Fall 2021

Lecture 1: Introduction to the course

Topics/Videos

• Title Sequence (just for fun)

• Motivation for this course

• Mini lecture. (If you can follow this, then you should do fine in this course)

• Course mechanics and requirements

Slides

• pdf

Optional Reading

• "Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications" Sorlie, et al Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74

• "Molecular Portraits of human breast tumors" Perou, et al Nature 406, 747-752, 2000

• "Gene expression profiling predicts clinical outcome of breast cancer" van't Veer, et al Nature. 2002 Jan 31;415(6871):530-6

• "Gene expression profiling in breast cancer: classification, prognostication, and prediction" Reis-Filho and Pusztai,

• How your surgeon could soon be replaced by a robot

Lecture 2: Medicine

Topics/Videos

• Medicine & Disease

• Personalized & Precision medicine

Slides

• pdf

Optional Reading

• "P4 Medicine: Personalized, Predictive, Preventive, Participatory A Change of View that Changes Everything", Hood and Galas, CCC. 2008

• Disease

• Medicine

• "The Role of Systems Biology in Predictive Health and Personalized Medicine", Voight and Brigham Open Pathology, 2008, 2, 68-70

Lecture 3: The healthcare industry

Topics/Videos

• Participants

• Medical Education & the Economics of Medicine in the US

Slides

• pdf

Required Reading

• None

Lecture 4: Evidence Based Medicine

Topics/Videos

• A brief history of medicine

• Evidence based medicine

  • Example: “Effect of Renin-Angiotensin-Aldosterone System Inhibitors in Patients with COVID-19: a Systematic Review and Meta-analysis of 28,872 Patients”, Baral et al Curr. Atherosclerosis Reports (2020) 22:61

Slides

• pdf

Required Reading

• “Effect of Renin-Angiotensin-Aldosterone System Inhibitors in Patients with COVID-19: a Systematic Review and Meta-analysis of 28,872 Patients”, Baral et al Curr. Atherosclerosis Reports (2020) 22:61

Optional Reading

• The Flexner Report

  • See also The State of Diversity in the Health Professions a Century After Flexner

• Evidence-based practice for individuals or groups: let’s make a difference, de Groot et al Perspect Med Educ (2013) 2:216–221

• Osteoporosis therapy: an example of putting evidence-basedmedicine into clinical practice, Hosking, Geusens, Rizzoli; QJM 98(6), pp. 403–413,

• "Why Most Published Research Findings Are False", Ioannidis, 2005, DOI: 10.1371/journal.pmed.0020124

• "Healthcare outcomes assessed with observational study designs compared with those assessed in randomized trials" , Anglemyer, et al Cochrane Database Syst Rev. 2014,Lancet. 2011 Nov 19;378(9805):1812-23. doi: 10.1016/S0140-6736(11)61539-0.

• "Clinical Versus Mechanical Prediction: A Meta Analysis" Grove et al Psychological Assessment, 2000 12(1) 19-30

• A Randomized Trial of Hydroxychloroquine as Postexposure Prophylaxis for Covid-19, Boulware, et al. N Engl J Med. 2020 doi: 10.1056/NEJMoa2016638

Lecture 5: Asthma Phenotyping

Topics/Videos

• Background

  • Clinical Phenotypes

  • Clinical Phenotype discovery via cluster analysis

• Today's paper

Slides

• pdf

Required Reading

• “Unsupervised phenotyping of Severe Asthma Research Program participants using expanded lung data.” J Allergy Clin Immunol. 133(5):1280-8

Optional Reading

• "Asthma phenotypes: the evolution from clinical to molecular approaches." Wenzel, Nat Med. 2012;18(5):716-25.

