distance-explainer 0.4.0__py3-none-any.whl
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Metadata-Version: 2.1
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Name: distance_explainer
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Version: 0.4.0
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Summary: XAI method to explain distances in embedded spaces
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Home-page: https://github.com/dianna-ai/distance_explainer
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Author: Christiaan Meijer
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Author-email: c.meijer@esciencecenter.nl
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Project-URL: Bug Tracker, https://github.com/dianna-ai/distance_explainer/issues
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Keywords: XAI,embedded spaces
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Classifier: Development Status :: 2 - Pre-Alpha
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Classifier: Intended Audience :: Developers
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Classifier: License :: OSI Approved :: Apache Software License
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Classifier: Natural Language :: English
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Requires-Python: >=3.9
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: dianna>=1.4
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Requires-Dist: numpy
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[](https://doi.org/10.5281/zenodo.10018768) [](https://pypi.python.org/project/distance_explainer/)
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# `distance_explainer`
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XAI method to explain distances in embedded spaces.
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## Installation
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To install distance_explainer from GitHub repository, do:
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```console
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git clone git@github.com:dianna-ai/distance_explainer.git
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cd distance_explainer
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python3 -m pip install .
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```
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## How to use
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See our [tutorial](tutorial.ipynb) how to use this package.
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In short:
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```python
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image1 = np.random.random((100, 100, 3))
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image2 = np.random.random((100, 100, 3))
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image2_embedded = model(image2)
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explainer = DistanceExplainer(axis_labels={2: 'channels'})
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attribution_map = explainer.explain_image_distance(model, image1, image2_embedded)
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```
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## Contributing
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If you want to contribute to the development of distance_explainer,
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have a look at the [contribution guidelines](docs/CONTRIBUTING.md).
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## Credits
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This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [NLeSC/python-template](https://github.com/NLeSC/python-template).
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distance_explainer.py,sha256=BAkMo621YLdX9Ox_MOFw5qQ0uPSJBM0IpC1lauxbAc8,10285
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distance_explainer-0.4.0.dist-info/LICENSE,sha256=OPzV6bHGPCXFylyiCR3GYAK-EP8seLDbcbgO87DYM1o,11359
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distance_explainer-0.4.0.dist-info/METADATA,sha256=AKFPmnjXNYWDviNQ0M9AFx_yi6FQsk7RO0bQXclXBkM,2962
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distance_explainer-0.4.0.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
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distance_explainer-0.4.0.dist-info/top_level.txt,sha256=Eb2RZ72DZmJ--Xbug_-bZ_zQGOlqmhZp_XZs0Vj9FEc,19
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distance_explainer-0.4.0.dist-info/RECORD,,
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distance_explainer
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distance_explainer.py
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"""Documentation about distance_explainer."""
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import logging
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import dianna.utils
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import numpy as np
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import numpy.typing
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from dianna.utils.maskers import generate_interpolated_float_masks_for_image
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from sklearn.metrics import pairwise_distances
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from tqdm import tqdm
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logging.getLogger(__name__).addHandler(logging.NullHandler())
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__author__ = "Christiaan Meijer"
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__email__ = "c.meijer@esciencecenter.nl"
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__version__ = "0.4.0"
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class DistanceExplainer:
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"""Explainer object to explain an image with respect to a reference point in an embedded space."""
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# axis labels required to be present in input image data
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required_labels = ('channels',)
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def __init__(self, n_masks=1000, feature_res=8, p_keep=.5, # pylint: disable=too-many-arguments
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mask_selection_range_max=0.2, mask_selection_range_min=0, mask_selection_negative_range_max=1,
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mask_selection_negative_range_min=0.8, axis_labels=None, batch_size=10,
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preprocess_function=None):
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"""Creates an explainer object to explain an image with respect to a reference point in an embedded space.
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Args:
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n_masks: Number of masks to use to mask the input image. More increases reliability and computation.
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feature_res: Number of features per dimension in the image. Determines the super pixel size in the masks.
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p_keep: Probability of keeping features unmasked. Higher means less masked input.
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batch_size: Number of masked inputs to process in a single batch by the model
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axis_labels: Axis labels
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preprocess_function: Preprocess function
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mask_selection_range_max: Top end of range of outcomes that will be selected.
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mask_selection_range_min: Lower end of range of outcomes that will be selected.
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mask_selection_negative_range_max: Top end of range of outcomes that will be selected and weighted -1.
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mask_selection_negative_range_min: Lower end of range of outcomes that will be selected and weighted -1.
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"""
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self.n_masks = n_masks
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self.feature_res = feature_res
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self.p_keep = p_keep
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self.preprocess_function = preprocess_function
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self.masks = None
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self.predictions = None
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self.axis_labels = axis_labels if axis_labels is not None else []
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self.mask_selection_range_max = mask_selection_range_max
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self.mask_selection_range_min = mask_selection_range_min
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self.mask_selection_negative_range_max = mask_selection_negative_range_max
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self.mask_selection_negative_range_min = mask_selection_negative_range_min
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self.batch_size = batch_size
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def explain_image_distance(self, model_or_function, input_data, embedded_reference, masks=None) -> tuple[
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numpy.typing.NDArray, float]:
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"""Explain an image with respect to a reference point in an embedded space.
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Args:
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model_or_function: Model that will encode the input_data into an embedded space
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input_data: Input data to be explained, by exploring what parts make it closer to the reference point.
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embedded_reference: Reference point in the embedded space
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masks: User specified masks, in case no autogenerated masks should be used.
