6.S897

Special Subject in Computer Science

Units arranged · Graduate

Covers subject matter not offered in the regular curriculum. Consult department to learn of offerings for a particular term.

Spring 2019 · Machine Learning for Healthcare

Topics

Introduction: What Makes Healthcare Unique?
Overview of Clinical Care
Deep Dive into Clinical Data
Risk Stratification, Part 2
Physiological Time-Series
Natural Language Processing (NLP), Part 2
Machine Learning for Differential Diagnosis
Causal Inference, Part 1
Causal Inference, Part 2
Disease Progression & Subtyping, Part 1
Disease Progression & Subtyping, Part 2
Precision Medicine
Automating Clinical Workflows
Fairness
Robustness to Dataset Shift
Interpretability

Readings

Ses #: 1 · Required Readings: No required readings. · Optional Readings: Bates, David, Suchi Saria, et al. “ Big Data In Health Care: Using Analytics to Identify and Manage High-Risk and High-Cost Patients. ” Health Affairs 33, no. 7 (July 2014): 1123–31. ↗
Reading assignment
Ses #: 2 · Required Readings: No required readings. · Optional Readings: No readings.
Reading assignment
Ses #: 3 · Required Readings: Agniel, Denis, Isaac Kohane, and Griffin Weber. “ Biases in Electronic Health Record Data Due to Processes Within the Healthcare System: Retrospective Observational Study. ” BMJ , 2018. · Optional Readings: No readings. ↗
Reading assignment
Razavian, Narges, Saul Blecker, et al. “ Population-Level Prediction of Type 2 Diabetes From Claims Data and Analysis of Risk Factors. ” Big Data 3, no. 4 (2015): 277–87. ↗
Listed reading
Pozen, Michael, Ralph D’Agostino, et al. “ A Predictive Instrument to Improve Coronary-Care-Unit Admission Practices in Acute Ischemic Heart Disease. ” New England Journal of Medicine 310, no. 20 (1984): 1273–78. ↗
Listed reading
Futoma, Joseph, Sanjay Hariharan, et al. “ An Improved Multi-Output Gaussian Process RNN With Real-Time Validation for Early Sepsis Detection. ” arXiv preprint arXiv:1708.05894 (2017). ↗
Listed reading
Caruana, Rich, Yin Lou, et al. “ Intelligible Models for HealthCare. ” Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD 15, 2015. ↗
Listed reading
Henry, Katharine, David Hager, et al. “ A Targeted Real-Time Early Warning Score (TREWScore) for Septic Shock. ” Science Translational Medicine 7, no. 299 (May 2015). ↗
Listed reading
Rodríguez, G. (2007). “ Chapter 7: Survival Models. ” In Lecture Notes on Generalized Linear Models. ↗
Listed reading
Quinn, J.A., C.K.I. Williams, and N. Mcintosh. “ Factorial Switching Linear Dynamical Systems Applied to Physiological Condition Monitoring. ” IEEE Transactions on Pattern Analysis and Machine Intelligence 31, no. 9 (2009): 1537–51. ↗
Listed reading
Hannun, Awni, Pranav Rajpurkar, et al. “ Cardiologist-Level Arrhythmia Detection and Classification in Ambulatory Electrocardiograms Using a Deep Neural Network. ” Nature Medicine 25, no. 3 (2019): 65–69. ↗
Listed reading
Ses #: 7 · Required Readings: Leaman, Robert, Ritu Khare, and Zhiyong Lu. “ Challenges in Clinical Natural Language Processing for Automated Disorder Normalization. ” Journal of Biomedical Informatics 57 (2015): 28–37. ↗
Reading assignment
Halpern, Yoni, Steven Horng, et al. “ Electronic Medical Record Phenotyping Using the Anchor and Learn Framework. ” Journal of the American Medical Informatics Association 23, no. 4 (2016): 731–40. ↗
Listed reading
Elhadad, N., and D. Demner-Fushman. “ Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing. ” Yearbook of Medical Informatics 25, no. 01 (2016): 224–33. ↗
Listed reading
Ses #: 8 · Required Readings: No required readings.
Reading assignment
Vaswani, Ashish, Noam Shazeer, et al. “ Attention Is All You Need. ” In Advances in Neural Information Processing Systems , pp. 5998-6008. 2017. ↗
Listed reading
Devlin, Jacob, Ming-Wei Chang, et al. “ Bert: Pre-Training of Deep Bidirectional Transformers for Language Understanding. ” arXiv preprint arXiv:1810.04805 (2018). ↗
Listed reading
Ses #: 9 · Required Readings: No required readings.
Reading assignment
Fihn, Stephan, Joseph Francis, et al. “ Insights From Advanced Analytics at the Veterans Health Administration. ” Health Affairs 33, no. 7 (2014): 1203–11. ↗
