I'm a CS PhD student at the University of Virginia advised by Prof. Jundong Li. My interests are broadly in AI for science, machine learning on graphs, and geometric deep learning.
Graph Neural Networks Are More Than Filters: Revisiting and Benchmarking from A Spectral Perspective Yushun Dong, Patrick Soga, Yinhan He, Song Wang, and Jundong LiICLR 2025.arXivDeep Interactions for Multimodal Molecular Property PredictionPatrick Soga, Zhenyu Lei, Camille Bilodeau, and Jundong LiPAKDD 2025 (Oral). Also in AIDrugX @ NeurIPS 2024.arXivExplaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective on Molecule Graphs Yinhan He, Zaiyi Zheng, Patrick Soga, Yaochen Zhu, Yushun Dong, and Jundong LiEMNLP (Findings) 2024.arXivSaludConectaMX: Lessons Learned from Deploying a Cooperative Mobile Health System for Pediatric Cancer Care in Mexico Jennifer J. Schnur*, Angélica Garcia-Martínez*, Patrick Soga*, Karla Badillo-Urquiola*, and othersCSCW 2024.arXivBridging Graph Position Encodings for Transformers with Weighted Graph-Walking AutomataPatrick Soga and David ChiangTMLR, 2023.arXivDeep Ensembles for Graphs with Higher-Order Dependencies Steven Krieg, William Burgis, Patrick Soga, and Nitesh ChawlaICLR 2023.arXivcode
In Submission
Energy-Based Models for Predicting Mutational Effects on ProteinsPatrick Soga, Zhenyu Lei, Yinhan He, Camille Bilodeau, and Jundong LiSubmitted 2025.arXivVirtualGCN — Enhancing Graph Collaborative Filtering with Virtual InteractionsPatrick Soga, Yushun Dong, Yaochen Zhu, Jundong Li, Tong Zhao, and Neil ShahSubmitted 2025. Collaboration with Snap.arXiv
Education
University of Virginia
8.2023 - present
Ph.D. in Computer Science ML for graphs, geometry, and life/physical sciences.
University of Notre Dame
8.2018 - 12.2022
B.S. in Computer Science, B.A. in Philosophy Cum Laude, Phi Beta Kappa.
Work Experience
Lucy Family Institute for Data and Society
6.2021 - 5.2022
Software Developer Web and mobile apps for health data management.
FloVision Solutions
6.2021 - 3.2022
Contracted Software Engineer Dashboards, deep vision models, and data pipelines.
Million Marker
2.2021 - 5.2021
Software Engineering Intern OCR for product labels.
RJ Reliance
12.2020 - 2.2021
Software Development Intern Mock data generation and dashboards.