PSB 2024 Online Proceedings

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Creative Commons License PSB 2024 proceedings are published as Open Access chapters by World Scientific Publishing Company and distributed under the terms of the Creative Commons Attribution (CC BY) 4.0 License.

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Contents

Preface

Artificial Intelligence in Clinical Medicine: Generative and Interactive Systems at the Human-Machine Interface

Session Introduction
Sajjad Fouladvand, Emma Pierson, Ivana Jankovic, David Ouyang, Jonathan H. Chen, Roxana Daneshjou;Pacific Symposium on Biocomputing 29:1-7(2024)
Clinfo.ai: An Open-Source Retrieval-Augmented Large Language Model System for Answering Medical Questions Using Scientific Literature
Alejandro Lozano, Scott L Fleming, Chia-Chun Chiang, Nigam Shah; Pacific Symposium on Biocomputing 29:8-23(2024)
A Conversational Agent for Early Detection of Neurotoxic Effects of Medications through Automated Intensive Observation
Serguei Pakhomov, Jacob Solinsky, Martin Michalowski, Veronika Bachanova; Pacific Symposium on Biocomputing 29:24-38(2024)
Leveraging 3D Echocardiograms to Evaluate AI Model Performance in Predicting Cardiac Function on Out-of-Distribution Data
Grant Duffy, Kai Christensen, David Ouyang; Pacific Symposium on Biocomputing 29:39-52(2024)
BrainSTEAM: A Practical Pipeline for Connectome-based fMRI Analysis towards Subject Classification
Alexis Li, Yi Yang, Hejie Cui, Carl Yang; Pacific Symposium on Biocomputing 29:53-64(2024)
MaTiLDA: An Integrated Machine Learning and Topological Data Analysis Platform for Brain Network Dynamics
Katrina Prantzalos, Dipak Upadhyaya, Nassim Shafiabadi, Guadalupe Fernandez-BacaVaca, Nick Gurski, Kenneth Yoshimoto, Subhashini Sivagnanam, Amitava Majumdar, Satya S. Sahoo; Pacific Symposium on Biocomputing 29:65-80(2024)
Zoish: A Novel Feature Selection Approach Leveraging Shapley Additive Values for Machine Learning Applications in Healthcare
< Hossein Javedani Sadaei, Salvatore Loguercio, Mahdi Shafiei Neyestanak, Ali Torkamani/i>; Pacific Symposium on Biocomputing 29:81-95(2024)
SynTwin: A Graph-Based Approach for Predicting Clinical Outcomes Using Digital Twins Derived from Synthetic Patients
Jason H. Moore, Xi Li, Jui-Hsuan Chang, Nicholas P. Tatonetti, Dan Theodorescu, Yong Chen, Folkert W. Asselbergs, Mythreye Venkatesan, Zhiping Paul Wang; Pacific Symposium on Biocomputing 29:96-107(2024)
Optimizing Computer-Aided Diagnosis with Cost-Aware Deep Learning Models
Charmi Patel, Yiyang Wang, Thiruvarangan Ramaraj, Roselyne Tchoua, Jacob Furst, Daniela Raicu; Pacific Symposium on Biocomputing 29:108-119(2024)
VetLLM: Large Language Model for Predicting Diagnosis from Veterinary Notes
Yixing Jiang, Jeremy A. Irvin, Andrew Y. Ng, James Zou; Pacific Symposium on Biocomputing 29:120-133(2024)
Impact of Measurement Noise on Genetic Association Studies of Cardiac Function
Milos Vukadinovic, Gauri Renjith, Victoria Yuan, Alan Kwan, Susan C. Cheng, Debiao Li, Shoa L. Clarke, David Ouyang; Pacific Symposium on Biocomputing 29:134-147(2024)
A Deep Neural Network Estimation of Brain Age Is Sensitive to Cognitive Impairment and Decline
Yisu Yang, Aditi Sathe, Kurt Schilling, Niranjana Shashikumar, Elizabeth Moore, Logan Dumitrescu, Kimberly Pechman, Bennett Landman, Katherine Gifford, Timothy Hohman, Angela Jefferson, Derek Archer; Pacific Symposium on Biocomputing 29:148-162(2024)

Digital health technology data in biocomputing: Research efforts and considerations for expanding access

