Education

Yale University

2022-present. Ph.D. in Computer Science

Columbia University

2018-2020. M.S. in Electrical Engineering.

Bucknell University

2014-2018. B.S. in Electrical Engineering.

Shanghai Foreign Language School

2007-2014. Middle and high school.

Experience

Senior Research Scientist @ GE Healthcare

2021-2022. Deep learning for medical imaging.

Research Software Engineer @ Matic

2021. Developed SLAM algorithms for housekeeping robots.

Research Assistant @ Columbia University Medical Center

2019-2020. Deep learning for medical imaging.

News

[11/2025] ImmunoStruct is accepted to Nature Machine Intelligence. bioRxiv

[09/2025] Brainteaser, a benchmark for LLM reasoning, is accepted to NeurIPS 2025. arXiv NeurIPS Dataset

[08/2025] CourtReasoner, a benchmark for legal LLMs, is accepted to EMNLP 2025. ACL

[06/2025] RNAGenScape is accepted to ICML 2025 GenBio workshop as a Spotlight & Oral. arXiv

[03/2025] Our paper on clinical time-series prediction for organ transplantation is accepted to Scientific Reports. nature

[01/2025] Geometry-Aware Generative Autoencoder (GAGA) is accepted to AISTATS 2025. arXiv

[12/2024] 3/3 papers (2 first-authored, both Oral) are accepted to ICASSP 2025. arXiv arXiv

[11/2024] I am recognized as a Top Reviewer at NeurIPS 2024.

[06/2024] CUTS, my first Ph.D. project, is accepted to MICCAI 2024. arXiv MICCAI Poster Dataset

[08/2022] I started my Ph.D. journey at Krishnaswamy Lab, Yale University.

[06/2022] I am recognized as an Outstanding Reviewer at ICML 2022.



Open Source Tools

[08/2024] I developed the first tool to calculate your GitHub Repo Star Percentile.

[07/2024] I developed the first free tool to generate your Google Scholar Citation World Map. PDF





Selected Recent Publications (Asterisk denotes co-first authorship)

Manifold learning Multimodal fusion Self-supervised learning

🧬 ImmunoStruct enables multimodal deep learning for immunogenicity prediction

bioRxiv PDF

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 immunogenicity-aware pairwise similarity and suppressing feature space collapse.

Kevin Bijan Givechian*, Joao Felipe Rocha*, Chen Liu* , Edward Yang, Sidharth Tyagi, Kerrie Greene, Rex Ying, Etienne Caron, Akiko Iwasaki, Smita Krishnaswamy

Nature Machine Intelligence, Impact Factor: 23.9 (2025)

Manifold learning Dynamics modeling Self-supervised learning

⏳ ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images

arXiv PDF ICASSP Poster Slides

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 Oral Presentation πŸ”Š

Manifold learning Self-supervised learning

βœ‚οΈ CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation

arXiv PDF MICCAI Poster Dataset

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



Conference Papers (Asterisk denotes co-first authorship)

PROBE: Self-Supervised Visual Prompting for Cross-Domain Road Damage Detection

arXiv PDF

Xi Xiao*, Zhuxuanzi Wang*, Mingqiao Mo*, Chen Liu , Chenrui Ma, Yanshu Li, Smita Krishnaswamy, Xiao Wang, Tianyang Wang

WACV 2026

🧠 Creativity or Brute Force? Using Brainteasers as a Window into the Problem-Solving Abilities of Large Language Models

arXiv PDF NeurIPS Dataset

Simeng Han*, Howard Dai*, Stephen Xia*, Grant Zhang*, Chen Liu* , Lichang Chen, Hoang Huy Nguyen, Hongyuan Mei, Jiayuan Mao, R. Thomas McCoy

NeurIPS 2025

Manifold learning Self-supervised learning

Dispersing Embeddings in Transformer Layers Improves Generalization of Language Models

