Chenyu You
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Chenyu You

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Chenyu You

Assistant Professor
Department of Applied Mathematics & Statistics
Department of Computer Science
Stony Brook University


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Introduction

Chenyu You is an Assistant Professor in the Department of Applied Mathematics & Statistics and Department of Computer Science at Stony Brook University. He is also affiliated with the CVLab, AI institute, and Institute for Advanced Computational Science. Previously, he received his Ph.D. in 2024 from Yale University under the advisement of James S. Duncan, his M.S. in 2019 from Stanford University under the advisement of Daniel Rubin, and his B.S. in 2017 from Rensselaer Polytechnic Institute under the advisement of Ge Wang, all in electrical engineering. He has also spent wonderful time at Facebook AI Research (FAIR), as well as Google Research.

Research

My group studies focuses on fundamental and applied problems in computer vision and machine learning, with a focus on AI for health. We build intelligent systems that learn from complex data, reason about and interact with the real world, and drive meaningful impact on healthcare. Besides learning algorithms, we ask: how AI should represent knowledge across imaging, text, and multi-omics data; what principles ensure robustness, trustworthy, and clinical reliability; and how algorithmic advances can translate into real-world healthcare domains. Our research aims to answer these questions by advancing machine learning methods in close collaboration with biomedical and clinical science.

  • Foundation: How do we build world foundation models that generalize across diverse clinical tasks?
    Representative projects :  MedSAM / MONA / ARCO / KGAE / UniHGKR
  • Reliability: How can we build complex AI systems that clinicians can trust and rely on?
    Representative projects :  SpuriousMemorization / CFR / CASTformer
  • Access: How can we turn advances in AI into efficient, deployable tools that improve healthcare and advance scientific discovery?
    Representative projects :  CSR / OTSurv / MORSE

Here is some information for prospective students and visitors.

News

  • [2026.01] PAPER Two papers accepted at ICLR 2026.

  • [2026.01] AWARD Thrilled to receive CPAL Rising Stars Award 2026. Many thanks for the acknowledgment!

  • [2026.01] AWARD Thrilled to receive Tinker Research Grant Award from Thinking Machines Lab!

  • [2025.12] AWARD Thrilled to receive IEEE Transactions on Medical Imaging Distinguished Associate Editor Certificate of Excellence!

  • [2025.12] SERVICE Invited to serve as Area Chair MIDL 2026.

  • [2025.11] EDITOR Thrilled to serve as Associate Editor for Medical Image Analysis!

  • [2025.11] PAPER Our work CoMA, a multi-agent complex human motion generation framework, is accepted at AAAI 2026. [Code]

  • [2025.11] AWARD Thrilled to receive AAAI New Faculty Highlights 2026. Many thanks for the acknowledgment!

  • [2025.11] EDITOR Thrilled to serve as Associate Editor for Transactions on Machine Learning Research.

  • [2025.10] PAPER One paper accepted at IEEE TMI (Impact Factor 9.8).

  • [2025.10] SERVICE Thrilled to serve on the SUNY AI Symposium Planning Committee!

  • [2025.09] PAPER Our work Martian World Model is accepted at NeurIPS 2025. [News]

  • [2025.09] PAPER One paper accepted at RSNA 2025 (Oral).

  • [2025.09] SERVICE Invited to serve as Area Chair CVPR 2026.

  • [2025.08] PAPER One paper accepted at EMNLP 2025.

  • [2025.07] AWARD Thrilled to receive the Excellence in Teaching Award for Spring 2025.

  • [2025.07] AWARD Congratulations to my Ph.D. student, Qin Ren, on winning the MICCAI 2025 NIH Registration Grant!

  • [2025.06] PAPER Our work Ouroboros on cycle-consistent rendering via diffusion models is accepted at ICCV 2025. [Code]

  • [2025.06] PAPER Our work OTSurv, leveraging Optimal Transport for survival analysis, is accepted at MICCAI 2025. [Code]

  • [2025.06] PAPER Our paper “Uncovering Memorization Effect in the Presence of Spurious Correlations” has been formally accepted by Nature Communications. [Code]

  • [2025.05] PAPER One paper accepted at ACL 2025.

  • [2025.05] PAPER Our work CSR, a state-of-the-art shortening embedding models (image/text/multimodal) with sparse coding, is accepted at ICML 2025 (Oral, Top ~1%). [ Code | Hugging Face Blog ]

  • [2025.04] SERVICE Invited to serve as Area Chair NeurIPS 2025.

