Graph Clustering

Clustering (Hierarchical):

Example of Hierarchical Clustering

import pandas as pd
from bioneuralnet.clustering import HierarchicalClustering

def main():
    try:
        print("Starting Hierarchical Clustering Workflow...")
        adjacency_matrix = pd.DataFrame({
            'GeneA': [1.0, 0.8, 0.3, 0.2],
            'GeneB': [0.8, 1.0, 0.4, 0.3],
            'GeneC': [0.3, 0.4, 1.0, 0.5],
            'GeneD': [0.2, 0.3, 0.5, 1.0]
        }, index=['GeneA', 'GeneB', 'GeneC', 'GeneD'])

        hierarchical_clustering = HierarchicalClustering(
            adjacency_matrix=adjacency_matrix,
            n_clusters=2,
            linkage='ward',       
            affinity='euclidean',  
            scale_data=True        
        )

        clustering_results = hierarchical_clustering.run()

        print("\nCluster Labels:")
        print(clustering_results['cluster_labels'])

        silhouette_score = clustering_results['silhouette_score']
        if silhouette_score is not None:
            print(f"\nSilhouette Score: {silhouette_score:.4f}")
        else:
            print("\nSilhouette Score could not be computed.")

        print("\nHierarchical Clustering Workflow completed successfully.")

    except Exception as e:
        print(f"An error occurred during execution: {e}")
        raise e

if __name__ == "__main__":
    main()

Clustering (PageRank):

Example of PageRank Clustering

from bioneuralnet.clustering import PageRank

def main():
    pagerank_cluster = PageRank(
        graph_file='input/GFEV1ac110.edgelist',
        omics_data_file='input/X.xlsx',
        phenotype_data_file='input/Y.xlsx',
        alpha=0.9,
        max_iter=100,
        tol=1e-6,
        k=0.9,
    )

    seed_nodes = [94] 
    results = pagerank_cluster.run(seed_nodes=seed_nodes)
    cluster_nodes = results['cluster_nodes']
    print(f"Identified cluster with {len(cluster_nodes)} nodes.")

    # Save results
    results.to_csv('output/pagerank_results.csv')
    print("PageRank clustering results saved to 'output/pagerank_results.csv'.")

if __name__ == "__main__":
    main()