biomedical-text-mining

There are 4 repositories under biomedical-text-mining topic.

dmis-lab / bern
A neural named entity recognition and multi-type normalization tool for biomedical text mining
biomedical-text-mining bert named-entity-recognition named-entity-linking api overlapped-entities-resolving
Language:Python 171
dmis-lab / BERN2
BERN2: an advanced neural biomedical namedentity recognition and normalization tool
biomedical-text-mining
Language:Python 166
yuzhimanhua / Multi-BioNER
Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)
bioinformatics biomedical-nlp biomedical-text-mining named-entity-recognition
Language:Python 130
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.
bioinformatics biomedical-named-entity-recognition biomedical-text-mining deep-learning information-extraction machine-learning spacy
Language:Python 102
BIDS-Xu-Lab / Me-LLaMA
A novel medical large language model family with 13/70B parameters, which have SOTA performances on various medical tasks
biomedical-nlp biomedical-text-mining chatgpt clinical-nlp large-language-models llama2 medical-medical-application medical-large-language-models medical-question-answering gpt-4 llama llm
Language:Python 75
AstraZeneca / KAZU
Fast, world class biomedical NER
biomedical-text-mining natural-language-processing nlp
Language:Python 62
yuzhimanhua / LM-LSTM-CRF
bioinformatics biomedical-nlp biomedical-text-mining named-entity-recognition
48
ncbi / BioConceptVec
biomedical-concept-embeddings biomedical-text-mining deep-learning text-mining word-embeddings protein-protein-interaction
Language:Jupyter Notebook 40
BioDEX
KarelDO / BioDEX
BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.
biomedical-text-mining drug-safety pharmacovigilance pubmed nlp
Language:Jupyter Notebook 37
datquocnguyen / BioPosDep
Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)
bionlp pos-tagging dependency-parsing tokenizer segmenter bioinformatics biomedical-text-mining
Language:Python 32
bayer-science-for-a-better-life / data2text-bioleaflets
Biomedical Data-to-Text Generation via Fine-Tuning Transformers
biomedical-text-mining data-to-text nlp-machine-learning transformers
Language:Python 28
lasigeBioTM / BiOnt
BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction
biomedical-text-mining deep-learning ontologies relation-extraction text-mining
Language:Python 26
biomedicalinformaticsgroup / cadmus
A full-text article retrieval pipeline for biomedical literature.
information-retrieval biomedical-text-mining corpus-generator bionlp python text-mining
Language:Python 17
disi-unibo-nlp / bio-ee-egv
[COLING22] Text-to-Text Extraction and Verbalization of Biomedical Event Graphs
event-extraction nlp semantic-parsing biomedical-text-mining data-to-text graph-to-text graph-verbalization text-to-graph text-to-text-transformer
Language:Python 12
lasigeBioTM / PGR
A Silver Standard Corpus of Human Phenotype-Gene Relations
biomedical-text-mining datasets genes phenotypes relation-extraction
Language:Python 12
vj1494 / PipelineIE
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 coreference-resolution entity information-extraction knowledge-graph pipeline natural-language-understanding corenlp spacy stanza biomedical-text-mining
Language:Python 10
yuzhimanhua / PENNER
PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature (BIBM'18)
bioinformatics biomedical-text-mining pattern-discovery
Language:Python 10
biomedicalinformaticsgroup / ParallelPyMetaMap
This code is to run MetaMap in parallel using Python.
bionlp named-entity-recognition metamap biomedical-text-mining python
Language:Python 8
BNLNLP / PPI-Relation-Extraction
Official implementation of PPI Relation Extraction (IEEE BigData 2022)
biomedical-text-mining ppi relation-extraction attention transformer nlp
Language:Python 8
lasigeBioTM / K-BiOnt
Biomedical Relation Extraction with Knowledge Graph-based Recommendations
bilstm biomedical-text-mining knowledge-graph nlp-machine-learning ontologies relation-extraction text-mining
Language:Python 8
lasigeBioTM / K-RET
K-RET: Knowledgeable Biomedical Relation Extraction System
bert-fine-tuning biomedical-text-mining deep-learning nlp-machine-learning relation-extraction text-mining bert
Language:Python 8
skoblov-lab / SciLK
SciLK: a Scientific natural Language Toolkit
natural-language-processing biomedical-text-mining deep-learning machine-learning
Language:Python 8
dmis-lab / bioner-generalization
How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?
