H2O for Medicine and Intro to H2O in Python
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Erin LeDell presents on machine learning for medicine using the H2O platform. She discusses how electronic health records, genomic data, medical images, and data from wearables can be used with machine learning for applications like predictive diagnostics, prognosis, and remote patient monitoring. H2O is an open source machine learning platform that provides algorithms like deep learning, random forests, and gradient boosting in an easy to use interface. It demonstrates an EEG example to predict eye state from brain signals.
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H2O for Medicine and Intro to H2O in Python
- 1. H2O.ai Machine Intelligence Machine Learning for Medicine Erin LeDell Ph.D. With an Intro to H2O in Python
- 2. H2O.ai Machine Intelligence Introduction • Statistician & Machine Learning Scientist at H2O.ai in Mountain View, California, USA • Ph.D. in Biostatistics with Designated Emphasis in Computational Science and Engineering from UC Berkeley (focus on Machine Learning) • Worked as a data scientist at several startups • Written a handful of machine learning R packages
- 3. H2O.ai Machine Intelligence H2O.ai H2O Company H2O Software • Team: 45. Founded in 2012, Mountain View, CA • Stanford Math & Systems Engineers • Open Source Software • Ease of Use via Web Interface • R, Python, Scala, Spark & Hadoop Interfaces • Distributed Algorithms Scale to Big Data
- 4. H2O.ai Machine Intelligence H2O.ai Founders SriSatish Ambati • CEO and Co-founder at H2O.ai • Past: Platfora, Cassandra, DataStax, Azul Systems, UC Berkeley • CTO and Co-founder at H2O.ai • Past: Azul Systems, Sun Microsystems • Developed the Java HotSpot Server Compiler at Sun • PhD in CS from Rice University Dr. Cliff Click
- 5. H2O.ai Machine Intelligence Scientific Advisory Council Dr. Trevor Hastie Dr. Rob Tibshirani Dr. Stephen Boyd • John A. Overdeck Professor of Mathematics, Stanford University • PhD in Statistics, Stanford University • Co-author, The Elements of Statistical Learning: Prediction, Inference and Data Mining • Co-author with John Chambers, Statistical Models in S • Co-author, Generalized Additive Models • 108,404 citations (via Google Scholar) • Professor of Statistics and Health Research and Policy, Stanford University • PhD in Statistics, Stanford University • COPPS Presidents’ Award recipient • Co-author, The Elements of Statistical Learning: Prediction, Inference and Data Mining • Author, Regression Shrinkage and Selection via the Lasso • Co-author, An Introduction to the Bootstrap • Professor of Electrical Engineering and Computer Science, Stanford University • PhD in Electrical Engineering and Computer Science, UC Berkeley • Co-author, Convex Optimization • Co-author, Linear Matrix Inequalities in System and Control Theory • Co-author, Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers
- 6. H2O.ai Machine Intelligence Agenda • Motivation • Medical Machine Learning • H2O Machine Learning • H2O Python Notebook Demo
- 7. H2O.ai Machine Intelligence Motivation Part 1 of 4 Machine Learning for Medicine
- 8. H2O.ai Machine Intelligence Data-Driven Preventative Care Precision Medicine • “The Future of Medicine is Precision Health” • President Obama’s Precision Medicine Initiative • Similar efforts at Stanford, UC Berkeley, UCSF Personalized
- 10. H2O.ai Machine Intelligence Genomic Data Genomics pioneer, Jun Wang, is one of China’s most famous scientists. Dr. Wang recently stepped down as head of BGI to create an AI health- monitoring system that would identify relationships between individual human genomic data, physiological traits (phenotypes) and lifestyle choices in order to provide advice on healthier living and to predict, and prevent, disease. Source: BGI
- 11. H2O.ai Machine Intelligence Wearables ABI Research has projected that by 2016, wearable wireless medical device sales will reach more than 100 million devices annually.
- 12. H2O.ai Machine Intelligence Open mHealth • FitBit • HealthVault • Jawbone • RunKeeper • Withings • HealthKit • HL7 EHR Open mHealth is a nonprofit start-up breaking down the barriers to integration and bringing clinical meaning to digital health data.
