Top 11 Python Medical Projects

• Huatuo-Llama-Med-Chinese

  1 4,272 6.9 Python

  Repo for BenTsao [original name: HuaTuo (华驼)], Instruction-tuning Large Language Models with Chinese Medical Knowledge. 本草（原名：华驼）模型仓库，基于中文医学知识的大语言模型指令微调

Project mention: Local medical LLM | /r/LocalLLaMA | 2023-06-09

Huatuo-Llama-Med-Chinese https://github.com/SCIR-HI/Huatuo-Llama-Med-Chinese

• paperai

  19 1,198 5.9 Python

  📄 🤖 Semantic search and workflows for medical/scientific papers

  

Project mention: Oracle of Zotero: LLM QA of Your Research Library | news.ycombinator.com | 2023-11-26

Nice project!

I've spent quite a lot of time in the medical/scientific literature space. With regards to LLMs, specifically RAG, how the data is chunked is quite important. With that, I have a couple projects that might be beneficial additions.

paperetl (https://github.com/neuml/paperetl) - supports parsing arXiv, PubMed and integrates with GROBID to handle parsing metadata and text from arbitrary papers.

paperai (https://github.com/neuml/paperai) - builds embeddings databases of medical/scientific papers. Supports LLM prompting, semantic workflows and vector search. Built with txtai (https://github.com/neuml/txtai).

While arbitrary chunking/splitting can work, I've found that integrating parsing that has knowledge of medical/scientific paper structure increases the overall accuracy and experience of downstream applications.

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• BCDU-Net

  1 676 0.0 Python

  BCDU-Net : Medical Image Segmentation

• INSIGHT

  2 393 7.3 Python

  INSIGHT is an autonomous AI that can do medical research! (by oneil512)

Project mention: RAG for Medical Research | news.ycombinator.com | 2023-10-21

• paperetl

  12 316 6.3 Python

  📄 ⚙️ ETL processes for medical and scientific papers

  

Project mention: Show HN: Open-source Rule-based PDF parser for RAG | news.ycombinator.com | 2024-01-23

• rdm

  2 106 0.0 Python

  Our regulatory documentation manager. Streamlines 62304, 14971, and 510(k) documentation for software projects. (by innolitics)

  

• can2RNET

  1 61 1.8 Python

  This repo has code and documentation to control power-wheelchairs with R-Net electronics.

• SaaSHub

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• attention-cnn-MS-segmentation

  1 14 5.0 Python

  An attention-based Fully Convolutional Densenet for Multiple Sclerosis lesion segmentation from FLAIR MRI

  

Project mention: Boosting multiple sclerosis lesion segmentation through attention mechanism | /r/computervision | 2023-06-16

We also released code and dataset (with pre-processing to be ready for training) here: https://github.com/ictlab-unict/attention-cnn-MS-segmentation

• ProteinStructurePrediction

  1 10 0.0 Python

  Protein structure prediction is the task of predicting the 3-dimensional structure (shape) of a protein given its amino acid sequence and any available supporting information. In this section, we will Install and inspect sidechainnet, a dataset with tools for predicting and inspecting protein structures, complete two simplified implementations of Attention based Networks for predicting protein angles from amino acid sequences, and visualize our predictions along the way.

• covid-ht

  3 2 0.0 Python

  covid-ht aims to provide a tool for implementing an AI layer on clinical classification effectively in order to improve detection, information availability and resource efficiency in medical environments.

• medprompt

  1 1 4.1 Python

  Collection of LLM prompts, tools, chains and agents for healthcare using LangChain & FHIR.

Project mention: Doctor interested in AI specifically how it will effect medicine - are there any good books to read on this? | /r/ArtificialInteligence | 2023-12-06

MedPrompt GitHub (note, not the medprompt from the first paper): https://github.com/dermatologist/medprompt

Python Medical related posts

• [P] Parse research papers into structured data

  2 projects | /r/MachineLearning | 28 Jan 2023

• Show HN: Semantic search and workflows for medical/scientific papers

  1 project | news.ycombinator.com | 24 Jan 2023

• Semantic search and workflows for medical/scientific papers

  1 project | /r/opensource | 24 Jan 2023

• Semantic search and workflows for medical/scientific papers

  1 project | /r/coolgithubprojects | 24 Jan 2023

• Semantic search and workflows for medical/scientific papers

  1 project | /r/LanguageTechnology | 24 Jan 2023

• Semantic search and workflows for medical/scientific papers

  1 project | /r/Python | 24 Jan 2023

• Semantic search and workflows for medical/scientific papers

  1 project | /r/programming | 24 Jan 2023
• A note from our sponsor - SaaSHub
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