Popular GitHub Repositories for Biomedical Informatics

Biomni: a general-purpose biomedical AI agent

A full spaCy pipeline and models for scientific/biomedical documents.

Deep Learning Papers on Medical Image Analysis

[pip install medmnist] 18x Standardized Datasets for 2D and 3D Biomedical Image Classification

Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

A tool for retrosynthetic planning

[NAACL 2021] QAGNN: Question Answering using Language Models and Knowledge Graphs ?

BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences

Code for our paper "Multi-scale Guided Attention for Medical Image Segmentation"

[ACL 2022] LinkBERT: A Knowledgeable Language Model ? Pretrained with Document Links

U-Net: Convolutional Networks for Biomedical Image Segmentation

A Python toolkit for pathology image analysis algorithms.

Tools for computational pathology

System for Medical Concept Extraction and Linking

Towards Generalist Biomedical AI

A vision-language foundation model for computational pathology - Nature Medicine

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

? A curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)

Image segmentation - general superpixel segmentation & center detection & region growing

A collection of UNet and hybrid architectures in PyTorch for 2D and 3D Biomedical Image segmentation