model_utils.py 20 KB
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# @author lucasmiranda42
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# encoding: utf-8
# module deepof

"""

Functions and general utilities for the deepof tensorflow models. See documentation for details

"""
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from itertools import combinations
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from typing import Any, Tuple
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import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf
import tensorflow_probability as tfp
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from tensorflow.keras import backend as K
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from tensorflow.keras.constraints import Constraint
from tensorflow.keras.layers import Layer

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tfd = tfp.distributions
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tfpl = tfp.layers
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# Helper functions and classes
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@tf.function
def compute_shannon_entropy(tensor):
    """Computes Shannon entropy for a given tensor"""

    tensor = tf.cast(tensor, tf.dtypes.int32)
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    bins = tf.math.bincount(tensor, dtype=tf.dtypes.float32) / tf.cast(
        tensor.shape[0], tf.float32
    )
    return -tf.reduce_sum(bins * tf.math.log(bins + 1e-5))


@tf.function
def get_k_nearest_neighbors(tensor, k, index):
    """Retrieve indices of the k nearest neighbors in tensor to the vector with the specified index"""

    query = tensor[index]
    distances = tf.norm(tensor - query, axis=1)
    max_distance = tf.sort(distances)[k]
    neighbourhood_mask = distances < max_distance
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    return tf.squeeze(tf.where(neighbourhood_mask))


@tf.function
def get_neighbourhood_entropy(tensor, clusters, k, index):

    neighborhood = get_k_nearest_neighbors(tensor, k, index)
    cluster_z = clusters[neighborhood]
    neigh_entropy = compute_shannon_entropy(cluster_z)

    return neigh_entropy
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class exponential_learning_rate(tf.keras.callbacks.Callback):
    """Simple class that allows to grow learning rate exponentially during training"""

    def __init__(self, factor):
        super().__init__()
        self.factor = factor
        self.rates = []
        self.losses = []

    # noinspection PyMethodOverriding
    def on_batch_end(self, batch, logs):
        """This callback acts after processing each batch"""

        self.rates.append(K.get_value(self.model.optimizer.lr))
        self.losses.append(logs["loss"])
        K.set_value(self.model.optimizer.lr, self.model.optimizer.lr * self.factor)


def find_learning_rate(
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    model, X, y, epochs=1, batch_size=32, min_rate=10 ** -5, max_rate=10
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):
    """Trains the provided model for an epoch with an exponentially increasing learning rate"""

    init_weights = model.get_weights()
    iterations = len(X) // batch_size * epochs
    factor = K.exp(K.log(max_rate / min_rate) / iterations)
    init_lr = K.get_value(model.optimizer.lr)
    K.set_value(model.optimizer.lr, min_rate)
    exp_lr = exponential_learning_rate(factor)
    model.fit(X, y, epochs=epochs, batch_size=batch_size, callbacks=[exp_lr])
    K.set_value(model.optimizer.lr, init_lr)
    model.set_weights(init_weights)
    return exp_lr.rates, exp_lr.losses


def plot_lr_vs_loss(rates, losses):  # pragma: no cover
    """Plots learing rate versus the loss function of the model"""

    plt.plot(rates, losses)
    plt.gca().set_xscale("log")
    plt.hlines(min(losses), min(rates), max(rates))
    plt.axis([min(rates), max(rates), min(losses), (losses[0] + min(losses)) / 2])
    plt.xlabel("Learning rate")
    plt.ylabel("Loss")


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def compute_kernel(x: tf.Tensor, y: tf.Tensor) -> tf.Tensor:
    """

    Computes the MMD between the two specified vectors using a gaussian kernel.

