How would you speed up the calculation of a custom centrality measure?

graph-tool
1

Hi - I am trying to find a way to speed up a calculation of straightness centrality, defined here: Centrality Analysis. Betweenness, Closeness, Straightness… | by AxU Platform | Medium

It’s effectively the euclidean_distance (stored as node attributes) / network_dist

I tried using Dask to speed it up but it is still slow; would anyone have any reccomendations to use graph-tools to speed it up?

# def euclidean_dist(x1, y1, x2, y2):
#     return math.sqrt((x1 - x2)**2 + (y1 - y2)**2)

# def bravo(target, k, vertID_dict, network_dist):
#     euclidean_distance = euclidean_dist(vertID_dict[k][0], vertID_dict[k][1], vertID_dict[target][0], vertID_dict[target][1])
#     return euclidean_distance / network_dist

# for k in tqdm(ego_graphs_2000):
#     ego_graph = ego_graphs_2000[k]["graph"]
#     straightness = 0
#     sp = gt.shortest_distance(ego_graph, k, target=gt.shortest_distance weights=ego_graph.edge_properties["mm_len"])

#     if len(sp.get_array()) > 0 and len(G) > 1:
#         for target, value in enumerate(sp):
#             if k != target:
#                 network_dist = sp_scattered[target]
#                 straightness += bravo(target, k, vertID_dict, network_dist)
#         straightness_df[k] = straightness * (1.0 / (len(vertID_dict.keys()) - 1.0))
#     else:
#         straightness_df[k] = 0
2

Doesn’t the square root taking consume considerable time? I know for non-floating point unit computing, it can have an effect, but I don’t know how much it really takes with math.sqrt, it might be a good idea to test it. If you could do with only using distancesquareds instead of the distances (thus, not having to take squares), you could consider using them instead

3

Unfortunately, it’s not possible to provide a solution to your problem or an answer to your question with the information provided.

To enable us to understand the situation, you need to provide a minimal working example that shows the problem.

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You need to provide us a complete example that runs and reproduces the problem you are observing.