Shiyi Du

Hello, I am Shiyi Du, a Ph.D. student at the School of Computer Science at Carnegie Mellon University, advised by Herbert A. Simon Professor Carl Kingsford. My current research focuses on agentic reinforcement learning and its biomedical applications, including developing autonomous AI agents for scientific discovery. I am grateful to be supported by the SoftBank Group-Arm Fellowship during 2025-2027.

During undergraduate research, I was advised by Prof. Qicheng Lao and Prof. Kang Li at the West China Hospital-SenseTime Joint Lab (2021-2022). I was subsequently advised by Prof.Xiaosong Wang , Prof. Zongwei Zhou , Prof. Alan Yuille and Dr.Junjun He (2022-2023).

I received my B.Eng. degree in Computer Science and Technology from Sichuan University, where I was enrolled in IDMR, advised by Prof.Gretchen Kalonji . During my undergraduate studies, I was honored with the National Scholarship (Top 0.2%).

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DNA Foundation Models for RNA Analyses
Shiyi Du, Litian Liang, Jiayi Li, Carl Kingsford*
arXiv

ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering
Jiayi Li, Litian Liang, Shiyi Du, Shijie Tang, Hong-Sheng Lai, Carl Kingsford*
bioarxiv

Boosting Dermatoscopic Lesion Segmentation via Diffusion Models with Visual and Textual Prompts
Shiyi Du, Xiaosong Wang, Yongyi Lu, Yuyin Zhou, Shaoting Zhang, Alan Yuille, Kang Li, Zongwei Zhou*
ISBI, 2024, Oral Presentation

Distilling Knowledge from Topological Representations for Pathological Complete Response Prediction
Shiyi Du, Qicheng Lao*, Qingbo Kang, Yiyue Li, Zekun Jiang, Yanfeng Zhao, Kang Li*
MICCAI, 2022 (Early Accepted 13%)

Self-Supervised Anomaly Detection, Staging and Segmentation for Retinal Images
Yiyue Li, Qicheng Lao*, Qingbo Kang, Zekun Jiang, Shiyi Du, Shaoting Zhang, Kang Li
Medical Image Analysis, 2022

Revisiting nnUNet for Iterative Pseudo Labeling and Efficient Sliding Window Inference
Ziyan Huang, Haoyu Wang, Jin Ye, Jingqi Niu, Can Tu, Yuncheng Yang, Shiyi Du, Zhongying Deng, Lixu Gu, Junjun He*
MICCAI FLARE Challenge, 2022, Winner

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