Session Introduction
Michelle Holko, Chris Lunt, Jessilyn Dunn;Pacific Symposium on Biocomputing 29:163-169(2024)
Expanding the Access of Wearable Silicone Wristbands in Community-Engaged Research Through Best Practices in Data Analysis and Integration
Lisa M. Bramer, Holly M. Dixon, David J. Degnan, Diana Rohlman, Julie B. Herbstman, Kim A. Anderson, Katrina M. Waters; Pacific Symposium on Biocomputing 29:170-186(2024)
Subject Harmonization of Digital Biomarkers: Improved Detection of Mild Cognitive Impairment from Language Markers
Bao Hoang, Yijiang Pang, Hiroko Dodge, Jiayu Zhou; Pacific Symposium on Biocomputing 29:187-200(2024)
Scalar-Function Causal Discovery for Generating Causal Hypotheses with Observational Wearable Device Data
Valeriya Rogovchenko, Austin Sibu, Yang Ni ; Pacific Symposium on Biocomputing 29:201-213(2024)
FedBrain: Federated Training of Graph Neural Networks for Connectome-based Brain Imaging Analysis
Yi Yang, Han Xie, Hejie Cui, Carl Yang; Pacific Symposium on Biocomputing 29:214-225(2024)

Drug-repurposing and discovery in the era of “big” Real-World Data: how the incorporation of observational data, genetics, and other -omic technologies can move us forward

Session Introduction
Megan M. Shuey, Jacklyn N. Hellwege, Nikhil Khankari, Marijana Vujkovic, Todd L. Edwards; Pacific Symposium on Biocomputing 29:226-231(2024)
Systematic Estimation of Treatment Effect on Hospitalization Risk as a Drug Repurposing Screening Method
Costa Georgantas, Jaume Banus, Roger Hullin, Jonas Richiardi; Pacific Symposium on Biocomputing 29:232-246(2024)
Transcript-Aware Analysis of Rare Predicted Loss-of-Function Variants in the UK Biobank Elucidate New Isoform-Trait Associations
Rachel A. Hoffing, Aimee M. Deaton, Aaron M. Holleman, Lynne Krohn, Philip J. LoGerfo, Mollie E. Plekan, Sebastian Akle Serrano, Paul Nioi, Lucas D. Ward; Pacific Symposium on Biocomputing 29:247-260(2024)
Generating new drug repurposing hypotheses using disease-specific hypergraphs
Ayush Jain, Marie-Laure Charpignon, Irene Y. Chen, Anthony Philippakis, Ahmed Alaa; Pacific Symposium on Biocomputing 29:261-275(2024)
Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies
Chinmaya U. Joisa, Kevin A. Chen, Samantha Beville, Timothy Stuhlmiller, Matthew E. Berginski, Denis Okumu, Brian T. Golitz, Michael P. East, Gary L. Johnson, Shawn M. Gomez; Pacific Symposium on Biocomputing 29:276-290(2024)
Creation of a Curated Database of Experimentally Determined Human Protein Structures for the Identification of Its Targetome
Armand Ovanessians, Carson Snow, Thomas Jennewein, Susanta Sarkar, Gil Speyer, Judith Klein-Seetharaman; Pacific Symposium on Biocomputing 29:291-305(2024)
Modeling Path Importance for Effective Alzheimer’s Disease Drug Repurposing
Shunian Xiang, Patrick J. Lawrence, Bo Peng, ChienWei Chiang, Dokyoon Kim, Li Shen, Xia Ning; Pacific Symposium on Biocomputing 29:306-321(2024)

