katielink

pyvol

volume calculation and segmentation

UniEval

Repository for EMNLP 2022 Paper: Towards a Unified Multi-Dimensional Evaluator for Text Generation

medalign

MedAlign is a clinician-generated dataset for instruction following with electronic medical records.

OpenMoE

A family of open-sourced Mixture-of-Experts (MoE) Large Language Models

SlicerJupyter

Extension for 3D Slicer that allows the application to be used from Jupyter notebook

FLAML

A fast library for AutoML and tuning. Join our Discord: https://discord.gg/Cppx2vSPVP.

generative_agents

Generative Agents: Interactive Simulacra of Human Behavior

silo-lm

SILO Language Models code repository

prompttools

Open-source tools for prompt testing and experimentation, with support for both LLMs (e.g. OpenAI, LLaMA) and vector databases (e.g. Chroma, Weaviate, LanceDB).

bertviz

BertViz: Visualize Attention in NLP Models (BERT, GPT2, BART, etc.)

TotalSegmentator

Tool for robust segmentation of >100 important anatomical structures in CT and MR images

biopython

Official git repository for Biopython (originally converted from CVS)

Computational-ADME

folding_tools

A collection of *fold* tools

evaluate

🤗 Evaluate: A library for easily evaluating machine learning models and datasets.

DeepPurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

medperf

An open benchmarking platform for medical artificial intelligence using Federated Evaluation.

LLM-ToolMaker

solvent

physionet

A collection of tools for working with the PhysioNet repository.

torchdrug

A powerful and flexible machine learning platform for drug discovery

graphein

Protein Graph Library

ehrshot-benchmark

A benchmark for few-shot evaluation of foundation models for electronic health records (EHRs)

scGPT

tiatoolbox

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

EventStreamGPT

Dataset and modelling infrastructure for modelling "event streams": sequences of continuous time, multivariate events with complex internal dependencies.

python-package-template

A template repo for Python packages

visual-med-alpaca

Visual Med-Alpaca is an open-source, multi-modal foundation model designed specifically for the biomedical domain, built on the LLaMa-7B.

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

ProteinFlow

Versatile computational pipeline for processing protein structure data for deep learning applications.