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    9 repositories

    • CombDNF

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • opt-synthdata-4tl

      Public
      This is the code repository for the paper "Optimizing ODE-derived Synthetic Data for Transfer Learning in Dynamical Biological Systems".
      transfer-learningtime-series-forecastingode-modelsbiological-systemsinformed-machine-learning
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•1•0•1•Updated Aug 9, 2024Aug 9, 2024

    • pepermint

      Public
      Graph Neural Network for Peptide Abundance Imputation in MS Proteomics Data
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 20, 2024May 20, 2024

    • pyproteonet

      Public
      Python package for imputation, peptide-to-protein aggregation as well as in silico data creation of proteomics data with a specific focus on the development and evaluation of imputation methods in proteomics. Also provides proteomics specific imputation methods based on graph neural networks.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 6, 2024Mar 6, 2024

    • GNN_imputer

      Public
      Graph Neural Network Driven Imputation of Missing Abundances in Mass Spectrometry-Based Proteomics
      Python
      •0•0•0•0•Updated Nov 2, 2023Nov 2, 2023

    • SimbaML

      Public
      SimbaML is an all-in-one framework for integrating prior knowledge of ODE models into the ML process by synthetic data augmentation. It allows for the convenient generation of realistic synthetic data by sparsifying and adding noise. Furthermore, our framework provides customizable pipelines for various ML experiments, such as transfer learning.
      open-sourcetransfer-learningordinary-differential-equationsdata-augmentationsynthetic-datatime-series-forecastingprior-knowledgeinformed-machine-learning
      Python
      •
      MIT License
      •1•4•6•0•Updated Oct 11, 2023Oct 11, 2023

    • pmotif_analytics

      Public
      Collection of tools to run analyses based on the pmotif_lib py-package
      HTML
      •1•0•0•0•Updated Jul 24, 2023Jul 24, 2023

    • pmotif_lib

      Public
      Perform motif detection, either with traditional frequency, or with positional metrics for each graphlet occurrence.
      Python
      •
      MIT License
      •2•0•0•0•Updated Jul 24, 2023Jul 24, 2023

    • SimbaML_examples

      Public
      Jupyter Notebook
      •2•1•0•0•Updated Apr 2, 2023Apr 2, 2023