Table of Contents

• Session IntroductionShefali Setia Verma, Anurag Verma, Dokyoon Kim, Christian Darabos. 1-7 [doi]
• Learning Contextual Hierarchical Structure of Medical Concepts with Poincairé Embeddings to Clarify PhenotypesBrett K. Beaulieu-Jones, Isaac S. Kohane, Andrew L. Beam. 8-17 [doi]
• The Effectiveness of Multitask Learning for Phenotyping with Electronic Health Records DataDaisy Yi Ding, Chloé Simpson, Stephen Pfohl, Dave C. Kale, Kenneth Jung, Nigam H. Shah. 18-29 [doi]
• ODAL: A one-shot distributed algorithm to perform logistic regressions on electronic health records data from multiple clinical sitesRui Duan, Mary Regina Boland, Jason H. Moore, Yong Chen. 30-41 [doi]
• PVC Detection Using a Convolutional Autoencoder and Random Forest ClassifierMax Gordon, Cranos Williams. 42-53 [doi]
• Removing Confounding Factors Associated Weights in Deep Neural Networks Improves the Prediction Accuracy for Healthcare ApplicationsHaohan Wang, Zhenglin Wu, Eric P. Xing. 54-65 [doi]
• DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectionalYuexu Jiang, Duolin Wang, Dong Xu 0002. 66-75 [doi]
• Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regionsZheng Liu, Yao Yao, Qi Wei, Benjamin Weeder, Stephen A. Ramsey. 76-87 [doi]
• DNA Steganalysis Using Deep Recurrent Neural NetworksHo Bae, Byunghan Lee, Sunyoung Kwon, Sungroh Yoon. 88-99 [doi]
• Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical LiteratureArjun Magge, Davy Weissenbacher, Abeed Sarker, Matthew Scotch, Graciela Gonzalez-Hernandez. 100-111 [doi]
• Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement LearningHaohan Wang, Xiang Liu, Yifeng Tao, Wenting Ye, Qiao Jin, William W. Cohen, Eric P. Xing. 112-123 [doi]
• Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategiesRashika Ramola, Shantanu Jain, Predrag Radivojac. 124-135 [doi]
• PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity PredictionKiley Graim, Verena Friedl, Kathleen E. Houlahan, Joshua M. Stuart. 136-147 [doi]
• Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survivalRachel M. Pyke, Raphael Genolet, Alexandre Harari, George Coukos, David Gfeller, Hannah Carter. 148-159 [doi]
• Exploring microRNA Regulation of Cancer with Context-Aware Deep Cancer ClassifierBlake Pyman, Alireza Sedghi, Shekoofeh Azizi, Kathrin Tyryshkin, Neil Renwick, Parvin Mousavi. 160-171 [doi]
• Implementing and Evaluating A Gaussian Mixture Framework for Identifying Gene Function from TnSeq DataKevin Li, Rachel Chen, William Lindsey, Aaron A. Best, Matthew DeJongh, Christopher Henry, Nathan L. Tintle. 172-183 [doi]
• SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPsShankara Anand, Laurynas Kalesinskas, Craig Smail, Yosuke Tanigawa. 184-195 [doi]
• Extracting allelic read counts from 250, 000 human sequencing runs in Sequence Read ArchiveBrian Tsui, Michelle Dow, Dylan Skola, Hannah Carter. 196-207 [doi]
• Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibilityArunima Srivastava, Ravali Adusumilli, Hunter Boyce, Daniel Garijo, Varun Ratnakar, Rajiv Mayani, Thomas Yu, Raghu Machiraju, Yolanda Gil, Parag Mallick. 208-219 [doi]
• Session introductionSteven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac. 220-223 [doi]
• CrowdVariant: a crowdsourcing approach to classify copy number variantsPeyton Greenside, Justin M. Zook, Marc Salit, Madeleine L. Cule, Ryan Poplin, Mark A. DePristo. 224-235 [doi]
• A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome dataWontack Han, Yuzhen Ye. 236-247 [doi]
• AICM: A Genuine Framework for Correcting Inconsistency Between Large Pharmacogenomics DatasetsZhiyue Tom Hu, Yuting Ye, Patrick A. Newbury, Haiyan Huang, Bin Chen. 248-259 [doi]
