BERN2: an advanced neural biomedical namedentity recognition and normalization tool
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Mar 28, 2024 - Python
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biomedical-text-mining
Here are 48 public repositories matching this topic...
A neural named entity recognition and multi-type normalization tool for biomedical text mining
api named-entity-recognition bert named-entity-linking biomedical-text-mining overlapped-entities-resolving
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Apr 18, 2022 - Python
A novel medical large language model family with 13/70B parameters, which have SOTA performances on various medical tasks
llama medical-application biomedical-text-mining clinical-nlp medical- medical-question-answering gpt-4 large-language-models llm chatgpt biomedical-nlp llama2 medical-large-language-models
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Jan 15, 2025 - Python
Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)
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Jul 25, 2024 - Python
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.
machine-learning bioinformatics deep-learning information-extraction spacy biomedical-text-mining biomedical-named-entity-recognition
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Jul 14, 2020 - Python
Fast, world class biomedical NER
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Mar 4, 2025 - Python
BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.
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Jan 29, 2024 - Jupyter Notebook
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Aug 30, 2023
text-mining deep-learning word-embeddings protein-protein-interaction biomedical-text-mining biomedical-concept-embeddings
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Feb 26, 2020 - Jupyter Notebook
Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)
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Apr 6, 2019 - Python
Biomedical Data-to-Text Generation via Fine-Tuning Transformers
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Dec 20, 2021 - Python
BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction
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Nov 30, 2023 - Python
A full-text article retrieval pipeline for biomedical literature.
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Jul 9, 2026 - Python
A Silver Standard Corpus of Human Phenotype-Gene Relations
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Oct 6, 2022 - Python
PipelineIE is a project that contains a pipeline for information extraction (currently triple) from free text and domain specific text (eg. biomedical domain) and also supports custom models making it flexible to support other domains. It takes care of coreference resolution and entity resolution by also allowing to test with different tools.
natural-language-processing text-mining pipeline entity information-extraction spacy knowledge-graph stanza corenlp natural-language-understanding coreference-resolution biomedical-text-mining
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Mar 15, 2021 - Python
PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature (BIBM'18)
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Apr 2, 2024 - Python
K-RET: Knowledgeable Biomedical Relation Extraction System
text-mining deep-learning nlp-machine-learning bert relation-extraction biomedical-text-mining bert-fine-tuning
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Feb 22, 2025 - Python
[COLING22] Text-to-Text Extraction and Verbalization of Biomedical Event Graphs
nlp event-extraction semantic-parsing biomedical-text-mining data-to-text graph-to-text text-to-graph graph-verbalization text-to-text-transformer
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Nov 5, 2022 - Python
Official implementation of PPI Relation Extraction (IEEE BigData 2022)
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Mar 3, 2023 - Python
This code is to run MetaMap in parallel using Python.
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Nov 25, 2025 - Python
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