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 :relieved:

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

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

🧬 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.

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

👑🦠 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.

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

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

Bi Master - Grupo de desafios de NLP: Classificação Multiclasse, BIOBERT, spaCy, NER, POS, Tópicos, Geração de Texto, sentence-bert, Tensorflow USEm.

AI powered symptom simulator and diagnostic trainer for medical students

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

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

A comprehensive web application built with Flask and BioBERT that provides intelligent information about cancer treatments, side effects, and medical guidance using advanced NLP processing and AI-powered question answering.

A simple binary prediction model that gets the Alzheimer's drugs' description texts as input. It classifies the drugs into two Small Molecules (SM) and Disease modifying therapies (DMT) categories. The model utilizes BERT for word embeddings.

NLP Named Entity Recognition dalam bidang Biomedis, mendeteksi teks dan membuat klasifikasi apakah teks tersebut mempunyai entitas plant atau disease, memberi label pada teks, menguji hubungan entitas plant dan disease, menilai kecocokan antara kedua entitas, membandingkan hasil uji dengan menggunakan models BERT

Ping Lab Intern Project, Summar, 2022: :octocat: Building Named Entity Recognition model with fine tuning BioBERT - a data engineering approach

Fine-tune with TEA

Advanced semantic search system for medical and scientific documentation using BioBERT and pgvector.

BioBert for Q&A

This project presents an adaptive token pruning framework for improving inference efficiency in BioBERT-based Biomedical Named Entity Recognition (NER). The system uses attention entropy and confidence-based scoring to identify low-importance tokens and dynamically prune them during inference.

Production-ready Clinical NER Pipeline using BioBERT for medical entity extraction from clinical notes — 95%+ accuracy | QuantumHelix.ai

This project is a demo for Bert Question Answering on medical data.