Fraunhofer SCAI Bioinformatics Department

All

38 repositories

index
Public
Intelligent data steward toolbox using Large Language Model embeddings for automated Data-Harmonization
embeddings data-harmonization semantic-mapping data-stewardship large-language-models
TypeScript
•
Apache License 2.0
•1•3•11•1•Updated Feb 24, 2025Feb 24, 2025
syndat
Public
Synthetic data quality evaluation & visualization
data-visualization data-quality synthetic-data
Python
•
MIT License
•0•2•3•0•Updated Feb 21, 2025Feb 21, 2025
datastew
Public
Python library for intelligent data stewardship using Large Language Model (LLM) embeddings
data-harmonization data-stewardship large-language-models
Python
•
Apache License 2.0
•0•5•16•1•Updated Feb 20, 2025Feb 20, 2025
tsnepad
Public
AD & PD cohort variable distributions
visualization t-sne alzheimers-disease parkinsons-disease data-harmonization
HTML
•
MIT License
•0•3•0•0•Updated Feb 17, 2025Feb 17, 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.
Jupyter Notebook
•0•0•0•0•Updated Feb 13, 2025Feb 13, 2025
BiomarkerOntology
Public
The Biomarker Ontology
0•0•0•0•Updated Feb 7, 2025Feb 7, 2025
ExMed-BERT
Public
Python
•1•6•0•0•Updated Feb 3, 2025Feb 3, 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•0•0•0•Updated Feb 3, 2025Feb 3, 2025
causal-npi-effects
Public
A causal machine learning framework to assess effects of non-pharmaceutical interventions on pandemic disease spread.
Python
•
Apache License 2.0
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
psystrata-explainerdashboard
Public
Prototype Dashboard explaining Treatment Resistance Models, based on explainerdashboard
explainable-ai
Python
•
MIT License
•337•1•0•0•Updated Jan 29, 2025Jan 29, 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
•
Apache License 2.0
•0•0•0•0•Updated Jan 28, 2025Jan 28, 2025
PDataViewer
Public
Parkinsons Disease cohort landscape visualization
visualization parkinsons-disease cohort-selection common-data-model
TypeScript
•
Apache License 2.0
•0•3•4•0•Updated Jan 14, 2025Jan 14, 2025
MMPK-SciML
Public
Official implementation of the paper Scientific Machine learning for predicting plasma concentrations in anti-cancer therapy
Python
•
MIT License
•0•0•0•0•Updated Sep 23, 2024Sep 23, 2024
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
•
Apache License 2.0
•1•1•1•0•Updated Jun 23, 2024Jun 23, 2024
MultiNODEs
Public
Python
•2•6•0•0•Updated Apr 30, 2024Apr 30, 2024
MultiNODEs_NewImplementation
Public
MultiNODEs New Implementation
Python
•
MIT License
•0•0•0•0•Updated Apr 30, 2024Apr 30, 2024
PD-progression-types
Public
R
•
Other
•1•1•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
•
Apache License 2.0
•1•0•0•0•Updated Feb 12, 2024Feb 12, 2024
MultiGML
Public
MultiGML
Python
•
Apache License 2.0
•4•9•1•0•Updated Feb 9, 2024Feb 9, 2024
tau-kg-benchmarking-GPT
Public
Benchmarking the performance of GPT-based LLMs against human curated Tau KG from Human Brain Pharmacome (HBP)
Jupyter Notebook
•
Apache License 2.0
•0•1•0•0•Updated Dec 13, 2023Dec 13, 2023
helm-upgrade-actions
Public
Template to automatically build & deploy services to Kubernetes (k8s) using helm and github actions
docker helm github-actions k8s helm-charts
HTML
•
Apache License 2.0
•0•1•0•0•Updated Dec 8, 2023Dec 8, 2023
sam
Public
Terminology management service
terminology-management
Java
•
MIT License
•0•1•2•0•Updated Dec 5, 2023Dec 5, 2023
ad-mapper
Public
alzheimers-disease data-harmonization common-data-model
Python
•
Creative Commons Attribution 4.0 International
•0•1•0•0•Updated Oct 31, 2023Oct 31, 2023
owl-tooling
Public
Helpers for importing OWL files, reasoning over OWL files, etc.
semantic-web owl ontology
Java
•
Apache License 2.0
•0•0•0•0•Updated Oct 4, 2023Oct 4, 2023
zetomap
Public
An AOP network visualizer and prediction tool for the ZET-O-MAP project.
TypeScript
•0•0•0•0•Updated Sep 20, 2023Sep 20, 2023
Web-of-Clint
Public
web of public health intelligence data tooling
semantic web detection anomaly
Java
•
Apache License 2.0
•0•2•0•0•Updated Jul 17, 2023Jul 17, 2023