Merge remote-tracking branch 'refs/remotes/origin/main'

Author: aloctavodia

.pre-commit-config.yaml

@@ -12,14 +12,14 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1
+    rev: v0.6.3
     hooks:
       - id: ruff
         args: ["--fix", "--output-format=full"]
       - id: ruff-format
         args: ["--line-length=100"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         args: [--ignore-missing-imports]

pymc_bart/utils.py

@@ -8,10 +8,11 @@
 import numpy as np
 import numpy.typing as npt
 import pytensor.tensor as pt
+from numba import jit
 from pytensor.tensor.variable import Variable
 from scipy.interpolate import griddata
 from scipy.signal import savgol_filter
-from scipy.stats import norm, pearsonr
+from scipy.stats import norm
 
 from .tree import Tree
 
@@ -700,8 +701,9 @@ def plot_variable_importance(  # noqa: PLR0915
     method: str = "VI",
     figsize: Optional[Tuple[float, float]] = None,
     xlabel_angle: float = 0,
-    samples: int = 100,
+    samples: int = 50,
     random_seed: Optional[int] = None,
+    plot_kwargs: Optional[Dict[str, Any]] = None,
     ax: Optional[plt.Axes] = None,
 ) -> Tuple[List[int], Union[List[plt.Axes], Any]]:
     """
@@ -733,6 +735,14 @@ def plot_variable_importance(  # noqa: PLR0915
         Number of predictions used to compute correlation for subsets of variables. Defaults to 100
     random_seed : Optional[int]
         random_seed used to sample from the posterior. Defaults to None.
+    plot_kwargs : dict
+        Additional keyword arguments for the plot. Defaults to None.
+        Valid keys are:
+        - color_r2: matplotlib valid color for error bars
+        - marker_r2: matplotlib valid marker for the mean R squared
+        - marker_fc_r2: matplotlib valid marker face color for the mean R squared
+        - ls_ref: matplotlib valid linestyle for the reference line
+        - color_ref: matplotlib valid color for the reference line
     ax : axes
         Matplotlib axes.
 
@@ -745,6 +755,9 @@ def plot_variable_importance(  # noqa: PLR0915
 
     all_trees = bartrv.owner.op.all_trees
 
+    if plot_kwargs is None:
+        plot_kwargs = {}
+
     if bartrv.ndim == 1:  # type: ignore
         shape = 1
     else:
@@ -773,6 +786,10 @@ def plot_variable_importance(  # noqa: PLR0915
         all_trees, X=X, rng=rng, size=samples, excluded=None, shape=shape
     )
 
+    r_2_ref = np.array(
+        [pearsonr2(predicted_all[j], predicted_all[j + 1]) for j in range(samples - 1)]
+    )
+
     if method == "VI":
         idxs = np.argsort(
             idata["sample_stats"]["variable_inclusion"].mean(("chain", "draw")).values
@@ -794,10 +811,7 @@ def plot_variable_importance(  # noqa: PLR0915
                 shape=shape,
             )
             r_2 = np.array(
-                [
-                    pearsonr(predicted_all[j].flatten(), predicted_subset[j].flatten())[0] ** 2
-                    for j in range(samples)
-                ]
+                [pearsonr2(predicted_all[j], predicted_subset[j]) for j in range(samples)]
             )
             r2_mean[idx] = np.mean(r_2)
             r2_hdi[idx] = az.hdi(r_2)
@@ -833,10 +847,7 @@ def plot_variable_importance(  # noqa: PLR0915
                 # Calculate Pearson correlation for each sample and find the mean
                 r_2 = np.zeros(samples)
                 for j in range(samples):
-                    r_2[j] = (
-                        (pearsonr(predicted_all[j].flatten(), predicted_subset[j].flatten())[0])
-                        ** 2
-                    )
+                    r_2[j] = pearsonr2(predicted_all[j], predicted_subset[j])
                 mean_r_2 = np.mean(r_2, dtype=float)
                 # Identify the least important combination of variables
                 # based on the maximum mean squared Pearson correlation
@@ -872,9 +883,21 @@ def plot_variable_importance(  # noqa: PLR0915
         ticks,
         r2_mean,
         np.array((r2_yerr_min, r2_yerr_max)),
-        color="C0",
+        color=plot_kwargs.get("color_r2", "k"),
+        fmt=plot_kwargs.get("marker_r2", "o"),
+        mfc=plot_kwargs.get("marker_fc_r2", "white"),
+    )
+    ax.axhline(
+        np.mean(r_2_ref),
+        ls=plot_kwargs.get("ls_ref", "--"),
+        color=plot_kwargs.get("color_ref", "grey"),
+    )
+    ax.fill_between(
+        [-0.5, n_vars - 0.5],
+        *az.hdi(r_2_ref),
+        alpha=0.1,
+        color=plot_kwargs.get("color_ref", "grey"),
     )
-    ax.axhline(r2_mean[-1], ls="--", color="0.5")
     ax.set_xticks(ticks, new_labels, rotation=xlabel_angle)
     ax.set_ylabel("R²", rotation=0, labelpad=12)
     ax.set_ylim(0, 1)
@@ -890,3 +913,13 @@ def generate_sequences(n_vars, i_var, include):
     else:
         sequences = [()]
     return sequences
+
+
+@jit(nopython=True)
+def pearsonr2(A, B):
+    """Compute the squared Pearson correlation coefficient"""
+    A = A.flatten()
+    B = B.flatten()
+    am = A - np.mean(A)
+    bm = B - np.mean(B)
+    return (am @ bm) ** 2 / (np.sum(am**2) * np.sum(bm**2))