BaderLab / saber
Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.
☆102Updated 4 years ago
Alternatives and similar repositories for saber:
Users that are interested in saber are comparing it to the libraries listed below
- Named Entity Recognition for biomedical entities☆47Updated 2 years ago
- A Python biomedical relation extraction package that uses a supervised approach (i.e. needs training data).☆157Updated 2 years ago
- Extracting biomedical relationships from literature with Snorkel 🏊☆58Updated 4 years ago
- Abbreviation definition dection library trained on PubMed abstracts☆47Updated 4 years ago
- ☆72Updated last year
- Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)☆33Updated 6 years ago
- A collection of annotated biomedical corpora, which can be used for training supervised machine learning methods for various tasks in bio…☆36Updated 6 years ago
- This repository contains the corpora and supplementary data, along with instructions for recreating the experiments, for our paper: "Towa…☆15Updated 5 years ago
- A neural named entity recognition and multi-type normalization tool for biomedical text mining☆177Updated 2 years ago
- ☆90Updated 5 years ago
- Table compiling the list of biomedically-related corpora available for named entity recognition (and some also suitable for association d…☆18Updated 7 years ago
- Crowdsourced ground truth for medical relation extraction.☆69Updated 6 years ago
- BioFLAIR: Pretrained Pooled Contextualized Embeddings for Biomedical Sequence Labeling Tasks☆42Updated 4 years ago
- Extracting scientific claims from biomedical abstracts (powered by AllenNLP)☆140Updated 3 years ago
- MedType: Improving Medical Entity Linking with Semantic Type Prediction☆116Updated 2 years ago
- ☆122Updated 6 years ago
- Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)☆135Updated 8 months ago
- BioBert Pytorch☆116Updated 2 years ago
- Conversion from brat-flavored standoff to CoNLL format☆51Updated 4 years ago
- Retrieve and process PubTator annotations☆44Updated last year
- Python library for work with BioCreative files☆13Updated 7 years ago
- A corpus of Biomedical papers annotated with mentions of UMLS entities.☆324Updated 3 years ago
- ACL'2020: Biomedical Entity Representations with Synonym Marginalization☆163Updated last year
- Python wraper for MetaMap☆171Updated 4 years ago
- This repository contains supplementary data, and links to the model and corpora used for the paper: Transfer learning for biomedical name…☆37Updated 6 years ago
- Fast and Effective Biomedical Entity Linking Using a Dual Encoder☆19Updated 2 years ago
- Text annotation tool for team collaboration☆40Updated last year
- Reach Biomedical Information Extraction☆97Updated 4 months ago
- NLP framework in python for entity recognition and relationship extraction☆114Updated 2 years ago
- NCBI disease corpus - related resources☆28Updated 7 years ago