PDF

Chen Liu* , Xingzhi Sun*, Alexandre Van Tassel*, Xi Xiao, Kristof Reimann, Danqi Liao, Ke Xu, Tianyang Wang, Xiao Wang, Smita Krishnaswamy

TAG-DS 2025, Flash Talk

Manifold learning Multimodal fusion

🧬 CellSpliceNet: Interpretable Multimodal Modeling of Alternative Splicing Across Neurons in C. elegans

bioRxiv PDF

Arman Afrasiyabi, Jake Kovalic, Chen Liu , Egbert Castro, Alexis Weinreb, Erdem Varol, David M. Miller III, Marc Hammarlund, Smita Krishnaswamy

NeurIPS 2025 FM4LS Workshop

CourtReasoner: Can LLM Agents Reason Like Judges?

PDF ACL

Simeng Han, Yoshiki Takashima, Shannon Zejiang Shen, Chen Liu , Yixin Liu, Roque K. Thuo, Sonia Knowlton, Ruzica Piskac, Scott J Shapiro, Arman Cohan

EMNLP 2025

Manifold learning

RNAGenScape: Property-guided Optimization and Interpolation of mRNA Sequences with Manifold Langevin Dynamics

arXiv PDF

Danqi Liao*, Chen Liu* , Xingzhi Sun, Dié Tang, Haochen Wang, Scott Elliot Youlten, Srikar Krishna Gopinath, Haejeong Lee, Ethan C. Strayer, Antonio J. Giraldez, Smita Krishnaswamy

ICML 2025 GenBio Workshop, Spotlight (top 16.6%) and Oral Presentation πŸ”Š (top 9.7%)

Manifold learning Dynamics modeling Self-supervised learning

⏳ ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images

arXiv PDF ICASSP Poster Slides

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 Oral Presentation πŸ”Š

Manifold learning Self-supervised learning

βš”οΈ DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images

arXiv PDF ICASSP Slides

Chen Liu* , Danqi Liao*, Alejandro Parada-Mayorga*, Alejandro Ribeiro, Marcello DiStasio, Smita Krishnaswamy

ICASSP 2025 Oral Presentation πŸ”Š

Manifold learning Self-supervised learning

🌐 Geometry-Aware Generative Autoencoders for Warped Riemannian Metric Learning and Generative Modeling on Data Manifolds

arXiv PDF

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 & AISTATS 2025

Self-supervised learning

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics

arXiv PDF ICASSP

Xingzhi Sun*, Charles Xu*, JoΓ£o F Rocha, Chen Liu , Benjamin Hollander-Bodie, Laney Goldman, Marcello DiStasio, Michael Perlmutter, Smita Krishnaswamy

ICASSP 2025

Manifold learning Self-supervised learning

βœ‚οΈ CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation

arXiv PDF MICCAI Poster Dataset

Chen Liu* , Matthew Amodio*, Liangbo L. Shen, Feng Gao, Arman Avesta, Sanjay Aneja, Jay C. Wang, Lucian V. Del Priore, Smita Krishnaswamy

MICCAI 2024

Manifold learning

🎲 Assessing Neural Network Representations During Training Using Noise-Resilient Diffusion Spectral Entropy

arXiv PDF CISS Slides Blog

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

Segmentation with Residual Attention U-Net and an Edge-Enhancement Approach Preserves Cell Shape Features

arXiv PDF EMBC

Nanyan Zhu*, Chen Liu* , Zakary S. Singer, Tal Danino, Andrew F. Laine, Jia Guo

IEEE EMBC 2022

Multimodal fusion

Deep Learning Identifies Neuroimaging Signatures of Alzheimer's Disease Using Structural and Synthesized Functional MRI Data

arXiv PDF ISBI

Nanyan Zhu*, Chen Liu* , Xinyang Feng, Dipika Sikka, Sabrina Gjerswold-Selleck, Scott A. Small, Jia Guo

