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BioTM, LASIGE, Fac. Ciências, Universidade de Lisboa

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63 repositories

LLAMIC
Public
Disease Named Entity Recognition and Relation Extraction with LLaMA-3 on Clinical Texts
Python
•0•0•0•0•Updated Oct 16, 2025Oct 16, 2025
XMR4EL
Public
Extreme Multi Label Ranking, Entity linking, BioInformatics
Python
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Other
•1•1•0•0•Updated Oct 14, 2025Oct 14, 2025
DiShIn
Public
Semantic Similarity Measures using Disjunctive Shared Information
Python
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Apache License 2.0
•4•25•1•0•Updated Oct 3, 2025Oct 3, 2025
EmergencyPatientsClustering
Public
Repository for a Master’s Thesis Project on profiling Emergency Department (ED) patients using Machine Learning techniques (clustering and PCA).
Python
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MIT License
•0•0•0•0•Updated Sep 23, 2025Sep 23, 2025
MiCRA
Public
Microbial Communities for Regenerative Agriculture
Python
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MIT License
•0•0•0•0•Updated Sep 18, 2025Sep 18, 2025
merpy
Public
MER python interface
Python
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Apache License 2.0
•5•12•2•1•Updated Sep 18, 2025Sep 18, 2025
MER
Public
Minimal Named-Entity Recognizer (MER)
Shell
•8•58•3•0•Updated Sep 18, 2025Sep 18, 2025
BioCreativeIX_Track1_MedHopQA
Public
lasigeBioTM at MedHop track : Can a Lean RAG-Enhanced Model Compete with MedGemma?
biocreative biomedical-question-answering
Python
•0•0•0•0•Updated Sep 8, 2025Sep 8, 2025
BioASQ13_2025
Public
lasigeBioTM: A Lean Biomedical QA System Empowered by Structured Knowledge
bioasq biomedical-question-answering
Python
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
BioASQ25-GutBrainIE
Public
BioASQ2025 Task6 -GutBrainIE
Python
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
BENT
Public
Biomedical Term Annotator
natural-language-processing text-mining information-extraction named-entity-recognition biomedical annotation-tool entity-linking entity-extraction named-entity-disambiguation
Python
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Apache License 2.0
•1•9•0•0•Updated Feb 24, 2025Feb 24, 2025
K-RET
Public
K-RET: Knowledgeable Biomedical Relation Extraction System
text-mining deep-learning nlp-machine-learning bert relation-extraction biomedical-text-mining bert-fine-tuning
Python
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Apache License 2.0
•2•10•0•0•Updated Feb 22, 2025Feb 22, 2025
knowledge-extraction-from-CORD-19
Public
Knowledge extraction from CORD-19 (COVID-19 Open Research Dataset)
Python
•2•2•0•1•Updated Oct 24, 2024Oct 24, 2024
CheRM
Public
Chemical Compounds Recommender Matrix
Python
•0•1•0•1•Updated Oct 24, 2024Oct 24, 2024
SemanticSimDBcreator
Public
Semantic Similarity Database Creator
Python
•0•0•0•1•Updated Oct 24, 2024Oct 24, 2024
ChemRecSys
Public
Python
•0•1•0•1•Updated Oct 24, 2024Oct 24, 2024
NILINKER
Public
Attention-based approach to NIL Entity Linking
natural-language-processing information-extraction entity-linking biomedical-text-mining
Python
•0•3•1•0•Updated Sep 4, 2024Sep 4, 2024
X-Linker
Public
Python
•1•1•0•0•Updated Aug 1, 2024Aug 1, 2024
REEL
Public
REEL: Relation Extraction for Entity Linking
Python
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Apache License 2.0
•3•10•0•2•Updated May 3, 2024May 3, 2024
MultiNEL-corpus
Public
A multilingual silver standard corpus containing English, Portuguese and Spanish clinical case reports annotated with medical diagnostic codes
Python
•1•4•0•1•Updated May 3, 2024May 3, 2024
BiOnt
Public
BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction
text-mining deep-learning ontologies relation-extraction biomedical-text-mining
Python
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Apache License 2.0
•6•27•1•0•Updated Nov 30, 2023Nov 30, 2023
K-BiOnt
Public
Biomedical Relation Extraction with Knowledge Graph-based Recommendations
text-mining knowledge-graph ontologies nlp-machine-learning relation-extraction biomedical-text-mining bilstm
Python
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Apache License 2.0
•5•8•0•0•Updated Nov 30, 2023Nov 30, 2023
biocreativeVII
Public
lasigeBioTM at BioCreative VII Track 1: Text mining drug and chemical-protein interactions using biomedical ontologies
Python
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Apache License 2.0
•0•1•0•0•Updated Nov 30, 2023Nov 30, 2023
biocreativeVIII_Track1
Public
Apache License 2.0
•0•1•0•0•Updated Nov 23, 2023Nov 23, 2023
K-RET-NEG
Public
Python
•0•0•0•0•Updated Sep 14, 2023Sep 14, 2023
SemEval2023_Task-7
Public
Python
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Apache License 2.0
•0•1•0•0•Updated Aug 21, 2023Aug 21, 2023
BLiR
Public
Biomarker Literature Retrieval
TeX
•2•5•0•2•Updated May 22, 2023May 22, 2023
BOE
Public
BOE: BiOnt Enhanced for Relation Extraction in Gene and Chemical Compounds interactions (DrugProt corpus)
Python
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MIT License
•0•4•0•0•Updated Mar 23, 2023Mar 23, 2023
exposome_NER_NEL
Public
Python
•0•0•0•0•Updated Feb 24, 2023Feb 24, 2023
BOLSTM
Public
Classifying Relations via Long Short-Term Memory Networks along Biomedical Ontologies
Python
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Apache License 2.0
•2•15•3•5•Updated Feb 15, 2023Feb 15, 2023