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mediqa-chat-2023

A repository for organizing our submission to the MEDIQA-Chat Tasks @ ACL-ClinicalNLP 2023

mfmap.py

This repository contains code for MFmap (model fidelity map), a semi-supervised generative model integrating gene expression, copy number and mutation data, matching cell lines to cancer subtypes. MFmap compresses high dimensional omics data of cell lines and bulk tumours into subtype informative low dimensional latent representations and predicts the subtype of cell lines with high accuracy and good generative performance. http://h2926513.stratoserver.net:3838/MFmap_shiny/

ms-da-mil-cnn

Multi-scale Domain-adversarial Multiple Instance Learning CNN (CVPR2020)

multimodal-clinical-pretraining

This is the official code for "Multimodal Pretraining of Medical Time Series and Notes" at Machine Learning for Health 2023

notes

pa-co

pancan_cin

pancan cancer CIN paper code

probtorch

Probabilistic Torch is library for deep generative models that extends PyTorch

protocols

ubuntu tool installation protocols

ptcharlieapp

Physiotherapy Case Study Generator

renv_files

rnawl

simulategpt

Large language models are universal biomedical simulators

snakemake-tutorial

Variance calling pipeline for sars-cov-2 genomic RNA sequencing data (omicron & delta strains)

virtualtumorevolution

Spatial Simulation of Tumor Growth