IEEE ISBI 2021

Substituting Gadolinium in Brain MRI Using DeepContrast

arXiv PDF ISBI

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

[Paper] [PDF] [IEEE]



Journal Publications (Asterisk denotes co-first authorship)

Manifold learning Multimodal fusion Self-supervised learning

🧬 ImmunoStruct enables multimodal deep learning for immunogenicity prediction

bioRxiv PDF

Kevin Bijan Givechian*, Joao Felipe Rocha*, Chen Liu* Edward Yang, Sidharth Tyagi, Kerrie Greene, Rex Ying, Etienne Caron, Akiko Iwasaki, Smita Krishnaswamy

Nature Machine Intelligence, Impact Factor: 23.9 (2025)

Dynamics modeling Multimodal fusion

πŸ₯ Deep learning unlocks the true potential of organ donation after circulatory death with accurate prediction of time-to-death

medRxiv PDF nature

Xingzhi Sun*, Edward De Brouwer*, Chen Liu , Smita Krishnaswamy, Ramesh Batra

Scientific Reports 2025, Impact Factor: 3.8 (2025)

Multimodal fusion

Deep learning of MRI contrast enhancement for mapping cerebral blood volume from single-modal non-contrast scans of aging and Alzheimer's disease brains

PDF FNAGI NIH PubMed

Chen Liu* , Nanyan Zhu*, Haoran Sun, Junhao Zhang, Xinyang Feng, Sabrina Gjerswold-Selleck, Dipika Sikka, Xuemin Zhu, Xueqing Liu, Tal Nuriel, Hong-Jian Wei, Cheng-Chia Wu, J Thomas Vaughan, Andrew F Laine, Frank A Provenzano, Scott A Small, Jia Guo

Frontiers in Aging Neuroscience 2022, Impact Factor: 5.7 (2022)

In vivo γ-aminobutyric acid increase as a biomarker of the epileptogenic zone: An unbiased metabolomics approach

PDF Epilepsia NIH PubMed Commentary

Sophie Hamelin, Vasile Stupar, Lucile Mazière, Jia Guo, Wafae Labriji, Chen Liu , Ludiwine Bretagnolle, Sandrine Parrot, Emmanuel L Barbier, Antoine Depaulis, Florence Fauvelle

Epilepsia 2021, Impact Factor: 6.7 (2021)

Reduced Hippocampal GABA is associated with Poorer Episodic Memory in Healthy Older Women: A Pilot Study

PDF FNEBH NIH PubMed

Joan JimΓ©nez-Balado, Alexandra Ycaza Herrera, Kay Igwe, Lynda Klem, Korhan Buyukturkoglu, Andrei Irimia, Chen Liu , Jia Guo, Adam M Brickman, Teal S Eich

Frontiers in Behavioral Neuroscience 2021, Impact Factor: 3.6 (2021)

Multimodal fusion

Understanding and Modeling Climate Impacts on Photosynthetic Dynamics with FLUXNET Data and Neural Networks

Energies

Nanyan Zhu, Chen Liu , Andrew F Laine, Jia Guo

Energies 2020, Impact Factor: 3.0 (2020)



Preprints (Asterisk denotes co-first authorship)

Manifold learning Dynamics modeling

Revealing dynamic temporal trajectories and underlying regulatory networks with Cflows

bioRxiv PDF

Xingzhi Sun*, Shabarni Gupta*, Alexander Tong*, Manik Kuchroo*, Dhananjay Bhaskar*, Chen Liu , Aarthi Venkat, Beatriz P. San Juan, Laura Rangel, Vanina Rodriguez, Brandon Zhu, John G. Lock, Christine L. Chaffer, Smita Krishnaswamy

bioRxiv 2025, under review at Nature Genetics

Manifold learning

Not All Directions Matter: Toward Structured and Task-Aware Low-Rank Adaptation

Xi Xiao, Chenrui Ma, Yunbei Zhang, Chen Liu , Zhuxuanzi Wang, Yanshu Li, Lin Zhao, Guosheng Hu, Tianyang Wang, Hao Xu