• Outgroup Machine Learning Approach Identifies Single Nucleotide Variants in Noncoding DNA Associated with Autism Spectrum DisorderMaya Varma, Kelley Marie Paskov, Jae-Yoon Jung, Brianna Sierra Chrisman, Nate Tyler Stockham, Peter Yigitcan Washington, Dennis Paul Wall. 260-271 [doi]
• Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE networkXinyuan Zhang, Yogasudha Veturi, Shefali Setia Verma, William Bone, Anurag Verma, Anastasia Lucas, Scott J. Hebbring, Joshua C. Denny, Ian Stanaway, Gail P. Jarvik, David R. Crosslin, Eric B. Larson, Laura Rasmussen-Torvik, Sarah A. Pendergrass, Jordan W. Smoller, Hakon Hakonarson, Patrick Sleiman, Chunhua Weng, David Fasel, Wei-Qi Wei, Iftikhar J. Kullo, Daniel J. Schaid, Wendy K. Chung, Marylyn D. Ritchie. 272-283 [doi]
• Integrating RNA expression and visual features for immune infiltrate predictionDerek Reiman, Lingdao Sha, Irvin Ho, Timothy Tan, Denise Lau, Aly A. Khan. 284-295 [doi]
• Influence of tissue context on gene prioritization for predicted transcriptome-wide association studiesBinglan Li, Yogasudha Veturi, Yukiko Bradford, Shefali S. Verma, Anurag Verma, Anastasia M. Lucas, David W. Haas, Marylyn D. Ritchie. 296-307 [doi]
• Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphismsFrancesca Vitali, Joanne Berghout, Jung-Wei Fan, Jianrong Li, Qike Li, Haiquan Li, Yves A. Lussier. 308-319 [doi]
• An Optimal Policy for Patient Laboratory Tests in Intensive Care UnitsLi-Fang Cheng, Niranjani Prasad, Barbara E. Engelhardt. 320-331 [doi]
• Session introductionLana X. Garmire, Guo-Cheng Yuan, Rong Fan, Gene W. Yeo, John Quackenbush. 332-337 [doi]
• LISA: Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq dataYang Chen, Yuping Zhang, Zhengqing Ouyang. 338-349 [doi]
• Topological Methods for Visualization and Analysis of High Dimensional Single-Cell RNA Sequencing DataTongxin Wang, Travis Johnson, Jie Zhang 0010, Kun Huang. 350-361 [doi]
• Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomicsQiwen Hu, Casey S. Greene. 362-373 [doi]
• Shallow Sparsely-Connected Autoencoders for Gene Set ProjectionMaxwell P. Gold, Alexander LeNail, Ernest Fraenkel. 374-385 [doi]
• Session IntroductionGamze Gürsoy, Arif Harmanci, Haixu Tang, Erman Ayday, Steven E. Brenner. 386-390 [doi]
• Leveraging summary statistics to make inferences about complex phenotypes in large biobanksAngela Gasdaska, Derek Friend, Rachel Chen, Jason Westra, Matthew Zawistowski, William Lindsey, Nathan L. Tintle. 391-402 [doi]
• Protecting Genomic Data Privacy with Probabilistic ModelingSean Simmons 0001, Bonnie Berger, Cenk S. Sahinalp. 403-414 [doi]
• Evaluation of patient re-identification using laboratory test orders and mitigation via latent space variablesKipp W. Johnson, Jessica K. De Freitas, Benjamin S. Glicksberg, Jason R. Bobe, Joel T. Dudley. 415-426 [doi]
• Implementing a universal informed consent process for the All of Us Research ProgramMegan Doerr, Shira Grayson, Sarah Moore, Christine Suver, John Wilbanks, Jennifer Wagner. 427-438 [doi]
• Merging heterogeneous clinical data to enable knowledge discoveryMartin G. Seneviratne, Michael G. Kahn, Tina Hernandez-Boussard. 439-443 [doi]
• Reading between the genes: interpreting non-coding DNA in high-throughputJoanne Berghout, Yves A. Lussier, Francesca Vitali, Martha L. Bulyk, Maricel G. Kann, Jason H. Moore. 444-448 [doi]
• Text Mining and Machine Learning for Precision MedicineGraciela Gonzalez, Zhiyong Lu, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen, Jingcheng Du, Juliane Fluck, Casey S. Greene, John Holmes, Aditya Kashyap, Rikke Linnemann Nielsen, Zhengqing Ouyang, Sebastian Schaaf, Jaclyn N. Taroni, Cui Tao, Yuping Zhang, Hongfang Liu. 449-454 [doi]
• Translational informatics of population Health: How large biomolecular and clinical datasets uniteYves A. Lussier, Atul J. Butte, Haiquan Li, Rong Chen, Jason H. Moore. 455 [doi]