Curated resources, architectures, prompts, and benchmark datasets for applying LLMs and Retrieval-Augmented Generation (RAG) in biomedicine and drug discovery.
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Aug 8, 2026 - Python
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pubmedbert
Here are 14 public repositories matching this topic...
Multimodal AI-powered plant disease diagnosis system integrating ResNet-18, Quantum Neural Networks (PennyLane), PubMedBERT, Gemini 2.5 Flash, Grad-CAM, and probabilistic ensemble fusion for explainable disease classification using computer vision, NLP, and quantum-enhanced deep learning.
nlp computer-vision deep-learning reactjs transformers grad-cam pytorch artificial-intelligence ensemble-learning quantum-machine-learning multimodal-learning explainable-ai gemini-api fastapi resnet18 medical-ai plant-disease-detection pennylane pubmedbert
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Jul 16, 2026 - Jupyter Notebook
Automated pharmacovigilance literature validation for ultra‑rare neurological diseases. Enter a drug name and an adverse event. The app searches PubMed with a multi‑tier cascade, extracts the most relevant evidence, and returns a verdict — Present or Absent — backed by a fine‑tuned PubMedBERT model.
open-source benchmark gradio signal-detection natural-language-inference zero-shot zero-shot-learning drug-safety few-shot pharmacovigilance few-shot-learning rare-disease huggingface faers ntd biomedical-nlp pubmedbert literature-validation
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Jun 21, 2026 - Python
AI-powered conversational medical assistant with RAG over MedLinePlus & MedQuAD datasets, Neo4j knowledge graph, Qdrant vector database, LangGraph agent orchestration, and voice I/O (Whisper STT + Edge TTS).
nlp embeddings graph-database voice-assistant rag medical-ai vector-database qdrant llm langchain graphrag langraph pubmedbert
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May 5, 2026 - Python
Exploring biomedical question answering using the PubMedQA dataset through natural language processing (NLP), comparing traditional machine learning approaches, text representation techniques, and fine-tuning of pretrained biomedical language models such as BioBERT and PubMedBERT.
python machine-learning natural-language-processing deep-learning text-classification pubmed fine-tuning biobert large-language-models trasformer pubmedbert
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May 25, 2025 - Jupyter Notebook
Classifying NHS patient questions by disease — TF-IDF+kNN baseline vs. fine-tuned BERT / BioBERT / PubMedBERT (UCL MSc, Advanced ML for Healthcare).
nlp machine-learning text-classification transformers pytorch bert huggingface healthcare-ai pubmedbert
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Jul 7, 2026 - Jupyter Notebook
Fine-tuned PubMedBERT bi-encoder on PubMedQA achieving NDCG@10=0.974. BM25 from scratch in pure NumPy. Self-improving multi-agent critic loop. Model live on HuggingFace Hub.
python information-retrieval multi-agent bm25 fine-tuning huggingface medical-ai sentence-transformers hybrid-search pubmedbert
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May 31, 2026 - Python
Adverse drug event NER on CADEC: feature-engineered CRF vs fine-tuned BioBERT/PubMedBERT, with class-imbalance and error analysis
crf named-entity-recognition pharmacovigilance clinical-nlp biobert cadec adverse-drug-events pubmedbert
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Oct 22, 2026 - Python
Transformer-based topic modeling (BERTopic) of six spine journals, 1978–2026 — 40,401 abstracts, 37 topics, with temporal trends and VOSviewer comparison.
python nlp text-mining transformers topic-modeling scientometrics umap hdbscan bibliometrics neurosurgery spine-surgery orthopedics bertopic biomedical-nlp research-trends pubmedbert
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Jun 2, 2026 - Python
How OCR errors break biomedical NER: BC5CDR abstracts rendered as degraded scans, read with docTR, gold spans projected by character alignment and tagged by PubMedBERT; entity F1 vs CER with bootstrap CIs and three fixes (OpenCV clean-up, noise-augmented fine-tuning, local-LLM correction).
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Oct 26, 2026 - Jupyter Notebook
Local multi-agent pipeline (LLaMa-3.1 via MLX + PubMedBERT RAG over Chroma) that fact-checks drug questions against authoritative medical sources and returns a cited answer with per-claim verdicts. Ships with a FastAPI + single-page web UI and a Typer CLI
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Apr 19, 2026 - Python
Fine-tuned PubMedBERT that labels each sentence of a medical abstract as background, objective, methods, results or conclusions, served over FastAPI
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Aug 13, 2026 - Jupyter Notebook
RAG clinical decision support for PCI vs CABG, grounded in 2021 ACC/AHA guidelines (FastAPI, LangChain, PubMedBERT, ChromaDB, Claude)
clinical-decision-support rag streamlit healthcare-ai chromadb retrieval-augmented-generation pubmedbert
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Oct 24, 2026 - Python
Agentic Corrective RAG over 484 ClinicalTrials.gov oncology protocols. LangGraph CRAG with LLM-as-judge grading + cross-encoder reranker for two-stage retrieval. Three independent refusal gates. PubMedBERT, FAISS, Groq Llama 3.3 70B. Live demo on Streamlit.
python data-science clinical-trials llama faiss reranker rag groq streamlit sentence-transformers healthcare-ai crag cross-encoder llm biomedical-nlp retrieval-augmented-generation corrective-rag agentic-ai langraph pubmedbert
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Oct 25, 2026 - Jupyter Notebook
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