Publications by authors named "Rex Ying"

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HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data.
Hiren Madhu, João Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying

ArXiv· December 2025

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STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Rex Ying, Wengong Jin

NPJ Digit Med· November 2025

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UNICORN: Towards universal cellular expression prediction with a multi-task learning framework.
Tianyu Liu, Tinglin Huang, Lijun Wang, Yingxin Lin, Rex Ying

Nat Commun· October 2025

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Interdisciplinary Development and Fine-Tuning of CARDIO, a Large Language Model for Cardiovascular Health Education in HIV Care: Tutorial.
Ryan Rullo, Ali Maatouk, Tinglin Huang, Jialin Chen, Weikang Qiu, Rex Ying

J Med Internet Res· September 2025

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RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design.
Rishabh Anand, Chaitanya K Joshi, Alex Morehead, Arian R Jamasb, Charles Harris, Rex Ying

ArXiv· August 2025

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Pre-training Genomic Language Model with Variants for Better Modeling Functional Genomics.
Tianyu Liu, Xiangyu Zhang, Jiecong Lin, Luca Pinello, Rex Ying

bioRxiv· August 2025

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spRefine Denoises and Imputes Spatial Transcriptomics with a Reference-Free Framework Powered by Genomic Language Model.
Tianyu Liu, Tinglin Huang, Wengong Jin, Tinyi Chu, Rex Ying

bioRxiv· July 2025

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ImmunoStruct: a multimodal neural network framework for immunogenicity prediction from peptide-MHC sequence, structure, and biochemical properties.
Smita Krishnaswamy, Kevin Givechian, João Rocha, Edward Yang, Chen Liu, Rex Ying

Res Sq· May 2025

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HEART: Learning better representation of EHR data with a heterogeneous relation-aware transformer.
Tinglin Huang, Syed Asad Rizvi, Rohan Krishna Thakur, Vimig Socrates, Meili Gupta, Rex Ying

J Biomed Inform· November 2024

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Bridging the Gap of AutoGraph Between Academia and Industry: Analyzing AutoGraph Challenge at KDD Cup 2020.
Zhen Xu, Lanning Wei, Huan Zhao, Rex Ying, Quanming Yao

Front Artif Intell· June 2022

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Hyperbolic Graph Convolutional Neural Networks.
Ines Chami, Rex Ying, Christopher Ré, Jure Leskovec

Adv Neural Inf Process Syst· December 2019

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GNNExplainer: Generating Explanations for Graph Neural Networks.
Rex Ying, Dylan Bourgeois, Jiaxuan You, Marinka Zitnik, Jure Leskovec

Adv Neural Inf Process Syst· December 2019

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A method for discrimination of noise and EMG signal regions recorded during rhythmic behaviors.
Rex Ying, Christine E Wall

J Biomech· December 2016

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