docs/changes/newsfragments/333.enh

@@ -0,0 +1 @@
+Add support for Chatterjee's xi correlation in :class:`.JuniferConnectivityMeasure` by `Synchon Mandal`_

junifer/external/nilearn/junifer_connectivity_measure.py

@@ -3,6 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import sys
+from itertools import product
 from typing import Callable, Optional
 
 import numpy as np
@@ -322,11 +324,13 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         The covariance estimator
         (default ``EmpiricalCovariance(store_precision=False)``).
     kind : {"covariance", "correlation", "spearman correlation", \
-            "partial correlation", "tangent", "precision"}, optional
+            "partial correlation", "xi correlation", "tangent", \
+            "precision"}, optional
         The matrix kind. The default value uses Pearson's correlation.
         If ``"spearman correlation"`` is used, the data will be ranked before
-        estimating the covariance. For the use of ``"tangent"`` see [1]_
+        estimating the covariance. For ``"xi correlation"``, the coefficient
-        (default "correlation").
+        is not symmetric and should be interpreted as a measure of dependence
+        [2]_ . For the use of ``"tangent"`` see [1]_ (default "correlation").
     vectorize : bool, optional
         If True, connectivity matrices are reshaped into 1D arrays and only
         their flattened lower triangular parts are returned (default False).
@@ -372,6 +376,12 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
            Springer.
            doi:10/cn2h9c.
 
+    .. [2] Chatterjee, S.
+           A new coefficient of correlation.
+           Journal of the American Statistical Association 116.536 (2021):
+           2009-2022.
+           doi:10.1080/01621459.2020.1758115.
+
     """
 
     def __init__(
@@ -420,6 +430,25 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
                 covariances_std.append(self.cov_estimator_.fit(x).covariance_)
 
             connectivities = [cov_to_corr(cov) for cov in covariances_std]
+        elif self.kind == "xi correlation":
+            if sys.version_info < (3, 10):  # pragma: no cover
+                raise_error(
+                    klass=RuntimeError,
+                    msg=(
+                        "scipy.stats.chatterjeexi is available from "
+                        "scipy 1.15.0 and that requires Python 3.10 and above."
+                    ),
+                )
+            connectivities = []
+            for x in X:
+                n_rois = x.shape[1]
+                connectivity = np.ones((n_rois, n_rois))
+                for i, j in product(range(n_rois), range(n_rois)):
+                    if i != j:
+                        connectivity[i, j] = stats.chatterjeexi(
+                            x[:, i], x[:, j], y_continuous=True
+                        ).statistic
+                connectivities.append(connectivity)
         else:
             covariances = [self.cov_estimator_.fit(x).covariance_ for x in X]
             if self.kind in ("covariance", "tangent"):

junifer/external/nilearn/tests/test_junifer_connectivity_measure.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 import copy
+import sys
 import warnings
 from math import cosh, exp, log, sinh, sqrt
 from typing import TYPE_CHECKING, Optional, Union
@@ -12,7 +13,11 @@ import numpy as np
 import pytest
 from nilearn.connectome.connectivity_matrices import sym_matrix_to_vec
 from nilearn.tests.test_signal import generate_signals
-from numpy.testing import assert_array_almost_equal, assert_array_equal
+from numpy.testing import (
+    assert_allclose,
+    assert_array_almost_equal,
+    assert_array_equal,
+)
 from pandas import DataFrame
 from scipy import linalg
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
@@ -1088,3 +1093,42 @@ def test_connectivity_measure_standardize(
         ).fit_transform(signals)
         for m in record:
             assert match not in m.message
+
+
+@pytest.mark.skipif(
+    sys.version_info > (3, 9),
+    reason="will have correct scipy version so no error",
+)
+def test_xi_correlation_error() -> None:
+    """Check xi correlation according to paper."""
+    with pytest.raises(RuntimeError, match="scipy.stats.chatterjeexi"):
+        JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+            np.zeros((2, 2))
+        )
+
+
+@pytest.mark.skipif(
+    sys.version_info < (3, 10),
+    reason=(
+        "needs scipy 1.15.0 and above which in turn requires "
+        "python 3.10 and above"
+    ),
+)
+def test_xi_correlation() -> None:
+    """Check xi correlation according to paper."""
+    rng = np.random.default_rng(25982435982346983)
+    x = rng.random(size=10)
+    y = rng.random(size=10)
+    arr = np.column_stack((x, y))
+    expected = np.array(
+        [
+            [
+                [1.0, -0.3030303],
+                [-0.18181818, 1.0],
+            ]
+        ]
+    )
+    got = JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+        [arr]
+    )
+    assert_allclose(expected, got)

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -143,14 +143,17 @@ class FunctionalConnectivityBase(BaseMarker):
             },
         )
         # Create dictionary for output
+        labels = aggregation["aggregation"]["col_names"]
         return {
             "functional_connectivity": {
                 "data": connectivity.fit_transform(
                     [aggregation["aggregation"]["data"]]
                 )[0],
-                # Create column names
+                "row_names": labels,
-                "row_names": aggregation["aggregation"]["col_names"],
+                "col_names": labels,
-                "col_names": aggregation["aggregation"]["col_names"],
+                # xi correlation coefficient is not symmetric
-                "matrix_kind": "tril",
+                "matrix_kind": (
+                    "full" if self.conn_method == "xi correlation" else "tril"
+                ),
             },
         }