8000 DOC Update biclustering documentation to point to used scipy algorith… · scikit-learn/scikit-learn@1fd6ca9 · GitHub
[go: up one dir, main page]
Skip to content

Commit 1fd6ca9

Browse files
notPlanchanotPlancha
authored
DOC Update biclustering documentation to point to used scipy algorithm (#29371)
1 parent 79afe99 commit 1fd6ca9

File tree

2 files changed

+10
-5
lines changed

2 files changed

+10
-5
lines changed

‎doc/modules/biclustering.rst

+3-2
Original file line numberDiff line numberDiff line change
@@ -288,7 +288,8 @@ available:
288288

289289
2. Assign biclusters from one set to another in a one-to-one fashion
290290
to maximize the sum of their similarities. This step is performed
291-
using the Hungarian algorithm.
291+
using :func:`scipy.optimize.linear_sum_assignment`, which uses a
292+
modified Jonker-Volgenant algorithm.
292293

293294
3. The final sum of similarities is divided by the size of the larger
294295
set.
@@ -302,4 +303,4 @@ are identical.
302303

303304
* Hochreiter, Bodenhofer, et. al., 2010. `FABIA: factor analysis
304305
for bicluster acquisition
305-
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881408/>`__.
306+
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881408/>`__.

‎sklearn/metrics/cluster/_bicluster.py

+7-3
Original file line numberDiff line numberDiff line change
@@ -57,8 +57,9 @@ def _pairwise_similarity(a, b, similarity):
5757
def consensus_score(a, b, *, similarity="jaccard"):
5858
"""The similarity of two sets of biclusters.
5959
60-
Similarity between individual biclusters is computed. Then the
61-
best matching between sets is found using the Hungarian algorithm.
60+
Similarity between individual biclusters is computed. Then the best
61+
matching between sets is found by solving a linear sum assignment problem,
62+
using a modified Jonker-Volgenant algorithm.
6263
The final score is the sum of similarities divided by the size of
6364
the larger set.
6465
@@ -83,9 +84,12 @@ def consensus_score(a, b, *, similarity="jaccard"):
8384
Consensus score, a non-negative value, sum of similarities
8485
divided by size of larger set.
8586
87+
See Also
88+
--------
89+
scipy.optimize.linear_sum_assignment : Solve the linear sum assignment problem.
90+
8691
References
8792
----------
88-
8993
* Hochreiter, Bodenhofer, et. al., 2010. `FABIA: factor analysis
9094
for bicluster acquisition
9195
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881408/>`__.

0 commit comments

Comments
 (0)
0