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BioNeuralNet 1.3.1 documentation
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BioNeuralNet 1.3.1 documentation

Contents:

  • Installation
  • Quick Start
    • Quick Start Guide
    • Quick Start for Biologists
    • Data Decision Framework
  • Notebooks
    • TCGA-BRCA - PAM50 Cancer Subtype Classification
    • TCGA-LGG (Lower Grade Glioma) - Binary Survival Prediction
    • TCGA-KIPAN - Binary Cancer Staging
    • ROSMAP (Alzheimer’s Disease) Biomarker Discovery
  • GNN Embeddings
  • Subgraph Detection & Biomarkers
  • Metrics and Visualization
  • Utils
  • Network Construction & Analysis
  • Downstream Tasks
  • Datasets Guide
  • More Examples
    • Example 1: SmCCNet + DPMON for Disease Prediction
    • Example 2: SmCCNet + GNN Embeddings + Subject Representation
  • External Tools
  • User API
    • bioneuralnet
      • bioneuralnet.clustering
        • bioneuralnet.clustering.correlated_louvain
        • bioneuralnet.clustering.correlated_pagerank
        • bioneuralnet.clustering.hybrid_louvain
        • bioneuralnet.clustering.louvain
      • bioneuralnet.datasets
        • bioneuralnet.datasets.dataset_loader
      • bioneuralnet.downstream_task
        • bioneuralnet.downstream_task.dpmon
        • bioneuralnet.downstream_task.subject_representation
      • bioneuralnet.external_tools
        • bioneuralnet.external_tools.extract_CVfold
      • bioneuralnet.metrics
        • bioneuralnet.metrics.correlation
        • bioneuralnet.metrics.plot
      • bioneuralnet.network
        • bioneuralnet.network.generate
        • bioneuralnet.network.pysmccnet
          • bioneuralnet.network.pysmccnet.analysis
          • bioneuralnet.network.pysmccnet.core
          • bioneuralnet.network.pysmccnet.math_helpers
          • bioneuralnet.network.pysmccnet.pipeline
          • bioneuralnet.network.pysmccnet.wrappers
        • bioneuralnet.network.tools
      • bioneuralnet.network_embedding
        • bioneuralnet.network_embedding.gnn_embedding
        • bioneuralnet.network_embedding.gnn_models
      • bioneuralnet.utils
        • bioneuralnet.utils.data
        • bioneuralnet.utils.feature_selection
        • bioneuralnet.utils.logger
        • bioneuralnet.utils.preprocess
        • bioneuralnet.utils.reproducibility
  • Acknowledgments
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