Ph.D. Student, Yale University
chen.liu.cl2482 at yale.edu
New Haven, CT & Mountain View, CA.
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Acknowledgements Many thanks to Zhuang Liu for kindly providing this website template, which was adapted from Zhe Cao's website.
Chen Liu
I am looking for a research internship (Summer 2025). Please let me know if you have opportunities in spatial-temporal modeling, multimodal learning, self-supervised learning, manifold learning, AI in healthcare, or related fields.
I am a Ph.D. student in computer science at Yale University (2022~) advised by Prof. Smita Krishnaswamy. I received my M.S. from Columbia University (2018~2020), and I did my undergraduate studies at Bucknell University, a liberal arts college featuring engineering education (2014~2018).
Research Areas I primarily work on manifold learning, a subfield of deep learning that studies how to best organize the representations in the latent space of neural networks.
Most of my research involve direct applications to healthcare or medicine, via analysis of medical images and omics (genomics, transcriptomics, proteomics) data. I also work on fusing multiple modalities, modeling time-varying dynamics, and learning from limited or no labels.
In the remaining years of my Ph.D., I would like to spend more time on taming neural networks, including generative models, to better comply with constraints such as physical laws, with applications in modeling the natural progression of diseases in time-varying medical images.
Experience Prior to my Ph.D., I first served as a full-time research assistant at Columbia University Medical Center (2020) in a medical imaging lab. The next year, I went to the industry and joined a startup company Matic (2021) and developed SLAM algorithms for housekeeping robots. Following that, I worked as a Senior Research Scientist at GE Healthcare (2021~2022), on deep learning in medical imaging applications, where I co-invented 2 patents.
News
[12/2024] 3/3 papers (2 first-authored) were accepted to ICASSP 2025.
[11/2024] I was recognized as a Top Reviewer at NeurIPS 2024 (top 9%).
[07/2024] I wrote a tool to generate your Google Scholar Citation World Map. [PDF] [Code]
[06/2024] My first project during my Ph.D. was accepted to MICCAI 2024. [Paper] [PDF] [Code] [MICCAI] [Poster]
[08/2022] I started my Ph.D. journey at Krishnaswamy Lab, Yale University.
[06/2022] I was recognized as an Outstanding Reviewer at ICML 2022 (top 10%).
Selected Recent Publications (* equal contribution)
⏳ ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images
I designed a position-parameterized neural ODE that flows the multiscale latent representations, so that we can predict a future image given an earlier image and the change in time. For example: ``Predict how this patient's eye will look like if we leave the disease untreated for 2 years.''
Chen Liu*, Ke Xu*, Liangbo L. Shen, Guillaume Huguet, Zilong Wang, Alexander Tong, Danilo Bzdok, Jay Stewart, Jay C. Wang, Lucian V. Del Priore, Smita Krishnaswamy
ICASSP 2025
ImmunoStruct: Integration of protein sequence, structure, and biochemical properties for immunogenicity prediction and interpretation
ImmunoStruct predicts immunogenicity of protein MHC complexes by fusing information from multiple biological modalities: sequence, structure and biochemical properties. I designed a novel cancer-wildtype contrastive learning objective to establish a new state of the art in the field, by encouraging pairwise similarity and suppressing feature space collapse.
Kevin Bijan Givechian, Joao Felipe Rocha, Edward Yang, Chen Liu, Kerrie Greene, Rex Ying, Etienne Caron, Akiko Iwasaki, Smita Krishnaswamy
bioRxiv 2024, updated version in submission
✂️ CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation
Chen Liu*, Matthew Amodio*, Liangbo L. Shen, Feng Gao, Arman Avesta, Sanjay Aneja, Jay C. Wang, Lucian V. Del Priore, Smita Krishnaswamy
I introduced CUTS, a novel multiscale unsupervised segmentation Framework. It first uses intra-image contrastive learning and local patch reconstruction to organize a meaningful pixel-level embedding space, and then produces multiscale assignments with diffusion condensation. On datasets with few training samples, CUTS performs on par or better than Segment Anything methods.
MICCAI 2024
[Paper] [PDF] [Code] [MICCAI] [Poster]
Conference Papers (* equal contribution)
⏳ ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images
Chen Liu*, Ke Xu*, Liangbo L. Shen, Guillaume Huguet, Zilong Wang, Alexander Tong, Danilo Bzdok, Jay Stewart, Jay C. Wang, Lucian V. Del Priore, Smita Krishnaswamy
ICASSP 2025
✂️ CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation
Chen Liu*, Matthew Amodio*, Liangbo L. Shen, Feng Gao, Arman Avesta, Sanjay Aneja, Jay C. Wang, Lucian V. Del Priore, Smita Krishnaswamy
MICCAI 2024
🎲 Assessing Neural Network Representations During Training Using Noise-Resilient Diffusion Spectral Entropy
Danqi Liao*, Chen Liu*, Benjamin W. Christensen, Alexander Tong, Guillaume Huguet, Guy Wolf, Maximilian Nickel, Ian Adelstein, Smita Krishnaswamy
ICML 2023 TAG-ML Workshop & IEEE CISS 2024
🌐 Geometry-Aware Generative Autoencoders for Warped Riemannian Metric Learning and Generative Modeling on Data Manifolds
Xingzhi Sun*, Danqi Liao*, Kincaid MacDonald*, Yanlei Zhang, Chen Liu, Guillaume Huguet, Guy Wolf, Ian Adelstein, Tim GJ Rudner, Smita Krishnaswamy
ICML 2024 GRaM Workshop & under review at a conference
Substituting Gadolinium in Brain MRI Using DeepContrast
Haoran Sun, Xueqing Liu, Xinyang Feng, Chen Liu, Nanyan Zhu, Sabrina J Gjerswold-Selleck, Hong-Jian Wei, Pavan S Upadhyayula, Angeliki Mela, Cheng-Chia Wu, Peter D Canoll, Andrew F Laine, J Thomas Vaughan, Scott A Small, Jia Guo
IEEE ISBI 2020