likelihood 1.5.8__tar.gz → 2.0.0__tar.gz

{likelihood-1.5.8 → likelihood-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: likelihood
-Version: 1.5.8
+Version: 2.0.0
 Summary: A package that performs the maximum likelihood algorithm.
 Home-page: https://github.com/jzsmoreno/likelihood/
 Author: J. A. Moreno-Guerra
@@ -20,9 +20,10 @@ Requires-Dist: pydocstyle>=6.3.0
 Requires-Dist: flake8>=6.0.0
 Requires-Dist: isort>=5.12.0
 Requires-Dist: mypy>=1.4.1
-Requires-Dist: numpy<2.0.0
+Requires-Dist: numpy<3.0.0,>=1.26.4
 Requires-Dist: pydot==2.0.0
 Requires-Dist: matplotlib
+Requires-Dist: packaging
 Requires-Dist: graphviz
 Requires-Dist: seaborn
 Requires-Dist: pyyaml
@@ -32,7 +33,7 @@ Requires-Dist: tqdm
 Provides-Extra: full
 Requires-Dist: networkx; extra == "full"
 Requires-Dist: pyvis; extra == "full"
-Requires-Dist: tensorflow==2.15.0; extra == "full"
+Requires-Dist: tensorflow>=2.15.0; extra == "full"
 Requires-Dist: keras-tuner; extra == "full"
 Requires-Dist: scikit-learn; extra == "full"
 Dynamic: author

likelihood-2.0.0/likelihood/graph/__init__.py

@@ -0,0 +1,9 @@
+import tensorflow as tf
+from packaging import version
+
+from .graph import *
+
+if version.parse(tf.__version__) > version.parse("2.15.0"):
+    from ._nn import *
+else:
+    from .nn import *

