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Patrick Soga

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.

Previously, I did my undergrad at the University of Notre Dame where I studied CS & philosophy of math/logic and worked under professors Nitesh Chawla and David Chiang.

Publications

(*) indicates equal contribution.

Graph Neural Networks Are More Than Filters: Revisiting and Benchmarking from A Spectral Perspective
Yushun Dong, Patrick Soga, Yinhan He, Song Wang, and Jundong Li
ICLR 2025.arXiv
Deep Interactions for Multimodal Molecular Property Prediction
Patrick Soga, Zhenyu Lei, Camille Bilodeau, and Jundong Li
PAKDD 2025 (Oral). Also in AIDrugX @ NeurIPS 2024.arXiv
Explaining 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 Li
EMNLP (Findings) 2024.arXiv
SaludConectaMX: 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 others
CSCW 2024.arXiv
Bridging Graph Position Encodings for Transformers with Weighted Graph-Walking Automata
Patrick Soga and David Chiang
TMLR, 2023.arXiv
Deep Ensembles for Graphs with Higher-Order Dependencies
Steven Krieg, William Burgis, Patrick Soga, and Nitesh Chawla
ICLR 2023.arXivcode

In Submission

Energy-Based Models for Predicting Mutational Effects on Proteins
Patrick Soga, Zhenyu Lei, Yinhan He, Camille Bilodeau, and Jundong Li
Submitted 2025.arXiv
VirtualGCN — Enhancing Graph Collaborative Filtering with Virtual Interactions
Patrick Soga, Yushun Dong, Yaochen Zhu, Jundong Li, Tong Zhao, and Neil Shah
Submitted 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.