mallikakhullar / healthcare_ml

A curated list of ML|NLP resources for healthcare.

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

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

Machine Learning Genomic Medicine

Deep learning for Genomics as Overview

Precision Medicine/Drug Discovery

Dr. VAE

Deep generative models of genetic variation capture the effects of mutations

Deep RL for Radiation Therapy

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.

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

Clinically Applicable deep learning for retinal disease diagnosis and referal

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

Dermatologist Level Skin Classification of skin cancer with deep neural networks

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

Hybrid Retrieval-Generation Reinforced Agent for Medical Image Report Generation

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

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...)

Detecting Hospital Acquired Infections with SVMs

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

Unsupervised Domain Adaptation for Clinical Negation Detection

Multitask Learning and Benchmarking with Clinical Time Series Data

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

Smart Hospital Hand Hygiene (Stanford)

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

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

Forecasting Treatment Responses Over Time Using Recurrent Marginal Structural Networks

Other and Multiple Categories

Datasets

Clinical Case Reports Dataset for machine comprehension

NLP Datasets from i2b2

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

EMR-Question and Answering Code

OncoKB

Conferences

Machine Learning for Healthcare Conference

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

Rework Healthcare 2018

Papers

Adversarial Attacks Against Medical Deep Learning Systems

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

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

Leveraging uncertainty information from deep neural networks for disease detection

Automated Medical Scribe for recording clinical encounters

Machine Learning for Medical Diagnosis PSU article 2006

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

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

Novel Exploration Techniques (NETs) for Malaria Policy Interventions

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

Additional Natural Language Processing for Healthcare Tools

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