likelihood-2.0.0/likelihood/graph/_nn.py

@@ -0,0 +1,421 @@
+import logging
+import os
+
+os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
+logging.getLogger("tensorflow").setLevel(logging.ERROR)
+
+import warnings
+from multiprocessing import Pool, cpu_count
+from typing import Any, List, Tuple
+
+import numpy as np
+import pandas as pd
+import tensorflow as tf
+from IPython.display import clear_output
+from pandas.core.frame import DataFrame
+from sklearn.metrics import f1_score
+
+tf.get_logger().setLevel("ERROR")
+
+from likelihood.tools import LoRALayer
+
+
+def compare_similarity_np(arr1: np.ndarray, arr2: np.ndarray, threshold: float = 0.05) -> int:
+    """Vectorized similarity comparison between two numeric/categorical arrays."""
+    arr1 = np.asarray(arr1)
+    arr2 = np.asarray(arr2)
+
+    is_numeric = np.vectorize(
+        lambda a, b: isinstance(a, (int, float)) and isinstance(b, (int, float))
+    )(arr1, arr2)
+
+    similarity = np.zeros_like(arr1, dtype=bool)
+
+    if np.any(is_numeric):
+        a_num = arr1[is_numeric].astype(float)
+        b_num = arr2[is_numeric].astype(float)
+
+        both_zero = (a_num == 0) & (b_num == 0)
+        nonzero = ~both_zero & (a_num != 0) & (b_num != 0)
+        ratio = np.zeros_like(a_num)
+        ratio[nonzero] = np.maximum(a_num[nonzero], b_num[nonzero]) / np.minimum(
+            a_num[nonzero], b_num[nonzero]
+        )
+        numeric_similar = both_zero | ((1 - threshold <= ratio) & (ratio <= 1 + threshold))
+
+        similarity[is_numeric] = numeric_similar
+
+    similarity[~is_numeric] = arr1[~is_numeric] == arr2[~is_numeric]
+
+    return np.count_nonzero(similarity)
+
+
+def compare_pair(pair, data, similarity, threshold):
+    i, j = pair
+    sim = compare_similarity_np(data[i], data[j], threshold=threshold)
+    return (i, j, 1 if sim >= similarity else 0)
+
+
+def cal_adjacency_matrix(
+    df: pd.DataFrame, exclude_subset: List[str] = [], sparse: bool = True, **kwargs
+) -> Tuple[dict, np.ndarray]:
+    """
+    Calculates the adjacency matrix for a given DataFrame using parallel processing.
+
+    Parameters
+    ----------
+    df : `DataFrame`
+        The input DataFrame containing the features.
+    exclude_subset : `List[str]`, `optional`
+        A list of features to exclude from the calculation of the adjacency matrix.
+    sparse : `bool`, `optional`
+        Whether to return a sparse matrix or a dense matrix.
+    **kwargs : `dict`
+        Additional keyword arguments to pass to the `compare_similarity` function.
+
+    Returns
+    -------
+    adj_dict : `dict`
+        A dictionary containing the features.
+    adjacency_matrix : `ndarray`
+        The adjacency matrix.
+
+    Keyword Arguments:
+    ----------
+    similarity: `int`
+        The minimum number of features that must be the same in both arrays to be considered similar.
+    threshold : `float`
+        The threshold value used in the `compare_similarity` function. Default is 0.0
+    """
+    if len(exclude_subset) > 0:
+        columns = [col for col in df.columns if col not in exclude_subset]
+        df_ = df[columns].copy()
+    else:
+        df_ = df.copy()
+
+    assert len(df_) > 0
+
+    similarity = kwargs.get("similarity", len(df_.columns) - 1)
+    threshold = kwargs.get("threshold", 0.05)
+    assert similarity <= df_.shape[1]
+
+    data = df_.to_numpy()
+    n = len(data)
+
+    adj_dict = {i: data[i].tolist() for i in range(n)}
+
+    def pair_generator():
+        for i in range(n):
+            for j in range(i, n):
+                yield (i, j)
+
+    with Pool(cpu_count()) as pool:
+        results = pool.starmap(
+            compare_pair, ((pair, data, similarity, threshold) for pair in pair_generator())
+        )
+
+    adjacency_matrix = np.zeros((n, n), dtype=np.uint8)
+    for i, j, val in results:
+        if val:
+            adjacency_matrix[i, j] = 1
+            adjacency_matrix[j, i] = 1
+
+    if sparse:
+        num_nodes = adjacency_matrix.shape[0]
+
+        indices = np.argwhere(adjacency_matrix != 0.0)
+        indices = tf.constant(indices, dtype=tf.int64)
+        values = tf.constant(adjacency_matrix[indices[:, 0], indices[:, 1]], dtype=tf.float32)
+        adjacency_matrix = tf.sparse.SparseTensor(
+            indices=indices, values=values, dense_shape=(num_nodes, num_nodes)
+        )
+
+    return adj_dict, adjacency_matrix
+
+
+class Data:
+    def __init__(
+        self,
+        df: DataFrame,
+        target: str | None = None,
+        exclude_subset: List[str] = [],
+        **kwargs,
+    ):
+        sparse = kwargs.get("sparse", True)
+        threshold = kwargs.get("threshold", 0.05)
+        _, adjacency = cal_adjacency_matrix(
+            df, exclude_subset=exclude_subset, sparse=sparse, threshold=threshold
+        )
+        if target is not None:
+            X = df.drop(columns=[target] + exclude_subset)