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Returns:
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attribution_map map
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"""
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full_preprocess_function, input_data = self._prepare_input_data(input_data)
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runner = dianna.utils.get_function(model_or_function, preprocess_function=full_preprocess_function)
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active_p_keep = 0.5 if self.p_keep is None else self.p_keep # Could autotune here (See #319)
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# data shape without batch axis and channel axis
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img_shape = input_data.shape[1:3]
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# Expose masks for to make user inspection possible
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if masks is None:
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self.masks = generate_interpolated_float_masks_for_image(img_shape, active_p_keep, self.n_masks,
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self.feature_res)
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else:
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self.masks = masks
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if self.masks.shape[0] != self.n_masks:
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raise ValueError(f"Configured n_masks ({self.n_masks}) is not equal to the number of masks passed "
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f"({self.masks.shape[0]}).")
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# Make sure multiplication is being done for correct axes
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masked = input_data * self.masks
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batch_predictions = []
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for i in tqdm(range(0, self.n_masks, self.batch_size), desc='Explaining'):
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new_predictions = runner(masked[i:i + self.batch_size])
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batch_predictions.append(new_predictions)
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self.predictions = np.concatenate(batch_predictions)
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def describe(x, name):
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return f'Description of {name}\nmean:{np.mean(x)}\nstd:{np.std(x)}\nmin:{np.min(x)}\nmax:{np.max(x)}'
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statistics = []
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highest_distances_masks, highest_mask_weights = self._get_lowest_distance_masks_and_weights(
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embedded_reference,
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self.predictions, self.masks,
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self.mask_selection_negative_range_min,
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self.mask_selection_negative_range_max)
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if len(highest_mask_weights) > 0:
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statistics.append(describe(highest_mask_weights, 'highest_mask_weights'))
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unnormalized_sal_highest = np.mean(highest_distances_masks, axis=0)
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else:
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unnormalized_sal_highest = 0
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lowest_distances_masks, lowest_mask_weights = self._get_lowest_distance_masks_and_weights(
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embedded_reference,
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self.predictions, self.masks,
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self.mask_selection_range_min,
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self.mask_selection_range_max)
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if len(lowest_mask_weights) > 0:
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statistics.append(describe(lowest_mask_weights, 'lowest_mask_weights'))
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unnormalized_sal_lowest = np.mean(lowest_distances_masks, axis=0)
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else:
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unnormalized_sal_lowest = 0
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self.statistics = '\n'.join(statistics)
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unnormalized_sal = unnormalized_sal_lowest - unnormalized_sal_highest
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attribution_map = unnormalized_sal
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return attribution_map
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@staticmethod
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def _get_lowest_distance_masks_and_weights(embedded_reference, predictions, masks, mask_selection_range_min,
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mask_selection_range_max):
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distances = DistanceExplainer.calculate_distances(predictions, embedded_reference[None, ...])
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lowest_distances_indices = np.argsort(distances, axis=0)[
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int(len(predictions) * mask_selection_range_min)
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:int(len(predictions) * mask_selection_range_max)]
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mask_weights = np.exp(-distances[lowest_distances_indices])
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lowest_distances_masks = masks[lowest_distances_indices]
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return lowest_distances_masks, mask_weights
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@staticmethod
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def calculate_distances(predictions: np.ndarray, embedded_reference: np.ndarray) -> np.ndarray:
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"""Calculate the distances to the reference point in an embedded space using cosine distance with range [0,1].
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Args:
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predictions: Batch of points in the embedded space for with distances are calculated
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embedded_reference: Point to calculate the distance to
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Returns:
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Distances from each point to the reference point
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"""
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distances = pairwise_distances(predictions, embedded_reference,
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metric='cosine') / 2 # divide by 2 to have [0.1] output range
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return distances
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def _prepare_input_data(self, input_data):
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input_data_xarray = dianna.utils.to_xarray(input_data, self.axis_labels, DistanceExplainer.required_labels)
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input_data_xarray_expanded = input_data_xarray.expand_dims('batch', 0)
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# ensure channels axis is last and keep track of where it was so we can move it back
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channels_axis_index = input_data_xarray_expanded.dims.index('channels')
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prepared_input_data = dianna.utils.move_axis(input_data_xarray_expanded, 'channels', -1)
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# create preprocessing function that puts model input generated by RISE into the right shape and dtype,
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# followed by running the user's preprocessing function
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full_preprocess_function = self._get_full_preprocess_function(channels_axis_index, prepared_input_data.dtype)
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return full_preprocess_function, prepared_input_data
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def _prepare_image_data(self, input_data):
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"""Transforms the data to be of the shape and type RISE expects.
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Args:
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input_data (xarray): Data to be explained
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Returns:
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transformed input data, preprocessing function to use with dianna.utils.get_function()
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"""
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# ensure channels axis is last and keep track of where it was so we can move it back
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channels_axis_index = input_data.dims.index('channels')
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input_data = dianna.utils.move_axis(input_data, 'channels', -1)
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# create preprocessing function that puts model input generated by RISE into the right shape and dtype,
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# followed by running the user's preprocessing function
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full_preprocess_function = self._get_full_preprocess_function(channels_axis_index, input_data.dtype)
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return input_data, full_preprocess_function
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def _get_full_preprocess_function(self, channel_axis_index, dtype):
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"""Creates a full preprocessing function.
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Creates a preprocessing function that incorporates both the (optional) user's
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preprocessing function, as well as any needed dtype and shape conversions
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Args:
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channel_axis_index (int): Axis index of the channels in the input data
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dtype (type): Data type of the input data (e.g. np.float32)
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Returns:
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Function that first ensures the data has the same shape and type as the input data,
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then runs the users' preprocessing function
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"""
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def moveaxis_function(data):
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return dianna.utils.move_axis(data, 'channels', channel_axis_index).astype(dtype).values
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if self.preprocess_function is None:
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return moveaxis_function
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return lambda data: self.preprocess_function(moveaxis_function(data))
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