        Parameters:
            - x (tf.Tensor): left tensor
            - y (tf.Tensor): right tensor

        Returns
            - kernel (tf.Tensor): returns the result of applying the kernel, for
            each training instance

    """

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    x_size = tf.shape(x)[0]
    y_size = tf.shape(y)[0]
    dim = tf.shape(x)[1]
    tiled_x = tf.tile(
        tf.reshape(x, tf.stack([x_size, 1, dim])), tf.stack([1, y_size, 1])
    )
    tiled_y = tf.tile(
        tf.reshape(y, tf.stack([1, y_size, dim])), tf.stack([x_size, 1, 1])
    )
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    kernel = tf.exp(
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        -tf.reduce_mean(tf.square(tiled_x - tiled_y), axis=2) / tf.cast(dim, tf.float32)
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    )
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    return kernel
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@tf.function
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def compute_mmd(tensors: Tuple[Any]) -> tf.Tensor:
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    """

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    Computes the MMD between the two specified vectors using a gaussian kernel.
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        Parameters:
            - tensors (tuple): tuple containing two tf.Tensor objects
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        Returns
            - mmd (tf.Tensor): returns the maximum mean discrepancy for each
            training instance
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    """
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    x = tensors[0]
    y = tensors[1]

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    x_kernel = compute_kernel(x, x)
    y_kernel = compute_kernel(y, y)
    xy_kernel = compute_kernel(x, y)
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    mmd = (
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        tf.reduce_mean(x_kernel)
        + tf.reduce_mean(y_kernel)
        - 2 * tf.reduce_mean(xy_kernel)
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    )
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    return mmd
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# Custom auxiliary classes
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class one_cycle_scheduler(tf.keras.callbacks.Callback):
    """

    One cycle learning rate scheduler.
    Based on https://arxiv.org/pdf/1506.01186.pdf

    """

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    def __init__(
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        self,
        iterations: int,
        max_rate: float,
        start_rate: float = None,
        last_iterations: int = None,
        last_rate: float = None,
        log_dir: str = ".",
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    ):
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        super().__init__()
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        self.iterations = iterations
        self.max_rate = max_rate
        self.start_rate = start_rate or max_rate / 10
        self.last_iterations = last_iterations or iterations // 10 + 1
        self.half_iteration = (iterations - self.last_iterations) // 2
        self.last_rate = last_rate or self.start_rate / 1000
        self.iteration = 0
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        self.history = {}
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        self.log_dir = log_dir
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    def _interpolate(self, iter1: int, iter2: int, rate1: float, rate2: float) -> float:
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        return (rate2 - rate1) * (self.iteration - iter1) / (iter2 - iter1) + rate1

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    # noinspection PyMethodOverriding,PyTypeChecker
    def on_batch_begin(self, batch: int, logs):
        """ Defines computations to perform for each batch """
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        self.history.setdefault("lr", []).append(K.get_value(self.model.optimizer.lr))

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        if self.iteration < self.half_iteration:
            rate = self._interpolate(
                0, self.half_iteration, self.start_rate, self.max_rate
            )
        elif self.iteration < 2 * self.half_iteration:
            rate = self._interpolate(
                self.half_iteration,
                2 * self.half_iteration,
                self.max_rate,
                self.start_rate,
            )
        else:
            rate = self._interpolate(
                2 * self.half_iteration,
                self.iterations,
                self.start_rate,
                self.last_rate,
            )
            rate = max(rate, self.last_rate)
        self.iteration += 1
        K.set_value(self.model.optimizer.lr, rate)
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    def on_epoch_end(self, epoch, logs=None):
        """Logs the learning rate to tensorboard"""

        writer = tf.summary.create_file_writer(self.log_dir)

        with writer.as_default():
            tf.summary.scalar(
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                "learning_rate",
                data=self.model.optimizer.lr,
                step=epoch,
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            )
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class neighbor_latent_entropy(tf.keras.callbacks.Callback):
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    """

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    Latent space entropy callback. Computes the entropy of cluster assignment across k nearest neighbors of a subset
    of samples in the latent space.
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    """

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    def __init__(
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        self,
        encoding_dim: int,
        validation_data: np.ndarray = None,
        k: int = 100,
        samples: int = 10000,
        log_dir: str = ".",
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    ):
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        super().__init__()
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        self.enc = encoding_dim
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        self.validation_data = validation_data
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        self.k = k
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        self.samples = samples
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        self.log_dir = log_dir
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    # noinspection PyMethodOverriding,PyTypeChecker
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    def on_epoch_end(self, epoch, logs=None):
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        """ Passes samples through the encoder and computes cluster purity on the latent embedding """