+        else:
+            X = df.drop(columns=exclude_subset)
+        self.columns = X.columns
+        X = X.to_numpy()
+        self.x = np.asarray(X).astype(np.float32)
+        self.adjacency = adjacency
+        if target is not None:
+            self.y = np.asarray(df[target].values).astype(np.int32)
+
+
+@tf.keras.utils.register_keras_serializable(package="Custom", name="VanillaGNNLayer")
+class VanillaGNNLayer(tf.keras.layers.Layer):
+    def __init__(self, dim_in, dim_out, rank=None, kernel_initializer="glorot_uniform", **kwargs):
+        super(VanillaGNNLayer, self).__init__(**kwargs)
+        self.dim_in = dim_in
+        self.dim_out = dim_out
+        self.rank = rank
+        self.kernel_initializer = kernel_initializer
+        self.linear = None
+
+    def build(self, input_shape):
+        if self.rank:
+            self.linear = LoRALayer(self.dim_out, rank=self.rank)
+        else:
+            self.linear = tf.keras.layers.Dense(
+                self.dim_out, use_bias=False, kernel_initializer=self.kernel_initializer
+            )
+        super(VanillaGNNLayer, self).build(input_shape)
+
+    def call(self, x, adjacency):
+        x = self.linear(x)
+        x = tf.sparse.sparse_dense_matmul(adjacency, x)
+        return x
+
+    def get_config(self):
+        config = super(VanillaGNNLayer, self).get_config()
+        config.update(
+            {
+                "dim_in": self.dim_in,
+                "dim_out": self.dim_out,
+                "rank": self.rank,
+                "kernel_initializer": (
+                    None
+                    if self.rank
+                    else tf.keras.initializers.serialize(self.linear.kernel_initializer)
+                ),
+            }
+        )
+        return config
+
+    @classmethod
+    def from_config(cls, config):
+        if config.get("kernel_initializer") is not None:
+            config["kernel_initializer"] = tf.keras.initializers.deserialize(
+                config["kernel_initializer"]
+            )
+        return cls(**config)
+
+
+class VanillaGNN:
+    def __init__(self, dim_in, dim_h, dim_out, rank=2, **kwargs):
+        self.dim_in = dim_in
+        self.dim_h = dim_h
+        self.dim_out = dim_out
+        self.rank = rank
+
+        self.gnn1 = VanillaGNNLayer(self.dim_in, self.dim_h, self.rank)
+        self.gnn2 = VanillaGNNLayer(self.dim_h, self.dim_h, self.rank)
+        self.gnn3 = VanillaGNNLayer(self.dim_h, self.dim_out, None)
+
+        self.build()
+
+    def build(self):
+        x_in = tf.keras.Input(shape=(self.dim_in,), name="node_features")
+        adjacency_in = tf.keras.Input(shape=(None,), sparse=True, name="adjacency")
+
+        gnn1 = VanillaGNNLayer(self.dim_in, self.dim_h, self.rank)
+        gnn2 = VanillaGNNLayer(self.dim_h, self.dim_h, self.rank)
+        gnn3 = VanillaGNNLayer(self.dim_h, self.dim_out, rank=None)
+
+        h = gnn1(x_in, adjacency_in)
+        h = tf.keras.activations.tanh(h)
+        h = gnn2(h, adjacency_in)
+        h = gnn3(h, adjacency_in)
+        out = tf.keras.activations.softmax(h, axis=-1)
+
+        self.model = tf.keras.Model(
+            inputs=[x_in, adjacency_in], outputs=out, name="VanillaGNN_Functional"
+        )
+
+    @tf.function
+    def __call__(self, x, adjacency):
+        return self.model([x, adjacency])
+
+    def f1_macro(self, y_true, y_pred):
+        return f1_score(y_true, y_pred, average="macro")
+
+    def compute_f1_score(self, logits, labels):
+        predictions = tf.argmax(logits, axis=1, output_type=tf.int32)
+        true_labels = tf.cast(labels, tf.int32)
+        return self.f1_macro(true_labels.numpy(), predictions.numpy())
+
+    def evaluate(self, x, adjacency, y):
+        y = tf.cast(y, tf.int32)
+        out = self(x, adjacency)
+        loss = tf.nn.sparse_softmax_cross_entropy_with_logits(labels=y, logits=out)
+        loss = tf.reduce_mean(loss)
+        f1 = round(self.compute_f1_score(out, y), 4)
+        return loss.numpy(), f1
+
+    def test(self, data):
+        data.x = tf.convert_to_tensor(data.x) if not tf.is_tensor(data.x) else data.x
+        out = self(data.x, data.adjacency)
+        test_f1 = self.compute_f1_score(out, data.y)
+        return round(test_f1, 4)
+
+    def predict(self, data):
+        data.x = tf.convert_to_tensor(data.x) if not tf.is_tensor(data.x) else data.x
+        out = self(data.x, data.adjacency)
+        return tf.argmax(out, axis=1, output_type=tf.int32).numpy()
+
+    def save(self, filepath, **kwargs):
+        """
+        Save the complete model including all components.
+
+        Parameters
+        ----------
+        filepath : str
+            Path where to save the model.
+        """
+        import os
+
+        # Create directory if it doesn't exist
+        os.makedirs(filepath, exist_ok=True)
+
+        self.model.save(os.path.join(filepath, "main_model.keras"))
+
