A neural named entity recognition and multi-type normalization tool for biomedical text mining
☆177Apr 18, 2022Updated 3 years ago
Alternatives and similar repositories for bern
Users that are interested in bern are comparing it to the libraries listed below
Sorting:
- CollaboNet for Biomedical Named Entity Recognition☆48Feb 5, 2019Updated 7 years ago
- BERN2: an advanced neural biomedical namedentity recognition and normalization tool☆203Mar 28, 2024Updated last year
- ACL'2020: Biomedical Entity Representations with Synonym Marginalization☆178Jul 7, 2023Updated 2 years ago
- ☆20Sep 28, 2021Updated 4 years ago
- This repository contains the corpora and supplementary data, along with instructions for recreating the experiments, for our paper: "Towa…☆15Jul 26, 2019Updated 6 years ago
- Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining☆2,186Aug 13, 2023Updated 2 years ago
- Pre-trained Language Model for Biomedical Question Answering☆125Mar 24, 2023Updated 2 years ago
- Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work …☆102Jul 14, 2020Updated 5 years ago
- BioBert Pytorch☆116Dec 9, 2022Updated 3 years ago
- A corpus of Biomedical papers annotated with mentions of UMLS entities.☆342Nov 9, 2021Updated 4 years ago
- Fast and Effective Biomedical Entity Linking Using a Dual Encoder☆18Apr 21, 2022Updated 3 years ago
- BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.☆296Jan 12, 2022Updated 4 years ago
- BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).☆588Mar 25, 2023Updated 2 years ago
- BioFLAIR: Pretrained Pooled Contextualized Embeddings for Biomedical Sequence Labeling Tasks☆42May 31, 2020Updated 5 years ago
- A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset☆725Jul 31, 2025Updated 7 months ago
- A full spaCy pipeline and models for scientific/biomedical documents.☆1,925Dec 4, 2025Updated 2 months ago
- System for Medical Concept Extraction and Linking☆432Aug 12, 2024Updated last year
- Named Entity Recognition for biomedical entities☆49Jan 11, 2023Updated 3 years ago
- Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)☆135Jul 25, 2024Updated last year
- covidAsk: Answering Questions on COVID-19 in Real-Time☆64Nov 9, 2022Updated 3 years ago
- ☆233Aug 15, 2017Updated 8 years ago
- ☆77Dec 20, 2023Updated 2 years ago
- A BERT model for scientific text.☆1,670Feb 22, 2022Updated 4 years ago
- A system for normalizing disorder mentions in biomedical data.☆19Jul 27, 2015Updated 10 years ago
- a module to calculate the MeSH similarity☆26Apr 13, 2021Updated 4 years ago
- Crowdsourced ground truth for medical relation extraction.☆69Mar 18, 2019Updated 6 years ago
- Transforming SemRep Predications into an Open Biomedical Linked Data Resource☆11Jan 26, 2018Updated 8 years ago
- EMNLP 2022: Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Framework☆11Aug 29, 2024Updated last year
- BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences☆611Aug 15, 2023Updated 2 years ago
- Medical Concept Annotation Tool☆522Jul 25, 2025Updated 7 months ago
- Extracting biomedical relationships from literature with Snorkel 🏊☆58Feb 1, 2021Updated 5 years ago
- Table compiling the list of biomedically-related corpora available for named entity recognition (and some also suitable for association d…☆18Mar 15, 2018Updated 7 years ago
- This repository aims to track the progress in BioNER and give a related paper list and an overview of the state-of-the-art (SOTA).☆201Feb 23, 2021Updated 5 years ago
- DEREK (Domain Entities and Relations Extraction Kit)☆10May 22, 2023Updated 2 years ago
- ☆10Jun 16, 2021Updated 4 years ago
- EMNLP'2021: Can Language Models be Biomedical Knowledge Bases?☆57Mar 9, 2023Updated 2 years ago
- Code and dataset of EMNLP 2020 paper "Infusing Disease Knowledge into BERT for Health Question Answering, Medical Inference and Disease N…☆69Jul 19, 2021Updated 4 years ago
- A collection of annotated biomedical corpora, which can be used for training supervised machine learning methods for various tasks in bio…☆36Sep 18, 2018Updated 7 years ago
- For icibm paper☆11Feb 23, 2017Updated 9 years ago