This repository contains files and information about step 2 of Kaphta Architecture: Information Extraction, using the R language.

Estudio del carácter patogénico de variantes humanas mediante deep learning. Fine-tuning de BERT para la representación de enfermedades: un método de aprendizaje sobre datasets de textos biomédicos.

A command-line tool to fetch and save data from articles available on PubMed using pubmed-lookup

This repository automatically requests and extracts abstract from 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 miner for PubMed abstracts

CureHunter XSL transformer for multithreaded conversion/transformation of a directory of XML files.

A Python tool for systematic review scraping PubMed articles based on specified search queries.

Clustering PubMed Abstracts using K-Means Algorithm

Unsupervised Discovery Of Trends In Biomedical Research Based On The PubMed Baseline Repository

CLinical Information Retrieval Evaluation Collection

BioMedical Language Processing with ELECTRA

Notebooks for fine-tuning and running of PubMedBERT-based classification models, used in the ANDDigest tool

Is a Django Python web application to download PubMed data into a Microsoft Excel spreadsheet and XML files.

It provides a method of how to fetch articles along with their features and text from PubMed API.

Analyzed PubMed Text abstracts using NLP and Topic Modeling techniques

Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J

A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework

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