uf-hobi-informatics-lab / ClinicalTransformerNERView external linksLinks
a library for named entity recognition developed by UF HOBI NLP lab featuring SOTA algorithms
☆155Sep 13, 2023Updated 2 years ago
Alternatives and similar repositories for ClinicalTransformerNER
Users that are interested in ClinicalTransformerNER are comparing it to the libraries listed below
Sorting:
- A project for developing transformer-based models for clinical relation extraction☆130Aug 15, 2023Updated 2 years ago
- ☆18Apr 8, 2024Updated last year
- A comprehensive NLP preprocessing package for clinical notes sentence boundary detection, tokenization☆32May 22, 2024Updated last year
- BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).☆588Mar 25, 2023Updated 2 years ago
- all scripts used in gatortron project☆130Nov 3, 2023Updated 2 years ago
- We evaluate many models used for biomedical and clinical nlp tasks, and train new models that perform much better.☆163Jul 29, 2021Updated 4 years ago
- repository for Publicly Available Clinical BERT Embeddings☆752Aug 25, 2020Updated 5 years ago
- Implementation of Nested Named Entity Recognition using BERT☆136Oct 29, 2021Updated 4 years ago
- ☆98Jul 7, 2023Updated 2 years ago
- Dataset containing 7,025 discharge summary notes from the MIMIC III dataset annotated for 7 SBDHs☆18Jun 18, 2022Updated 3 years ago
- Library for clinical NLP with spaCy.☆632Aug 4, 2025Updated 6 months ago
- BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.☆296Jan 12, 2022Updated 4 years ago
- Medical Concept Annotation Tool☆522Jul 25, 2025Updated 6 months ago
- Large medical text dataset curated for abbreviation disambiguation, designed for natural language understanding pre-training in the medic…☆282Oct 18, 2023Updated 2 years ago
- Clinical XLNet: Modeling Sequential Clinical Notes and Predicting Prolonged Mechanical Ventilation☆51Aug 12, 2021Updated 4 years ago
- Embedding Complexity In the Data Representation Instead of In the Model (arXiv:1802.04233)☆24Feb 14, 2018Updated 8 years ago
- BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences☆611Aug 15, 2023Updated 2 years ago
- Full named-entity (i.e., not tag/token) evaluation metrics based on SemEval’13☆204Sep 6, 2025Updated 5 months ago
- Implementation of the BLUE benchmark with Transformers.☆20Feb 16, 2024Updated 2 years ago
- A corpus of Biomedical papers annotated with mentions of UMLS entities.☆342Nov 9, 2021Updated 4 years ago
- Rare disease identification from free-text clinical notes with ontologies and weak supervision☆32May 6, 2023Updated 2 years ago
- Code for Contextual Autocomplete paper published in MLHC2020☆13Aug 7, 2021Updated 4 years ago
- ☆15Apr 28, 2020Updated 5 years ago
- Clinical NLP workshop for ODSC☆40Oct 31, 2019Updated 6 years ago
- ☆44Jul 13, 2023Updated 2 years ago
- A Python Natural Language Processing Toolkit for Medical Text Generation☆83May 24, 2025Updated 8 months ago
- ☆38Mar 27, 2022Updated 3 years ago
- ☆13Oct 20, 2022Updated 3 years ago
- ☆55Apr 9, 2020Updated 5 years ago
- Implementation of Nested Named Entity Recognition using Flair☆24Oct 29, 2021Updated 4 years ago
- skweak: A software toolkit for weak supervision applied to NLP tasks☆926Sep 2, 2024Updated last year
- [ACL 2022] LinkBERT: A Knowledgeable Language Model 😎 Pretrained with Document Links☆449Apr 5, 2022Updated 3 years ago
- ☆63Jul 4, 2023Updated 2 years ago
- Med-BERT, contextualized embedding model for structured EHR data☆314Feb 19, 2024Updated last year
- ☆19Jul 7, 2025Updated 7 months ago
- Language model fine-tuning on NER with an easy interface and cross-domain evaluation. "T-NER: An All-Round Python Library for Transformer…☆396May 11, 2023Updated 2 years ago
- Fall Detection in EHR using Word Embeddings and Deep Learning☆16Nov 23, 2020Updated 5 years ago
- A python module for evaluating NERC and NEL system performances as defined in the HIPE shared tasks (formerly CLEF-HIPE-2020-scorer).☆15Jun 4, 2024Updated last year
- MedAlign is a clinician-generated dataset for instruction following with electronic medical records.☆97May 17, 2025Updated 8 months ago