hi-ml
latest

Working with Azure

  • First steps: How to run your Python code in the cloud
  • Setting up Azure
  • Connecting to Azure
  • Datasets
  • Hyperparameter Search via Hyperdrive (AML SDK v1)
  • Hyperparameter Search in AML SDK v2
  • Using Cheap Low Priority VMs
  • Commandline tools
  • Downloading from/ uploading to Azure ML
  • Examples

Working with Amulet

  • Submitting jobs to Singularity using Amulet
  • Example Trainer Script for Amulet

Machine Learning

  • Logging metrics when training models in and outside AzureML
  • Performance Diagnostics
  • Running ML experiments with hi-ml
  • Checkpoint Utils

Histopathology

  • HI-ML Tools for Computational Pathology
  • Using Public Datasets PANDA and TCGA-Crck
  • DeepMIL model for tumor grading on PANDA dataset
  • DeepMIL model for genetic mutation on TCGA-CRCK
  • Pre-training of an image encoder using self-supervised learning
  • Digital Slide Archive
  • Creating montages from whole slide images (WSIs)
  • Histopathology Scripts

Multimodal learning

  • HI-ML Multimodal Toolbox
  • API

Self supervised learning

  • Training of self-supervised models

Developers

  • Contributing to this toolbox
  • Design and Coding Guidelines
  • Setting up the Development Environment
  • Software Development Process
  • Debugging and Profiling

Guidelines

  • Loading Images as Torch Tensors
  • Whole Slide Images

Changelog

  • Changelog

API

  • health_azure Package
  • health_ml Package
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