Notable Publications

The following is a sample of publications indicative of the research conducted by the HEADS Center.

• Beyond discrimination: a comparison of calibration methods and clinical usefulness of predictive models of readmission risk
  Walsh CG, Sharman K, Hripcsak G
  Journal of Biomedical Informatics. 2017; 76: 9-18.

• Calibration drift in regression and machine learning models for acute kidney injury
  Davis SE, Lasko TA, Chen G, Siew ED, Matheny ME
  Journal of the American Medical Informatics Association. 2017; 24(6): 1052-1061.

• Classifying patient portal messages using convolutional neural networks
  Sulieman L, Gilmore D, French C, Cronin R, Jackson GP, Russell M, Fabbri D
  Journal of Biomedical Informatics. 2017; 74: 59-70.

• A comparison of rule-based and machine learning approaches for classifying patient portal messages
  Cronin RM, Fabbri D, Denny JC, Rosenbloom ST, Jackson GP
  International Journal of Medical Informatics. 2017; 105: 110-120.

• Computational phenotype discovery using unsupervised feature learning over noisy, sparse, and irregular clinical data
  Lasko TA, Denny JC, Levy MA
  PLoS One. 2013; 8(6): e66341.

• A community effort to protect genomic data sharing, collaboration and outsourcing
  Wang S, Jiang X, Tang H, Wang X, Bu D, Carey K, Dyke S, Fox D, Jiang C, Lauter K, Malin B, Sofia H, Telenti A, Wang L, Wang W, Ohno-Machado L
  Genomic Medicine. 2017; 2: 33.

• CP tensor decomposition with cannot-link intermode constraints
  Henderson J, Malin B, Denny JC, Kho A, Sun J, Ghosh J, Ho J
  Proceedings of the SIAM Data Mining Conference. 2019: in press.

• Deep learning predicts extreme preterm birth from electronic health records
  Gao C, Osmundson S, Edwards DR, Purcell G, Malin B, Chen Y
  Journal of Biomedical Informatics. 2019: in press.

• Development of an automated phenotyping algorithm for hepatorenal syndrome
  Koola J, Davis S, Al-Nimri O, Parr S, Fabbri D, Malin B, Ho SB, Matheny M
  Journal of Biomedical Informatics. 2018; 80: 87-95.

• DMMS: a decentralized blockchain ledger for the management of medication histories
  Li P, Nelson SP, Malin B, Chen Y
  Blockchain in Healthcare Today. 2019; 2.

• Does communication help people coordinate?
  Vorobeychik Y, Joveski Z, Yu S
  PLoS One. 2017; 12(2): e0170780.

• Efficient active learning for electronic medical record de-identification
  Li M, Scaiano M, El Emam K, Malin B
  Proceedings of the AMIA Informatics Summit. 2019: 462-471.

• Enabling claims-based decision support through non-interruptive capture of admission diagnoses and provider billing codes
  Walsh CG, Vawdrey DK, Stetson PD, Fred MR, Hripcsak G
  Proceedings of the American Medical Informatics Association Fall Symposium. 2014: 1950-1959.

• Enabling open science initiatives in clinical psychology and psychiatry without sacrificing patient privacy: current practices and future challenges
  Walsh CG, Xia W, Li M, Denny J, Harris P, Malin B
  Advances in Methods and Practices in Psychological Science. 2018; 1(1): 104-114.

• Ensuring patient privacy in data sharing for postapproval research
  Sarpatwari A, Kesselheim AS, Malin BA, Gagne JJ, Schneeweiss S
  New England Journal of Medicine. 2014; 371(17): 1644-1649.

• Evaluating EHR data availability for cohort selection in retrospective studies
  Harrell M, Fabbri D, Levy M
  Proceedings of the IEEE International Conference on Healthcare Informatics. 2016: 380-387.

• Expanding access to large-scale genomic data while promoting privacy: a game theoretic approach
  Wan Z, Vorobeychik Y, Xia W, Clayton EW, Kantarcioglu M, Malin B
  American Journal of Human Genetics. 2017; 100(2): 316-322.

• Explanation-based auditing
  Fabbri D, LeFevre K
  Proceedings of the Very Large Data Bases Endowment (VLDB). 2011; 5(1): 1-12.

• Extracting similar terms from multiple EMR-based semantic embeddings to support chart reviews
  Cheng Y, Fabbri D
  Journal of Biomedical Informatics. 2018; 83: 63-72.

• Identifying collaborative care teams through electronic medical record utilization patterns
  Chen Y, Lorenzi NM, Sandberg WS, Wolgast K, Malin B
  Journal of the American Medical Informatics Association. 2017: 24(e1): e111-e120.

• Interaction patterns of trauma providers are associated with length of stay
  Chen Y, McNaughton C, Patel M, Malin B
  Journal of the American Medical Informatics Association. 2018: 25(7): 790-799.

• Learning bundled care opportunities from electronic medical records
  Chen Y, Kho A, Liebovitz D, Ivory C, Osmundson O, Bian J, Malin B
  Journal of Biomedical Informatics. 2018; 77: 1-10.

• Learning clinical workflows to identify subgroups of heart failure patients
  Yan C, Yin Z, Xiang S, Chen Y, Vorobeychik Y, Fabbri D, Kho A, Liebovitz D, Malin B
  Proceedings of the American Medical Informatics Association Fall Symposium. 2016: 1248-1257.