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        if self.validation_data is not None:
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            # Get encoer and grouper from full model
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            latent_distribution = [
                layer
                for layer in self.model.layers
                if layer.name == "latent_distribution"
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            ][0]
            cluster_assignment = [
                layer
                for layer in self.model.layers
                if layer.name == "cluster_assignment"
            ][0]

            encoder = tf.keras.models.Model(
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                self.model.layers[0].input, latent_distribution.output
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            )
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            grouper = tf.keras.models.Model(
                self.model.layers[0].input, cluster_assignment.output
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            )

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            # Use encoder and grouper to predict on validation data
            encoding = encoder.predict(self.validation_data)
            groups = grouper.predict(self.validation_data)
            hard_groups = groups.argmax(axis=1)
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            max_groups = groups.max(axis=1)
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            # Iterate over samples and compute purity across neighbourhood
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            self.samples = np.min([self.samples, encoding.shape[0]])
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            random_idxs = np.random.choice(
                range(encoding.shape[0]), self.samples, replace=False
            )
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            # Add result to pre allocated array
            purity_vector = get_neighbourhood_entropy(encodings, random_idxs)
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            writer = tf.summary.create_file_writer(self.log_dir)
            with writer.as_default():
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                tf.summary.scalar(
                    "number_of_populated_clusters",
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                    data=len(set(hard_groups[max_groups >= 0.25])),
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                    step=epoch,
                )
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                tf.summary.scalar(
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                    "average_neighborhood_cluster_entropy",
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                    data=np.average(purity_vector, weights=max_groups[random_idxs]),
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                    step=epoch,
                )
                tf.summary.scalar(
                    "average_confidence_in_selected_cluster",
                    data=np.average(max_groups),
                    step=epoch,
                )
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class uncorrelated_features_constraint(Constraint):
    """

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    tf.keras.constraints.Constraint subclass that forces a layer to have uncorrelated features.
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    Useful, among others, for auto encoder bottleneck layers

    """

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    def __init__(self, encoding_dim, weightage=1.0):
        self.encoding_dim = encoding_dim
        self.weightage = weightage

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    def get_config(self):  # pragma: no cover
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        """Updates Constraint metadata"""
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        config = super().get_config().copy()
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        config.update({"encoding_dim": self.encoding_dim, "weightage": self.weightage})
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        return config

    def get_covariance(self, x):
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        """Computes the covariance of the elements of the passed layer"""

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        x_centered_list = []

        for i in range(self.encoding_dim):
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            x_centered_list.append(x[:, i] - K.mean(x[:, i]))
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        x_centered = tf.stack(x_centered_list)
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        covariance = K.dot(x_centered, K.transpose(x_centered)) / tf.cast(
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            x_centered.get_shape()[0], tf.float32
        )

        return covariance

    # Constraint penalty
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    # noinspection PyUnusedLocal
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    def uncorrelated_feature(self, x):
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        """Adds a penalty on feature correlation, forcing more independent sets of weights"""

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        if self.encoding_dim <= 1:  # pragma: no cover
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            return 0.0
        else:
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            output = K.sum(
                K.square(
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                    self.covariance
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                    - tf.math.multiply(self.covariance, tf.eye(self.encoding_dim))
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                )
            )
            return output

    def __call__(self, x):
        self.covariance = self.get_covariance(x)
        return self.weightage * self.uncorrelated_feature(x)


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# Custom Layers
class MCDropout(tf.keras.layers.Dropout):
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    """Equivalent to tf.keras.layers.Dropout, but with training mode enabled at prediction time.
    Useful for Montecarlo predictions"""

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    def call(self, inputs, **kwargs):
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        """Overrides the call method of the subclassed function"""
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        return super().call(inputs, training=True)


class DenseTranspose(Layer):
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    """Mirrors a tf.keras.layers.Dense instance with transposed weights.
    Useful for decoder layers in autoencoders, to force structure and
    decrease the effective number of parameters to train"""

