Table of Contents

• Session IntroductionRoxana Daneshjou, Lukasz Kidzinski, Olga Afanasiev, Jonathan H. Chen. 1-6 [doi]
• Predicting Longitudinal Outcomes of Alzheimer's Disease via a Tensor-Based Joint Classification andRegression ModelLodewijk Brand, Kai Nichols, Hua Wang 0007, Heng Huang, Li Shen 0001. 7-18 [doi]
• Robustly Extracting Medical Knowledge from EHRs: A Case Study of Learning a Health KnowledgeGraphIrene Y. Chen, Monica Agrawal, Steven Horng, David A. Sontag. 19-30 [doi]
• Increasing Clinical Trial Accrual via Automated Matching of Biomarker CriteriaJessica W. Chen, Christian A. Kunder, Nam Bui, James L. Zehnder, Helio A. Costa, Henning Stehr. 31-42 [doi]
• Addressing the Credit Assignment Problem in Treatment Outcome Prediction Using Temporal DifferenceLearningSahar Harati, Andrea Crowell, Helen S. Mayberg, Shamim Nemati. 43-54 [doi]
• Multiclass Disease Classification from Microbial Whole-Community MetagenomesSaad Khan 0004, Libusha Kelly. 55-66 [doi]
• LitGen: Genetic Literature Recommendation Guided by Human ExplanationsAllen Nie, Arturo L. Pineda, Matt W. Wright, Hannah Wand, Bryan Wulf, Helio A. Costa, Ronak Y. Patel, Carlos D. Bustamante, James Zou. 67-78 [doi]
• From Genome to Phenome: Predicting Multiple Cancer Phenotypes Based on Somatic GenomicAlterations via the Genomic Impact TransformerYifeng Tao, Chunhui Cai, William W. Cohen, Xinghua Lu. 79-90 [doi]
• Automated Phenotyping of Patients with Non-Alcoholic Fatty Liver Disease Reveals Clinically RelevantDisease SubtypesMaxence Vandromme, Tomi Jun, Ponni Perumalswami, Joel T. Dudley, Andrea Branch, Li Li 0062. 91-102 [doi]
• Monitoring ICU Mortality Risk with a Long Short-Term Memory Recurrent Neural NetworkKe Yu, Mingda Zhang, Tianyi Cui, Milos Hauskrecht. 103-114 [doi]
• Multilevel Self-Attention Model and Its Use on Medical Risk PredictionXianlong Zeng, Yunyi Feng, Soheil Moosavinasab, Deborah Lin, Simon M. Lin, Chang Liu 0028. 115-126 [doi]
• Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary CarePhysiciansHaoran Zhang, Elisa Candido, Andrew S. Wilton, Raquel Duchen, Liisa Jaakkimainen, Walter P. Wodchis, Quaid Morris. 127-138 [doi]
• Obtaining Dual-Energy Computed Tomography (CT) Information from a Single-Energy CT Image forQuantitative Imaging Analysis of Living Subjects by Using Deep LearningWei Zhao, Tianling Lv, Rena Lee, Yang Chen 0008, Lei Xing. 139-148 [doi]
• Session IntroductionLukasz A. Kurgan, Predrag Radivojac, Joel L. Sussman, A. Keith Dunker. 149-158 [doi]
• Many-to-One Binding by Intrinsically Disordered Protein RegionsWei-Lun Alterovitz, Eshel Faraggi, Christopher J. Oldfield, Jingwei Meng, Bin Xue, Fei Huang, Pedro Romero, Andrzej Kloczkowski, Vladimir N. Uversky, A. Keith Dunker. 159-170 [doi]
• Disordered Function Conjunction: On the In-Silico Function Annotation of Intrinsically DisorderedRegionsSina Ghadermarzi, Akila Katuwawala, Christopher J. Oldfield, Amita Barik, Lukasz A. Kurgan. 171-182 [doi]
• De novo Ensemble Modeling Suggests that AP2-Binding to Disordered Regions Can Increase StericVolume of Epsin but Not Eps15N. Suhas Jagannathan, Christopher W. V. Hogue, Lisa Tucker-Kellogg. 183-194 [doi]
• Modulation of p53 Transactivation Domain Conformations by Ligand Binding and Cancer-AssociatedMutationsXiaorong Liu, Jianhan Chen. 195-206 [doi]
• Exploring Relationships Between the Density of Charged Tracts Within Disordered Regions and PhaseSeparationRamiz Somjee, Diana M. Mitrea, Richard W. Kriwacki. 207-218 [doi]
• Session IntroductionMax D. M. Leiserson, Teresa M. Przytycka, Roded Sharan. 219-225 [doi]
• PhySigs: Phylogenetic Inference of Mutational Signature DynamicsSarah Christensen, Mark D. M. Leiserson, Mohammed El-Kebir. 226-237 [doi]
• TrackSigFreq: Subclonal Reconstructions Based on Mutation Signatures and Allele FrequenciesCaitlin F. Harrigan, Yulia Rubanova, Quaid Morris, Alina Selega. 238-249 [doi]
• Impact of Mutational Signatures on microRNA and Their Response ElementsEirini Stamoulakatou, Pietro Pinoli, Stefano Ceri, Rosario M. Piro. 250-261 [doi]
• DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignaturesDamian Wójtowicz, Mark D. M. Leiserson, Roded Sharan, Teresa M. Przytycka. 262-273 [doi]
• Genome Gerrymandering: Optimal Division of the Genome into Regions with Cancer Type SpecificDifferences in Mutation RatesAdamo Young, Jacob Chmura, Yoon-Sik Park, Quaid Morris, Gurnit Atwal. 274-285 [doi]
• Session IntroductionShilpa Nadimpalli Kobren, Brett Beaulieu-Jones, Christian Darabos, Dokyoon Kim, Anurag Verma. 286-294 [doi]
• Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical DataAndrew L. Beam, Benjamin Kompa, Allen Schmaltz, Inbar Fried, Griffin M. Weber, Nathan P. Palmer, Xu Shi, Tianxi Cai, Isaac S. Kohane. 295-306 [doi]
• Assessment of Imputation Methods for Missing Gene Expression Data in Meta-Analysis of DistinctCohorts of Tuberculosis PatientsCarly A. Bobak, Lauren McDonnell, Matthew D. Nemesure, Justin Lin, Jane E. Hill. 307-318 [doi]
• Towards Identifying Drug Side Effects from Social Media Using Active Learning andCrowd SourcingSophie Burkhardt, Julia Siekiera, Josua Glodde, Miguel A. Andrade-Navarro, Stefan Kramer 0001. 319-330 [doi]
• Microvascular Dynamics from 4D Microscopy Using Temporal SegmentationShir Gur, Lior Wolf, Lior Golgher, Pablo Blinder. 331-342 [doi]
• Using Transcriptional Signatures to Find Cancer Drivers with LUREDavid Haan, Ruikang Tao, Verena Friedl, Ioannis N. Anastopoulos, Christopher K. Wong, Alana S. Weinstein, Joshua M. Stuart. 343-354 [doi]
• PAGE-Net: Interpretable and Integrative Deep Learning for Survival Analysis Using HistopathologicalImages and Genomic DataJie Hao, Sai Chandra Kosaraju, Nelson Zange Tsaku, Dae Hyun Song, Mingon Kang. 355-366 [doi]
• Machine Learning Algorithms for Simultaneous Supervised Detection of Peaks in Multiple Samples andCell TypesToby Dylan Hocking, Guillaume Bourque. 367-378 [doi]
• Learning a Latent Space of Highly Multidimensional Cancer DataBenjamin Kompa, Beau Coker. 379-390 [doi]
• Scaling Structural Learning with NO-BEARS to Infer Causal Transcriptome NetworksHao-Chih Lee, Matteo Danieletto, Riccardo Miotto, Sarah T. Cherng, Joel T. Dudley. 391-402 [doi]
• PathFlowAI: A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation inDigital PathologyJoshua J. Levy, Lucas A. Salas, Brock C. Christensen, Aravindhan Sriharan, Louis J. Vaickus. 403-414 [doi]
• Improving Survival Prediction Using a Novel Feature Selection and Feature Reduction FrameworkBased on the Integration of Clinical and Molecular DataLisa Neums, Richard Meier, Devin C. Koestler, Jeffrey A. Thompson. 415-426 [doi]
• Bayesian Semi-Nonnegative Matrix Tri-Factorization to Identify Pathways Associated with CancerPhenotypesSunHo Park, Nabhonil Kar, Jae-Ho Cheong, TaeHyun Hwang. 427-438 [doi]
• Graph-Based Information Diffusion Method for Prioritizing Functionally Related Genes in Protein-Protein Interaction NetworksMinh Pham, Olivier Lichtarge. 439-450 [doi]
• Tree-Weighting for Multi-Study Ensemble LearnersMaya Ramchandran, Prasad Patil, Giovanni Parmigiani. 451-462 [doi]
• A Literature-Based Knowledge Graph Embedding Method for Identifying Drug RepurposingOpportunities in Rare DiseasesDaniel N. Sosa, Alexander Derry, Margaret Guo, Eric Wei, Connor Brinton, Russ B. Altman. 463-474 [doi]
• PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms usingproteogenomicsArunima Srivastava, Michael Sharpnack, Kun Huang 0001, Parag Mallick, Raghu Machiraju. 475-486 [doi]
• Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue ProteaseJacob T. Stanley, Alison R. Gilchrist, Alex C. Stabell, Mary A. Allen, Sara L. Sawyer, Robin D. Dowell. 487-498 [doi]
• Network Representation of Large-Scale Heterogeneous RNA Sequences with Integration of DiverseMulti-omics, Interactions, and Annotations DataNhat Tran, Jean Gao. 499-510 [doi]
• Enhancing Model Interpretability and Accuracy for Disease Progression Prediction via Phenotype-BasedPatient Similarity LearningYue Wang, Tong Wu, Yunlong Wang, Gao Wang. 511-522 [doi]