under review at an NLP conference

Manifold learning

CTR-LoRA: curvature-aware and trust-region guided low-rank adaptation for large language models

arXiv PDF

Zhuxuanzi Wang, Mingqiao Mo, Xi Xiao, Chen Liu , Chenrui Ma, Yunbei Zhang, Xiao Wang, Smita Krishnaswamy, Tianyang Wang

arXiv 2025, under review at ICASSP

Self-supervised learning

Frequency Prior Guided Matching: A Data Augmentation Approach for Generalizable Semi-Supervised Polyp Segmentation

arXiv PDF

Haoran Xi, Chen Liu , Xiaolin Li

arXiv 2025, under review at Pattern Recognition

Adversarial Focal Loss: Asking Your Discriminator for Hard Examples

arXiv PDF

Chen Liu , Xiaomeng Dong, Michael Potter, Hsi-Ming Chang, Ravi Soni

arXiv 2022



Patents (Asterisk denotes co-first authorship)

System and Method for Obtaining Accurate Measurements and Quantification of X-Ray Image from Estimation of Key Anatomical Locations

Patent PDF

Gireesha Chinthamani Rao, Ravi Soni, Gopal B Avinash, Poonam Dalal, Chen Liu , Molin Zhang, Zita Herczeg

U.S. Patent App.

X-Ray Lead Marker Detection System for X-Ray Imaging System

Patent PDF

Gireesha Chinthamani Rao, Ravi Soni, Poonam Dalal, Chen Liu , PATI Dibyajyoti, Katelyn Nye

U.S. Patent, granted in 2025.



Conference Abstracts, excluding those published elsewhere (Asterisk denotes co-first authorship)

DL-BET-A Deep Learning Based Tool for Automatic Brain Extraction from Structural Magnetic Resonance Images in Mice

PDF

Sabrina Gjerswold-Selleck, Nanyan Zhu, Haoran Sun, Dipika Sikka, Jie Shi, Chen Liu , Tal Nuriel, Scott A Small, Jia Guo

ISMRM 2021

JET-A Matlab Toolkit for Automated J-Difference-Edited MR Spectra Processing of In Vivo Mouse MEGA-PRESS Study at 9.4 T

PDF

Chen Liu , David Jing Ma, Nanyan Zhu, Kay Igwe, Jochen Weber, Roshell Li, Emily Turner Wood, Wafae Labriji, Vasile Stupar, Yanping Sun, Neil Harris, Antoine Depaulis, Florence Fauvelle, Scott A Small, Douglas L Rothman, Jia Guo

ISMRM 2021 Oral Presentation πŸ”Š

Predicting Gadolinium Contrast Enhancement for Structural Lesion Analysis using DeepContrast

PDF

Dipika Sikka, Nanyan Zhu, Chen Liu , Scott Small, Jia Guo

ISMRM 2021 Oral Presentation πŸ”Š

Blogs and Side Projects (Asterisk denotes co-first authorship)

🌏 CitationMap: A Python Tool to Identify and Visualize Your Google Scholar Citations Around the World

TechRxiv PDF

Chen Liu

TechRxiv, Authorea Preprints

A Technical Deep Dive into Drag Your GAN (DragGAN)

PDF

Chen Liu

Blog

Towards a Large-Scale Unbiased Machine Learning Benchmark for Cell Instance Segmentation: Final Report for CPSC 537 Intro to Database Systems

PDF

Chen Liu , Danqi Liao, Shuangge Wang

Course Project

Others

Service  I'm a regular reviewer for conferences NeurIPS, ICML, ICLR, MICCAI, ICASSP and journals TNNLS, TMLR.


Fun fact 1  I am the father of two cats.

Fun fact 2  My spirit animal is a fox.