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    def __init__(self, dense, output_dim, activation=None, **kwargs):
        self.dense = dense
        self.output_dim = output_dim
        self.activation = tf.keras.activations.get(activation)
        super().__init__(**kwargs)

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    def get_config(self):  # pragma: no cover
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        """Updates Constraint metadata"""

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        config = super().get_config().copy()
        config.update(
            {
                "dense": self.dense,
                "output_dim": self.output_dim,
                "activation": self.activation,
            }
        )
        return config

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    # noinspection PyAttributeOutsideInit
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    def build(self, batch_input_shape):
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        """Updates Layer's build method"""

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        self.biases = self.add_weight(
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            name="bias",
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            shape=self.dense.get_input_at(-1).get_shape().as_list()[1:],
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            initializer="zeros",
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        )
        super().build(batch_input_shape)

    def call(self, inputs, **kwargs):
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        """Updates Layer's call method"""

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        z = tf.matmul(inputs, self.dense.weights[0], transpose_b=True)
        return self.activation(z + self.biases)

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    def compute_output_shape(self, input_shape):  # pragma: no cover
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        """Outputs the transposed shape"""

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        return input_shape[0], self.output_dim


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class KLDivergenceLayer(tfpl.KLDivergenceAddLoss):
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    """
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    Identity transform layer that adds KL Divergence
    to the final model loss.
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    """

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    def __init__(self, iters, warm_up_iters, annealing_mode, *args, **kwargs):
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        super(KLDivergenceLayer, self).__init__(*args, **kwargs)
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        self.is_placeholder = True
        self._iters = iters
        self._warm_up_iters = warm_up_iters
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        self._annealing_mode = annealing_mode
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    def get_config(self):  # pragma: no cover
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        """Updates Constraint metadata"""

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        config = super().get_config().copy()
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        config.update({"is_placeholder": self.is_placeholder})
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        config.update({"_iters": self._iters})
        config.update({"_warm_up_iters": self._warm_up_iters})
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        config.update({"_annealing_mode": self._annealing_mode})
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        return config

    def call(self, distribution_a):
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        """Updates Layer's call method"""

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        # Define and update KL weight for warmup
        if self._warm_up_iters > 0:
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            if self._annealing_mode in ["linear", "sigmoid"]:
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                kl_weight = tf.cast(
                    K.min([self._iters / self._warm_up_iters, 1.0]), tf.float32
                )
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                if self._annealing_mode == "sigmoid":
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                    kl_weight = tf.math.sigmoid(
                        (2 * kl_weight - 1) / (kl_weight - kl_weight ** 2)
                    )
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            else:
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                raise NotImplementedError(
                    "annealing_mode must be one of 'linear' and 'sigmoid'"
                )
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        else:
            kl_weight = tf.cast(1.0, tf.float32)

        kl_batch = kl_weight * self._regularizer(distribution_a)

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        self.add_loss(kl_batch, inputs=[distribution_a])
        self.add_metric(
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            kl_batch,
            aggregation="mean",
            name="kl_divergence",
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        )
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        # noinspection PyProtectedMember
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        self.add_metric(kl_weight, aggregation="mean", name="kl_rate")
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        return distribution_a


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class MMDiscrepancyLayer(Layer):
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    """
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    Identity transform layer that adds MM Discrepancy
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    to the final model loss.
    """

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    def __init__(
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        self, batch_size, prior, iters, warm_up_iters, annealing_mode, *args, **kwargs
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    ):
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        super(MMDiscrepancyLayer, self).__init__(*args, **kwargs)
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        self.is_placeholder = True
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        self.batch_size = batch_size
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        self.prior = prior
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        self._iters = iters
        self._warm_up_iters = warm_up_iters
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        self._annealing_mode = annealing_mode
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    def get_config(self):  # pragma: no cover
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        """Updates Constraint metadata"""

