risk-network 0.0.8b27__py3-none-any.whl → 0.0.9__py3-none-any.whl

risk/neighborhoods/community.py

@@ -4,186 +4,409 @@ risk/neighborhoods/community
 """
 
 import community as community_louvain
+import igraph as ig
+import markov_clustering as mc
 import networkx as nx
 import numpy as np
-import markov_clustering as mc
-from networkx.algorithms.community import asyn_lpa_communities, greedy_modularity_communities
+from leidenalg import find_partition, RBConfigurationVertexPartition
+from networkx.algorithms.community import greedy_modularity_communities
+from scipy.sparse import csr_matrix
+
+from risk.log import logger
 
 
-def calculate_greedy_modularity_neighborhoods(network: nx.Graph) -> np.ndarray:
-    """Calculate neighborhoods using the Greedy Modularity method.
+def calculate_greedy_modularity_neighborhoods(
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
+) -> csr_matrix:
+    """Calculate neighborhoods using the Greedy Modularity method with CSR matrix output.
 
     Args:
-        network (nx.Graph): The network graph to analyze for community structure.
+        network (nx.Graph): The network graph.
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
+            subgraphs before clustering. Defaults to 1.0.
 
     Returns:
-        np.ndarray: A binary neighborhood matrix where nodes in the same community have 1, and others have 0.
+        csr_matrix: A binary neighborhood matrix (CSR) where nodes in the same community have 1, and others have 0.
     """
+    # Create a subgraph with the shortest edges based on the rank fraction
+    subnetwork = _create_percentile_limited_subgraph(
+        network, fraction_shortest_edges=fraction_shortest_edges
+    )
     # Detect communities using the Greedy Modularity method
-    communities = greedy_modularity_communities(network)
-    # Create a binary neighborhood matrix
-    n_nodes = network.number_of_nodes()
-    neighborhoods = np.zeros((n_nodes, n_nodes), dtype=int)
-    # Create a mapping from node to index in the matrix
-    node_index = {node: i for i, node in enumerate(network.nodes())}
-    # Fill in the neighborhood matrix for nodes in the same community
+    communities = greedy_modularity_communities(subnetwork)
+    # Get the list of nodes in the original NetworkX graph
+    nodes = list(network.nodes())
+    node_index_map = {node: idx for idx, node in enumerate(nodes)}
+    # Prepare data for CSR matrix
+    row_indices = []
+    col_indices = []
     for community in communities:
-        # Iterate through all pairs of nodes in the same community
-        for node_i in community:
-            idx_i = node_index[node_i]
-            for node_j in community:
-                idx_j = node_index[node_j]
-                # Set them as neighbors (1) in the binary matrix
-                neighborhoods[idx_i, idx_j] = 1
+        mapped_indices = [node_index_map[node] for node in community]
+        for i in mapped_indices:
+            for j in mapped_indices:
+                row_indices.append(i)
+                col_indices.append(j)
+
+    # Create a CSR matrix
+    num_nodes = len(nodes)
+    data = np.ones(len(row_indices), dtype=int)
+    neighborhoods = csr_matrix((data, (row_indices, col_indices)), shape=(num_nodes, num_nodes))
 
     return neighborhoods
 
 
-def calculate_label_propagation_neighborhoods(network: nx.Graph) -> np.ndarray:
+def calculate_label_propagation_neighborhoods(
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
+) -> csr_matrix:
     """Apply Label Propagation to the network to detect communities.
 
     Args:
         network (nx.Graph): The network graph.
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
+            subgraphs before clustering. Defaults to 1.0.
 
