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Graph algorithms written in GraphBLAS
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python-graphblas/graphblas-algorithms
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graphblas-algorithms
is a collection of GraphBLAS algorithms written usingpython-graphblas
.It may be used directly or as an experimentalbackend to NetworkX.
Why use GraphBLAS Algorithms? Because it isfast,flexible, andfamiliar by using the NetworkX API.
Are we missing anyalgorithms that you want?Please let us know!
conda install -c conda-forge graphblas-algorithms
pip install graphblas-algorithms
First, create a GraphBLAS Matrix.
importgraphblasasgbM=gb.Matrix.from_coo( [0,0,1,2,2,3], [1,3,0,0,1,2], [1.,2.,3.,4.,5.,6.],nrows=4,ncols=4,dtype='float32')
Next wrap the Matrix asga.Graph
.
importgraphblas_algorithmsasgaG=ga.Graph(M)
Finally call an algorithm.
hubs,authorities=ga.hits(G)
When the result is a value per node, agb.Vector
will be returned.In the case ofHITS,two Vectors are returned representing the hubs and authorities values.
Algorithms whose result is a subgraph will returnga.Graph
.
Dispatching to plugins is a new feature in Networkx 3.0.When bothnetworkx
andgraphblas-algorithms
are installed in anenvironment, calls to NetworkX algorithms can be dispatched to theequivalent version ingraphblas-algorithms
.
importnetworkxasnximportgraphblas_algorithmsasga# Generate a random graph (5000 nodes, 1_000_000 edges)G=nx.erdos_renyi_graph(5000,0.08)# Explicitly convert to ga.GraphG2=ga.Graph.from_networkx(G)# Pass G2 to NetworkX's k_trussT5=nx.k_truss(G2,5)
G2
is not anx.Graph
, but it does have an attribute__networkx_plugin__ = "graphblas"
. This tells NetworkX todispatch the k_truss call to graphblas-algorithms. This linkconnection exists because graphblas-algorithms registersitself as a "networkx.plugin" entry point.
The resultT5
is aga.Graph
representing the 5-truss structure of theoriginal graph. To convert to a NetworkX Graph, use:
T5.to_networkx()
Note that even with the conversions to and fromga.Graph
, this example still runs 10xfaster than using the native NetworkX k-truss implementation. Speed improvements scalewith graph size, so larger graphs will see an even larger speed-up relative to NetworkX.
The following NetworkX algorithms have been implementedby graphblas-algorithms and can be used following thedispatch pattern shown above.
graphblas_algorithms.nxapi├── boundary│ ├── edge_boundary│ └── node_boundary├── centrality│ ├── degree_alg│ │ ├── degree_centrality│ │ ├── in_degree_centrality│ │ └── out_degree_centrality│ ├── eigenvector│ │ └── eigenvector_centrality│ └── katz│ └── katz_centrality├── cluster│ ├── average_clustering│ ├── clustering│ ├── generalized_degree│ ├── square_clustering│ ├── transitivity│ └── triangles├── community│ └── quality│ ├── inter_community_edges│ └── intra_community_edges├── components│ ├── connected│ │ ├── is_connected│ │ └── node_connected_component│ └── weakly_connected│ └── is_weakly_connected├── core│ └── k_truss├── cuts│ ├── boundary_expansion│ ├── conductance│ ├── cut_size│ ├── edge_expansion│ ├── mixing_expansion│ ├── node_expansion│ ├── normalized_cut_size│ └── volume├── dag│ ├── ancestors│ └── descendants├── dominating│ └── is_dominating_set├── efficiency_measures│ └── efficiency├── generators│ └── ego│ └── ego_graph├── isolate│ ├── is_isolate│ ├── isolates│ └── number_of_isolates├── isomorphism│ └── isomorph│ ├── fast_could_be_isomorphic│ └── faster_could_be_isomorphic├── linalg│ ├── bethehessianmatrix│ │ └── bethe_hessian_matrix│ ├── graphmatrix│ │ └── adjacency_matrix│ ├── laplacianmatrix│ │ ├── laplacian_matrix│ │ └── normalized_laplacian_matrix│ └── modularitymatrix│ ├── directed_modularity_matrix│ └── modularity_matrix├── link_analysis│ ├── hits_alg│ │ └── hits│ └── pagerank_alg│ ├── google_matrix│ └── pagerank├── lowest_common_ancestors│ └── lowest_common_ancestor├── operators│ ├── binary│ │ ├── compose│ │ ├── difference│ │ ├── disjoint_union│ │ ├── full_join│ │ ├── intersection│ │ ├── symmetric_difference│ │ └── union│ └── unary│ ├── complement│ └── reverse├── reciprocity│ ├── overall_reciprocity│ └── reciprocity├── regular│ ├── is_k_regular│ └── is_regular├── shortest_paths│ ├── dense│ │ ├── floyd_warshall│ │ ├── floyd_warshall_numpy│ │ └── floyd_warshall_predecessor_and_distance│ ├── generic│ │ └── has_path│ ├── unweighted│ │ ├── all_pairs_shortest_path_length│ │ ├── single_source_shortest_path_length│ │ └── single_target_shortest_path_length│ └── weighted│ ├── all_pairs_bellman_ford_path_length│ ├── bellman_ford_path│ ├── bellman_ford_path_length│ ├── negative_edge_cycle│ └── single_source_bellman_ford_path_length├── simple_paths│ └── is_simple_path├── smetric│ └── s_metric├── structuralholes│ └── mutual_weight├── tournament│ ├── is_tournament│ ├── score_sequence│ └── tournament_matrix├── traversal│ └── breadth_first_search│ ├── bfs_layers│ └── descendants_at_distance└── triads └── is_triad
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