diff --git a/.gigaide/gigaide.properties b/.gigaide/gigaide.properties new file mode 100644 index 0000000..652f4a7 --- /dev/null +++ b/.gigaide/gigaide.properties @@ -0,0 +1,1246 @@ +## changed at Sun Dec 15 17:50:53 MSK 2024 +#Sun Dec 15 17:50:53 MSK 2024 +com.gigaide.elements.ext.marker.solution.BeanMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.ConfigMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.DataMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.EndpointMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.EntryMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.FactoryMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.MessageMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.TaskMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.TransactionMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.type.AnnotationTypePsi.shouldMark=true 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+com.gigaide.elements.ext.marker.solution.DataMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.EndpointMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.EntryMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.FactoryMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.MessageMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.TaskMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.solution.TransactionMarkedPsi.shouldMark=true +com.gigaide.elements.ext.marker.type.AnnotationTypePsi.shouldMark=true +com.gigaide.elements.ext.marker.type.CallTypePsi.shouldMark=true +com.gigaide.elements.ext.marker.type.ImplTypePsi.shouldMark=true +com.gigaide.elements.ext.menu.ToFrameworkMarkerAction.shouldAct=true +com.gigaide.elements.ext.menu.ToSolutionMarkerAction.shouldAct=true +com.gigaide.elements.ext.stack.allure.AddAttachmentCall.checkElement=true 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+com.gigaide.elements.service.stack.config.StackConfigHolder.autoLoadableNotify=false +com.gigaide.elements.service.stack.config.StackConfigHolder.includeTests=false diff --git a/hc/README.md b/hc/README.md new file mode 100644 index 0000000..68fae6e --- /dev/null +++ b/hc/README.md @@ -0,0 +1,134 @@ +# Hypergraph Clustering + +## Описание +Библиотека предоставляет инструменты для агломеративной кластеризации гиперграфов. Она включает методы преобразования гиперграфов в матрицы инцидентности и смежности, автоматический выбор количества кластеров, а также метрики оценки качества кластеризации. + +Кластеризация гиперграфов полезна в задачах анализа данных, таких как: +- Социальные сети +- Транспортные системы +- Биологические сети +- Анализ текстов и документов + +Библиотека использует возможности `scikit-learn` и `scipy` для вычислений. + +--- + +## Установка +1. Установите зависимости и проект: + ```bash + pip install -e . + ``` + +--- + +## Использование + +### Пример 1: Кластеризация гиперграфа с заданным количеством кластеров +```python +from hypergraph_clustering.utils.graph_conversion import hypergraph_to_incidence_matrix, incidence_to_adjacency +from hypergraph_clustering.clustering.agglomerative import AgglomerativeHypergraphClustering + +# Пример гиперграфа +hyperedges = [[0, 1, 2], [1, 2, 3], [3, 4]] + +# Преобразуем гиперграф в матрицы +incidence_matrix = hypergraph_to_incidence_matrix(hyperedges) +adjacency_matrix = incidence_to_adjacency(incidence_matrix) + +# Кластеризация +clustering = AgglomerativeHypergraphClustering(n_clusters=2) +labels = clustering.fit(adjacency_matrix) + +print("Кластеры:", labels) +``` + +### Пример 2: Автоматический выбор количества кластеров +```python +from hypergraph_clustering.clustering.auto_clustering import AutoClusterHypergraphClustering + +clustering = AutoClusterHypergraphClustering(linkage="average", max_clusters=5, scoring="silhouette") +labels = clustering.fit(adjacency_matrix) + +print("Кластеры:", labels) +print("Лучшее количество кластеров:", clustering.best_n_clusters) +print("Оценка:", clustering.best_score) +``` + +--- + +## Теоретическая справка + +Пример гиперграфа: +- Узлы: {0, 1, 2, 3, 4} +- Гиперрёбра: {{0, 1, 2}, {1, 2, 3}, {3, 4}} + +#### Преобразования гиперграфа +Для применения алгоритмов кластеризации гиперграфы преобразуются: +1. **Матрица инцидентности**: показывает связь между узлами и гиперрёбрами. +2. **Матрица смежности**: вычисляется на основе матрицы инцидентности, показывает связи между узлами. + +--- + +### Алгоритмы кластеризации + +#### Агломеративная кластеризация +Метод «снизу вверх», который начинает с представления каждого узла как отдельного кластера и объединяет их итеративно на основе заданного метода связи (`ward`, `complete`, `average`, `single`). + +- **Ward**: минимизирует увеличение внутрикластерной дисперсии. +- **Complete**: учитывает максимальное расстояние между узлами. +- **Average**: основывается на среднем расстоянии между узлами. +- **Single**: минимизирует минимальное расстояние между узлами. + +#### Автоматический выбор количества кластеров +Для автоматического выбора количества кластеров используется одна из метрик: +- **Silhouette**: оценивает, насколько хорошо данные сгруппированы. +- **Calinski-Harabasz**: измеряет плотность и разделение кластеров. +- **Davies-Bouldin**: оценивает близость между кластерами (меньше лучше). + +--- + +## Структура проекта + +``` +hypergraph_clustering/ +├── clustering/ +│ ├── agglomerative.py # Класс для агломеративной кластеризации +│ ├── auto_clustering.py # Класс для автоматического выбора количества кластеров +│ └── __init__.py +├── metrics/ +│ ├── evaluation.py # Метрики для оценки кластеризации +│ └── __init__.py +├── tests/ +│ ├── test_agglomerative.py # Тесты для агломеративной кластеризации +│ ├── test_auto_clustering.py # Тесты для автоматического выбора кластеров +│ ├── test_graph_conversion.py # Тесты для преобразования гиперграфов +│ └── __init__.py +├── utils/ +│ ├── graph_conversion.py # Утилиты для работы с гиперграфами +│ ├── examples.py # Примеры гиперграфов +│ └── __init__.py +├── README.md # Документация +├── setup.py # Файл установки +├── requirements.txt # Зависимости +└── data/ # Примеры гиперграфов в формате JSON + ├── social_network.json + ├── transport_network.json + └── biological_network.json +``` + +--- + +## Тестирование проекта +Для проверки работоспособности проекта доступны тесты. Запустите их с помощью: +```bash +pytest hypergraph_clustering/tests/ +``` + +--- + +## Источники +- [Scikit-learn Documentation](https://scikit-learn.org/stable/) +- [Silhouette Coefficient](https://en.wikipedia.org/wiki/Silhouette_(clustering)) +- [Agglomerative Clustering](https://en.wikipedia.org/wiki/Hierarchical_clustering) + +--- \ No newline at end of file diff --git a/hc/data/biological_network.json b/hc/data/biological_network.json new file mode 100644 index 0000000..3d537a0 --- /dev/null +++ b/hc/data/biological_network.json @@ -0,0 +1,44 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2, + 3, + 4 + ], + [ + 2, + 4, + 5, + 6 + ], + [ + 6, + 7, + 8, + 9, + 10 + ], + [ + 3, + 8, + 11, + 12 + ], + [ + 1, + 9, + 10, + 13, + 14 + ], + [ + 5, + 7, + 12, + 13 + ] + ], + "num_nodes": 15 +} \ No newline at end of file diff --git a/hc/data/education_network.json b/hc/data/education_network.json new file mode 100644 index 0000000..72eeeed --- /dev/null +++ b/hc/data/education_network.json @@ -0,0 +1,38 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2 + ], + [ + 2, + 3, + 4, + 5 + ], + [ + 5, + 6, + 7 + ], + [ + 3, + 6, + 8, + 9 + ], + [ + 8, + 9, + 10 + ], + [ + 1, + 7, + 9, + 10 + ] + ], + "num_nodes": 11 +} \ No newline at end of file diff --git a/hc/data/electric_network.json b/hc/data/electric_network.json