- 13. H2O.ai Machine Intelligence Medical ML Part 2 of 4 Machine Learning for Medicine
- 14. H2O.ai Machine Intelligence Machine Learning in Medicine • Predict Viral Failure in AIDS patients • Parkinson’s disease progression prediction from mobile phone accelerometer data • Personalized diagnostics • Clinical research: Identify which genes are associated with breast cancer relapse • Prognosis: Predict probability of survival in 5 years • Real-time predictions using data from wearables • Medication adherence monitoring • Clinical research: MRI and PET scans & Deep Learning • Cellular image analysis: genotype, phenotype, classification, identification, cell tracking Diagnostic Testing Oncology Medical Imaging Remote Patient Monitoring
- 15. H2O.ai Machine Intelligence H2O Platform Part 3 of 4 Machine Learning for Medicine
- 16. H2O.ai Machine Intelligence H2O Software H2O is an open source, distributed, Java machine learning library. APIs are available for: R, Python, Scala & JSON
- 17. H2O.ai Machine Intelligence H2O Software Overview Speed Matters! No Sampling Interactive UI Cutting-Edge Algorithms • Time is valuable • In-memory is faster • Distributed is faster • High speed AND accuracy • Scale to big data • Access data links • Use all data without sampling • Web-based modeling with H2O Flow • Model comparison • Suite of cutting-edge machine learning algorithms • Deep Learning & Ensembles • NanoFast Scoring Engine
- 18. H2O.ai Machine Intelligence Current Algorithm Overview Statistical Analysis • Linear Models (GLM) • Cox Proportional Hazards • Naïve Bayes Ensembles • Random Forest • Distributed Trees • Gradient Boosting Machine • R Package - Super Learner Ensembles Deep Neural Networks • Multi-layer Feed-Forward Neural Network • Auto-encoder • Anomaly Detection • Deep Features Clustering • K-Means Dimension Reduction • Principal Component Analysis • Generalized Low Rank Models Solvers & Optimization • Generalized ADMM Solver • L-BFGS (Quasi Newton Method) • Ordinary Least-Square Solver • Stochastic Gradient Descent Data Munging • Integrated R-Environment • Slice, Log Transform
- 21. H2O.ai Machine Intelligence EEG Demo Part 4 of 4 Machine Learning for Medicine
- 22. H2O.ai Machine Intelligence EEG for Eye Detection Problem Data • Goal is to accurately predict the eye state using minimal, surface level EEG data. • Binary outcome: Open vs Closed • Data from Emotiv Neuralheadset. • Predictor variables describe signals from 14 EEG channels placed on the surface of the head. Source: http://archive.ics.uci.edu/ml/datasets/EEG+Eye+State
- 23. H2O.ai Machine Intelligence EEG Data in H2O Flow
- 24. H2O.ai Machine Intelligence H2O Python Demo https://github.com/h2oai/h2o-3/blob/master/ h2o-py/demos/H2O_tutorial_eeg_eyestate.ipynb For comparison, there is scikit-learn version: https://github.com/h2oai/h2o-3/blob/master/h2o-py/demos/ EEG_eyestate_sklearn_NOPASS.ipynb
- 25. H2O.ai Machine Intelligence H2O on https://www.kaggle.com/mlandry • H2O starter scripts available on Kaggle • H2O is used in many competitions on Kaggle • Mark Landry, H2O Data Scientist and Competitive Kaggler
- 26. H2O.ai Machine Intelligence Where to learn more? • H2O Online Training (free): http://learn.h2o.ai • H2O Slidedecks: http://www.slideshare.net/0xdata • H2O Video Presentations: https://www.youtube.com/user/0xdata • H2O Community Events & Meetups: http://h2o.ai/events • Machine Learning & Data Science courses: http://coursebuffet.com
- 28. H2O.ai Machine Intelligence Questions? @ledell on Twitter, GitHub erin@h2o.ai http://www.stat.berkeley.edu/~ledell