Fraunhofer SCAI Bioinformatics Department

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46 repositories

kitsune
Public
Kitsune is a next-generation data steward and harmonization tool.
embeddings data-harmonization semantic-mapping data-stewardship large-language-models
TypeScript
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Apache License 2.0
•1•3•8•0•Updated Aug 5, 2025Aug 5, 2025
covid-NDD-image-based-information-extraction
Public
Extracting structured knowledge from biomedical images using LLMs, focusing on COVID-19 and neurodegeneration. Leverages GPT-4o for image analysis and semantic triple extraction to build a biomedical knowledge graph.
Python
•0•0•0•0•Updated Aug 5, 2025Aug 5, 2025
datastew
Public
Python library for intelligent data stewardship using Large Language Model (LLM) embeddings
data-harmonization data-stewardship large-language-models
Python
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Apache License 2.0
•0•5•12•2•Updated Aug 4, 2025Aug 4, 2025
syndat
Public
Synthetic data quality evaluation & visualization
data-visualization data-quality synthetic-data
Python
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MIT License
•0•3•4•0•Updated Aug 1, 2025Aug 1, 2025
BiomarkerOntology
Public
The Biomarker Ontology
0•0•1•0•Updated Jul 31, 2025Jul 31, 2025
primekg-rag
Public
RAG-based method for mapping variables to PrimeKG subgraphs with textual graph descriptions.
knowledge-graph rag llm primekg graph-retrieval
Python
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Apache License 2.0
•0•1•0•0•Updated Jul 30, 2025Jul 30, 2025
covid-NDD-comorbidity-NLP
Public
This work aims to integrate diverse, curated biological databases with a comprehensive analysis of the growing body of literature on the potential long-term neurological consequences of COVID-19 infections, employing advanced natural language processing and text mining techniques.
Jupyter Notebook
•0•3•0•0•Updated Jul 29, 2025Jul 29, 2025
ADHTEB
Public
ADHTEB - Alzheimers Disease Harmonization Text Embedding Benchmark
benchmark alzheimers-disease data-harmonization llms
Python
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Apache License 2.0
•0•1•0•1•Updated Jul 28, 2025Jul 28, 2025
pytmle
Public
A Flexible Python Implementation of Targeted Estimation for Survival and Competing Risks Analysis
Python
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Apache License 2.0
•1•1•0•1•Updated Jul 17, 2025Jul 17, 2025
CBM-Comorbidity-KG
Public
a manually curated, comorbidity-centric knowledge graph linking COVID-19 to neurodegenerative diseases
Cypher
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Apache License 2.0
•0•0•0•0•Updated Jun 12, 2025Jun 12, 2025
cv-extraction
Public
Web-Tool for LLM based CV extraction
text-mining resume-parser llm
Python
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Apache License 2.0
•0•1•2•0•Updated May 5, 2025May 5, 2025
PD-diagnostic-delay
Public
Parkinson's disease diagnostic delay analysis
0•1•0•0•Updated Mar 31, 2025Mar 31, 2025
radar-ad-rmt-analysis
Public
Python
•0•0•0•0•Updated Mar 26, 2025Mar 26, 2025
ollama-docker
Public
Pre-build docker containers for different LLMs using Ollama
docker llm ollama
Shell
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Apache License 2.0
•0•1•0•0•Updated Mar 24, 2025Mar 24, 2025
PDataViewer
Public
Parkinsons Disease cohort landscape visualization
visualization parkinsons-disease cohort-selection common-data-model
TypeScript
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Apache License 2.0
•0•3•4•0•Updated Mar 21, 2025Mar 21, 2025
causal-npi-effects
Public
A causal machine learning framework to assess effects of non-pharmaceutical interventions on pandemic disease spread.
Python
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Apache License 2.0
•0•0•0•0•Updated Mar 18, 2025Mar 18, 2025
MMPK-SciML
Public
Official implementation of the paper Scientific Machine learning for predicting plasma concentrations in anti-cancer therapy
Python
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MIT License
•0•1•0•0•Updated Mar 11, 2025Mar 11, 2025
psystrata-explainerdashboard
Public
Prototype Dashboard explaining Treatment Resistance Models, based on explainerdashboard
explainable-ai
Python
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MIT License
•344•1•0•0•Updated Feb 26, 2025Feb 26, 2025
tsnepad
Public
AD & PD cohort variable distributions
visualization t-sne alzheimers-disease parkinsons-disease data-harmonization
HTML
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MIT License
•0•3•0•0•Updated Feb 17, 2025Feb 17, 2025
ExMed-BERT
Public
Python
•1•7•0•0•Updated Feb 3, 2025Feb 3, 2025
SEEDS
Public
SEEDS (Similarity based Expert Embedding Decision System) is a Retrieval-Augmented Generation (RAG) based agricultural question-answering (QA) system. It is built upon a domain-specific knowledge graph (KG), representing Cedar Apple Rust disease.
Python
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Apache License 2.0
•1•1•0•0•Updated Jan 28, 2025Jan 28, 2025
Dynamic_Ensemble
Public
A Dynamic Ensemble Model for short-term Forecasting in Pandemic Situations
Python
•0•0•0•0•Updated Sep 18, 2024Sep 18, 2024
wasterwater_analysis
Public
Jupyter Notebook
•0•0•0•0•Updated Sep 18, 2024Sep 18, 2024
service-template
Public
0•0•0•0•Updated Jul 3, 2024Jul 3, 2024
mirna-disease-association-detection
Public
MiRNA-disease association detection through text mining methods.
Python
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Apache License 2.0
•1•1•1•0•Updated Jun 23, 2024Jun 23, 2024
MultiNODEs
Public
Python
•2•8•0•0•Updated Apr 30, 2024Apr 30, 2024
MultiNODEs_NewImplementation
Public
MultiNODEs New Implementation
Python
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MIT License
•0•0•0•0•Updated Apr 30, 2024Apr 30, 2024
PD-progression-types
Public
R
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Other
•1•3•0•0•Updated Apr 29, 2024Apr 29, 2024
tau-kg-extension-nlp
Public
Extending the Tau subgraph within the pharmacome using NLP.
Jupyter Notebook
•0•0•0•0•Updated Mar 27, 2024Mar 27, 2024
adr-detection-with-knowledge-fusion
Public
ADR Deteciton with Knowledge Fusion Approaches
Python
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Apache License 2.0
•1•0•0•0•Updated Feb 12, 2024Feb 12, 2024