Table Of Contents

• Machine Learning for Healthcare
  • Introduction
  • Genomics
  • Precision Medicine/Drug Discovery
    • Tools
  • Medical Imaging
    • Papers
    • Blogs, blog posts, and reddit discussions
    • Conferences and Workshops
    • Research Groups
    • Competitions
    • Videos
    • Datasets
    • Code Repositories
    • Tools
    • Other
  • Hospital Operations (i.e. OR Utilization, Scheduling, Discharge planning, HAIs...)
  • Signal processing, forecasting, and adverse event prediction
    • Papers
  • Other and Multiple Categories
    • Datasets
    • Conferences
    • Papers
• Companies

Machine Learning for Healthcare

This repository is a list of the all the relevant resources on applying machine learning to healthcare. If you see an article, repository, or other useful addition please make a pull request. At the moment structure of the repository is as follows: instead of being broken down by machine learning domains as you would technically expect (i.e. computer vision, NLP, audio...etc), it is broken down by application area (i.e. precision medicine, genomics, medical imaging/radiology, hospital operations...). Papers, conferences, tools, or courses that cover multiple areas of healthcare are moved to the "other/overlapping" category. If you think that this is confusing or there is a better way of doing things please post in the issues discussion

Introduction

Genomics

AffinityNet

Bayesian multi-domain learning for cancer subtype discovery from next-generation sequencing count data

Machine Learning Genomic Medicine

Deep learning for Genomics a Overview

Precision Medicine/Drug Discovery

Assessing Disparate Impacts of Personalized Interventions: Identifiability and Bounds

Adapting Neural Networks for the Estimation of Treatment Effects

Attentive State-Space Modeling of Disease Progression

Dr. VAE

Deep generative models of genetic variation capture the effects of mutations

Deep learning with multimodal representation for pancancer prognosis prediction

Deep RL for Radiation Therapy

GAMENet: Graph Augmented MEmory Networks for Recommending Medication Combination

The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology

End-to-end training of deep probabilistic CCA for joint modeling of paired biomedical observations

Fréchet ChemNet Distance: A metric for generative models for molecules in drug discovery

Lesson Learned from Natural Language Inference in the Clinical Domain

Molecular De Novo design using Recurrent Neural Networks and Reinforcement Learning Code

NAACL Paper on Cross Speciality Entity Recognition for Medicine

Natural Language Processing for Precision Medicine ACL 2017 Tutorial.

Near-Optimal Reinforcement Learning in Dynamic Treatment Regimes

Predicting drug response of tumors from integrated genomic profiles by deep neural networks

Regression tree methods for precision medicine talk by Wei-Yin Loh University of Wisconsin-Madison, USA.

Survey of Computational Methods for Drug Discovery

Tools

DeepChem

Medical Imaging

Papers

A Two-Stream Mutual Attention Network for Semi-supervised Biomedical Segmentation with Noisy Labels

Clinically Applicable deep learning for retinal disease diagnosis and referal

CheXNet: Radiologist-Level Pneumonia Detection on Chest X-Rays with Deep Learning

Domain Generalization via Model-Agnostic Learning of Semantic Features (with application to medical image segmentation

Dermatologist Level Skin Classification of skin cancer with deep neural networks

Discrepancy Ratio: Evaluating Model Performance When Even Experts Disagree on the Truth

Explanation by Progressive Exaggeration

Overview of Deep Learning in Medical Imaging

On the Automatic Generation of Medical Imaging Reports

OBELISK - One Kernel to Solve Nearly Everything: Unified 3D Binary Convolutions for Image Analysis

PGANs: Personalized Generative Adversarial Networks for ECG Generation to improve Patient-Specific Deep ECG Classification

Hybrid Retrieval-Generation Reinforced Agent for Medical Image Report Generation

Recurrent Registration Neural Networks for Deformable Image Registration

Robust breast cancer detection in mammography and digital breast tomosynthesis using annotation-efficient deep learning approach

Transfusion: Understanding Transfer Learning for Medical Imaging

Towards Deep Cellular Phenotyping in Placental Histology

Blogs, blog posts, and reddit discussions

Luke Oakden Rayner's blog

A case study of text annotation for medical imaging - LightTag

Conferences and Workshops

Deep learning for healthcare video series MIT

Harvard Digital Doctor Symposium

Medical Imaging with deep learning MIDL

Medical Imaging meets NIPS

Medical Imaging Summer School 2014

Medical Image Computing and Computer Assisted Intervention

Machine Learning in Medical Imaging

SIM Conference on Machine Intelligence in Medical Imaging

CVPR 2018 Medical Imaging Workshop

Research Groups

Imperial University

Images Science Institute at Utrecht

Competitions

Digital Mammography Recall Challenge

Kaggle 2017 Data Science Bowl-Lung diagnosis

NIPS 2018 Prothestics Challenge

LUNA 16

Kaggle 2016 Data Science Bowl-Measuring ejection fraction

Videos

Learning to read deep learning papers -i.e. dicussion of ChexNet by Stanford

Datasets

CheX-Ray14

Code Repositories

Tools

DeepInfer

Other

Medical Image Analysis Network (UK)

Hospital Operations (i.e. OR Utilization, Scheduling, Discharge planning, HAIs, EMRs...)