  • [2025.04] PAPER One paper accepted at AIME 2025.

  • [2025.04] PAPER One paper accepted at EMBC 2025 (Oral, Top Paper Award).

  • [2025.03] PAPER One paper accepted at ACM TKDD.

  • [2025.03] PAPER Our work UniHGKR, a universal retrieval-augmented generation framework, is accept at NAACL 2025 (Oral). [Code]

  • [2025.02] SERVICE Invited to serve as Area Chair EMNLP 2025.

  • [2025.02] SERVICE Invited to serve as Area Chair COLM 2025.

  • [2025.02] TALK Invited as panel speaker at the AAAI Bridge: AI for Medicine and Healthcare.

  • [2025.02] SERVICE Invited to serve on scientific committee for the 11th Workshop on Medical Computer Vision at CVPR 2025.

  • [2025.01] PAPER One paper accepted at Nature Reviews Bioengineering.

  • [2025.01] SERVICE Invited to serve as Area Chair MICCAI 2025!

  • [2025.01] EDITOR Thrilled to serve as Guest Associate Editor for IEEE Transactions on Medical Imaging!

  • [2024.12] PAPER One paper accepted at MedIA (Impact Factor 10.9).

  • [2024.12] PAPER One paper accepted at IEEE TMI (Impact Factor 8.9).

  • [2024.10] PAPER One paper accepted at Computerized Medical Imaging and Graphics.

  • [2024.10] AWARD Thrilled to be recognized as IEEE Transactions on Medical Imaging (TMI) Platinum Distinguished Reviewer (Highest award).

  • [2024.10] PAPER One paper accepted at MedIA (Impact Factor 10.9).

  • [2024.09] AWARD World’s Top 2% Scientists by Stanford University.

  • [2024.09] PAPER Our paper MONA has been formally accepted by IEEE-TPAMI (Impact Factor 20.8). [Code]

  • [2024.07] PAPER One paper accepted at BMVC 2024 (Oral).

  • [2024.06] PAPER Our paper “Medical image registration via neural fields” accepted by Medical Image Analysis (MedIA) (Impact Factor 10.9). Congrats to Shanlin, and all collaborators!

  • [2024.06] PAPER One paper accepted at MICCAI 2024.

  • [2024.04] PAPER One paper accepted at UAI 2024.

  • [2024.04] AWARD Privileged to be elected into Sigma Xi!

  • [2024.03] SERVICE Thrilled to serve as Area Chair MICCAI 2024!

  • [2024.02] PAPER Our paper “Calibrating Multi-modal Representations: A Pursuit of Group Robustness without Annotations” has been accepted at CVPR 2024. [Code]

  • [2024.02] PAPER One paper accepted at CVPR 2024.

  • [2024.01] PAPER One paper accepted at ICLR 2024.

  • [2024.01] AWARD Thrilled to be recognized as WACV 2024 Outstanding Reviewer.

  • [2024.01] PAPER One paper accepted at Imaging Neuroscience.

  • [2023.12] PAPER One paper accepted at IEEE SaTML 2023.

  • [2023.11] PAPER Our paper “Segment Anything in Medical Images” has been formally accepted by Nature Communications. [Code]

  • [2023.10] PAPER Two papers accepted at WACV 2024.

  • [2023.10] PAPER One paper accepted at IEEE BIBM 2023.

  • [2023.10] AWARD Thrilled to be recognized as IEEE Transactions on Medical Imaging (TMI) Platinum Distinguished Reviewer.

  • [2023.09] PAPER Our paper “Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective” has been accepted at NeurIPS 2023! [Code]

  • [2023.09] PAPER Two papers accepted at NeurIPS 2023!

  • [2023.09] PAPER One paper accepted at npj Digital Medicine (Impact Factor 15.357).

  • [2023.09] PAPER One paper accepted at Physics in Medicine and Biology.

  • [2023.07] PAPER One paper accepted at MICCAI-MLCN 2023.

  • [2023.06] PAPER Four papers accepted at IEEE NSS-MIC-RTSD 2023 (1 Oral).

  • [2023.06] PAPER Six papers accepted at MICCAI 2023.

  • [2023.05] PAPER One paper accepted at Investigative Radiology (Impact Factor: 10.065).

  • [2023.05] PAPER Three papers early accepted at MICCAI 2023!

