Popular GitHub Repositories for Pubmed

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

BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

NLP framework in python for entity recognition and relationship extraction

SciFive: a text-text transformer model for biomedical literature

生物医学模型上下文协议

An agentic AI application that allows you to chat with your papers and gather also information from papers on ArXiv and on PubMed

ReCiter: an enterprise open source author disambiguation system for academic institutions

Pull high-quality, efficient embeddings for PubMed, arXiv and Wikipedia from Huggingface and use for local LLM inference/Retrieval Augmented Generation (RAG)

This is a RAG implementation using Open Source stack. BioMistral 7B has been used to build this app along with PubMedBert as an embedding model, Qdrant as a self hosted Vector DB, and Langchain & Llama CPP as an orchestration frameworks.

MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extraction (COLING 2022)

Official Repository for different models based on MultiHead VGAEs.

A library that facilitates the process of building a machine learning pipeline using PubMed as a data source

Word2Vec word embedding analysis on Autism Spectrum Disorder (ASD) articles abstracts available on Pubmed.

Paper Peek is a project based on Natural Language Processing which helps the medical professional to read abstracts from the Randomized controlled trials (RCTs) abstracts into sub sections such as Background, Objective etc.

Text Mining (PubMed Search) with NLP & LLM

Enhanced biomedical literature search combining semantic understanding with traditional keyword search for PubMed articles

The LLM Health Assistant is an AI-driven health consultation platform using LLM and RAG for intelligent Q&A, supporting text/voice interaction, PubMed retrieval, and user data management.

PICO Extraction using BERT NER for PubMed Data Sources

? AI-powered medical journal crawler that provides comprehensive literature reviews from PubMed articles using GPT-4 and semantic search

A python based web scrapper for scientific papers created for my Bio-Hacking.Blog