Listed reading
Amland, Robert C., and Kristin E. Hahn-Cover. “ Clinical Decision Support for Early Recognition of Sepsis. ” American Journal of Medical Quality 31, no. 2 (March 2016): 103–10. ↗
Listed reading
Ses #: 10 · Required Readings: Ranschaert, Erik, Sergey Morozov, and Paul Algra. “Chapter 13: Artificial Intelligence and Computer-Assisted Evaluation of Chest Pathology.” In Artificial Intelligence in Medical Imaging: Opportunities, Applications and Risks . Cham, Switzerland: Springer, 2019. ISBN: 9783319948775.
Reading assignment
Zhang, Jeffrey, Sravani Gajjala, et al. “ Fully Automated Echocardiogram Interpretation in Clinical Practice: Feasibility and Diagnostic Accuracy. ” Circulation 138, no. 16 (2018): 1623-1635. ↗
Listed reading
Lieman-Sifry, Jesse, Matthieu Le, et al. “ FastVentricle: Cardiac Segmentation with ENet. ” Functional Imaging and Modelling of the Heart Lecture Notes in Computer Science (2017): 127–38. ↗
Listed reading
Ses #: 11 · Required Readings: Rotmensch, Maya, Yoni Halpern, et al. “ Learning a Health Knowledge Graph from Electronic Medical Records. ” Scientific Reports 7, no. 1 (2017): 5994. ↗
Reading assignment
Shwe, M. A., D. E. Heckerman, et al. “ Probabilistic Diagnosis Using a Reformulation of the INTERNIST-1/QMR Knowledge Base. ” Methods of Information in Medicine 30, no. 04 (1991): 241–55. ↗
Listed reading
Pople, H. E., Jr. “ Heuristic Methods for Imposing Structure on Ill-Structured Problems: The Structuring of Medical Diagnostics. ” In Szolovits, P. (Ed.) Artificial Intelligence in Medicine. 1982. ↗
Listed reading
Ses #: 12 · Required Readings: Wang, Dayong, Aditya Khosla, et al. “ Deep Learning for Identifying Metastatic Breast Cancer. ” arXiv preprint arXiv:1606.05718 (2016). · Optional Readings: Oakden-Rayner, Luke. “ Exploring the ChestXray14 Dataset: Problems. ” Rayner, December 18, 2017. ↗
Reading assignment
Ses #: 13 · Required Readings: Ranschaert, Erik, Sergey Morozov, and Paul Algra. “Chapter 14: Deep Learning in Breast Cancer Screening.” In Artificial Intelligence in Medical Imaging: Opportunities, Applications and Risks . Cham, Switzerland: Springer, 2019. ISBN: 9783319948775. · Optional Readings: Lehman, Constance, Adam Yala, et al. “ Mammographic Breast Density Assessment Using Deep Learning: Clinical Implementation. ” Radiology 290, no. 1 (2019): 52–58. ↗
Reading assignment
Ses #: 14 · Required Readings: Hernán MA, Robins JM. Causal Inference: What If . Boca Raton: Chapman & Hall/CRC, forthcoming. Chapter 1. 2019. ↗
Reading assignment
Brat, Gabriel, Denis Agniel, et al. “ Postsurgical Prescriptions for Opioid Naive Patients and Association with Overdose and Misuse: Retrospective Cohort Study. ” BMJ , 2018. ↗
Listed reading
Bertsimas, Dimitris, Nathan Kallus, et al. “ Personalized Diabetes Management Using Electronic Medical Records. ” Diabetes Care 40, no. 2 (Feb 2017): 210–17. ↗
Listed reading
Huszar, Ferenc. “ Causal Inference 3: Counterfactuals. ” inFERENCe. January 24, 2019. ↗
Listed reading
Ses #: 15 · Required Readings: No required readings.
Reading assignment
Rosenbaum, Paul R. “ From Association to Causation in Observational Studies: The Role of Tests of Strongly Ignorable Treatment Assignment. ” Journal of the American Statistical Association 79, no. 385 (1984): 41. ↗
Listed reading
Kallus, Nathan, and Angela Zhou. “ Confounding-Robust Policy Improvement. ” In Advances in Neural Information Processing Systems , pp. 9269-9279. 2018. ↗
Listed reading
Louizos, Christos, Uri Shalit, et al “ Causal Effect Inference with Deep Latent-Variable Models. ” In Advances in Neural Information Processing Systems , pp. 6446-6456. 2017. ↗
Listed reading
Ses #: 16 · Required Readings: Prasad, Niranjani, Li-Fang Cheng, et al. “ A Reinforcement Learning Approach to Weaning of Mechanical Ventilation in Intensive Care Units. ” arXiv preprint arXiv:1704.06300 (2017). ↗
Reading assignment
Chakraborty, Bibhas, and Erica Moodie. Statistical Methods for Dynamic Treatment Regimes. Section 2.1, 2.2, and Chapter 3. Springer, 2013. ISBN: 9781461474272.
Listed reading
