Merge branch 'dev' of https://github.com/stefanradev93/BayesFlow into dev

Author: stefanradev93

bayesflow/diagnostics/plots/loss.py

@@ -15,11 +15,13 @@ def loss(
     train_key: str = "loss",
     val_key: str = "val_loss",
     per_training_step: bool = False,
+    smoothing_factor: float = 0.8,
     figsize: Sequence[float] = None,
     train_color: str = "#132a70",
     val_color: str = "black",
-    lw_train: float = 2.5,
-    lw_val: float = 2.5,
+    lw_train: float = 2.0,
+    lw_val: float = 2.0,
+    grid_alpha: float = 0.2,
     legend_fontsize: int = 14,
     label_fontsize: int = 14,
     title_fontsize: int = 16,
@@ -38,17 +40,21 @@ def loss(
         The validation loss key to look for in the history
     per_training_step : bool, optional, default: False
         A flag for making loss trajectory detailed (to training steps) rather than per epoch.
+    smoothing_factor : float, optional, default: 0.8
+        If greater than zero, smooth the loss curves by applying an exponential moving average.
     figsize            : tuple or None, optional, default: None
         The figure size passed to the ``matplotlib`` constructor.
         Inferred if ``None``
-    train_color        : str, optional, default: '#8f2727'
+    train_color        : str, optional, default: '#132a70'
         The color for the train loss trajectory
-    val_color          : str, optional, default: black
+    val_color          : str, optional, default: None
         The color for the optional validation loss trajectory
-    lw_train           : int, optional, default: 1
+    lw_train           : int, optional, default: 2
         The linewidth for the training loss curve
     lw_val             : int, optional, default: 2
         The linewidth for the validation loss curve
+    grid_alpha          : float, optional, default: 0.2
+        The transparency of the background grid
     legend_fontsize    : int, optional, default: 14
         The font size of the legend text
     label_fontsize     : int, optional, default: 14
@@ -91,28 +97,60 @@ def loss(
 
     # Loop through loss entries and populate plot
     for i, ax in enumerate(axes.flat):
-        # Plot train curve
-        ax.plot(train_step_index, train_losses.iloc[:, i], color=train_color, lw=lw_train, alpha=0.9, label="Training")
+        if smoothing_factor > 0:
+            # plot unsmoothed train loss
+            ax.plot(
+                train_step_index, train_losses.iloc[:, 0], color=train_color, lw=lw_train, alpha=0.3, label="Training"
+            )
+
+            # plot smoothed train loss
+            smoothed_train_loss = train_losses.iloc[:, 0].ewm(alpha=1.0 - smoothing_factor, adjust=True).mean()
+            ax.plot(
+                train_step_index,
+                smoothed_train_loss,
+                color=train_color,
+                lw=lw_train,
+                alpha=0.8,
+                label="Training (Moving Average)",
+            )
+        else:
+            # plot unsmoothed train loss
+            ax.plot(
+                train_step_index, train_losses.iloc[:, 0], color=train_color, lw=lw_train, alpha=0.8, label="Training"
+            )
 
         # Plot optional val curve
         if val_losses is not None:
-            if i < val_losses.shape[1]:
-                ax.plot(
-                    val_step_index,
-                    val_losses.iloc[:, i],
-                    linestyle="--",
-                    marker="o",
-                    markersize=5,
-                    color=val_color,
-                    lw=lw_val,
-                    label="Validation",
-                )
+            if val_color is not None:
+                if smoothing_factor > 0:
+                    # plot unsmoothed val loss
+                    ax.plot(
+                        val_step_index, val_losses.iloc[:, 0], color=val_color, lw=lw_val, alpha=0.3, label="Validation"
+                    )
+
+                    # plot smoothed val loss
+                    smoothed_val_loss = val_losses.iloc[:, 0].ewm(alpha=1.0 - smoothing_factor, adjust=True).mean()
+                    ax.plot(
+                        val_step_index,
+                        smoothed_val_loss,
+                        color=val_color,
+                        lw=lw_val,
+                        alpha=0.8,
+                        label="Validation (Moving Average)",
+                    )
+                else:
+                    # plot unsmoothed val loss
+                    ax.plot(
+                        val_step_index, val_losses.iloc[:, 0], color=val_color, lw=lw_val, alpha=0.8, label="Validation"
+                    )
 
         sns.despine(ax=ax)
-        ax.grid(alpha=0.5)
+        ax.grid(alpha=grid_alpha)
 
