Popular GitHub Repositories for Biomedical

Biomni: a general-purpose biomedical AI agent

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

[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

[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

Tools for computational pathology

Towards Generalist Biomedical AI

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

[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach

[ICLR 2022 spotlight]GreaseLM: Graph REASoning Enhanced Language Models for Question Answering

[NAACL'21 & ACL'21] SapBERT: Self-alignment pretraining for BERT & XL-BEL: Cross-Lingual Biomedical Entity Linking.

PheKnowLator: Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models