     Returns:
-        np.ndarray: Binary neighborhood matrix on Label Propagation.
+        csr_matrix: A binary neighborhood matrix (CSR) on Label Propagation.
     """
+    # Create a subgraph with the shortest edges based on the rank fraction
+    subnetwork = _create_percentile_limited_subgraph(
+        network, fraction_shortest_edges=fraction_shortest_edges
+    )
     # Apply Label Propagation for community detection
-    communities = nx.algorithms.community.label_propagation.label_propagation_communities(network)
-    # Create a binary neighborhood matrix
-    num_nodes = network.number_of_nodes()
-    neighborhoods = np.zeros((num_nodes, num_nodes), dtype=int)
-    # Create a mapping from node to index in the matrix
-    node_index = {node: i for i, node in enumerate(network.nodes())}
-    # Assign neighborhoods based on community labels
+    communities = nx.algorithms.community.label_propagation.label_propagation_communities(
+        subnetwork
+    )
+    # Get the list of nodes in the network
+    nodes = list(network.nodes())
+    node_index_map = {node: idx for idx, node in enumerate(nodes)}
+    # Prepare data for CSR matrix
+    row_indices = []
+    col_indices = []
+    # Assign neighborhoods based on community labels using the mapped indices
     for community in communities:
-        for node_i in community:
-            idx_i = node_index[node_i]
-            for node_j in community:
-                idx_j = node_index[node_j]
-                neighborhoods[idx_i, idx_j] = 1
+        mapped_indices = [node_index_map[node] for node in community]
+        for i in mapped_indices:
+            for j in mapped_indices:
+                row_indices.append(i)
+                col_indices.append(j)
+
+    # Create a CSR matrix
+    num_nodes = len(nodes)
+    data = np.ones(len(row_indices), dtype=int)
+    neighborhoods = csr_matrix((data, (row_indices, col_indices)), shape=(num_nodes, num_nodes))
+
+    return neighborhoods
+
+
+def calculate_leiden_neighborhoods(
+    network: nx.Graph,
+    resolution: float = 1.0,
+    fraction_shortest_edges: float = 1.0,
+    random_seed: int = 888,
+) -> csr_matrix:
+    """Calculate neighborhoods using the Leiden method with CSR matrix output.
+
+    Args:
+        network (nx.Graph): The network graph.
+        resolution (float, optional): Resolution parameter for the Leiden method. Defaults to 1.0.
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
+            subgraphs before clustering. Defaults to 1.0.
+        random_seed (int, optional): Random seed for reproducibility. Defaults to 888.
+
+    Returns:
+        csr_matrix: A binary neighborhood matrix (CSR) where nodes in the same community have 1, and others have 0.
+    """
+    # Create a subgraph with the shortest edges based on the rank fraction
+    subnetwork = _create_percentile_limited_subgraph(
+        network, fraction_shortest_edges=fraction_shortest_edges
+    )
+    # Convert NetworkX graph to iGraph
+    igraph_network = ig.Graph.from_networkx(subnetwork)
+    # Apply Leiden algorithm using RBConfigurationVertexPartition, which supports resolution
+    partition = find_partition(
+        igraph_network,
+        partition_type=RBConfigurationVertexPartition,
+        resolution_parameter=resolution,
+        seed=random_seed,
+    )
+    # Get the list of nodes in the original NetworkX graph
+    nodes = list(network.nodes())
+    node_index_map = {node: idx for idx, node in enumerate(nodes)}
+    # Prepare data for CSR matrix
+    row_indices = []
+    col_indices = []
+    for community in partition:
+        mapped_indices = [node_index_map[igraph_network.vs[node]["_nx_name"]] for node in community]
+        for i in mapped_indices:
+            for j in mapped_indices:
+                row_indices.append(i)
+                col_indices.append(j)
+
+    # Create a CSR matrix
+    num_nodes = len(nodes)
+    data = np.ones(len(row_indices), dtype=int)
+    neighborhoods = csr_matrix((data, (row_indices, col_indices)), shape=(num_nodes, num_nodes))
 
     return neighborhoods
 
 
 def calculate_louvain_neighborhoods(
-    network: nx.Graph, resolution: float, random_seed: int = 888
-) -> np.ndarray:
+    network: nx.Graph,
+    resolution: float = 0.1,
+    fraction_shortest_edges: float = 1.0,
+    random_seed: int = 888,
+) -> csr_matrix:
     """Calculate neighborhoods using the Louvain method.
 
     Args:
         network (nx.Graph): The network graph.
-        resolution (float): Resolution parameter for the Louvain method.
+        resolution (float, optional): Resolution parameter for the Louvain method. Defaults to 0.1.
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
+            subgraphs before clustering. Defaults to 1.0.
         random_seed (int, optional): Random seed for reproducibility. Defaults to 888.
 