+        # Save configuration
+        import json
+
+        config = self.get_config()
+
+        with open(os.path.join(filepath, "config.json"), "w") as f:
+            json.dump(config, f, indent=2)
+
+    @classmethod
+    def load(cls, filepath):
+        """
+        Load a complete model from saved components.
+
+        Parameters
+        ----------
+        filepath : str
+            Path where the model was saved.
+
+        Returns
+        -------
+        VanillaGNN
+            The loaded model instance.
+        """
+        import json
+        import os
+
+        # Load configuration
+        with open(os.path.join(filepath, "config.json"), "r") as f:
+            config = json.load(f)
+
+        # Create new instance
+        instance = cls(**config)
+
+        instance.model = tf.keras.models.load_model(os.path.join(filepath, "main_model.keras"))
+
+        return instance
+
+    def get_config(self):
+        return {
+            "dim_in": self.dim_in,
+            "dim_h": self.dim_h,
+            "dim_out": self.dim_out,
+            "rank": self.rank,
+        }
+
+    @classmethod
+    def from_config(cls, config):
+        return cls(
+            dim_in=config["dim_in"],
+            dim_h=config["dim_h"],
+            dim_out=config["dim_out"],
+            rank=config["rank"],
+        )
+
+    def get_build_config(self):
+        config = {
+            "dim_in": self.dim_in,
+            "dim_h": self.dim_h,
+            "dim_out": self.dim_out,
+            "rank": self.rank,
+        }
+        return config
+
+    @classmethod
+    def build_from_config(cls, config):
+        return cls(**config)
+
+    @tf.function
+    def train_step(self, batch_x, batch_adjacency, batch_y, optimizer):
+        with tf.GradientTape() as tape:
+            out = self(batch_x, batch_adjacency)
+            loss = tf.nn.sparse_softmax_cross_entropy_with_logits(labels=batch_y, logits=out)
+            loss = tf.reduce_mean(loss)
+        gradients = tape.gradient(loss, self.model.trainable_variables)
+        optimizer.apply_gradients(zip(gradients, self.model.trainable_variables))
+        return loss
+
+    def fit(self, data, epochs, batch_size, test_size=0.2, optimizer="adam"):
+        optimizers = {
+            "sgd": tf.keras.optimizers.SGD(),
+            "adam": tf.keras.optimizers.Adam(),
+            "adamw": tf.keras.optimizers.AdamW(),
+            "adadelta": tf.keras.optimizers.Adadelta(),
+            "rmsprop": tf.keras.optimizers.RMSprop(),
+        }
+        optimizer = optimizers[optimizer]
+        train_losses = []
+        train_f1_scores = []
+        val_losses = []
+        val_f1_scores = []
+
+        num_nodes = len(data.x)
+        split_index = int((1 - test_size) * num_nodes)
+
+        X_train, X_test = data.x[:split_index], data.x[split_index:]
+        y_train, y_test = data.y[:split_index], data.y[split_index:]
+
+        adjacency_train = tf.sparse.slice(data.adjacency, [0, 0], [split_index, split_index])
+        adjacency_test = tf.sparse.slice(
+            data.adjacency,
+            [split_index, split_index],
+            [num_nodes - split_index, num_nodes - split_index],
+        )
+
+        batch_starts = np.arange(0, len(X_train), batch_size)
+        for epoch in range(epochs):
+            np.random.shuffle(batch_starts)
+            for start in batch_starts:
+                end = start + batch_size
+                batch_x = X_train[start:end, :]
+                batch_adjacency = tf.sparse.slice(
+                    adjacency_train, [start, start], [batch_size, batch_size]
+                )
+                batch_y = y_train[start:end]
+                train_loss = self.train_step(batch_x, batch_adjacency, batch_y, optimizer)
+
+            train_loss, train_f1 = self.evaluate(X_train, adjacency_train, y_train)
+            train_losses.append(train_loss)
+            train_f1_scores.append(train_f1)
+
+            if epoch % 5 == 0:
+                clear_output(wait=True)
+                val_loss, val_f1 = self.evaluate(X_test, adjacency_test, y_test)
+                val_losses.append(val_loss)
+                val_f1_scores.append(val_f1)
+                print(
+                    f"Epoch {epoch:>3} | Train Loss: {train_loss:.4f} | Train F1: {train_f1:.4f} | Val Loss: {val_loss:.4f} | Val F1: {val_f1:.4f}"
+                )
+
+        return train_losses, train_f1_scores, val_losses, val_f1_scores
+
+
+if __name__ == "__main__":
+    print("Examples will be running below")

likelihood-2.0.0/likelihood/models/deep/__init__.py

@@ -0,0 +1,12 @@
+import tensorflow as tf
+from packaging import version
+
+if version.parse(tf.__version__) > version.parse("2.15.0"):
+    from ._autoencoders import *
+    from ._predictor import GetInsights
+else:
+    from .autoencoders import *
+    from .predictor import GetInsights
+
+from .gan import *
+from .rl import *