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        config = super().get_config().copy()
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        config.update({"batch_size": self.batch_size})
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        config.update({"_iters": self._iters})
        config.update({"_warmup_iters": self._warm_up_iters})
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        config.update({"prior": self.prior})
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        config.update({"_annealing_mode": self._annealing_mode})
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        return config

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    def call(self, z, **kwargs):
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        """Updates Layer's call method"""

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        true_samples = self.prior.sample(self.batch_size)
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        # Define and update MMD weight for warmup
        if self._warm_up_iters > 0:
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            if self._annealing_mode in ["linear", "sigmoid"]:
                mmd_weight = tf.cast(
                    K.min([self._iters / self._warm_up_iters, 1.0]), tf.float32
                )
                if self._annealing_mode == "sigmoid":
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                    mmd_weight = tf.math.sigmoid(
                        (2 * mmd_weight - 1) / (mmd_weight - mmd_weight ** 2)
                    )
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            else:
                raise NotImplementedError(
                    "annealing_mode must be one of 'linear' and 'sigmoid'"
                )
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        else:
            mmd_weight = tf.cast(1.0, tf.float32)

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        mmd_batch = mmd_weight * compute_mmd((true_samples, z))
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        self.add_loss(K.mean(mmd_batch), inputs=z)
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        self.add_metric(mmd_batch, aggregation="mean", name="mmd")
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        self.add_metric(mmd_weight, aggregation="mean", name="mmd_rate")
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        return z
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class ClusterOverlap(Layer):
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    """
    Identity layer that measures the overlap between the components of the latent Gaussian Mixture
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    using the the entropy of the nearest neighbourhood. If self.loss_weight > 0, it adds a regularization
    penalty to the loss function
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    """

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    def __init__(
        self,
        encoding_dim: int,
        k: int = 100,
        loss_weight: float = False,
        samples: int = 512,
        *args,
        **kwargs
    ):
        self.enc = encoding_dim
        self.k = k
        self.loss_weight = loss_weight
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        self.min_confidence = 0.25
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        self.samples = samples
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        super(ClusterOverlap, self).__init__(*args, **kwargs)
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    def get_config(self):  # pragma: no cover
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        """Updates Constraint metadata"""

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        config = super().get_config().copy()
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        config.update({"enc": self.enc})
        config.update({"k": self.k})
        config.update({"loss_weight": self.loss_weight})
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        config.update({"min_confidence": self.min_confidence})
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        config.update({"samples": self.samples})
        return config

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    @tf.function
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    def call(self, encodings, categorical, **kwargs):
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        """Updates Layer's call method"""
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        hard_groups = tf.math.argmax(categorical, axis=1)
        max_groups = tf.reduce_max(categorical, axis=1)
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        # Iterate over samples and compute purity across neighbourhood
        self.samples = tf.reduce_min([self.samples, encodings.shape[0]])
        random_idxs = range(encoding.shape[0])
        random_idxs = tf.random.categorical(
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            tf.expand_dims(random_idxs / tf.reduce_sum(random_idxs), 0), self.samples
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        )
        purity_vector = tf.zeros(self.samples)
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        for i, sample in enumerate(random_idxs):
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            neighborhood = get_k_nearest_neighbors(encodings, sample, self.k)
            neighborhood = tf.reshape(neighborhood, neighborhood.shape[1])
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            z = hard_groups[neighborhood]

            # Compute Shannon entropy across samples
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            neigh_entropy = compute_shannon_entropy(z)
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            # Add result to pre allocated array
            purity_vector[i] = neigh_entropy

        neighbourhood_entropy = purity_vector * max_groups[random_idxs]

        self.add_metric(
            len(set(hard_groups[max_groups >= self.min_confidence])),
            aggregation="mean",
            name="number_of_populated_clusters",
        )

        self.add_metric(
            max_groups,
            aggregation="mean",
            name="average_confidence_in_selected_cluster",
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        )
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        self.add_metric(
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            neighbourhood_entropy, aggregation="mean", name="neighbourhood_entropy"
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        )
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        if self.loss_weight:
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            self.add_loss(neighbourhood_entropy, inputs=[target, categorical])
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        return encodings