Gottesman, Omer, Fredrik Johansson, et al. “ Guidelines for Reinforcement Learning in Healthcare. ” Nature Medicine 25, no. 1 (2019): 16–18. ↗
Listed reading
Ses #: 17 · Required Readings: Komorowski, Matthieu, Leo Celi, et al. “ The Artificial Intelligence Clinician learns optimal treatment strategies for sepsis in intensive care. ” Nature Medicine 24, no. 11 (2018): 1716. ↗
Reading assignment
Dickerman, Barbra, Edward Giovannucci, et al. “ Guideline-Based Physical Activity and Survival Among US Men With Nonmetastatic Prostate Cancer. ” American Journal of Epidemiology 188, no. 3 (2018): 579–86. ↗
Listed reading
Ses #: 18 · Required Readings: Schulam, Peter, and Suchi Saria. “ Integrative Analysis Using Coupled Latent Variable Models for Individualizing Prognoses. ” The Journal of Machine Learning Research 17, no. 232 (2016): 1–35. · Optional Readings: No readings. ↗
Reading assignment
Ses #: 19 · Required Readings: Young, Alexandra, Razvan Marinescu, et al. “ Uncovering the Heterogeneity and Temporal Complexity of Neurodegenerative Diseases with Subtype and Stage Inference. ” Nature Communications 9, no. 1 (2018): 4273. ↗
Reading assignment
Wang, Xiang, David Sontag, and Fei Wang. “ Unsupervised Learning of Disease Progression Models. ” In Proceedings of the 20th ACM SIGKDD international conference on Knowledge discovery and data mining , pp. 85-94. ACM, 2014. ↗
Listed reading
Pierson, Emma, Pang Wei Koh, et al. “ Inferring Multi-Dimensional Rates of Aging from Cross-Sectional Data. ” arXiv preprint arXiv:1807.04709 (2018). ↗
Listed reading
Saelens, Wouter, Robrecht Cannoodt, et al. “ A Comparison of Single-Cell Trajectory Inference Methods. ” Nature Biotechnology 37, no. 5 (2019): 547–54. ↗
Listed reading
Campbell, Kieran R., and Christopher Yau. “ Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference. ” PLOS Computational Biology 12, no. 11 (2016). ↗
Listed reading
Ses #: 20 · Required Readings: Udler, Miriam S., Jaegil Kim, et al. “ Type 2 Diabetes Genetic Loci Informed by Multi-Trait Associations Point to Disease Mechanisms and Subtypes: A Soft Clustering Analysis. ” PLoS Medicine 15, no. 9 (2018): e1002654. · Optional Readings: Denny, Joshua, Marylyn Ritchie, et al. “ PheWAS: Demonstrating the Feasibility of a Phenome-Wide Scan to Discover Gene–Disease Associations. ” Bioinformatics 26, no. 9 (2010): 1205-1210. ↗
Reading assignment
Ses #: 21 · Required Readings: No required readings.
Reading assignment
Zhang, Yiye, Rema Padman, and Nirav Patel. “ Paving the COWpath: Learning and Visualizing Clinical Pathways from Electronic Health Record Data. ” Journal of Biomedical Informatics 58 (2015): 186–97. ↗
Listed reading
Gawande, Atul. “ A Life-Saving Checklist. ” The New Yorker . The New Yorker, December 3, 2007. ↗
Listed reading
Ses #: 22 · Required Readings: US Food and Drug Administration. “ Proposed Regulatory Framework for Modifications to Artificial Intelligence/Machine Learning (AI/ML)-Based Software as a Medical Device (SaMD)-Discussion Paper and Request for Feedback. ” (2019). ↗
Reading assignment
Coravos, Andy. “ The Doctor Prescribes Video Games and Virtual Reality Rehab. ” Wired . Conde Nast, November 20, 2018. ↗
Listed reading
Coravos, Andy, Irene Chen, et al. “ We Should Treat Algorithms like Prescription Drugs. ” Quartz . Quartz, February 19, 2019. ↗
Listed reading
“ Want to Create Meaningful Change in the US Healthcare System? Serve a ‘Tour of Duty’ in the Government. ” Rock Health . March 25, 2019. ↗
Listed reading
Hsiang, Mina. “ If You Want to Make Government Programs Work Better, Submit a Public Comment. ” Medium . Medium, March 23, 2019. ↗
Listed reading
Ses #: 23–25 · Required Readings: No required readings. · Optional Readings: No readings.
Reading assignment

Prerequisites & course information

Prereq: Permission of instructor G (Fall) Not offered regularly; consult department Units arranged Can be repeated for credit.

Sources

Course catalogue ↗2026–2027
MIT OpenCourseWare ↗Spring 2019
MIT OCW calendar ↗
MIT OCW readings ↗
MIT OCW syllabus ↗
Historical MIT OpenCourseWare offering. Named reading entries and schedule topics are automatically extracted from the linked source pages.