• Mining the best observational window to model social phenomena
  Chao Y, Li B, Chen Y, Liebovitz D, Malin B
  Proceedings of the 4th IEEE International Conference on Collaboration and Internet Computing (CIC). 2018: 46-55.

• The need for better data breach statistics
  Fabbri D, Frisse M, Malin B
  JAMA Internal Medicine. 2017; 177(11): 1696.

• Nonstationary Gaussian process regression for evaluating clinical laboratory test sampling strategies
  Lasko TA
  Proceedings of the 30th AAAI Conference on Artificial Intelligence. 2015: 1777-1783.

• PARAMO: a PARAllel predictive MOdeling platform for healthcare analytic research using electronic health records
  Ng K, Ghoting A, Steinhubl SR, Stewart WF, Malin B, Sun J 
  Journal of Biomedical Informatics. 2014; 48: 160-170.

• Phenotyping through semi-supervised tensor factorization
  Henderson J, He H, Malin B, Denny J, Kho A, Ghosh J, Ho J
  Proceedings of the American Medical Informatics Association Annual Fall Symposium (AMIA). 2018;  564-573.

• The Power of the Patient Voice: Learning Indicators of Hormonal Therapy Adherence From an Online Breast Cancer Forum
  Yin Z, Malin B, Warner J, Hsueh PY, Chen CH
  Proceedings of the AAAI Conference on Weblogs and Social Media (ICWSM). 2017: 337-346.

• #PrayforDad: learning the semantics behind why social media users disclose health information
  Yin Z, Chen Y, Sun J, Fabbri D, Malin B
  Proceedings of the AAAI Conference on Web and Social Media (ICWSM), 2016: 456-465.

• Predicting changes in hypertension control using electronic health records from a chronic disease management program
  Sun J, McNaughton C, Zhang P, Perer A, Gkoulalas-Divanis A, Denny JC, Kirby J, Lasko T, Saip A, Malin B
  Journal of the American Medical Informatics Association. 2014; 21(2): 337-344.

• Predicting discharge dates from the NICU using progress note data
  Temple MW, Lehmann CU, Fabbri D
  Pediatrics. 2015; 136(2): e395-e405.

• Predicting negative events: using post-discharge data to detect high-risk patients
  Sulieman L, Fabbri D, Wang F, Hu J, Malin B
  Proceedings of the American Medical Informatics Association Fall Symposium. 2016: 1169-1178.

• Predicting length of stay for obstetric patients via electronic medical records
  Gao C, Kho A, Ivory C, Osmundson S, Malin B, Chen Y
  Proceedings of the 16th World Congress on Medical and Health Informatics - MEDINFO. 2017; 245:1 019-1023.

• Predicting neonatal encephalopathy from maternal data in electronic health records
  Li T, Gao C, Yan C, Osmundson S, Malin B, Chen Y
  Proceedings of the American Medical Informatics Association Informatics Summit. 2018: 359-368.

• Predicting risk of suicide attempts over time through machine learning
  Walsh CG, Ribeiro JD, Franklin JC
  Clinical Psychological Science. 2017; 5(3): 457-469.

• Protecting genomic data analytics in the cloud: state of the art and opportunities
  Tang H, Jiang X, Wang X, Wang S, Sofia H, Fox D, Lauter K, Malin B, Telenti A, Xiong L, Ohno-Machado L 
  BMC Med Genomics. 2016; 9(1): 63.

• A scalable framework to detect personal health mentions on Twitter
  Yin Z, Fabbri D, Rosenbloom ST, Malin B
  Journal of Medical Internet Research. 2015;  17(6): e138.

• Scalable Iterative Classification for Sanitizing Large-Scale Datasets
  Li B, Vorobeychik Y, Li M, Malin B
  IEEE Transactions on Knowledge and Data Engineering. 2017; 29(3): 698-711.

• Schedule-based metrics for the evaluation of clinic performance and potential recovery of cancelled appointments
  Monahan K, Fabbri D
  International Journal of Medical Informatics. 2018;109: 49-54.

• A system for automated determination of perioperative patient acuity
  Zhang L, Fabbri D, Lasko TA, Ehrenfeld, Wanderer J
  Journal of Medical Systems. 2018; 42(7): 123.

• A systematic literature review of machine learning in online personal health data
  Yin Z, Sulieman L, Malin B
  Journal of the American Medical Informatics Association. 2019; 26(6): 561-576.

• Systematizing genome privacy research: a privacy-enhancing technologies perspective
  Mittos A, Malin B, de Cristofaro E
  Proceedings of the 19th Privacy Enhancing Technologies Symposium. 2019: 87-107.

• The therapy is making me sick: how online portal communications between breast cancer patients and physicians indicate medication discontinuation
  Yin Z, Harrell M, Warner J, Chen Q, Fabbri D, Malin B
  Journal of the American Medical Informatics Assocatiation. 2018; 25(11): 1444-1451.

• Time-dependent severity change during treatment of pediatric patients hospitalized for acute asthma exacerbations
  Walsh CG, Sills MR, Arnold DH
  Annals of Allergy, Asthma, & Immunology. 2017; 118(2): 226-227.

• Toward content based image retrieval with deep convolutional neural networks
  Sklan JES, Plassard AJ, Fabbri D, Landman BA
  sPIE Medical Imaging. 2015: 9417.