PSB 2025 Online Proceedings
PSB 2025 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.
A PDF of the full PSB 2025 Proceedings is available.
Table of Contents
- Preface
- 30 Years of PSB Impact
- AI and Machine Learning in Clinical Medicine: Generative and Interactive Systems at the Human-Machine Interface
- Precision Medicine: Multi-modal and multi-scale methods to promote mechanistic understanding of disease
- Translating Big Data Imaging Genomics Findings to the Individual: Prediction of Risks and Outcomes in Neuropsychiatric Illnesses
- Overcoming health disparities in precision medicine
- Workshops
- Earth Friendly Computation: Applying Indigenous Data Lifecycles in Medical and Sovereign AI
- Erratum
Preface
30 Years of PSB Impact
- A Comprehensive Bibliometric Analysis: Celebrating the Thirtieth Anniversary of the Pacific Symposium on Biocomputing
- Rachit Kumar, Rasika Venkatesh, David Y. Zhang, Teri E. Klein, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 30:1-15(2025)
- Charting the Evolution and Transformative Impact of the Pacific Symposium on Biocomputing Through a 30-Year Retrospective Analysis of Collaborative Networks and Themes Using Modern Computational Tools
- Leah Zhang, Sameeksha Garg, Edward Zhang, Sean McOsker, Carly Bobak, Kristine Giffin, Brock Christensen, Joshua Levy; Pacific Symposium on Biocomputing 30:16-32(2025)
AI and Machine Learning in Clinical Medicine: Generative and Interactive Systems at the Human-Machine Interface
- Session Introduction
- Fateme Nateghi Haredasht, Dokyoon Kim, Joseph D. Romano, Geoff Tison, Roxana Daneshjou, Jonathan H. Chen;Pacific Symposium on Biocomputing 30:33-39(2025)
- A Visual Analytics Framework for Assessing Interactive AI for Clinical Decision Support
- Eric Prince, Todd C. Hankinson, Carsten Görg;Pacific Symposium on Biocomputing 30:40-53(2025)
- QUEST-AI: A System for Question Generation, Verification, and Refinement using AI for USMLE-Style Exams
- Suhana Bedi, Scott L. Fleming Chia-Chun Chiang, Keith Morse, Aswathi Kumar, Birju Patel, Jenelle A. Jindal, Conor Davenport, Craig Yamaguchi, Nigam H. Shah;Pacific Symposium on Biocomputing 30:54-69(2025)
- ReXErr: Synthesizing Clinically Meaningful Errors in Diagnostic Radiology Reports
- Vishwanatha M. Rao, Serena Zhang, Julian N. Acosta, Subathra Adithan, Pranav Rajpurkar;Pacific Symposium on Biocomputing 30:70-81(2025)
- LLM-CGM: A Benchmark for Large Language Model-Enabled Querying of Continuous Glucose Monitoring Data for Conversational Diabetes Management
- Elizabeth Healey, Isaac Kohane;Pacific Symposium on Biocomputing 30:82-93(2025)
- Artificial Allies: Validation of Synthetic Text for Peer Support Tools through Data Augmentation in NLP Model Development
- Josué Godeme, Julia Hill, Stephen P. Gaughan, Wade J. Hirschbuhl, Amanda J. Emerson, Christian Darabos, Carly A. Bobak, Karen L. Fortuna;Pacific Symposium on Biocomputing 30:94-108(2025)
- A Prospective Comparison of Large Language Models for Early Prediction of Sepsis
- Supreeth P. Shashikumar, Shamim Nemati;Pacific Symposium on Biocomputing 30:109-120(2025)
- Using Large Language Models for Efficient Cancer Registry Coding in the Real Hospital Setting: A Feasibility Study
- Chen-Kai Wang, Cheng-Rong Ke, Ming-Siang Huang, Inn-Wen Chong, Yi-Hsin Yang, Vincent S. Tseng, Hong-Jie Dai;Pacific Symposium on Biocomputing 30:121-137(2025)
- Automated Evaluation of Antibiotic Prescribing Guideline Concordance in Pediatric Sinusitis Clinical Notes
- Davy Weissenbacher, Lauren Dutcher, Mickael Boustany, Leigh Cressman, Karen O'Connor, Keith W. Hamilton, Jeffrey Gerber, Robert Grundmeier, Graciela Gonzalez-Hernandez;Pacific Symposium on Biocomputing 30:138-153(2025)
- Implications of An Evolving Regulatory Landscape on the Development of AI and ML in Medicine
- Nicole Rincon, Sara Gerke, Jennifer K. Wagner;Pacific Symposium on Biocomputing 30:154-166(2025)
