biobert

Browse Covid-19 & SARS-CoV-2 Scientific Papers with Transformers 🦠 📖

NER and Relation Extraction from Electronic Health Records (EHR).

Implementation and demo of explainable coding of clinical notes with Hierarchical Label-wise Attention Networks (HLAN)

MIL-RBERT: A Data-driven Approach for Noise Reduction in Distantly Supervised Biomedical Relation Extraction (BioNLP @ ACL 2020)

Ready to use BioBert pytorch weights for HuggingFace pytorch BertModel 😌

Relation Extraction using BERT and BioBERT - using BERT, we achieved new state of the art results

Computational Strategies in Nutrigenetics: Constructing a Reference Dataset of Nutrition-Associated Genetic Polymorphisms https://doi.org/10.1101/2023.08.04.23293659

🧬 Fine-Tuning Large Language and Protein Models on a single T4 GPU via Distillation, Quantization and Low-Rank Adaptation to run inference on proteins functions.

This project applies Fine-tuning BERT & BioBERT on BC5CDR for biomedical named entity recognition (diseases + chemicals).

COVID-19 Open Research Dataset Challenge (CORD-19)

The traditional machine learning models give a lot of pain when we do not have sufficient labeled data for the specific task or domain we care about to train a reliable model. Transfer learning allows us to deal with these scenarios by leveraging the already existing labeled data of some related task or domain. We try to store this knowledge gai…

👑🦠 Annotating PMC and PubMed articles for Covid-related entities

This repository contains data and BioBert based NER model monologg/biobert_v1.1_pubmed from community-uploaded Hugging Face models for detecting entities such as chemical and disease.

Prompts, datasets, and scripts for evaluating frontier LLMs as biomedical text-mining annotators, including instruction retrieval, two-step inference, and synthetic-data distillation.

The repo consists of an ML model based on BioBERT by virtue of transfer learning, to detect adverse drug reactions (ADRs). It also consists of the data used by the model.

Code for my Master thesis on "Intelligent Drug-Drug Interaction Extraction: A Natural Language Processing Approach to Biomedical Text Analysis".

A tool capable of parsing datasets of papers from pubmed, annotating entities that appear using bio-BERT, creating a network of cooccurrences on which to perform analysis with various algorithms

Question Answering tool for CliCR dataset developed using BERT and BioBERT

A cost-sensitive BERT that handles the class imbalance for the task of biomedical NER.

Training and computational/visualization analysis of BERT and BioBERT using PyTorch and huggingface.