new file mode 100644 index 0000000..75a5839 --- /dev/null +++ b/hc/data/electric_network.json @@ -0,0 +1,39 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2 + ], + [ + 2, + 3, + 4, + 5 + ], + [ + 5, + 6, + 7 + ], + [ + 3, + 6, + 8, + 9 + ], + [ + 8, + 9, + 10, + 11 + ], + [ + 1, + 4, + 7, + 10 + ] + ], + "num_nodes": 12 +} \ No newline at end of file diff --git a/hc/data/healthcare_network.json b/hc/data/healthcare_network.json new file mode 100644 index 0000000..8b2e61f --- /dev/null +++ b/hc/data/healthcare_network.json @@ -0,0 +1,35 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2 + ], + [ + 2, + 3, + 4 + ], + [ + 4, + 5, + 6 + ], + [ + 6, + 7, + 8 + ], + [ + 1, + 4, + 7 + ], + [ + 0, + 3, + 6 + ] + ], + "num_nodes": 9 +} \ No newline at end of file diff --git a/hc/data/hypergraph_social_network.json b/hc/data/hypergraph_social_network.json new file mode 100644 index 0000000..5498aea --- /dev/null +++ b/hc/data/hypergraph_social_network.json @@ -0,0 +1,12 @@ +{ + "hyperedges": [ + [0, 1, 2], + [2, 3, 4, 5], + [5, 6, 7], + [7, 8, 9, 10], + [10, 11, 12], + [1, 3, 8, 12] + ], + "num_nodes": 13 + } + \ No newline at end of file diff --git a/hc/data/iot_network.json b/hc/data/iot_network.json new file mode 100644 index 0000000..8b2e61f --- /dev/null +++ b/hc/data/iot_network.json @@ -0,0 +1,35 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2 + ], + [ + 2, + 3, + 4 + ], + [ + 4, + 5, + 6 + ], + [ + 6, + 7, + 8 + ], + [ + 1, + 4, + 7 + ], + [ + 0, + 3, + 6 + ] + ], + "num_nodes": 9 +} \ No newline at end of file diff --git a/hc/data/logistics_network.json b/hc/data/logistics_network.json new file mode 100644 index 0000000..1771b71 --- /dev/null +++ b/hc/data/logistics_network.json @@ -0,0 +1,40 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2, + 3 + ], + [ + 3, + 4, + 5, + 6 + ], + [ + 6, + 7, + 8 + ], + [ + 1, + 4, + 7 + ], + [ + 2, + 5, + 8, + 9, + 10 + ], + [ + 0, + 3, + 7, + 10 + ] + ], + "num_nodes": 14 +} \ No newline at end of file diff --git a/hc/data/sample_hypergraph.json b/hc/data/sample_hypergraph.json new file mode 100644 index 0000000..0fa1c4c --- /dev/null +++ b/hc/data/sample_hypergraph.json @@ -0,0 +1,5 @@ +{ + "hypergraph_1": [[0, 1, 2], [1, 2, 3], [3, 4]], + "hypergraph_2": [[0, 1], [2, 3], [4]], + "hypergraph_3": [[0, 1, 2, 3]] +} diff --git a/hc/data/social_network.json b/hc/data/social_network.json new file mode 100644 index 0000000..9f01168 --- /dev/null +++ b/hc/data/social_network.json @@ -0,0 +1,38 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2 + ], + [ + 2, + 3, + 4, + 5 + ], + [ + 5, + 6, + 7 + ], + [ + 7, + 8, + 9, + 10 + ], + [ + 10, + 11, + 12 + ], + [ + 1, + 3, + 8, + 12 + ] + ], + "num_nodes": 13 +} \ No newline at end of file diff --git a/hc/data/supply_chain.json b/hc/data/supply_chain.json new file mode 100644 index 0000000..8b2e61f --- /dev/null +++ b/hc/data/supply_chain.json @@ -0,0 +1,35 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2 + ], + [ + 2, + 3, + 4 + ], + [ + 4, + 5, + 6 + ], + [ + 6, + 7, + 8 + ], + [ + 1, + 4, + 7 + ], + [ + 0, + 3, + 6 + ] + ], + "num_nodes": 9 +} \ No newline at end of file diff --git a/hc/data/transport_network.json b/hc/data/transport_network.json new file mode 100644 index 0000000..2a4bf1d --- /dev/null +++ b/hc/data/transport_network.json @@ -0,0 +1,46 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2, + 3 + ], + [ + 3, + 4, + 5, + 6 + ], + [ + 6, + 7, + 8 + ], + [ + 1, + 4, + 7 + ], + [ + 2, + 5, + 8, + 9, + 10 + ], + [ + 10, + 11, + 12, + 13 + ], + [ + 0, + 13, + 6, + 9 + ] + ], + "num_nodes": 14 +} \ No newline at end of file diff --git a/hc/data/urban_infrastructure.json b/hc/data/urban_infrastructure.json new file mode 100644 index 0000000..8b2e61f --- /dev/null +++ b/hc/data/urban_infrastructure.json @@ -0,0 +1,35 @@ +{ + "hyperedges": [ + [ + 0, + 1, + 2 + ], + [ + 2, + 3, + 4 + ], + [ + 4, + 5, + 6 + ], + [ + 6, + 7, + 8 + ], + [ + 1, + 4, + 7 + ], + [ + 0, + 3, + 6 + ] + ], + "num_nodes": 9 +} \ No newline at end of file diff --git a/hc/hypergraph_clustering/__init__.py b/hc/hypergraph_clustering/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/hc/hypergraph_clustering/clustering/__init__.py b/hc/hypergraph_clustering/clustering/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/hc/hypergraph_clustering/clustering/agglomerative.py b/hc/hypergraph_clustering/clustering/agglomerative.py new file mode 100644 index 0000000..ed11379 --- /dev/null +++ b/hc/hypergraph_clustering/clustering/agglomerative.py @@ -0,0 +1,138 @@ +from sklearn.cluster import AgglomerativeClustering +from sklearn.metrics import silhouette_score, calinski_harabasz_score, davies_bouldin_score +from scipy.spatial.distance import squareform, pdist +import numpy as np + + +class AgglomerativeHypergraphClustering: + def __init__(self, n_clusters=2, linkage="ward", normalize=True): + """ + Класс для агломеративной кластеризации гиперграфов. + + :param n_clusters: Количество кластеров. + :param linkage: Метод связи ('ward', 'complete', 'average', 'single'). + :param normalize: Нормализовать ли матрицу смежности перед кластеризацией. + """ + self.n_clusters = n_clusters + self.linkage = linkage + self.normalize = normalize + self.model = None + + def normalize_adjacency(self, adjacency_matrix): + """ + Нормализует матрицу смежности с использованием нормализации строки. + + :param adjacency_matrix: np.ndarray, матрица смежности. + :return: np.ndarray, нормализованная матрица. + """ + row_sums = adjacency_matrix.sum(axis=1, keepdims=True) + normalized_matrix = adjacency_matrix / np.maximum(row_sums, 1e-10) + return normalized_matrix + + def compute_distance_matrix(self, adjacency_matrix): + """ + Преобразует матрицу смежности в матрицу расстояний. + + :param adjacency_matrix: np.ndarray, матрица смежности. + :return: np.ndarray, матрица расстояний. + """ + max_distance = np.max(adjacency_matrix) + 1 + distance_matrix = np.where( + adjacency_matrix > 0, + 1 / adjacency_matrix, # Инвертируем веса для положительных значений + max_distance # Устанавливаем большое значение для недостижимых узлов + ) + np.fill_diagonal(distance_matrix, 0) # Убираем петли + return distance_matrix + + def compute_laplacian(self, adjacency_matrix): + """ + Вычисляет матрицу Лапласа графа. + + :param adjacency_matrix: np.ndarray, матрица смежности. + :return: np.ndarray, матрица Лапласа. + """ + degree_matrix = np.diag(adjacency_matrix.sum(axis=1)) + laplacian_matrix = degree_matrix - adjacency_matrix + return laplacian_matrix + + def fit(self, adjacency_matrix): + """ + Выполняет кластеризацию на основе матрицы смежности. + + :param adjacency_matrix: np.ndarray, матрица смежности графа. + :return: np.ndarray, метки кластеров. + """ + max_distance = np.max(adjacency_matrix) + 1 + + # Исправляем проблему деления на ноль + distance_matrix = np.zeros_like(adjacency_matrix, dtype=float) + non_zero_indices = adjacency_matrix > 0 + distance_matrix[non_zero_indices] = 1 / adjacency_matrix[non_zero_indices] + distance_matrix[~non_zero_indices] = max_distance + np.fill_diagonal(distance_matrix, 0) + + if self.linkage == "ward": + # Для ward используем матрицу признаков (смежности) + self.model = AgglomerativeClustering( + n_clusters=self.n_clusters, + linkage=self.linkage + ) + labels = self.model.fit_predict(adjacency_matrix) + else: + # Для остальных методов используем метрику "precomputed" + condensed_distance_matrix = squareform(distance_matrix) + self.model = AgglomerativeClustering( + n_clusters=self.n_clusters, + metric="precomputed", + linkage=self.linkage + ) + labels = self.model.fit_predict(squareform(condensed_distance_matrix)) + + self.labels_ = labels + return labels + + + def evaluate(self, adjacency_matrix): + """ + Оценивает качество кластеризации с использованием различных метрик. + + :param adjacency_matrix: np.ndarray, матрица смежности графа. + :return: dict, значения метрик. + """ + if not hasattr(self, "labels_"): + raise ValueError("Кластеризация не выполнена. Сначала вызовите fit().") + + metrics = { + "silhouette_score": silhouette_score(adjacency_matrix, self.labels_, metric="precomputed"), + "calinski_harabasz_score": calinski_harabasz_score(adjacency_matrix, self.labels_), + "davies_bouldin_score": davies_bouldin_score(adjacency_matrix, self.labels_), + } + return metrics + + def spectral_embedding(self, adjacency_matrix, n_components=2): + """ + Выполняет спектральное вложение на основе матрицы Лапласа. + + :param adjacency_matrix: np.ndarray, матрица смежности. + :param n_components: int, количество компонент вложения. + :return: np.ndarray, спектральные вложения. + """ + laplacian = self.compute_laplacian(adjacency_matrix) + eigenvalues, eigenvectors = np.linalg.eigh(laplacian) + return eigenvectors[:, :n_components] + + def plot_clusters(self, adjacency_matrix): + """ + Визуализирует кластеры с использованием спектрального вложения. + + :param adjacency_matrix: np.ndarray, матрица смежности. + """ + import matplotlib.pyplot as plt + embeddings = self.spectral_embedding(adjacency_matrix) + plt.scatter(embeddings[:, 0], embeddings[:, 1], c=self.labels_, cmap="viridis", s=50) + plt.title("Clusters Visualization") + plt.xlabel("Component 1") + plt.ylabel("Component 2") + plt.colorbar(label="Cluster") + plt.show() diff --git a/hc/hypergraph_clustering/clustering/auto_clustering.py b/hc/hypergraph_clustering/clustering/auto_clustering.py new file mode 100644 index 0000000..435c064 --- /dev/null +++ b/hc/hypergraph_clustering/clustering/auto_clustering.py @@ -0,0 +1,104 @@ +from sklearn.cluster import AgglomerativeClustering +from sklearn.metrics import silhouette_score, calinski_harabasz_score, davies_bouldin_score +import numpy as np + +class AutoClusterHypergraphClustering: + """ + Класс для агломеративной кластеризации гиперграфов с автоматическим определением оптимального числа кластеров. + + Этот класс выполняет кластеризацию на основе матрицы смежности графа, автоматически + выбирая количество кластеров по заданным метрикам качества. Поддерживает различные методы связи, + а также позволяет варьировать максимальное количество кластеров для анализа. + + Атрибуты: + ---------- + linkage : str + Метод связи для агломеративного алгоритма ('ward', 'complete', 'average', 'single'). + + max_clusters : int + Максимальное число кластеров для анализа, среди которых выбирается оптимальное. + + scoring : str + Метрика для оценки качества кластеризации и выбора наилучшего количества кластеров. + Доступны следующие метрики: 'silhouette', 'calinski', 'davies'. + + best_n_clusters : int + Число кластеров, которое было определено как оптимальное. + + best_score : float + Оценка качества кластеризации для выбранного числа кластеров. + + labels_ : np.ndarray + Массив меток кластеров для каждой точки, вычисленных по оптимальной кластеризации. + + Методы: + ------- + fit(adjacency_matrix): + Выполняет кластеризацию на основе заданной матрицы смежности, выбирая оптимальное число кластеров. + + Примечание: + ----------- + Этот класс использует библиотеку sklearn для агломеративной кластеризации и оценки, + поэтому ожидается, что входная матрица смежности представлена в формате numpy.ndarray. + """ + + def __init__(self, linkage="ward", max_clusters=10, scoring="silhouette"): + """ + Класс для агломеративной кластеризации гиперграфов с автоматическим выбором количества кластеров. + + :param linkage: str, метод связи ('ward', 'complete', 'average', 'single'). + :param max_clusters: int, максимальное количество кластеров для анализа. + :param scoring: str, метрика для выбора лучшего количества кластеров ('silhouette', 'calinski', 'davies'). + """ + self.linkage = linkage + self.max_clusters = max_clusters + self.scoring = scoring + self.best_n_clusters = None + self.best_score = None + self.labels_ = None + + def fit(self, adjacency_matrix): + """ + Выполняет кластеризацию на основе матрицы смежности с автоматическим выбором количества кластеров. + + :param adjacency_matrix: np.ndarray, матрица смежности графа. + :return: np.ndarray, метки кластеров. + """ + max_distance = np.max(adjacency_matrix) + 1 # Максимальное расстояние + distance_matrix = np.where( + adjacency_matrix > 0, + 1 / adjacency_matrix, + max_distance + ) + np.fill_diagonal(distance_matrix, 0) + + scores = [] + for n_clusters in range(2, self.max_clusters + 1): + model = AgglomerativeClustering( + n_clusters=n_clusters, + metric="precomputed" if self.linkage != "ward" else None, + linkage=self.linkage + ) + labels = model.fit_predict(distance_matrix if self.linkage != "ward" else adjacency_matrix) + + # Оценка качества кластеризации + if self.scoring == "silhouette": + score = silhouette_score(distance_matrix if self.linkage != "ward" else adjacency_matrix, labels) + elif self.scoring == "calinski": + score = calinski_harabasz_score(adjacency_matrix, labels) + elif self.scoring == "davies": + score = -davies_bouldin_score(adjacency_matrix, labels) # Отрицательное значение, чтобы максимизировать + else: + raise ValueError(f"Неизвестная метрика оценки: {self.scoring}") + + scores.append((n_clusters, score)) + + # Находим лучшее количество кластеров + self.best_n_clusters, self.best_score = max(scores, key=lambda x: x[1]) + self.model = AgglomerativeClustering( + n_clusters=self.best_n_clusters, + metric="precomputed" if self.linkage != "ward" else None, + linkage=self.linkage + ) + self.labels_ = self.model.fit_predict(distance_matrix if self.linkage != "ward" else adjacency_matrix) + return self.labels_ diff --git a/hc/hypergraph_clustering/metrics/evaluation.py b/hc/hypergraph_clustering/metrics/evaluation.py new file mode 100644 index 0000000..1aae8da --- /dev/null +++ b/hc/hypergraph_clustering/metrics/evaluation.py @@ -0,0 +1,15 @@ +from sklearn.metrics import silhouette_score, calinski_harabasz_score, davies_bouldin_score + +def evaluate_clustering(adjacency_matrix, labels): + """ + Оценивает качество кластеризации. + + :param adjacency_matrix: np.ndarray, матрица смежности. + :param labels: np.ndarray, метки кластеров. + :return: dict, значения метрик. + """ + return { + "silhouette_score": silhouette_score(adjacency_matrix, labels, metric="precomputed"), + "calinski_harabasz_score": calinski_harabasz_score(adjacency_matrix, labels), + "davies_bouldin_score": davies_bouldin_score(adjacency_matrix, labels), + } diff --git a/hc/hypergraph_clustering/tests/__init__.py b/hc/hypergraph_clustering/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/hc/hypergraph_clustering/tests/test_agglomerative.py b/hc/hypergraph_clustering/tests/test_agglomerative.py new file mode 100644 index 0000000..ae161f2 --- /dev/null +++ b/hc/hypergraph_clustering/tests/test_agglomerative.py @@ -0,0 +1,28 @@ +import pytest +import json +import os +import numpy as np +from hypergraph_clustering.utils.graph_conversion import hypergraph_to_incidence_matrix, incidence_to_adjacency +from hypergraph_clustering.clustering.agglomerative import AgglomerativeHypergraphClustering + +# Путь к JSON-файлам +DATA_DIR = "data" + +@pytest.mark.parametrize("filename", [ + "social_network.json", + "transport_network.json", + "biological_network.json" +]) +@pytest.mark.parametrize("linkage", ["ward", "complete", "average", "single"]) +def test_agglomerative_clustering(filename, linkage): + with