• Hadoop and PySpark for Reproducibility and Scalability of Genomic Sequencing StudiesNicholas R. Wheeler, Penelope Benchek, Brian W. Kunkle, Kara L. Hamilton-Nelson, MikeWarfe, Jeremy R. Fondran, Jonathan L. Haines, William S. Bush. 523-534 [doi]
• CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPsYao Yao 0007, Stephen A. Ramsey. 535-546 [doi]
• Session IntroductionSteven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti. 547-550 [doi]
• Integrated Cancer Subtyping using Heterogeneous Genome-Scale Molecular DatasetsSuzan Arslanturk, Sorin Draghici, Tin Nguyen 0001. 551-562 [doi]
• AnomiGAN: Generative Adversarial Networks for Anonymizing Private Medical DataHo Bae, Dahuin Jung, Hyun Soo Choi, Sungroh Yoon. 563-574 [doi]
• Frequency of ClinVar Pathogenic Variants in Chronic Kidney Disease Patients Surveyed for Return ofResearch Results at a Cleveland Public HospitalDana C. Crawford, John Lin, Jessica Cooke Bailey, Tyler Kinzy, John R. Sedor, John F. O'Toole, William S. Bush. 575-586 [doi]
• Assessment of Coverage for Endogenous Metabolites and Exogenous Chemical Compounds Using anUntargeted Metabolomics PlatformSek Won Kong, Carles Hernandez-Ferrer. 587-598 [doi]
• Coverage Profile Correction of Shallow-Depth Circulating Cell-Free DNA Sequencing via Multi-Distance LearningNicholas B. Larson, Melissa C. Larson, Jie Na, Carlos P. Sosa, Chen Wang, Jean-Pierre A. Kocher, Ross A. Rowsey. 599-610 [doi]
• PGxMine: Text Mining for Curation of PharmGKBJake Lever, Julia M. Barbarino, Li Gong, Rachel Huddart, Katrin Sangkuhl, Ryan Whaley, Michelle Whirl Carrillo, Mark Woon, Teri E. Klein, Russ B. Altman. 611-622 [doi]
• Network-Based Matching of Patients and Targeted Therapies for Precision OncologyQingzhi Liu, Min Jin Ha, Rupam Bhattacharyya, Lana X. Garmire, Veerabhadran Baladandayuthapani. 623-634 [doi]
• The Power of Dynamic Social Networks to Predict Individuals' Mental HealthShikang Liu, David Hachen, Omar Lizardo, Christian Poellabauer, Aaron Striegel, Tijana Milenkovic. 635-646 [doi]
• Implementing a Cloud Based Method for Protected Clinical Trial Data SharingGaurav Luthria, Qingbo Wang. 647-658 [doi]
• Phenome-wide Association Studies on Cardiovascular Health and Fatty Acids Considering PhenotypeQuality Control Practices for Epidemiological DataKristin Passero, Xi He, Jiayan Zhou, Bertram Müller-Myhsok, Marcus E. Kleber, Winfried März, Molly A. Hall. 659-670 [doi]
• Pathway and Network Embedding Methods for Prioritizing Psychiatric DrugsYash Pershad, Margaret Guo, Russ B. Altman. 671-682 [doi]
• aTEMPO: Pathway-Specific Temporal Anomalies for Precision TherapeuticsChristopher Michael Pietras, Liam Power, Donna K. Slonim. 683-694 [doi]
• Robust-ODAL: Learning from Heterogeneous Health Systems Without Sharing Patient-LevelDataJiayi Tong, Rui Duan, Ruowang Li, Martijn J. Scheuemie, Jason H. Moore, Yong Chen 0016. 695-706 [doi]
• Feature Selection and Dimension Reduction of Social Autism DataPeter Washington 0001, Kelley Marie Paskov, Haik Kalantarian, Nate Tyler Stockham, Catalin Voss, Aaron Kline, Ritik Patnaik, Brianna Sierra Chrisman, Maya Varma, Qandeel Tariq, Kaitlyn Dunlap, Jessey Schwartz, Nick Haber, Dennis P. Wall. 707-718 [doi]
• Computationally Efficient, Exact, Covariate-Adjusted Genetic Principal Component Analysis byLeveraging Individual Marker Summary Statistics from Large BiobanksJack Wolf, Martha Barnard, Xueting Xia, Nathan Ryder, Jason Westra, Nathan L. Tintle. 719-730 [doi]
• AI Ethics and Values in Biomedicine - Technical Challenges and SolutionsDragutin Petkovic, Lester Kobzik, Reza Ghanadan. 731-735 [doi]
• Navigating Ethical Quandaries with the Privacy Dilemma of Biomedical DatasetsGamze Gürsoy, Megan Doerr, John Wilbanks, Jennifer K. Wagner, Haixu Tang, Steven E. Brenner. 736-738 [doi]
• Packaging Biocomputing Software to Maximize Distribution and ReuseWilliam S. Bush, Nicholas Wheeler, Brett K. Beaulieu-Jones, Christian Darabos. 739-742 [doi]
• Translational Bioinformatics: Biobanks in the Precision Medicine EraMarylyn D. Ritchie, Jason H. Moore, Ju Han Kim. 743-747 [doi]