Lecture 6: Comorbidity Phenotyping

Topics/Videos

• Background

  • Electronic Health Records

  • Comorbidities

  • The Diagnostic and Statistical Manual of Mental Disorders (DSM)

• Today's paper

Slides

• pdf

Required Reading

• Comorbidity Clusters in Autism Spectrum Disorders: An Electronic Health Record Time-Series Analysis. Doshi-Velez et al Pediatrics. 2014, 133(1):e54-63

Lecture 7: Intensive Care Phenotyping

Topics/Videos

• Background

  • Intensive Care Medicine

• Today's paper

Slides

• pdf

Required Reading

• Prognostic Physiology: Modeling Patient Severity in Intensive Care Units Using Radial Domain Folding. AMIA Annu Symp Proc. 2012; 2012: 1276–1283

Lecture 8: Phenotyping via Tensor Factorization

Topics/Videos

• Background

  • Clustering via Matrix Decompositions

  • Tensors and Tensor Decompositions

• Today's paper

Slides

• pdf

Required Reading

• Rubik: Knowledge guided tensor factorization and completion for health data analytics, Wang et al. KDD 2015, pp. 1265–1274

Lecture 9: Gene Set Enrichment Analysis

Topics/Videos

• Background

  • Biomarkers & Biomarker Discovery

  • Feature Selection

• Today's Paper

Slides

• pdf

Required Reading

• Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, Subramanian et al PNAS, 2005, 102 (43) 15545-15550

Lecture 10: Biomarker discovery for indolent prostate cancer

Topics/Videos

• Background

  • Odds ratios

  • Survival Analysis

  • Histology

  • Cancer Staging

  • Tissue microarrays

• Today's paper

Slides

• pdf

Required Reading

• A Molecular Signature Predictive of Indolent Prostate Cancer, Irshad et al Sci Transl Med. 2013; 5(202) doi: 10.1126/scitranslmed.3006408

Lecture 11: Finding Genomic Markers

Topics/Videos

• Background

  • DNA sequencing technologies

  • Types of genomic variations

• Today's paper

Slides

• pdf

Required Reading

• "Identification of novel mutations by exome sequencing in African American colorectal cancer patients", Ashktorab et al Cancer, 121(1):34-42, 2014

Lecture 12: Finding Phylogenetic Markers

Topics/Videos

• Background

  • Single cell analyses

  • Phylogenetics

• Today's paper

• Requirements for course projects

Slides

• pdf

Required Reading

• Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis, Heselmeyer-Haddad et al Am J Pathol. 2014 Oct;184(10):2671-86

Lecture 13: Detecting high-risk surgical patients

Topics/Videos

• Background

• Today's paper

Slides

• pdf

Required Reading

• Development and validation of machine learning models to identify high-risk surgical patients using automatically curated electronic health record data (Pythia): A retrospective, single-site study Corey, et al PLOS Medicine, 2018

Lecture 14: Detecting Autism from video

Topics/Videos

• Background

• Today's paper

Slides

• pdf

Required Reading

• •Mobile detection of autism through machine learning on home video: A development and prospective validation study, Tariq, et al PLOS Medicine, 2017

Lecture 15: Predicting cancer survival using deep learning

Topics/Videos

• Background

  • Neural Networks & Deep Learning

  • Convolutional Neural Networks

  • Pre-trained CNNs

• Today's paper

Slides

• pdf

Required Reading

• Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study, Kathner, et al PLOS Medicine, 2019

Lecture 16: Detecting onset of heart failure via deep learning

Topics/Videos

• Background

  • Modeling time-varying processes

  • Recurrent Neural Networks

• Today's paper

Slides

• pdf

Required Reading

• •Using recurrent neural network models for early detection of heart failure onset, Choi et al J Am Med Inform Assoc. 2017 Mar; 24(2): 361–370

Lecture 17: Learning causal interactions

Topics/Videos

• Background

  • Causality & Causal Discovery

  • Four techniques for causal modeling

  • Structure Learning in Bayesian Networks

• Today's paper

Slides

• pdf

Required Reading

• •An algorithm for direct causal learning of influences on patient outcomes, Rathnam C, Lee S, Jiang X, Artif Intell Med. 2017 Jan; 75: 1-15