Overcoming health disparities in precision medicine

Session Introduction
Francisco M. De La Vega, Kathleen C. Barnes, Keolu Fox, Alexander Ioannidis, Eimear Kenny, Rasika A. Mathias, Bogdan Pasaniuc;Pacific Symposium on Biocomputing 29:322-326(2024)
PopGenAdapt: Semi-Supervised Domain Adaptation for Genotype-to-Phenotype Prediction in Underrepresented Populations
Marçal Comajoan Cara, Daniel Mas Montserrat, Alexander G. Ioannidis; Pacific Symposium on Biocomputing 29:327-340(2024)
LA-GEM: Imputation of Gene Expression with Incorporation of Local Ancestry
Mrinal Mishra, Layan Nahlawi, Yizhen Zhong, Tanima De, Guang Yang, Cristina Alarcon, Minoli A Perera; Pacific Symposium on Biocomputing 29:341-358(2024)
Cluster Analysis Reveals Socioeconomic Disparities Among Elective Spine Surgery Patients
Alena Orlenko, Philip J. Freda, Attri Ghosh, Hyunjun Choi, Nicholas Matsumoto, Tiffani J. Bright, Corey T. Walker, Tayo Obafemi-Ajayi, Jason H. Moore; Pacific Symposium on Biocomputing 29:359-373(2024)
Evidence of Recent and Ongoing Admixture in the U.S. and Influences on Health and Disparities
Hannah M. Seagle, Jacklyn N. Hellwege, Brian S. Mautz, Chun Li, Yaomin Xu, Siwei Zhang, Dan M. Roden, Tracy L. McGregor, Digna R. Velez Edwards, Todd L. Edwards; Pacific Symposium on Biocomputing 29:374-388(2024)
Evaluating the Relationships Between Genetic Ancestry and the Clinical Phenome
Jacqueline A. Piekos and Jeewoo Kim, Jacob M. Keaton, Jacklyn N. Hellwege, Todd L. Edwards and Digna R. Velez Edwards; Pacific Symposium on Biocomputing 29:389-403(2024)
Machine Learning Strategies for Improved Phenotype Prediction in Underrepresented Populations
David Bonet, May Levin, Daniel Mas Montserrat, Alexander G. Ioannidis; Pacific Symposium on Biocomputing 29:404-418(2024)
Quantifying Health Outcome Disparity in Invasive Methicillin-Resistant Staphylococcus aureus Infection using Fairness Algorithms on Real-World Data
Inyoung Jun, Sarah E. Ser, Scott A. Cohen, Jie Xu, Robert J. Lucero, Jiang Bian, Mattia Prosperi; Pacific Symposium on Biocomputing 29:419-432(2024)
Imputation of Race and Ethnicity Categories Using Genetic Ancestry from Real-World Genomic Testing Data
Brooke Rhead, Paige E. Haffener, Yannick Pouliot, Francisco M. De La Vega; Pacific Symposium on Biocomputing 29:433-445(2024)

Precision Medicine: Innovative methods for advanced understanding of molecular underpinnings of disease

