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    25 repositories

    • MCF

      Public
      Code for the paper "Persistent Homology of the Multiscale Clustering Filtration" by Dominik J. Schindler and Mauricio Barahona: https://arxiv.org/abs/2305.04281
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Nov 21, 2024Nov 21, 2024

    • PyGenStability

      Public
      PyGenStability: Multiscale community detection with generalized Markov Stability
      clusteringcommunity-detectionpython3multiscalelouvain-algorithmleiden-algorithm
      C++
      •
      GNU General Public License v3.0
      •12•33•2•0•Updated Nov 14, 2024Nov 14, 2024

    • raman-unmixing-aes

      Public
      Codebase supporting "Hyperspectral unmixing for Raman spectroscopy via physics-constrained autoencoders"
      Jupyter Notebook
      •
      MIT License
      •1•5•0•0•Updated Oct 16, 2024Oct 16, 2024

    • RamanSPy

      Public
      RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis
      pythonartificial-intelligencedata-analysischemometricsanalytical-chemistryraman-spectroscopy
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •17•84•7•2•Updated Aug 14, 2024Aug 14, 2024

    • mfds-resources

      Public
      0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • LGDE

      Public
      Python code for the paper "LGDE: Local Graph-based Dictionary Expansion" by Dominik J Schindler, Sneha Jha, Xixuan Zhang, Kilian Buehling, Annett Heft and Mauricio Barahona: http://arxiv.org/abs/2405.07764
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • severability

      Public
      Code for the severability component quality function
      Python
      •
      GNU General Public License v2.0
      •1•2•3•1•Updated Jul 2, 2024Jul 2, 2024

    • PissaridesReview

      Public
      Pissarides Review webpage
      HTML
      •1•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • hcga

      Public
      Highly Comparative Graph Analysis - Code for network phenotyping
      feature-extractionnetworksclassification-algorithmgraph-embeddinggraph-featuresinterpretable-featuresgraph-analysis-toolbox
      Python
      •
      GNU General Public License v3.0
      •14•44•11•1•Updated Jun 4, 2024Jun 4, 2024

    • ICE-NODE

      Public
      Integration of Clinical Embeddings with Neural ODEs
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•10•0•1•Updated Jan 21, 2024Jan 21, 2024

    • dHSIC_ts

      Public
      Higher order interactions python package
      Python
      •1•1•0•0•Updated Nov 3, 2023Nov 3, 2023

    • streitberg-interaction

      Public
      Repository for 'Interaction Measures, Partition Lattices and Kernel Tests for High-Order Interactions'
      Python
      •
      GNU Affero General Public License v3.0
      •1•1•0•0•Updated Oct 26, 2023Oct 26, 2023

    • MultiscaleMobilityPatterns

      Public
      Code for the paper "Multiscale mobility patterns and the restriction of human movement" by Dominik J Schindler, Jonathan M Clarke and Mauricio Barahona: https://arxiv.org/abs/2201.06323
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 20, 2023Sep 20, 2023

    • scIHPF

      Public
      single-cell Integrative Hierarchical Poisson Factorisation
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Aug 25, 2023Aug 25, 2023

    • BayesFactorSimilarity

      Public
      Code for the paper "Similarity Measure for Sparse Time Course Data Based on Gaussian Processes" by Z Liu and M Barahona, accepted at UAI 2021, https://arxiv.org/abs/2102.12342
      time-series-analysisclustering-methods
      MATLAB
      •0•1•0•0•Updated Feb 3, 2023Feb 3, 2023

    • POPs

      Public
      POPs: Propensity Optimised Paths
      Python
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Jan 16, 2023Jan 16, 2023

    • DynGDim

      Public
      Dynamic Graph Dimensionality is a methodology for computing the relative, local and global dimension of complex networks.
      graphsmathsdimension
      Python
      •
      GNU General Public License v3.0
      •3•10•0•0•Updated Sep 15, 2021Sep 15, 2021

    • MultiscaleCentrality

      Public
      Graph centrality is a question of scale - Multiscale centrality (MSC) is a scale dependent measure of centrality on complex networks.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •8•7•1•0•Updated Jun 28, 2021Jun 28, 2021

    • RMST

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•1•2•0•Updated Jun 7, 2021Jun 7, 2021

    • StEP

      Public
      Contact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce linked networks of individuals based on a binary decision of contact which can be hampered by missing data and indirect contacts. Here, we present our Spatial-temporal Epidemiological Proximity (S…
      R
      •0•0•0•0•Updated Apr 10, 2021Apr 10, 2021

    • GDR

      Public
      Graph Diffusion Reclassification - Code from the paper "Semi-supervised classification on graphs using explicit diffusion dynamics" by RL Peach, A Arnaudon and M Barahona, Foundations of Data Science 2 (1), 19-33 (2020)
      Python
      •
      GNU General Public License v3.0
      •3•5•0•0•Updated Jan 10, 2021Jan 10, 2021

    • GraphBasedClustering

      Public
      Multiresolution clustering of data using geometric graphs --- Code from "Graph-based data clustering via multiscale community detection" by Z Liu and M Barahona, Applied Network Science, 5 (3) (2020). See also: https://wwwf.imperial.ac.uk/~mpbara/Partition_Stability/
      Common Lisp
      •
      GNU General Public License v3.0
      •4•4•0•0•Updated Mar 31, 2020Mar 31, 2020

    • Chemotaxis-In-Rugged-Landscapes

      Public
      Code for the paper: Gosztolai, A., Barahona, M. "Cellular memory enhances bacterial chemotactic navigation in rugged environments". Commun Phys 3, 47 (2020). https://doi.org/10.1038/s42005-020-0312-8 . The code allows the simulation of bacterial chemotaxis based on run-and-tumble motion in rugged chemoattractant landscapes.
      Mathematica
      •0•0•0•0•Updated Aug 12, 2019Aug 12, 2019

    • OptimalNavigation

      Public
      Code from the paper "Collective Search With Finite Perception: Transient Dynamics and Search Efficiency" (2019, Front. Phys., https://doi.org/10.3389/fphy.2018.00153). Computes the time evolution of the ON model of interacting random walkers optimising their diffusion on a landscape over a finite-horizon using optimal transport.
      MATLAB
      •0•0•0•0•Updated Aug 4, 2019Aug 4, 2019

    • Stationary-bounds-for-continuous-time-chains

      Public
      Code from the paper: "Bounding the stationary distributions of the chemical master equation via mathematical programming" J. Chem. Phys. 151, 034109 (2019); https://doi.org/10.1063/1.5100670
      MATLAB
      •0•0•0•0•Updated Jun 8, 2019Jun 8, 2019