-        # Only add legend if there is a validation curve
-        if val_losses is not None:
+        ax.set_xlim(train_step_index[0], train_step_index[-1])
+
+        # Only add the legend if there are multiple curves
+        if val_losses is not None or smoothing_factor > 0:
             ax.legend(fontsize=legend_fontsize)
 
     # Add labels, titles, and set font sizes

bayesflow/utils/plot_utils.py

@@ -4,6 +4,11 @@
 import matplotlib.pyplot as plt
 import seaborn as sns
 
+from matplotlib.collections import LineCollection
+from matplotlib.colors import Normalize
+from matplotlib.patches import Rectangle
+from matplotlib.legend_handler import HandlerPatch
+
 from .validators import check_estimates_prior_shapes
 from .dict_utils import dicts_to_arrays
 
@@ -260,3 +265,96 @@ def make_quadratic(ax: plt.Axes, x_data: np.ndarray, y_data: np.ndarray):
         alpha=0.9,
         linestyle="dashed",
     )
+
+
+def gradient_line(x, y, c=None, cmap: str = "viridis", lw: float = 2.0, alpha: float = 1, ax=None):
+    """
+    Plot a 1D line with color gradient determined by `c` (same shape as x and y).
+    """
+    if ax is None:
+        ax = plt.gca()
+
+    # Default color value = y
+    if c is None:
+        c = y
+
+    # Create segments for LineCollection
+    points = np.array([x, y]).T.reshape(-1, 1, 2)
+    segments = np.concatenate([points[:-1], points[1:]], axis=1)
+
+    norm = Normalize(np.min(c), np.max(c))
+    lc = LineCollection(segments, array=c, cmap=cmap, norm=norm, linewidth=lw, alpha=alpha)
+
+    ax.add_collection(lc)
+    ax.set_xlim(np.min(x), np.max(x))
+    ax.set_ylim(np.min(y), np.max(y))
+    return lc
+
+
+def gradient_legend(ax, label, cmap, norm, loc="upper right"):
+    """
+    Adds a single gradient swatch to the legend of the given Axes.
+
+    Parameters
+    ----------
+    - ax: matplotlib Axes
+    - label: str, label to display in the legend
+    - cmap: matplotlib colormap
+    - norm: matplotlib Normalize object
+    - loc: legend location (default 'upper right')
+    """
+
+    # Custom dummy handle to represent the gradient
+    class _GradientSwatch(Rectangle):
+        pass
+
+    # Custom legend handler that draws a horizontal gradient
+    class _HandlerGradient(HandlerPatch):
+        def create_artists(self, legend, orig_handle, xdescent, ydescent, width, height, fontsize, trans):
+            gradient = np.linspace(0, 1, 256).reshape(1, -1)
+            im = ax.imshow(
+                gradient,
+                aspect="auto",
+                extent=[xdescent, xdescent + width, ydescent, ydescent + height],
+                transform=trans,
+                cmap=cmap,
+                norm=norm,
+            )
+            return [im]
+
+    # Add to existing legend entries
+    handles, labels = ax.get_legend_handles_labels()
+    handles.append(_GradientSwatch((0, 0), 1, 1))
+    labels.append(label)
+
+    ax.legend(handles=handles, labels=labels, loc=loc, handler_map={_GradientSwatch: _HandlerGradient()})
+
+
+def add_gradient_plot(
+    x,
+    y,
+    ax,
+    cmap: str = "viridis",
+    lw: float = 3.0,
+    marker: bool = True,
+    marker_type: str = "o",
+    marker_size: int = 34,
+    alpha: float = 1,
+    label: str = "Validation",
+):
+    gradient_line(x, y, c=x, cmap=cmap, lw=lw, alpha=alpha, ax=ax)
+
+    # Optionally add markers
+    if marker:
+        ax.scatter(
+            x,
+            y,
+            c=x,
+            cmap=cmap,
+            marker=marker_type,
+            s=marker_size,
+            zorder=10,
+            edgecolors="none",
+            label=label,
+            alpha=0.01,
+        )

bayesflow/workflows/basic_workflow.py

@@ -348,7 +348,7 @@ def plot_default_diagnostics(
     ) -> dict[str, plt.Figure]:
         """
         Generates default diagnostic plots to evaluate the quality of inference. The function produces several
-        diagnostic plots, including:
+        diagnostic plots, including
         - Loss history (if training history is available).
         - Parameter recovery plots.
         - Calibration ECDF plots.

