HealthML

self-supervised-3d-tasks

ContIG

This is the official implementation of the method ContIG, for self-supervised learning from medical imaging with genomics

active-segmentation

ActiveSegmentation: A Simulation Framework for Benchmarking Active Learning Strategies for 3D Medical Image Segmentation

Deep-Learning-Lecture

HPI Deep Learning Lecture

explainability-requires-interactivity

Code to reproduce experiments in the paper "Explainability Requires Interactivity". See https://github.com/HealthML/StyleGAN2-Hypotheses-Explorer/ for the implementation of the interactive framework.

ukb-200k-wes-vep

UK Biobank 200k whole exome sequencing variant effect predictions

Math4ML-Lecture

HPI Mathematics for Machine Learning Lecture

StyleGAN2-Hypotheses-Explorer

Implementation of the interactive framework from the paper "Explainability Requires Interactivity". See https://github.com/HealthML/explainability-requires-interactivity for the code to reproduce experiments from the paper.

AntiSplodge

Spatial Transcriptomics deconvolution pipeline

seak

faatpipe

Functional Annotation and Association Testing Pipeline

lucid-torch

AdaScreen

AdaScreen - Ensembles of Screening Rules

AntiSplodge_Turorial

Tutorial for AntiSplodge with all the required datasets to get going!

d2l-en

Dive into Deep Learning, Berkeley STAT 157 (Spring 2019) textbook. With code, math, and discussions.

deep-learning-notes

My CS231n lecture notes

FaST-LMM

Python version of Factored Spectrally Transformed Linear Mixed Models

gadgetron

Gadgetron - Medical Image Reconstruction Framework

manim

Animation engine for explanatory math videos

math4ml

Notes on mathematical topics that pertain to machine learning

Math4ML-Code

Python Code for the Mathematics for Machine Learning Lecture

MFD

mml-book.github.io

Companion webpage to the book "Mathematics For Machine Learning"

neurocor

A repository to calculate genetic correlations with brain imaging phenotypes

Nextflow-pipeline

The pipeline for analyzing the UKBiobank data, with variant annotation tool VEP and some in-house tools

pathology-ml-model-training

A tool to enable biologists to train a machine learning model for their pathology images.

PySnpTools

A Python library for reading and manipulating genetic data.

spectral

A jekyll theme for the spectral template by html5up.net (@ajlkn). Demo: http://arkadianriver.github.io/spectral. How to jekyll: http://jekyllrb.com/docs/home/. If you intend to use this theme as a blog site with more than a few pages, have a look at my fork at https://github.com/arkadianriver/arkadianriver.com

STATS331

Lecture notes for an introductory undergraduate course in Bayesian Inference

transfer-gwas-brain-mri