biobert

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 😌

Explainable clinical reasoning engine combining Graph Attention Networks (GAT), BioBERT embeddings, and Neo4j knowledge graphs for disease prediction and dietary contraindications.

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.

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

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.

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.

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.

Fine-tune with TEA

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

Cross-modal attention fusion of chest X-rays (ViT), clinical notes (BioBERT), and 48-hour vitals (BiLSTM) for explainable 14-label CheXpert classification. Includes Grad-CAM/SHAP/attention-rollout XAI and a FastAPI + React dashboard.

Biomedical NLP tool that analyses PubMed abstracts using BioBERT. Extracts diseases, medications, and lab values. Classifies disease area and summarises in plain English. Live on Streamlit.

BioBert for Q&A

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

🧠 Multimodal Agentic RAG system for medical imaging — UNet-ResNet34 segmentation + BioBERT RAG + LangGraph reasoning → structured differential diagnosis

Production clinical NLP pipeline — BERT/BioBERT text classification, NER, and sentiment analysis on medical records. 93% classification accuracy. HuggingFace · spaCy · FastAPI · MLflow · Docker.