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25th PSB 2020: Fairmont Orchid, Hawaii, USA
- Pacific Symposium on Biocomputing 2020, Fairmont Orchid, Hawaii, USA, January 3-7, 2020. 2020
Artificial Intelligence for Enhancing Clinical Medicine
- Roxana Daneshjou, Lukasz Kidzinski, Olga Afanasiev, Jonathan H. Chen:
Session Introduction. 1-6 - Lodewijk Brand, Kai Nichols, Hua Wang, Heng Huang, Li Shen:
Predicting Longitudinal Outcomes of Alzheimer's Disease via a Tensor-Based Joint Classification andRegression Model. 7-18 - Irene Y. Chen, Monica Agrawal, Steven Horng, David A. Sontag:
Robustly Extracting Medical Knowledge from EHRs: A Case Study of Learning a Health KnowledgeGraph. 19-30 - Jessica W. Chen, Christian A. Kunder, Nam Bui, James L. Zehnder, Helio A. Costa, Henning Stehr:
Increasing Clinical Trial Accrual via Automated Matching of Biomarker Criteria. 31-42 - Sahar Harati, Andrea Crowell, Helen S. Mayberg, Shamim Nemati:
Addressing the Credit Assignment Problem in Treatment Outcome Prediction Using Temporal DifferenceLearning. 43-54 - Saad Khan, Libusha Kelly:
Multiclass Disease Classification from Microbial Whole-Community Metagenomes. 55-66 - Allen Nie, Arturo L. Pineda, Matt W. Wright, Hannah Wand, Bryan Wulf, Helio A. Costa, Ronak Y. Patel, Carlos D. Bustamante, James Zou:
LitGen: Genetic Literature Recommendation Guided by Human Explanations. 67-78 - Yifeng Tao, Chunhui Cai, William W. Cohen, Xinghua Lu:
From Genome to Phenome: Predicting Multiple Cancer Phenotypes Based on Somatic GenomicAlterations via the Genomic Impact Transformer. 79-90 - Maxence Vandromme, Tomi Jun, Ponni Perumalswami, Joel T. Dudley, Andrea Branch, Li Li:
Automated Phenotyping of Patients with Non-Alcoholic Fatty Liver Disease Reveals Clinically RelevantDisease Subtypes. 91-102 - Ke Yu, Mingda Zhang, Tianyi Cui, Milos Hauskrecht:
Monitoring ICU Mortality Risk with a Long Short-Term Memory Recurrent Neural Network. 103-114 - Xianlong Zeng, Yunyi Feng, Soheil Moosavinasab, Deborah Lin, Simon M. Lin, Chang Liu:
Multilevel Self-Attention Model and Its Use on Medical Risk Prediction. 115-126 - Haoran Zhang, Elisa Candido, Andrew S. Wilton, Raquel Duchen, Liisa Jaakkimainen, Walter P. Wodchis, Quaid Morris:
Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary CarePhysicians. 127-138 - Wei Zhao, Tianling Lv, Rena Lee, Yang Chen, Lei Xing:
Obtaining Dual-Energy Computed Tomography (CT) Information from a Single-Energy CT Image forQuantitative Imaging Analysis of Living Subjects by Using Deep Learning. 139-148
Intrinsically Disordered Proteins (IDPS) and their Functions
- Lukasz A. Kurgan, Predrag Radivojac, Joel L. Sussman, A. Keith Dunker:
Session Introduction. 149-158 - Wei-Lun Alterovitz, Eshel Faraggi, Christopher J. Oldfield, Jingwei Meng, Bin Xue, Fei Huang, Pedro Romero, Andrzej Kloczkowski, Vladimir N. Uversky, A. Keith Dunker:
Many-to-One Binding by Intrinsically Disordered Protein Regions. 159-170 - Sina Ghadermarzi, Akila Katuwawala, Christopher J. Oldfield, Amita Barik, Lukasz A. Kurgan:
Disordered Function Conjunction: On the In-Silico Function Annotation of Intrinsically DisorderedRegions. 171-182 - N. Suhas Jagannathan, Christopher W. V. Hogue, Lisa Tucker-Kellogg:
De novo Ensemble Modeling Suggests that AP2-Binding to Disordered Regions Can Increase StericVolume of Epsin but Not Eps15. 183-194 - Xiaorong Liu, Jianhan Chen:
Modulation of p53 Transactivation Domain Conformations by Ligand Binding and Cancer-AssociatedMutations. 195-206 - Ramiz Somjee, Diana M. Mitrea, Richard W. Kriwacki:
Exploring Relationships Between the Density of Charged Tracts Within Disordered Regions and PhaseSeparation. 207-218
Mutational Signatures
- Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan:
Session Introduction. 219-225 - Sarah A. Christensen, Mark D. M. Leiserson, Mohammed El-Kebir:
PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. 226-237 - Caitlin F. Harrigan, Yulia Rubanova, Quaid Morris, Alina Selega:
TrackSigFreq: Subclonal Reconstructions Based on Mutation Signatures and Allele Frequencies. 238-249 - Eirini Stamoulakatou, Pietro Pinoli, Stefano Ceri, Rosario M. Piro:
Impact of Mutational Signatures on microRNA and Their Response Elements. 250-261 - Damian Wójtowicz, Mark D. M. Leiserson, Roded Sharan, Teresa M. Przytycka:
DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures. 262-273 - Adamo Young, Jacob Chmura, Yoon-Sik Park, Quaid Morris, Gurnit Atwal:
Genome Gerrymandering: Optimal Division of the Genome into Regions with Cancer Type SpecificDifferences in Mutation Rates. 274-285
Pattern Recognition in Biomedical Data: Challenges in Putting Big Data to Work
- Shilpa Nadimpalli Kobren, Brett K. Beaulieu-Jones, Christian Darabos, Dokyoon Kim, Anurag Verma:
Session Introduction. 286-294 - Andrew L. Beam, Benjamin Kompa, Allen Schmaltz, Inbar Fried, Griffin M. Weber, Nathan P. Palmer, Xu Shi, Tianxi Cai, Isaac S. Kohane:
Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical Data. 295-306 - Carly A. Bobak, Lauren McDonnell, Matthew D. Nemesure, Justin Lin, Jane E. Hill:
Assessment of Imputation Methods for Missing Gene Expression Data in Meta-Analysis of DistinctCohorts of Tuberculosis Patients. 307-318 - Sophie Burkhardt, Julia Siekiera, Josua Glodde, Miguel A. Andrade-Navarro, Stefan Kramer:
Towards Identifying Drug Side Effects from Social Media Using Active Learning andCrowd Sourcing. 319-330 - Shir Gur, Lior Wolf, Lior Golgher, Pablo Blinder:
Microvascular Dynamics from 4D Microscopy Using Temporal Segmentation. 331-342 - David Haan, Ruikang Tao, Verena Friedl, Ioannis N. Anastopoulos, Christopher K. Wong, Alana S. Weinstein, Joshua M. Stuart:
Using Transcriptional Signatures to Find Cancer Drivers with LURE. 343-354 - Jie Hao, Sai Chandra Kosaraju, Nelson Zange Tsaku, Dae Hyun Song, Mingon Kang:
PAGE-Net: Interpretable and Integrative Deep Learning for Survival Analysis Using HistopathologicalImages and Genomic Data. 355-366 - Toby Dylan Hocking, Guillaume Bourque:
Machine Learning Algorithms for Simultaneous Supervised Detection of Peaks in Multiple Samples andCell Types. 367-378 - Benjamin Kompa, Beau Coker:
Learning a Latent Space of Highly Multidimensional Cancer Data. 379-390 - Hao-Chih Lee, Matteo Danieletto, Riccardo Miotto, Sarah T. Cherng, Joel T. Dudley:
Scaling Structural Learning with NO-BEARS to Infer Causal Transcriptome Networks. 391-402 - Joshua J. Levy, Lucas A. Salas, Brock C. Christensen, Aravindhan Sriharan, Louis J. Vaickus:
PathFlowAI: A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation inDigital Pathology. 403-414 - Lisa Neums, Richard Meier, Devin C. Koestler, Jeffrey A. Thompson:
Improving Survival Prediction Using a Novel Feature Selection and Feature Reduction FrameworkBased on the Integration of Clinical and Molecular Data. 415-426 - Sunho Park, Nabhonil Kar, Jae-Ho Cheong, TaeHyun Hwang:
Bayesian Semi-Nonnegative Matrix Tri-Factorization to Identify Pathways Associated with CancerPhenotypes. 427-438 - Minh Pham, Olivier Lichtarge:
Graph-Based Information Diffusion Method for Prioritizing Functionally Related Genes in Protein-Protein Interaction Networks. 439-450 - Maya Ramchandran, Prasad Patil, Giovanni Parmigiani:
Tree-Weighting for Multi-Study Ensemble Learners. 451-462 - Daniel N. Sosa, Alexander Derry, Margaret G. Guo, Eric Wei, Connor Brinton, Russ B. Altman:
A Literature-Based Knowledge Graph Embedding Method for Identifying Drug RepurposingOpportunities in Rare Diseases. 463-474 - Arunima Srivastava, Michael F. Sharpnack, Kun Huang, Parag Mallick, Raghu Machiraju:
PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms usingproteogenomics. 475-486 - Jacob T. Stanley, Alison R. Gilchrist, Alex C. Stabell, Mary A. Allen, Sara L. Sawyer, Robin D. Dowell:
Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease. 487-498 - Nhat Tran, Jean Gao:
Network Representation of Large-Scale Heterogeneous RNA Sequences with Integration of DiverseMulti-omics, Interactions, and Annotations Data. 499-510 - Yue Wang, Tong Wu, Yunlong Wang, Gao Wang:
Enhancing Model Interpretability and Accuracy for Disease Progression Prediction via Phenotype-BasedPatient Similarity Learning. 511-522 - Nicholas R. Wheeler, Penelope Benchek, Brian W. Kunkle, Kara L. Hamilton-Nelson, MikeWarfe, Jeremy R. Fondran, Jonathan L. Haines, William S. Bush:
Hadoop and PySpark for Reproducibility and Scalability of Genomic Sequencing Studies. 523-534 - Yao Yao, Stephen A. Ramsey:
CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPs. 535-546
Precision Medicine: Addressing the Challenge of Sharing, Analysis, and Privacy at Scale
- Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti:
Session Introduction. 547-550 - Suzan Arslanturk, Sorin Draghici, Tin Nguyen:
Integrated Cancer Subtyping using Heterogeneous Genome-Scale Molecular Datasets. 551-562 - Ho Bae, Dahuin Jung, Hyun-Soo Choi, Sungroh Yoon:
AnomiGAN: Generative Adversarial Networks for Anonymizing Private Medical Data. 563-574 - Dana C. Crawford, John Lin, Jessica Cooke Bailey, Tyler Kinzy, John R. Sedor, John F. O'Toole, William S. Bush:
Frequency of ClinVar Pathogenic Variants in Chronic Kidney Disease Patients Surveyed for Return ofResearch Results at a Cleveland Public Hospital. 575-586 - Sek Won Kong, Carles Hernandez-Ferrer:
Assessment of Coverage for Endogenous Metabolites and Exogenous Chemical Compounds Using anUntargeted Metabolomics Platform. 587-598 - Nicholas B. Larson, Melissa C. Larson, Jie Na, Carlos P. Sosa, Chen Wang, Jean-Pierre A. Kocher, Ross A. Rowsey:
Coverage Profile Correction of Shallow-Depth Circulating Cell-Free DNA Sequencing via Multi-Distance Learning. 599-610 - Jake Lever, Julia M. Barbarino, Li Gong, Rachel Huddart, Katrin Sangkuhl, Ryan Whaley, Michelle Whirl Carrillo, Mark Woon, Teri E. Klein, Russ B. Altman:
PGxMine: Text Mining for Curation of PharmGKB. 611-622 - Qingzhi Liu, Min Jin Ha, Rupam Bhattacharyya, Lana X. Garmire, Veerabhadran Baladandayuthapani:
Network-Based Matching of Patients and Targeted Therapies for Precision Oncology. 623-634 - Shikang Liu, David Hachen, Omar Lizardo, Christian Poellabauer, Aaron Striegel, Tijana Milenkovic:
The Power of Dynamic Social Networks to Predict Individuals' Mental Health. 635-646 - Gaurav Luthria, Qingbo Wang:
Implementing a Cloud Based Method for Protected Clinical Trial Data Sharing. 647-658 - Kristin Passero, Xi He, Jiayan Zhou, Bertram Müller-Myhsok, Marcus E. Kleber, Winfried März, Molly A. Hall:
Phenome-wide Association Studies on Cardiovascular Health and Fatty Acids Considering PhenotypeQuality Control Practices for Epidemiological Data. 659-670 - Yash Pershad, Margaret G. Guo, Russ B. Altman:
Pathway and Network Embedding Methods for Prioritizing Psychiatric Drugs. 671-682 - Christopher Michael Pietras, Liam Power, Donna K. Slonim:
aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics. 683-694 - Jiayi Tong, Rui Duan, Ruowang Li, Martijn J. Scheuemie, Jason H. Moore, Yong Chen:
Robust-ODAL: Learning from Heterogeneous Health Systems Without Sharing Patient-LevelData. 695-706 - Peter Washington, Kelley Marie Paskov, Haik Kalantarian, Nate Tyler Stockham, Catalin Voss, Aaron Kline, Ritik Patnaik, Brianna Sierra Chrisman, Maya Varma, Qandeel Tariq, Kaitlyn Dunlap, Jessey N. Schwartz, Nick Haber, Dennis P. Wall:
Feature Selection and Dimension Reduction of Social Autism Data. 707-718 - Jack M. Wolf, Martha Barnard, Xueting Xia, Nathan Ryder, Jason Westra, Nathan L. Tintle:
Computationally Efficient, Exact, Covariate-Adjusted Genetic Principal Component Analysis byLeveraging Individual Marker Summary Statistics from Large Biobanks. 719-730
Workshops
- Dragutin Petkovic, Lester Kobzik, Reza Ghanadan:
AI Ethics and Values in Biomedicine - Technical Challenges and Solutions. 731-735 - Gamze Gürsoy, Megan Doerr, John Wilbanks, Jennifer K. Wagner, Haixu Tang, Steven E. Brenner:
Navigating Ethical Quandaries with the Privacy Dilemma of Biomedical Datasets. 736-738 - William S. Bush, Nicholas Wheeler, Brett K. Beaulieu-Jones, Christian Darabos:
Packaging Biocomputing Software to Maximize Distribution and Reuse. 739-742 - Marylyn D. Ritchie, Jason H. Moore, Ju Han Kim:
Translational Bioinformatics: Biobanks in the Precision Medicine Era. 743-747
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