     Returns:
-        np.ndarray: Binary neighborhood matrix on the Louvain method.
+        csr_matrix: A binary neighborhood matrix in CSR format.
     """
+    # Create a subgraph with the shortest edges based on the rank fraction
+    subnetwork = _create_percentile_limited_subgraph(
+        network, fraction_shortest_edges=fraction_shortest_edges
+    )
     # Apply Louvain method to partition the network
     partition = community_louvain.best_partition(
-        network, resolution=resolution, random_state=random_seed
+        subnetwork, resolution=resolution, random_state=random_seed
     )
-    # Create a binary neighborhood matrix
-    num_nodes = network.number_of_nodes()
-    neighborhoods = np.zeros((num_nodes, num_nodes), dtype=int)
-    # Create a mapping from node to index in the matrix
-    node_index = {node: i for i, node in enumerate(network.nodes())}
+    # Get the list of nodes in the network and create a mapping to indices
+    nodes = list(network.nodes())
+    node_index_map = {node: idx for idx, node in enumerate(nodes)}
     # Group nodes by community
     community_groups = {}
     for node, community in partition.items():
         community_groups.setdefault(community, []).append(node)
 
-    # Assign neighborhoods based on community partitions
-    for community, nodes in community_groups.items():
-        for node_i in nodes:
-            idx_i = node_index[node_i]
-            for node_j in nodes:
-                idx_j = node_index[node_j]
-                neighborhoods[idx_i, idx_j] = 1
+    # Prepare data for CSR matrix
+    row_indices = []
+    col_indices = []
+    for community_nodes in community_groups.values():
+        mapped_indices = [node_index_map[node] for node in community_nodes]
+        for i in mapped_indices:
+            for j in mapped_indices:
+                row_indices.append(i)
+                col_indices.append(j)
+
+    # Create a CSR matrix
+    num_nodes = len(nodes)
+    data = np.ones(len(row_indices), dtype=int)
+    neighborhoods = csr_matrix((data, (row_indices, col_indices)), shape=(num_nodes, num_nodes))
 
     return neighborhoods
 
 
-def calculate_markov_clustering_neighborhoods(network: nx.Graph) -> np.ndarray:
-    """Apply Markov Clustering (MCL) to the network.
+def calculate_markov_clustering_neighborhoods(
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
+) -> csr_matrix:
+    """Apply Markov Clustering (MCL) to the network and return a binary neighborhood matrix (CSR).
 
     Args:
         network (nx.Graph): The network graph.
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
+            subgraphs before clustering. Defaults to 1.0.
 
     Returns:
-        np.ndarray: Binary neighborhood matrix on Markov Clustering.
+        csr_matrix: A binary neighborhood matrix (CSR) on Markov Clustering.
+
+    Warning:
+        This function temporarily converts the adjacency matrix to a dense format, which may lead to
+        high memory consumption for large graphs.
     """
-    # Convert the graph to an adjacency matrix
-    adjacency_matrix = nx.to_numpy_array(network)
-    # Run Markov Clustering (MCL)
-    result = mc.run_mcl(adjacency_matrix)  # MCL with default parameters
-    # Get clusters (communities) from MCL result
+    # Create a subgraph with the shortest edges based on the rank fraction
+    subnetwork = _create_percentile_limited_subgraph(
+        network, fraction_shortest_edges=fraction_shortest_edges
+    )
+    # Check if the subgraph has edges
+    if subnetwork.number_of_edges() == 0:
+        raise ValueError("The subgraph has no edges. Adjust the fraction_shortest_edges parameter.")
+
+    # Step 1: Convert the subnetwork to an adjacency matrix (CSR)
+    subnetwork_nodes = list(subnetwork.nodes())
+    adjacency_matrix = nx.to_scipy_sparse_array(subnetwork, nodelist=subnetwork_nodes)
+    # Ensure the adjacency matrix is valid
+    if adjacency_matrix.shape[0] == 0 or adjacency_matrix.shape[1] == 0:
+        raise ValueError(
+            "The adjacency matrix is empty. Check the input graph or filtering criteria."
+        )
+
+    # Convert the sparse matrix to dense format for MCL
+    dense_matrix = adjacency_matrix.toarray()
+    # Step 2: Run Markov Clustering (MCL) on the dense adjacency matrix
+    try:
+        result = mc.run_mcl(dense_matrix)
+    except Exception as e:
+        raise RuntimeError(f"Markov Clustering failed: {e}")
+
     clusters = mc.get_clusters(result)
-    # Create a binary neighborhood matrix
-    num_nodes = network.number_of_nodes()
-    neighborhoods = np.zeros((num_nodes, num_nodes), dtype=int)
-    # Create a mapping from node to index in the matrix
-    node_index = {node: i for i, node in enumerate(network.nodes())}
-    # Assign neighborhoods based on MCL clusters
+    # Step 3: Prepare the original network nodes and indices
+    nodes = list(network.nodes())
+    node_index_map = {node: idx for idx, node in enumerate(nodes)}
+    num_nodes = len(nodes)
+    # Step 4: Prepare data for CSR matrix
+    row_indices = []
+    col_indices = []
     for cluster in clusters:
         for node_i in cluster:
-            idx_i = node_index[node_i]
             for node_j in cluster:
-                idx_j = node_index[node_j]
-                neighborhoods[idx_i, idx_j] = 1
+                # Map the indices back to the original network's node indices
+                original_node_i = subnetwork_nodes[node_i]
+                original_node_j = subnetwork_nodes[node_j]
+                if original_node_i in node_index_map and original_node_j in node_index_map:
+                    idx_i = node_index_map[original_node_i]
+                    idx_j = node_index_map[original_node_j]
+                    row_indices.append(idx_i)
+                    col_indices.append(idx_j)
+
+    # Step 5: Create a CSR matrix
+    data = np.ones(len(row_indices), dtype=int)
+    neighborhoods = csr_matrix((data, (row_indices, col_indices)), shape=(num_nodes, num_nodes))
 
