Comments (6)
Hi! Thanks for the details. Would you be able to produce a minimal code example which illustrates the issue?
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Hi!, Yes I can. The code example is below. Thanks.
Define filter function
filter_func = umap.UMAP(n_neighbors=5)
Define cover
cover = CubicalCover(kind='balanced', n_intervals=10, overlap_frac=0.2)
#cover = CubicalCover(n_intervals=10, overlap_frac=0.2)
Choose clustering algorithm
clusterer = DBSCAN(eps=10)
Initialise pipeline
pipe = make_mapper_pipeline(
filter_func=filter_func,
cover=cover,
clusterer=clusterer,
verbose=True,
n_jobs=-1,
)
Plot Mapper graph where df_refined is a Pandas dataframe
fig = plot_static_mapper_graph(pipe, df_refined, color_data = df_refined)
fig.show(config={'scrollZoom': True})
#Node_elements from attributes.
graph = pipe.fit_transform(df_refined)
node_elements = graph.vs["node_elements"]
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When I hover over the nodes in the plot_static_mapper graph and match the same node in the node_elements, the node sizes are different. Thanks
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Thanks @jnukpezah! I can reproduce using the example provided.
The issue does not seem to come from giotto-tda
but rather from UMAP
. Indeed, the UMAP
class constructor has a random_state
parameter, which is by default set to None
, meaning that a "random random seed" is generated every time fit
is called. Thus, running the UMAP
part of the Mapper pipeline gives different results every time.
To have a fully reproducible pipeline, and solve your issue, set random_state
in UMAP
to some integer value of your choice.
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Hi @ulupo Got it! Thanks for the insight. Will do so! Great library btw!
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Great! Happy to help!
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