- Investigating the Differential Impact of Psychosocial Factors by Patient Characteristics and Demographics on Veteran Suicide Risk Through Machine Learning Extraction of Cross-Modal Interactions
- Joshua Levy, Monica Dimambro, Alos Diallo, Jiang Gui, Brian Shiner, Maxwell Levis;Pacific Symposium on Biocomputing 30:167-184(2025)
- ReXamine-Global: A Framework for Uncovering Inconsistencies in Radiology Report Generation Metrics
- Oishi Banerjee, Agustina Saenz, Kay Wu, Warren Clements, Adil Zia, Dominic Buensalido, Helen Kavnoudias, Alain S. Abi-Ghanem, Nour El Ghawi, Cibele Luna, Patricia Castillo, Khaled Al-Surimi, Rayyan A. Daghistani, Yuh-Min Chen, Heng-sheng Chao, Lars Heiliger, Moon Kim, Johannes Haubold, Frederic Jonske, Pranav Rajpurkar;Pacific Symposium on Biocomputing 30:185-198(2025)
- Improving Retrieval-Augmented Generation in Medicine with Iterative Follow-up Questions
- Guangzhi Xiong, Qiao Jin, Xiao Wang, Minjia Zhang, Zhiyong Lu, Aidong Zhang;Pacific Symposium on Biocomputing 30:199-214(2025)
- ClinValAI: A framework for developing Cloud-based infrastructures for the External Clinical Validation of AI in Medical Imaging
- Ojas A. Ramwala, Kathryn P. Lowry, Daniel S. Hippe, Matthew P.N. Unrath, Matthew J. Nyflot, Sean D. Mooney, Christoph I. Lee;Pacific Symposium on Biocomputing 30:215-228(2025)
- PGxQA: A Resource for Evaluating LLM Performance for Pharmacogenomic QA Tasks
- Karl Keat, Rasika Venkatesh, Yidi Huang, Rachit Kumar, Sony Tuteja, Katrin Sangkuhl, Binglan Li, Li Gong, Michelle Whirl-Carrillo, Teri E. Klein, Marylyn D. Ritchie, Dokyoon Kim;Pacific Symposium on Biocomputing 30:229-246(2025)
- Session Introduction
- Francisco M. De La Vega, Kathleen C. Barnes, Harris Bland, Todd Edwards, Keolu Fox, Alexander Ioannidis, Eimear Kenny, Rasika A. Mathias, Bogdan Pasaniuc, Jada Benn Torres, Digna R Velez Edwards;Pacific Symposium on Biocomputing 30:247-250(2025)
- The Impact of Ancestry on Genome-Wide Association Studies
- Steven Christopher Jones, Katie M. Cardone, Yuki Bradford, Sarah A. Tishkoff, Marylyn D. Ritchie;Pacific Symposium on Biocomputing 30:251-267(2025)
- Constructing a multi-ancestry polygenic risk score for uterine fibroids using publicly available data highlights need for inclusive genetic research
- Jessica L.G. Winters, Jacqueline A. Piekos, Jacklyn N. Hellwege, Ozan Dikilitas, Iftikhar J. Kullo, Daniel J. Schaid, Todd L. Edwards, Digna R. Velez Edwards;Pacific Symposium on Biocomputing 30:268-280(2025)
- Uterine fibroids show evidence of shared genetic architecture with blood pressure traits
- Alexis T. Akerele, Jacqueline A. Piekos, Jeewoo Kim, Nikhil K. Khankari, Jacklyn N. Hellwege, Todd L. Edwards, Digna R. Velez Edwards;Pacific Symposium on Biocomputing 30:281-295(2025)
- Social Determinants of Health and Lifestyle Risk Factors Modulate Genetic Susceptibility for Women’s Health Outcomes
- Lindsay A Guare, Jagyashila Das, Lannawill Caruth, Shefali Setia-Verma;Pacific Symposium on Biocomputing 30:296-313(2025)
- Social risk factors and cardiovascular risk in obstructive sleep apnea: a systematic assessment of clinical predictors in community health centers
- Diego R. Mazzotti, Ryan Urbanowicz, Marta Jankowska;Pacific Symposium on Biocomputing 30:314-329(2025)
- Detecting clinician implicit biases in diagnoses using proximal causal inference
- Kara Liu, Russ Altman, Vasilis Syrgkanis;Pacific Symposium on Biocomputing 30:330-345(2025)
- Spatial Clustering for Carolina Breast Cancer Study
- Hongqian Niu, Melissa Troester, Didong Li;Pacific Symposium on Biocomputing 30:346-59(2025)
- Assessment of Drug Impact on Laboratory Test Results in Hospital Settings
- Victorine P. Muse, Amalie D. Haue, Cristina L. Rodríguez, Alejandro A. Orozco, Jorge H. Biel, Søren Brunak;Pacific Symposium on Biocomputing 30:360-376(2025)
- Session Introduction