tests/conftest.py

@@ -1,6 +1,6 @@
-import logging
-
 import keras
+import logging
+import matplotlib
 import pytest
 
 BACKENDS = ["jax", "numpy", "tensorflow", "torch"]
@@ -25,6 +25,16 @@ def pytest_runtest_setup(item):
 
         jax.config.update("jax_traceback_filtering", "off")
 
+    # use a non-GUI plotting backend for tests
+    matplotlib.use("Agg")
+
+
+def pytest_runtest_teardown(item, nextitem):
+    import matplotlib.pyplot as plt
+
+    # close all plots at the end of each test
+    plt.close("all")
+
 
 def pytest_make_parametrize_id(config, val, argname):
     return f"{argname}={repr(val)}"

tests/test_diagnostics/conftest.py

@@ -1,3 +1,4 @@
+import keras
 import numpy as np
 import pytest
 from bayesflow.utils.numpy_utils import softmax
@@ -61,3 +62,19 @@ def pred_models(true_models):
     pred_models = np.random.normal(loc=true_models)
     pred_models = softmax(pred_models, axis=-1)
     return pred_models
+
+
+@pytest.fixture()
+def history():
+    h = keras.callbacks.History()
+
+    step = np.linspace(0, 1, 10_000)
+    train_loss = (1.0 - step) ** 2 + np.random.normal(loc=0, scale=0.02, size=step.shape)
+    validation_loss = 0.1 + (0.75 - step) ** 2 + np.random.normal(loc=0, scale=0.02, size=step.shape)
+
+    h.history = {
+        "loss": train_loss.tolist(),
+        "val_loss": validation_loss.tolist(),
+    }
+
+    return h

tests/test_diagnostics/test_diagnostics_plots.py

@@ -6,6 +6,15 @@ def num_variables(x: dict):
     return sum(arr.shape[-1] for arr in x.values())
 
 
+def test_backend():
+    import matplotlib.pyplot as plt
+
+    # if the local testing backend is not Agg
+    # then you may run into issues once you run workflow tests
+    # on GitHub, since these use the Agg backend
+    assert plt.get_backend() == "Agg"
+
+
 def test_calibration_ecdf(random_estimates, random_targets, var_names):
     # basic functionality: automatic variable names
     out = bf.diagnostics.plots.calibration_ecdf(random_estimates, random_targets)
@@ -45,6 +54,12 @@ def test_calibration_histogram(random_estimates, random_targets):
     assert out.axes[0].title._text == "beta_0"
 
 
+def test_loss(history):
+    out = bf.diagnostics.loss(history)
+    assert len(out.axes) == 1
+    assert out.axes[0].title._text == "Loss Trajectory"
+
+
 def test_recovery(random_estimates, random_targets):
     # basic functionality: automatic variable names
     out = bf.diagnostics.plots.recovery(random_estimates, random_targets)

tests/test_networks/test_inference_networks.py

@@ -96,7 +96,7 @@ def f(x):
     numerical_output, numerical_jacobian = jacobian(f, random_samples, return_output=True)
 
     # output should be identical, otherwise this test does not work (e.g. for stochastic networks)
-    assert keras.ops.all(keras.ops.isclose(output, numerical_output))
+    assert_allclose(output, numerical_output)
 
     log_prob = generative_inference_network.base_distribution.log_prob(output)
 

tests/test_networks/test_summary_networks.py

@@ -47,9 +47,8 @@ def test_variable_set_size(summary_network, random_set):
     summary_network.build(keras.ops.shape(random_set))
 
     # run with another set size
-    for _ in range(10):
+    for s in [3, 4, 5]:
         b = keras.ops.shape(random_set)[0]
-        s = np.random.randint(1, 10)
         new_input = keras.ops.zeros((b, s, keras.ops.shape(random_set)[2]))
         summary_network(new_input)
 

tests/test_workflows/test_basic_workflow.py

@@ -1,7 +1,7 @@
 import bayesflow as bf
 
 
-def test_classifier_two_sample_test(inference_network, summary_network):
+def test_basic_workflow(inference_network, summary_network):
     workflow = bf.BasicWorkflow(
         inference_network=inference_network,
         summary_network=summary_network,