Attend and Diagnose

Adversarial Learning of Privacy-Preserving Text Representations for De-Identification of Medical Records

Detecting Hospital Acquired Infections with SVMs

Deep EHR: a survey of recent deep learning techniques for EHR analysis

Emergency Department Online Patient-Caregiver Scheduling

Few-Shot and Zero-Shot Multi-Label Learning for Structured Label Spaces (focuses on ICD Coding)

Learning to predict post-hospitalization VTE risk from EHR data

Multitask Learning and Benchmarking with Clinical Time Series Data

Machine-learning Algorithm to Predict Hypotension Based on High- delity Arterial Pressure Waveform Analysis

Privacy-Preserving Classification of Personal Text Messages with Secure Multi-Party Computation

Smart Hospital Hand Hygiene (Stanford)

Unsupervised Domain Adaptation for Clinical Negation Detection

Vision Based Prediction of ICU Mobility with RNNs

Signal processing, forecasting, and adverse event prediction

Papers

Analysing and Improving the Diagnosis of Ischaemic Heart Disease with Machine Learning NIH Article

Asthma Incidence Prediction with DNN

Doctor AI: Predicting Clinical Events via Recurrent Neural Networks published in MLR

Cardiologist level classification of arrhythmia (Stanford)

Dynamic Bayesian Flu Forecasting

Deep Self Organization with application to ICU

Interpretable AI for beat-to-beat cardiac function assessment

GRU-ODE-Bayes: Continuous modeling of sporadically-observed time series

Manifold-regression to predict from MEG/EEG brain signals without source modeling

U-Time: A Fully Convolutional Network for Time Series Segmentation Applied to Sleep Staging

Forecasting Treatment Responses Over Time Using Recurrent Marginal Structural Networks

Other and Multiple Categories

Datasets

Clinical Case Reports Dataset for machine comprehension

HEAD-QA: A Healthcare Dataset for Complex Reasoning

NLP Datasets from i2b2

EBM-NLP 5,000 richly annotated abstracts of medical articles

EMR-Question and Answering Code

OncoKB

MeDAL: A large medical text dataset curated for abbreviation disambiguation

[MIMIC - Medical Information Mart for Intensive Care - A large dataset by MIT and made available through Github] (https://mimic.mit.edu/)

Conferences

BioNLP Workshops

Clinical NLP

Machine Learning for Healthcare Conference

HealthTac

Trec Clinical Decision Support

Machine Learning for Healthcare 2018

2017 ICML Healthcare Related Talks

ICML AI and Health Workshop

Ninth Workshop on Health Text Mining at EMNLP

NAACL 2019 On Tutorial Applications of Natural Language Processing in Clinical Research and Practice

Rework Healthcare 2018

Papers

Active Learning for Decision-Making from Imbalanced Observational Data (application to personalized treatment

Adversarial Attacks Against Medical Deep Learning Systems

Annotating a Large Representative Corpus of Clinical Notes for Parts of Speech

Automated Medical Scribe for recording clinical encounters

Deep Learning for Healthcare Review, Opportunities, Challenges published Oxford Academic.

[Deep Neural Models for Medical Concept Normalization in User-Generated Texts](link coming)

Direct Uncertainty Prediction for Medical Second Opinions

EMER-QA A large corpus for question answering on electronic medical records

GAMENet: Graph Augmented MEmory Networks for Recommending Medication Combination

Leveraging uncertainty information from deep neural networks for disease detection

Label-aware Double Transfer Learning for Cross-Specialty Medical Named Entity Recognition

Machine Learning for Medical Diagnosis PSU article 2006

MiME: Multilevel Medical Embedding of Electronic Health Records for Predictive Healthcare

Novel Exploration Techniques (NETs) for Malaria Policy Interventions

Opportunistic Learning: Budgeted Cost-Sensitive Learning from Data Streams with application to diabetes

Patient2Vec: A Personalized Interpretable Deep Representation of the Longitudinal Electronic Health Record

Towards Automating Healthcare Question Answering in a Noisy Multilingual Low-Resource Setting

Learning Phenotypes and Dynamic Patient Representations via RNN Regularized Collective Non-negative Tensor Factorization

Uncertainty-Aware Attention for Reliable Interpretation and Prediction

Additional Natural Language Processing for Healthcare Tools

BioBERT

Clinical Named Entity Recognition system (CliNER)

Clinical Text Analysis Knowledge Extraction System (cTAKES)

Courses

Machine Learning for Medicine MIT Course

Companies

Companies are arranged alphabetical order.

Benevolent AI

Camereyes

Center Clinical Data Science Mass General

Deep Genomics

Etiometry

Heartflow

Hemonitor

Healthcare at Google

Insitrio

Path.AI

RadAI

Recursion Pharmaceuticals

Siemens AI Document