8000 Enable dice metric for UMAP and pairwise_distances by aamijar · Pull Request #6842 · rapidsai/cuml · GitHub
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Enable dice metric for UMAP and pairwise_distances #6842

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Enable dice metric for UMAP and pairwise_distances #6842

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612b2e3
init umap-dice-coefficient-update
aamijar Jun 3, 2025
73bfd05
Merge branch 'branch-25.08' into umap-dice-coefficient-update
aamijar Jun 3, 2025
3218954
add dice to pairwise_distances
aamijar Jun 4, 2025
2e67aaf
Merge branch 'branch-25.08' into umap-dice-coefficient-update
aamijar Jun 4, 2025
617760a
test ci with local cuvs
aamijar Jun 4, 2025
ffb5ff2
merge
aamijar Jun 4, 2025
4ccc848
Merge branch 'branch-25.08' into umap-dice-coefficient-update
aamijar Jun 4, 2025
d182930
test ci
aamijar Jun 4, 2025
3321fbf
test ci
aamijar Jun 4, 2025
f54ff1b
test ci
aamijar Jun 4, 2025
dc63226
Merge branch 'branch-25.08' into umap-dice-coefficient-update
aamijar Jun 4, 2025
e44e9c4
test ci
aamijar Jun 4, 2025
4f0191b
test ci
aamijar Jun 4, 2025
8551d19
test ci
aamijar Jun 6, 2025
c313bd4
Merge branch 'branch-25.08' into umap-dice-coefficient-update
aamijar Jun 6, 2025
99d3659
fix ci
aamijar Jun 12, 2025
c10d8f1
pin cuvs
aamijar Jun 12, 2025
f0c70ae
Merge branch 'branch-25.08' into umap-dice-coefficient-update
aamijar Jun 12, 2025
18d8640
rerun CI
aamijar Jun 12, 2025
ab4c7a4
Merge branch 'branch-25.08' into umap-dice-coefficient-update
aamijar Jun 13, 2025
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4 changes: 2 additions & 2 deletions cpp/cmake/thirdparty/get_cuvs.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,8 @@ endfunction()
# To use a different CUVS locally, set the CMake variable
# CPM_cuvs_SOURCE=/path/to/local/cuvs
find_and_configure_cuvs(VERSION ${CUML_MIN_VERSION_cuvs}
FORK rapidsai
PINNED_TAG branch-${CUML_BRANCH_VERSION_cuvs}
FORK aamijar
PINNED_TAG umap-dice-coefficient
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EXCLUDE_FROM_ALL ${CUML_EXCLUDE_CUVS_FROM_ALL}
# When PINNED_TAG above doesn't match cuml,
# force local cuvs clone in build directory
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5 changes: 4 additions & 1 deletion python/cuml/cuml/manifold/umap_utils.pyx
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Expand Up @@ -147,7 +147,8 @@ _METRICS = {
"hellinger": DistanceType.HellingerExpanded,
"hamming": DistanceType.HammingUnexpanded,
"jaccard": DistanceType.JaccardExpanded,
"canberra": DistanceType.Canberra
"canberra": DistanceType.Canberra,
"dice": DistanceType.DiceExpanded,
}

_SUPPORTED_METRICS = {
Expand All @@ -168,6 +169,7 @@ _SUPPORTED_METRICS = {
DistanceType.L2Expanded,
DistanceType.Linf,
DistanceType.LpUnexpanded,
DistanceType.DiceExpanded,
)),
"dense": frozenset((
DistanceType.Canberra,
Expand All @@ -181,6 +183,7 @@ _SUPPORTED_METRICS = {
DistanceType.L2Expanded,
DistanceType.Linf,
DistanceType.LpUnexpanded,
DistanceType.DiceExpanded,
))
}
}
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7 changes: 4 additions & 3 deletions python/cuml/cuml/metrics/pairwise_distances.pyx
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Expand Up @@ -82,7 +82,8 @@ PAIRWISE_DISTANCE_METRICS = {
"hamming": DistanceType.HammingUnexpanded,
"kldivergence": DistanceType.KLDivergence,
"russellrao": DistanceType.RusselRaoExpanded,
"nan_euclidean": DistanceType.L2Expanded
"nan_euclidean": DistanceType.L2Expanded,
"dice": DistanceType.DiceExpanded
}

PAIRWISE_DISTANCE_SPARSE_METRICS = {
Expand Down Expand Up @@ -350,7 +351,7 @@ def pairwise_distances(X, Y=None, metric="euclidean", handle=None,
if metric in ['nan_euclidean']:
return nan_euclidean_distances(X, Y, **kwds)

if metric in ['russellrao'] and not np.all(X.data == 1.):
if metric in ['russellrao', 'dice'] and not np.all(X.data == 1.):
warnings.warn("X was converted to boolean for metric {}"
.format(metric))
X = np.where(X != 0., 1.0, 0.0)
Expand All @@ -377,7 +378,7 @@ def pairwise_distances(X, Y=None, metric="euclidean", handle=None,
if (n_samples_x == 1 or n_features_x == 1):
input_order = "K"

if metric in ['russellrao'] and not np.all(Y.data == 1.):
if metric in ['russellrao', 'dice'] and not np.all(Y.data == 1.):
warnings.warn("Y was converted to boolean for metric {}"
.format(metric))
Y = np.where(Y != 0., 1.0, 0.0)
Expand Down
2 changes: 2 additions & 0 deletions python/cuml/cuml/tests/test_umap.py
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< 7B98 td id="diff-75f3a48b4080eb063594a8c29961c09a4ad9110e6bf7eeb3d622781c03d6a8d5L699" data-line-number="699" class="blob-num blob-num-context js-linkable-line-number">
Original file line number Diff line number Diff line change
Expand Up @@ -699,6 +699,7 @@ def test_fuzzy_simplicial_set(n_rows, n_features, n_neighbors):
@pytest.mark.parametrize(
"metric,build_algo,supported",
[
("dice", "brute_force_knn", True),
("l2", "brute_force_knn", True),
("euclidean", "brute_force_knn", True),
("sqeuclidean", "brute_force_knn", True),
Expand Down Expand Up @@ -767,6 +768,7 @@ def test_umap_distance_metrics_fit_transform_trust(
@pytest.mark.parametrize(
"metric,supported,umap_learn_supported",
[
("dice", True, False),
("l2", True, False),
("euclidean", True, True),
("sqeuclidean", True, False),
Expand Down
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