generalization ability through unsupervised data augmentation.

Predicting Molecular Properties with a Rotationally Invariant Graph Neural Network

First Author | Advisor: Prof. Jinjin Li | AIMS Lab, SJTU

• Designed a graph neural network (RotNet) with a rotationally invariant transformation, overcoming the generalization deficiency caused by rotations of molecules.
• Generalized well to various molecular conformations and achieved 2% relative loss, outperforming prior state-of-the-art methods.

Predicting Protein Energy Changes upon Single-Point Amino Acid Mutations

First Author | Advisor: Prof. Jinjin Li | AIMS Lab, SJTU

• Designed the Clustered Tree Regression (CTR) method, integrating unsupervised and supervised learning.
• Achieved a 6% improvement in accuracy compared to previous methods, using protein sequences alone as input.
• Developed software for CTR with copyright license No. 2022SR1040914 granted in China.

Teaching Assistant

Machine Learning Department, Carnegie Mellon University

10-701 Introduction to Machine Learning (PhD)

• Created homework assignments and exams, hosted recitations and office hours, and mentored projects.

Teaching Assistant

Machine Learning Department, Carnegie Mellon University

10-701 Introduction to Machine Learning (PhD)

• Created homework assignments and exams, hosted recitations and office hours, and mentored projects.

Learning genome-wide interactions of intrinsically disordered proteins with DNA using U-DisCo

Under Review

Tu, H., Zhang, Y., & Ma, J.

RotNet: A Rotationally Invariant Graph Neural Network for Quantum Mechanical Calculations

Small Methods

Tu, H., Han, Y., Wang, Z., Chen, A., Tao, K., Ye, S., ... & Li, J.

Clustered tree regression to learn protein energy change with mutated amino acid

Briefings in Bioinformatics

Tu, H., Han, Y., Wang, Z., & Li, J.

Chiang Chen Overseas Fellowship

Chiang Chen Industrial Charity Foundation

$50,000, 10 awardees in mainland China

Outstanding Graduate of Shanghai Jiao Tong University

Shanghai Jiao Tong University

Rong Chang Technology and Innovation Scholarship

Shanghai Rong Chang Public Welfare Foundation

¥30,000 (~$4,300)