     return neighborhoods
 
 
-def calculate_spinglass_neighborhoods(network: nx.Graph) -> np.ndarray:
-    """Apply Spin Glass Community Detection to the network.
+def calculate_spinglass_neighborhoods(
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
+) -> csr_matrix:
+    """Apply Spinglass Community Detection to the network, handling disconnected components.
 
     Args:
         network (nx.Graph): The network graph.
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
+            subgraphs before clustering. Defaults to 1.0.
 
     Returns:
-        np.ndarray: Binary neighborhood matrix on Spin Glass communities.
+        csr_matrix: A binary neighborhood matrix (CSR) based on Spinglass communities.
     """
-    # Apply Asynchronous Label Propagation (LPA)
-    communities = asyn_lpa_communities(network)
-    # Create a binary neighborhood matrix
-    num_nodes = network.number_of_nodes()
-    neighborhoods = np.zeros((num_nodes, num_nodes), dtype=int)
-    # Create a mapping from node to index in the matrix
-    node_index = {node: i for i, node in enumerate(network.nodes())}
-    # Assign neighborhoods based on community labels from LPA
-    for community in communities:
-        for node_i in community:
-            idx_i = node_index[node_i]
-            for node_j in community:
-                idx_j = node_index[node_j]
-                neighborhoods[idx_i, idx_j] = 1
+    # Create a subgraph with the shortest edges based on the rank fraction
+    subnetwork = _create_percentile_limited_subgraph(
+        network, fraction_shortest_edges=fraction_shortest_edges
+    )
+    # Step 1: Find connected components in the graph
+    components = list(nx.connected_components(subnetwork))
+    # Prepare data for CSR matrix
+    nodes = list(network.nodes())
+    node_index_map = {node: idx for idx, node in enumerate(nodes)}
+    row_indices = []
+    col_indices = []
+    # Step 2: Run Spinglass on each connected component
+    for component in components:
+        # Extract the subgraph corresponding to the current component
+        subgraph = network.subgraph(component)
+        # Convert the subgraph to an iGraph object
+        igraph_subgraph = ig.Graph.from_networkx(subgraph)
+        # Ensure the subgraph is connected before running Spinglass
+        if not igraph_subgraph.is_connected():
+            logger.error("Warning: Subgraph is not connected. Skipping...")
+            continue
+
+        # Apply Spinglass community detection
+        try:
+            communities = igraph_subgraph.community_spinglass()
+        except Exception as e:
+            logger.error(f"Error running Spinglass on component: {e}")
+            continue
+
+        # Step 3: Assign neighborhoods based on community labels
+        for community in communities:
+            mapped_indices = [
+                node_index_map[igraph_subgraph.vs[node]["_nx_name"]] for node in community
+            ]
+            for i in mapped_indices:
+                for j in mapped_indices:
+                    row_indices.append(i)
+                    col_indices.append(j)
+
+    # Step 4: Create a CSR matrix
+    num_nodes = len(nodes)
+    data = np.ones(len(row_indices), dtype=int)
+    neighborhoods = csr_matrix((data, (row_indices, col_indices)), shape=(num_nodes, num_nodes))
 
     return neighborhoods
 
 
-def calculate_walktrap_neighborhoods(network: nx.Graph) -> np.ndarray:
-    """Apply Walktrap Community Detection to the network.
+def calculate_walktrap_neighborhoods(
+    network: nx.Graph, fraction_shortest_edges: float = 1.0
+) -> csr_matrix:
+    """Apply Walktrap Community Detection to the network with CSR matrix output.
 