- Hannah Carter, Steven Brenner, Yana Bromberg;Pacific Symposium on Biocomputing 30:377-381(2025)
- Understanding TCR T cell knockout behavior using interpretable machine learning
- Marcus Blennemann, Archit Verma, Stefanie Bachl, Julia Carnevale, Barbara E Engelhardt;Pacific Symposium on Biocomputing 30:382-393(2025)
- Amyloid, Tau, and APOE in Alzheimer's Disease: Impact on White Matter Tracts
- Bramsh Qamar Chandio, Julio E. Villalon-Reina, Talia M. Nir, Sophia I. Thomopoulos, Yixue Feng, Sebastian Benavidez, Neda Jahanshad, Jaroslaw Harezlak, Eleftherios Garyfallidis, Paul M. Thompson;Pacific Symposium on Biocomputing 30:394-411(2025)
- A Pathway-Level Information ExtractoR (PLIER) framework to gain mechanistic insights into obesity in Down syndrome
- Sutanu Nandi, Yuehua Zhu, Lucas A. Gillenwater, Marc Subirana-Granés, Haoyu Zhang, Negar Janani, Casey Greene, Milton Pividori, Maria Chikina, James C. Costello;Pacific Symposium on Biocomputing 30:412-425(2025)
- Cross-Species Modeling Identifies Gene Signatures in Type 2 Diabetes Mouse Models Predictive of Inflammatory and Estrogen Signaling Pathways Associated with Alzheimer’s Disease Outcomes in Humans
- Brendan K. Ball, Elizabeth A. Proctor, Douglas K. Brubaker;Pacific Symposium on Biocomputing 30:426-440(2025)
- Biologically Enhanced Machine Learning Model to uncover Novel Gene-Drug Targets for Alzheimer’s Disease
- Alena Orlenko, Mythreye Venkatesan, Li Shen, Marylyn D. Ritchie, Zhiping Paul Wang, Tayo Obafemi-Ajayi, Jason H. Moore;Pacific Symposium on Biocomputing 30:441-456(2025)
- Identifying DNA methylation sites affecting drug response using electronic health record–derived GWAS summary statistics
- Delaney A. Smith, Stephanie A. Arteaga, Marie C. Sadler, Russ B. Altman;Pacific Symposium on Biocomputing 30:457-472(2025)
- Spherical Manifolds Capture Drug-Induced Changes in Tumor Cell Cycle Behavior
- Olivia Wen, Samuel C. Wolff, Wayne Stallaert, Didong Li, Jeremy E. Purvis, Tarek M. Zikry;Pacific Symposium on Biocomputing 30:473-487(2025)
- Astrocyte Reactivity Polygenic Risk Score May Predict Cognitive Decline in Alzheimer’s Disease
- Jared M Phillips, Julie A Schneider, David A Bennett, Paul K Crane, Shannon L Risacher, Andrew J Saykin, Logan C Dumitrescu, Timothy J Hohman; the Alzheimer’s Disease Neuroimaging Initiative;Pacific Symposium on Biocomputing 30:488-503(2025)
- Connecting intermediate phenotypes to disease using multi-omics in heart failure
- Anni Moore, Rasika Venkatesh, Michael G. Levin, Scott M. Damrauer, Nosheen Reza, Thomas P. Cappola, Marylyn D. Ritchie;Pacific Symposium on Biocomputing 30:504-521(2025)
- Plasma protein-based and polygenic risk scores serve complementary roles in predicting inflammatory bowel disease
- Jakob Woerner, Thomas Westbrook, Seokho Jeong, Manu Shivakumar, Allison R. Greenplate, Sokratis A. Apostolidis, Seunggeun Lee, Yonghyun Nam, Dokyoon Kim;Pacific Symposium on Biocomputing 30:522-534(2025)
- Integrated exposomic analysis of lipid phenotypes: Leveraging GE.db in environment by environment interaction studies
- Andre Luis Garao Rico, Nicole Palmiero, Marylyn D. Ritchie, Molly A. Hall;Pacific Symposium on Biocomputing 30:535-550(2025)
- Frequency of adding salt is a stronger predictor of chronic kidney disease in individuals with genetic risk
- Manu Shivakumar, Yanggyun Kim, Sang-Hyuk Jung, Jakob Woerner, Dokyoon Kim;Pacific Symposium on Biocomputing 30:551-564(2025)
- Enhancing Privacy-Preserving Cancer Classification with Convolutional Neural Networks
- Aurora A. F. Colombo, Luca Colombo, Alessandro Falcetta, Manuel Roveri;Pacific Symposium on Biocomputing 30:565-579(2025)
- One-Versus-Others Attention: Scalable Multimodal Integration for Biomedical Data
- Michal Golovanevsky, Eva Schiller, Akira Nair, Eric Han, Ritambhara Singh, Carsten Eickhoff;Pacific Symposium on Biocomputing 30:580-593(2025)
- Session Introduction