biomedical-text-mining bioner bionlp named-entity-recognition
Language:Python 6
covid
Aequivinius / covid
👑🦠 Annotating PMC and PubMed articles for Covid-related entities
biobert biomedical-text-mining pubannotation pmids
Language:Jupyter Notebook 5
SciCrunch / bio_electra
Bio-Electra - Small and efficient discriminatively pre-trained language representation models for biomedical text mining
language-model biomedical-text-mining question-answering relation-extraction named-entity-recognition transformers
Language:Python 4
Dimas263 / NLP_NER_BERT_BILSTM_CRF_Named_Entity_Recognition
NLP Named Entity Recognition dalam bidang Biomedis, mendeteksi teks dan membuat klasifikasi apakah teks tersebut mempunyai entitas plant atau disease, memberi label pada teks, menguji hubungan entitas plant dan disease, menilai kecocokan antara kedua entitas, membandingkan hasil uji dengan menggunakan models BERT-BILSTM-CRF
bert-bilstm-crf bilstm-model biomedical-text-mining crf-model data-mining jupyter-notebook named-entity-recognition natural-language-processing plant-disease-classification python bert information-extraction ner pytorch transformer nlp keras tensorflow dimas-dwi-putra dimas263
Language:Jupyter Notebook 3
kuldeep7688 / BioMedicalBertNer
Named Entity Recognition using BERT
ner jnlpba bert bioinformatics biomedical-data-science machine-learning deeplearning biomedical-text-mining biomedical-named-entity-recognition natural-language-processing
Language:Python 3
ncbi / biocreative_litcovid
Evaluation scripts of the Biocreative LitCovid track
biomedical-text-mining biocreative machine-learning natural-language-processing deep-learning
Language:Python 3
lasigeBioTM / NILINKER
Attention-based approach to NIL Entity Linking
biomedical-text-mining entity-linking information-extraction natural-language-processing
Language:Python 2
lasigeBioTM / PGR-crowd
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing
biomedical-text-mining crowdsourcing datasets distant-supervision relation-extraction text-mining
Language:Python 2
oligogenic / Deep_active_learning_bioRE
Framework to study the use of deep active learning for biomedical relation extraction
active-learning active-learning-in-nlp annotation biomedical biomedical-text-mining relation-extraction
Language:Python 2
psaegert / pmtrendviz
Unsupervised Discovery Of Trends In Biomedical Research Based On The PubMed Baseline Repository
biomedical-text-mining clustering data-science document-representation pubmed pubmed-abstracts text-analysis trends
Language:Python 2
awakenedhaki / navigating-my-reference-manager
Navigating My Reference Manager
biomedical-text-mining data-analysis nlp r text-mining
Language:R 1
biomedicalinformaticsgroup / pm_abs_extr
This repository automatically requests and extracts abstract from PubMed.
bionlp pubmed-abstracts biomedical-text-mining python text-mining
Language:Python 1
Dimas263 / NLP_NER_BERT_Named_Entity_Recognition
NLP Named Entity Recognition dalam bidang Biomedis, mendeteksi teks dan membuat klasifikasi apakah teks tersebut mempunyai entitas plant atau disease, memberi label pada teks, menguji hubungan entitas plant dan disease, menilai kecocokan antara kedua entitas, membandingkan hasil uji dengan menggunakan models BERT
bert-fine-tuning bert-model biobert biomedical-text-mining jupyter-notebook named-entity-recognition natural-language-processing plant-disease-classification python ner nlp pytorch transformer crf dimas dimas-dwi-putra dimas263 information-extraction relation-extraction
Language:Jupyter Notebook 1
disi-unibo-nlp / ddegk
Implementation of Deep Divergence Event Graph Kernels
event-embedding graph-representation-learning graph-similarity-learning graph-kernels graph-neural-networks event-extraction biomedical-text-mining
Language:Jupyter Notebook 1