Session Introduction
Yana Bromberg, Hannah Carter, Steven E. Brenner;Pacific Symposium on Biocomputing 29:446-449(2024)
Enhancing Spatial Transcriptomics Analysis by Integrating Image-Aware Deep Learning Methods
Jiarong Song, Josh Lamstein, Vivek Gopal Ramaswamy, Michelle Webb, Gabriel Zada, Steven Finkbeiner, David W. Craig; Pacific Symposium on Biocomputing 29:450-463(2024)
Spatial Omics Driven Crossmodal Pretraining Applied to Graph-based Deep Learning for Cancer Pathology Analysis
Zarif L. Azher, Michael Fatemi, Yunrui Lu, Gokul Srinivasan, Alos B. Diallo, Brock C. Christensen, Lucas A. Salas, Fred W. Kolling IV, Laurent Perreard, Scott M. Palisoul, Louis J. Vaickus, Joshua J. Levy; Pacific Symposium on Biocomputing 29:464-476(2024)
Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining
Gokul Srinivasan, Matthew J. Davis, Matthew R. LeBoeuf, Michael Fatemi, Zarif L. Azher, Yunrui Lu, Alos B. Diallo, Marietta K. Saldias Montivero, Fred W. Kolling IV, Laurent Perrard, Lucas A. Salas, Brock C. Christensen, Thomas J. Palys , Margaret R. Karagas, Scott M. Palisoul, Gregory J. Tsongalis, Louis J. Vaickus, Sarah M. Preum, Joshua J. Levy; Pacific Symposium on Biocomputing 29:477-491(2024)
PEPSI: Polarity Measurements from Spatial Proteomics Imaging Suggest Immune Cell Engagement
Eric Wu, Zhenqin Wu, Aaron T. Mayer, Alexandro E. Trevino, James Zou ; Pacific Symposium on Biocomputing 29:492-505(2024)
KombOver: Efficient K-Core and K-Truss Based Characterization of Perturbations Within the Human Gut Microbiome
Nicolae Sapoval, Marko Tanevski, Todd J. Treangen; Pacific Symposium on Biocomputing 29:506-520(2024)
nSEA: n-Node Subnetwork Enumeration Algorithm Identifies Lower Grade Glioma Subtypes with Altered Subnetworks and Distinct Prognostics
Zhihan Zhang, Christiana Wang, Ziyin Zhao, Ziyue Yi, Arda Durmaz, Jennifer S. Yu, Gurkan Bebek; Pacific Symposium on Biocomputing 29:521-533(2024)
Application of Quantile Discretization and Bayesian Network Analysis to Publicly Available Cystic Fibrosis Data Sets
Kiyoshi Ferreira Fukutani, Thomas H. Hampton, Carly A. Bobak, Todd A. MacKenzie, Bruce A. Stanton; Pacific Symposium on Biocomputing 29:534-548(2024)
Low- and High-Level Information Analyses of Transcriptome Connecting Endometrial-Decidua-Placental Origin of Preeclampsia Subtypes: A Preliminary Study
Herdiantri Sufriyana, Yu-Wei Wu, Emily Chia-Yu Su; Pacific Symposium on Biocomputing 29:549-563(2024)
Deconvolution of Nascent Sequencing Data Using Transcriptional Regulatory Elements
Zachary Maas, Rutendo Sigauke, Robin Dowelli; Pacific Symposium on Biocomputing 29:564-578(2024)
Splitpea: Quantifying Protein Interaction Network Rewiring Changes Due to Alternative Splicing in Cancer
Ruth Dannenfelser, Vicky Yao; Pacific Symposium on Biocomputing 29:579-593(2024)
Lymphocyte Count Derived Polygenic Score and Interindividual Variability in CD4 T-cell Recovery in Response to Antiretroviral Therapy
Kathleen M. Cardone, Scott Dudek, Karl Keat, Yuki Bradford, Zinhle Cindi, Eric S. Daar, Roy Gulick, Sharon A. Riddler, Jeffrey L. Lennox, Phumla Sinxadi, David W. Haas, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 29:594-610(2024)
Polygenic Risk Scores for Cardiometabolic Traits Demonstrate Importance of Ancestry for Predictive Precision Medicine
Rachel Kember, Shefali Verma, Anurag Verma, Brenda Xiao, Anastasia Lucas, Colleen Kripke, Renae Judy, Jinbo Chen, Scott Damrauer, Daniel Rader, Marylyn Ritchie; Pacific Symposium on Biocomputing 29:611-626(2024)
intCC: An Efficient Weighted Integrative Consensus Clustering of Multimodal Data
Can Huang, Pei Fen Kuan; Pacific Symposium on Biocomputing 29:627-640(2024)

Workshops

Large Language Models (LLMs) and ChatGPT for Biomedicine
Cecilia Arighi, Steven Brenner, Zhiyong Lu;Pacific Symposium on Biocomputing 29:641-644(2024)
Practical Approaches to Enhancing Fairness, Social Responsibility and the Inclusion of Diverse Viewpoints in Biomedicine
Daphne O. Martschenko, Nicole Martinez-Martin, Meghan Halley; Pacific Symposium on Biocomputing 29:645-649(2024)
Risk prediction: Methods, Challenges, and Opportunities
Ruowang Li, Rui Duan, Lifang He, Jason H. Moore; Pacific Symposium on Biocomputing 29:650-653(2024)
Statistical Analysis of single-cell protein data
Brooke L Fridley, Simon Vandekar, Inna Chervoneva, Julia Wrobel, Siyuan Ma; Pacific Symposium on Biocomputing 29:654-660(2024)
Tools for assembling the cell: Towards the era of cell structural bioinformatics
Mengzhou Hu, Xikun Zhang, Andrew Latham, Andrej Sali, Trey Ideker, and Emma Lundberg; Pacific Symposium on Biocomputing 29:661-665(2024)

Erratum

How Fitbit data are being made available to registered researchers in All of Us Research Program
Hiral Master, Aymone Kouame, Kayla Marginean, Melissa Basford, Paul Harris, Michelle Holko

Funding for this conference was made possible (in part) by R13LM006766 from the National Library of Medicine. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.

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Updated: December 13, 2023