Optional Reading

• Reduction of HIV concentration during acute infection: independence from a specific immune response, A.N. Phillips, Science 1996 271(5248):497-9. doi: 10.1126/science.271.5248.497

Lecture 18: Association Rule Learning

Topics/Videos

• Background

  • Association Rule Learning

• Today's paper

Slides

• pdf

Required Reading

• Learning temporal rules to forecast instability in continuously monitored patients, Guillame-Bert, et al J Am Med Inform Assoc. 2017 Jan;24(1):47-53

Lecture 19: Agent Based Modeling

Topics/Videos

• Background

  • Agent Based Modeling/Simulation

• Today's paper

Slides

• pdf

Required Reading

• A Multi-Host Agent-Based Model for a Zoonotic, Vector-Borne Disease. A Case Study on Trypanosomiasis in Eastern Province, Zambia, Alderton, et al PLOS NTD

Lecture 20: PK/PD modeling

Topics/Videos

• Background

  • Pharmacology & PK/PD modeling

• Today's paper

Slides

• pdf

Required Reading

• A population pharmacokinetic/pharmacodynamic model of thrombocytopenia characterizing the effect of trastuzumab emtansine (T-DM1) on platelet counts in patients with HER2-positive metastatic breast cancer. Bender, et al Cancer Chemother Pharmacol (2012) 70:591–601

Optional Reading

• Pharmacokinetic/Pharmacodynamic Modeling for Drug Development in Oncology, Garralda et al, DOI: 10.1200/EDBK_180460 American Society of Clinical Oncology Educational Book 37, 2018, pp. 210-215

Lecture 21: Designing Therapeutic Proteins

Topics/Videos

• Background

  • Therapeutic proteins

  • Immune system’s response to therapeutic proteins

• Today's papers

Slides

• pdf

Required Reading

• Optimization algorithms for functional deimmunization of therapeutic proteins, Parker et al BMC Bioinformatics 2010 11:180 DOI: 10.1186/1471-2105-11-180

Optional Reading

• Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate, PLoS Comput Biol. 2015;11(1):e1003988. doi: 10.1371/journal.pcbi.1003988. eCollection 2015

Lecture 22: Robot-assisted surgery

Topics/Videos

• Background

  • Kalman Filters

  • Gaussian Processes

• Today's paper

Slides

• pdf

Required Reading

• •Inequality Constrained Kalman Filtering for the Localization and Registration of a Surgical Robot, Tully, et al IROS 2011

Optional Reading

• Using Bayesian Optimization to Guide Probing of a Flexible Environment for Simultaneous Registration and Stiffness Mapping, Ayvali et al ICRA 2016

Lecture 23: Reinforcement Learning in Medicine

Topics

• Background

  • Reinforcement Learning

• Today's paper

Slides

• pdf

Required Reading

• The Artificial Intelligence Clinician learns optimal treatment strategies for sepsis in intensive care, Komorowski, et al Nature Medicine, 2018 (24), pages 1716–1720

Lecture 24: Interpretable/Explainable AI

Topics

• Background & Today's paper

Slides

• pdf

Required Reading

• Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells, Kuenzi, et al, Cancer Cell Volume 38, Issue 5, 9 November 2020, Pages 672-684.e6

Lecture 25: Algorithmic Bias in AI and Machine Learning

Topics

• Background & Today's paper

Slides

• pdf

Required Reading

• Dissecting racial bias in an algorithm used to manage the health of populations, Obermeyer et al, Science, Vol. 366, Issue 6464, pp. 447-453; DOI: 10.1126/science.aax2342

Lecture 26: Wearable Devices; Course Summary

Topics

• Background & Today's paper

• Course summary

Slides

• pdf

Required Reading

• End-to-end Deep Learning from Raw Sensor Data: Atrial Fibrillation Detection using Wearables, Gotlibovych, et al, KDD Deep Learning Day, 2018