     Args:
         network (nx.Graph): The network graph.
+        fraction_shortest_edges (float, optional): Shortest edge rank fraction threshold for creating
+            subgraphs before clustering. Defaults to 1.0.
 
     Returns:
-        np.ndarray: Binary neighborhood matrix on Walktrap communities.
+        csr_matrix: A binary neighborhood matrix (CSR) on Walktrap communities.
     """
-    # Apply Asynchronous Label Propagation (LPA)
-    communities = asyn_lpa_communities(network)
-    # Create a binary neighborhood matrix
-    num_nodes = network.number_of_nodes()
-    neighborhoods = np.zeros((num_nodes, num_nodes), dtype=int)
-    # Create a mapping from node to index in the matrix
-    node_index = {node: i for i, node in enumerate(network.nodes())}
-    # Assign neighborhoods based on community labels from LPA
+    # Create a subgraph with the shortest edges based on the rank fraction
+    subnetwork = _create_percentile_limited_subgraph(
+        network, fraction_shortest_edges=fraction_shortest_edges
+    )
+    # Convert NetworkX graph to iGraph
+    igraph_network = ig.Graph.from_networkx(subnetwork)
+    # Apply Walktrap community detection
+    communities = igraph_network.community_walktrap().as_clustering()
+    # Get the list of nodes in the original NetworkX graph
+    nodes = list(network.nodes())
+    node_index_map = {node: idx for idx, node in enumerate(nodes)}
+    # Prepare data for CSR matrix
+    row_indices = []
+    col_indices = []
     for community in communities:
-        for node_i in community:
-            idx_i = node_index[node_i]
-            for node_j in community:
-                idx_j = node_index[node_j]
-                neighborhoods[idx_i, idx_j] = 1
+        mapped_indices = [node_index_map[igraph_network.vs[node]["_nx_name"]] for node in community]
+        for i in mapped_indices:
+            for j in mapped_indices:
+                row_indices.append(i)
+                col_indices.append(j)
+
+    # Create a CSR matrix
+    num_nodes = len(nodes)
+    data = np.ones(len(row_indices), dtype=int)
+    neighborhoods = csr_matrix((data, (row_indices, col_indices)), shape=(num_nodes, num_nodes))
 
     return neighborhoods
+
+
+def _create_percentile_limited_subgraph(G: nx.Graph, fraction_shortest_edges: float) -> nx.Graph:
+    """Create a subgraph containing the shortest edges based on the specified rank fraction
+    of all edge lengths in the input graph.
+
+    Args:
+        G (nx.Graph): The input graph with 'length' attributes on edges.
+        fraction_shortest_edges (float): The rank fraction (between 0 and 1) to filter edges.
+
+    Returns:
+        nx.Graph: A subgraph with nodes and edges where the edges are within the shortest
+        specified rank fraction.
+    """
+    # Step 1: Extract edges with their lengths
+    edges_with_length = [(u, v, d) for u, v, d in G.edges(data=True) if "length" in d]
+    if not edges_with_length:
+        raise ValueError(
+            "No edge lengths found in the graph. Ensure edges have 'length' attributes."
+        )
+
+    # Step 2: Sort edges by length in ascending order
+    edges_with_length.sort(key=lambda x: x[2]["length"])
+    # Step 3: Calculate the cutoff index for the given rank fraction
+    cutoff_index = int(fraction_shortest_edges * len(edges_with_length))
+    if cutoff_index == 0:
+        raise ValueError("The rank fraction is too low, resulting in no edges being included.")
+
+    # Step 4: Create the subgraph by selecting only the shortest edges within the rank fraction
+    subgraph = nx.Graph()
+    subgraph.add_nodes_from(G.nodes(data=True))  # Retain all nodes from the original graph
+    subgraph.add_edges_from(edges_with_length[:cutoff_index])
+    # Step 5: Remove nodes with no edges
+    subgraph.remove_nodes_from(list(nx.isolates(subgraph)))
+    # Step 6: Check if the resulting subgraph has no edges and issue a warning
+    if subgraph.number_of_edges() == 0:
+        raise Warning("The resulting subgraph has no edges. Consider adjusting the rank fraction.")
+
+    return subgraph