  • [2023.05] PAPER Two papers accepted at ACL 2023.

  • [2023.02] PAPER Our paper ACTION has been accepted at IPMI 2023. [Code]

  • [2023.02] PAPER One paper accepted at IPMI 2023.

  • [2023.01] PAPER One paper accepted at Medical Physics.

  • [2022.10] PAPER One paper accepted at WACV 2023.

  • [2022.09] PAPER Our paper CASTformer has been accepted at NeurIPS 2022!

  • [2022.09] PAPER Two papers accepted at NeurIPS 2022!

  • [2022.08] TALK Gave a talk at Meta AI Research (FAIR) Eastcoast Vision Group about Contrastive Learning.

  • [2022.08] AWARD Very honored to be recognized as IEEE Transactions on Medical Imaging (TMI) Platinum Distinguished Reviewer.

  • [2022.08] PAPER One paper accepted at WACV 2023.

  • [2022.07] PAPER One paper accepted at MICCAI-STACOM 2022.

  • [2022.07] PAPER One paper accepted at MICCAI-DeCaF 2022.

  • [2022.07] PAPER One paper accepted at MICCAI-DGM4MICCAI 2022.

  • [2022.06] PAPER Two papers accepted at MICCAI 2022.

  • [2022.05] PAPER One paper early accepted at MICCAI 2022!

  • [2022.04] PAPER One paper accepted at NAACL 2022.

  • [2022.03] PAPER Our paper SimCVD has been formally accepted by IEEE-TMI (Impact Factor: 10.048).

  • [2022.03] PAPER One paper accepted at ICLR-PAIR2Struct 2022.

  • [2022.03] STATUS I will be interning at Facebook AI Research (FAIR), New York, starting from June 2022.

  • [2022.02] AWARD Very proud to be recognized as a Distinguished Referee for Medical Physics.

  • [2021.12] AWARD Awarded 2021 - 2022 Yale Fellowship.

  • [2021.12] PAPER One paper accepted at AAAI 2022.

  • [2021.11] PAPER One paper has been formally accepted by IEEE Transactions on Pattern Analysis and Machine Intelligence (IEEE-TPAMI) (Impact Factor 17.861).

  • [2021.10] PAPER One paper accepted at WACV 2022.

  • [2021.09] PAPER One paper accepted at NeurIPS 2021.

  • [2021.08] PAPER One paper accepted at EMNLP 2021.

  • [2021.06] PAPER Three papers accepted at Interspeech 2021.

  • [2021.05] AWARD Glad to be recognized as CVPR 2021 outstanding reviewer.

  • [2021.04] PAPER One paper accepted at IJCAI 2021 (Acceptance Rate: 13.9%).

  • [2021.03] AWARD Very proud to be recognized as Medical Physics Journal Distinguished Reviewer.

  • [2021.02] AWARD Very honored to be recognized as IEEE Transactions on Medical Imaging (TMI) Distinguished Reviewer.

  • [2021.01] PAPER Two papers accepted at IEEE-ICASSP 2021.

  • [2021.01] PAPER One paper accepted at ICLR 2021 (Spotlight).

  • [2020.11] AWARD Awarded 2020 - 2021 Yale Fellowship.

  • [2020.10] AWARD Proud to be an Outstanding Reviewer for MICCAI 2020.

  • [2020.08] PAPER One paper accepted at MICCAI-MIL3ID 2020.

  • [2020.07] PAPER Our work NuSeT, a high quality tool box for cell segmentation and analysis, accepted at PLOS Computational Biology. [Code]

  • [2019.10] AWARD Awarded 2019 - 2020 Yale Fellowship.

  • [2019.09] PAPER Three full papers accepted at Proceedings of SPIE.

  • [2019.06] AWARD Our paper “Recovery of Latent Vectors and Exploration of Latent Space from StyleGAN” received the Stanford CS230 Final Project Prize , mentored by Prof. Andrew Ng.

  • [2019.06] PAPER Our paper “CT Super-resolution GAN Constrained by the Identical, Residual, and Cycle Learning Ensemble(GAN-CIRCLE)” has been formally accepted by IEEE Transactions on Medical Imaging (IEEE-TMI) (Impact Factor: 10.048). [Code]

  • [2019.01] PAPER One papers accepted at Medical Physics.

Contact

  • Email: chenyu.you [AT] stonybrook [DOT] edu

  • Address: Physics A-148, Stony Brook, NY 11794