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Fix Leiden multi-pair null-model normalisation to match Louvain (#111) #115

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Fix Leiden multi-pair null-model normalisation to match Louvain (#111) #115

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4 changes: 2 additions & 2 deletions src/pygenstability/constructors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -298,8 +298,8 @@ def prepare(self, **kwargs):
adj_neg = -self.graph.copy()
adj_neg[self.graph > 0] = 0.0

deg_plus = adj_pos.sum(1).flatten()
deg_neg = adj_neg.sum(1).flatten()
deg_plus = np.asarray(adj_pos.sum(1)).flatten()
deg_neg = np.asarray(adj_neg.sum(1)).flatten()

deg_norm = deg_plus.sum() + deg_neg.sum()
# silence divide-by-zero when the graph has only positive or only negative edges
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9 changes: 7 additions & 2 deletions src/pygenstability/pygenstability.py
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Original file line number Diff line number Diff line change
Expand Up @@ -470,12 +470,15 @@ def _optimise(

partitions = []
n_null = int(len(null_model) / 2)
# The CPM null-model contribution is quadratic in node_sizes, so scaling by
# sqrt(n_null) makes each layer contribute n_null * pair_k; after Leiden's
# 1/n_null averaging below this yields sum_k pair_k, matching the Louvain backend.
for null in null_model[::2]:
partitions.append(
leidenalg.CPMVertexPartition(
G,
weights=quality_values,
node_sizes=null.tolist(),
node_sizes=(np.sqrt(n_null) * null).tolist(),
correct_self_loops=True,
)
)
Expand Down Expand Up @@ -517,13 +520,15 @@ def _evaluate_quality(
# evaluate using Leiden method
if method == "leiden":
n_null = int(len(null_model) / 2)
# Scale node_sizes by sqrt(n_null) so the quadratic CPM null term matches the
# Louvain backend once the 1/n_null averaging is applied (see _optimise).
quality = np.sum(
[
leidenalg.CPMVertexPartition(
ig.Graph(edges=zip(*quality_indices), directed=True),
initial_membership=partition_id,
weights=quality_values,
node_sizes=null.tolist(),
node_sizes=(np.sqrt(n_null) * null).tolist(),
correct_self_loops=True,
).quality()
for null in null_model[::2]
Expand Down
176 changes: 88 additions & 88 deletions tests/data/test_constructor_signed_modularity.yaml
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Original file line number Diff line number Diff line change
@@ -1,92 +1,92 @@
null_model:
- - - 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.053763440860215055
- 0.010752688172043012
- 0.010752688172043012
- 0.053763440860215055
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- - - 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.053763440860215055
- 0.010752688172043012
- 0.010752688172043012
- 0.053763440860215055
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- - - .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- - - 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- - 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.053763440860215055
- 0.010752688172043012
- 0.010752688172043012
- 0.053763440860215055
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- - 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.053763440860215055
- 0.010752688172043012
- 0.010752688172043012
- 0.053763440860215055
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- 0.04838709677419355
- - .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- .nan
- - 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
quality:
- - 0.0
- 0.005376344086021506
Expand Down
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