News

[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)

Weak supervision Manifold learning

✂️ 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

[Paper] [PDF] [Code] [MICCAI] [Poster]

Spatial-temporal dynamics Manifold learning

⏳ 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

arXiv 2024

[Paper] [PDF] [Slides] [Code]



Conference Papers (* equal contribution)

Weak supervision Manifold learning

✂️ 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

[Paper] [PDF] [Code] [MICCAI] [Poster]

Weak supervision Manifold learning

🎲 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

[Paper] [PDF] [Slides] [Code]

Manifold learning

🌐 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

[Paper] [PDF]

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

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

IEEE EMBC 2022

[Paper] [PDF] [Code]

Multimodal fusion

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

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

IEEE ISBI 2021

[Paper] [PDF] [IEEE]

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

[Paper] [PDF] [IEEE]



Journal Publications (* equal contribution)

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

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)

[Paper] [PDF] [NIH PubMed]

In Vivo γ-Aminobutyric Acid Increase as a Biomarker of the Epileptogenic Zone: An Unbiased Metabolomics Approach

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)

[Paper] [PDF] [NIH PubMed]

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

Joan Jiménez-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)

[Paper] [PDF] [NIH PubMed]



Preprints (* equal contribution)

Multimodal fusion

Deep Learning Unlocks the True Potential of Organ Donation after Circulatory Death with Accurate Prediction of Time-to-Death

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

medRxiv 2024, under review at a journal

[Paper] [PDF]

Multimodal fusion Manifold learning

ImmunoStruct: Integration of protein sequence, structure, and biochemical properties for immunogenicity prediction and interpretation

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

bioRxiv 2024

[Paper] [PDF]

Weak supervision Manifold learning

⚔️ DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images

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

arXiv 2024, under review at a conference

[Paper] [PDF] [Slides] [Code]

Spatial-temporal dynamics Manifold learning

⏳ 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

arXiv 2024, under review at a conference

[Paper] [PDF] [Slides] [Code]

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics

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

arXiv 2024, under review at a conference

[Paper] [PDF]

Adversarial Focal Loss: Asking Your Discriminator for Hard Examples

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

arXiv 2022

[Paper] [PDF]



Patents (* equal contribution)

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

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

U.S. Patent App.

[Patent] [PDF]

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

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

U.S. Patent App.

[Patent] [PDF]



Conference Abstracts (Excluding those published elsewhere) (* equal contribution)

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

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

ISMRM 2021

[PDF]

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

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

[PDF]

Predicting Gadolinium Contrast Enhancement for Structural Lesion Analysis using DeepContrast

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

ISMRM 2021 Oral Presentation

[PDF]

Blogs and Side Projects (* equal contribution)

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

Chen Liu

TechRxiv, Authorea Preprints

[Paper] [PDF] [Code]

A Novel Entropy and Mutual Information Measure for High Dimensional Data and Deep Neural Networks

Chen Liu

Blog

[PDF]

A Technical Deep Dive into Drag Your GAN (DragGAN)

Chen Liu

Blog

[PDF]

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

Chen Liu

Course Project

[PDF]


Others

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


Fun fact 1  I am the father of two cats.

Fun fact 2  My spirit animal is a fox.

Joker 🤡 story 1  I still haven't published at NeurIPS, ICML or ICLR despite having served as a reviewer for 3 years and having won two outstanding/top reviewer awards.

Joker 🤡 story 2  I have applied for Ph.D. positions three times. I got rejected from all applications in the first two attempts, and only received 1 offer out of 16 applications in the third attempt.