- Peter Kochunov, Li Shen, Zhongming Zhao, Paul M Thompson;Pacific Symposium on Biocomputing 30:594-598(2025)
- Electronic Health Record Analysis for Personalized Medicine: Predicting Malnutrition-Related Health Outcomes and Secondary Neuropsychiatric Health Concerns
- Pinar Gurkas, Gunnur Karakurt;Pacific Symposium on Biocomputing 30:599-613(2025)
- Unsupervised Dimensionality Reduction Techniques for the Assessment of ASD Biomarkers
- Zachary Jacokes, Ian Adoremos. Arham Hussain, Benjamin Newman, Kevin Pelphrey, John Van Horn, ACE GENDAAR Consortium;Pacific Symposium on Biocomputing 30:614-630(2025)
- Uncovering Important Diagnostic Features for Alzheimer’s, Parkinson’s and Other Dementias Using Interpretable Association Mining Methods
- Kazi Noshin, Mary Regina Boland, Bojian Hou, Victoria Lu, Carol Manning, Li Shen, Aidong Zhang;Pacific Symposium on Biocomputing 30:631-646(2025)
- Exploring the Granularity of the Illnesses-Related Changes in Regional Homogeneity in Major Depressive Disorder using the UKBB Data
- Yewen Huang, Syed Ibrar Hussain, Demetrio Labate, Robert Azencott, Paul Thompson, Bhim Adhikari, Peter Kochunov;Pacific Symposium on Biocomputing 30:647-663(2025)
- Multi-modal Imaging-based Pseudotime Analysis of Alzheimer progression
- Bing He, Shu Zhang, Shannon L. Risacher, Andrew J. Saykin, Jingwen Yan;Pacific Symposium on Biocomputing 30:664-674(2025)
- A Dynamic Model for Early Prediction of Alzheimer’s Disease by Leveraging Graph Convolutional Networks and Tensor Algebra
- Cagri Ozdemir, Mohammad Al Olaimat, Serdar Bozdag, Alzheimer’s Disease Neuroimaging Initiative;Pacific Symposium on Biocomputing 30:675-689(2025)
- All Together Now: Data Work to Advance Privacy, Science, and Health in the Age of Synthetic Data
- Lindsay Fernández-Rhodes, Jennifer K. Wagner;Pacific Symposium on Biocomputing 30:690-695(2025)
- Command line to pipeLine: Cross-biobank analyses with Nextflow
- Anurag Verma, Zachary Rodriguez, Lindsay Guare, Katie Cardone, Christopher Carson ; Pacific Symposium on Biocomputing 30:696-701(2025)
- Leveraging Foundational Models in Computational Biology: Validation, Understanding, and Innovation
- Brett Beaulieu-Jones, Steven Brenner; Pacific Symposium on Biocomputing 30:702-705(2025)
- Opportunities and Pitfalls with Large Language Models for Biomedical Annotation
- Cecilia Arighi, Jin-Dong Kim, Zhiyong Lu, Fabio Rinaldi; Pacific Symposium on Biocomputing 30:706-710(2025)
- Earth Friendly Computation: Applying Indigenous Data Lifecycles in Medical and Sovereign AI
- Keolu Fox, Krystal Tsosie, Alex Ioannidis, Kaja Wasik, Alec Calac, Eric Dawson; Pacific Symposium on Biocomputing 30:711-716(2025)
- Indigenous Data Sovereignty, Circular Systems, and Solarpunk Solutions for a Sustainable Future
- Ka'ulawena Alipio, Javier García-Colón, Nima Boscarino, Keolu Fox; Pacific Symposium on Biocomputing 30:717-733(2025)
- AI in Point-of-Care - A Sustainable Healthcare Revolution at the Edge
- Yousuf Rajput, Tarek Tarif, Akira Wolfe, Eric Dawson, Keolu Fox; Pacific Symposium on Biocomputing 30:734-747(2025)
- Polygenic risk scores for cardiometabolic traits demonstrate importance of ancestry for predictive precision medicine
- Rachel L. Kember, Shefali S. Verma, Anurag Verma, Brenda Xiao, Anastasia Lucas, Colleen M. Kripke, Renae Judy, Jinbo Chen, Scott M. Damrauer, Daniel J. Rader, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 30:748-765(2025)
Overcoming Health Disparities in Precision Medicine: Intersectional Approaches in Precision Medicine
Precision Medicine: Multi-Modal and Multi-Scale Methods to Promote Mechanistic Understanding of Disease
Translating Big Data Imaging Genomics Findings to Individual: Prediction of Risks and Outcomes in Neuropsychiatric Illness
Workshops
Hybrid Session/Workshop
Erratum
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.
Updated: October 25, 2024