open(os.path.join(DATA_DIR, filename), "r") as f: + hypergraph = json.load(f) + + incidence_matrix = hypergraph_to_incidence_matrix(hypergraph["hyperedges"]) + adjacency_matrix = incidence_to_adjacency(incidence_matrix) + + clustering = AgglomerativeHypergraphClustering(n_clusters=2, linkage=linkage) + labels = clustering.fit(adjacency_matrix) + + assert len(labels) == adjacency_matrix.shape[0] + assert set(labels).issubset({0, 1}) diff --git a/hc/hypergraph_clustering/tests/test_auto_clustering.py b/hc/hypergraph_clustering/tests/test_auto_clustering.py new file mode 100644 index 0000000..aa6b5da --- /dev/null +++ b/hc/hypergraph_clustering/tests/test_auto_clustering.py @@ -0,0 +1,26 @@ +import os +import pytest +import json +import numpy as np +from hypergraph_clustering.clustering.auto_clustering import AutoClusterHypergraphClustering +from hypergraph_clustering.utils.graph_conversion import hypergraph_to_incidence_matrix, incidence_to_adjacency + +DATA_DIR = "data" + +@pytest.mark.parametrize("filename", [ + "social_network.json", + "transport_network.json" +]) +def test_auto_clustering(filename): + with open(os.path.join(DATA_DIR, filename), "r") as f: + hypergraph = json.load(f) + + incidence_matrix = hypergraph_to_incidence_matrix(hypergraph["hyperedges"]) + adjacency_matrix = incidence_to_adjacency(incidence_matrix) + + clustering = AutoClusterHypergraphClustering(linkage="average", max_clusters=5, scoring="silhouette") + labels = clustering.fit(adjacency_matrix) + + assert len(labels) == adjacency_matrix.shape[0] + assert clustering.best_n_clusters is not None + assert clustering.best_score is not None diff --git a/hc/hypergraph_clustering/tests/test_evaluation.py b/hc/hypergraph_clustering/tests/test_evaluation.py new file mode 100644 index 0000000..62868b1 --- /dev/null +++ b/hc/hypergraph_clustering/tests/test_evaluation.py @@ -0,0 +1,29 @@ +import pytest +import json +import os +import numpy as np +from hypergraph_clustering.utils.graph_conversion import hypergraph_to_incidence_matrix, incidence_to_adjacency +from hypergraph_clustering.clustering.agglomerative import AgglomerativeHypergraphClustering +from hypergraph_clustering.metrics.evaluation import evaluate_clustering + +DATA_DIR = "data" + +@pytest.mark.parametrize("filename", [ + "social_network.json", + "transport_network.json" +]) +def test_evaluation_metrics(filename): + with open(os.path.join(DATA_DIR, filename), "r") as f: + hypergraph = json.load(f) + + incidence_matrix = hypergraph_to_incidence_matrix(hypergraph["hyperedges"]) + adjacency_matrix = incidence_to_adjacency(incidence_matrix) + + clustering = AgglomerativeHypergraphClustering(n_clusters=2, linkage="ward") + labels = clustering.fit(adjacency_matrix) + + metrics = evaluate_clustering(adjacency_matrix, labels) + + assert metrics["silhouette_score"] >= -1 and metrics["silhouette_score"] <= 1 + assert metrics["calinski_harabasz_score"] > 0 + assert metrics["davies_bouldin_score"] > 0 diff --git a/hc/hypergraph_clustering/tests/test_graph_conversion.py b/hc/hypergraph_clustering/tests/test_graph_conversion.py new file mode 100644 index 0000000..2d0c247 --- /dev/null +++ b/hc/hypergraph_clustering/tests/test_graph_conversion.py @@ -0,0 +1,42 @@ +import pytest +import json +import os +from hypergraph_clustering.utils.graph_conversion import hypergraph_to_incidence_matrix, incidence_to_adjacency + +# Путь к JSON-файлам +DATA_DIR = "data" + +@pytest.mark.parametrize("filename", [ + "biological_network.json", + "electric_network.json" +]) +def test_hypergraph_to_incidence_matrix(filename): + # Загружаем гиперграф из JSON + with open(os.path.join(DATA_DIR, filename), "r") as f: + hypergraph = json.load(f) + + # Преобразуем гиперграф в матрицу инцидентности + incidence_matrix = hypergraph_to_incidence_matrix(hypergraph["hyperedges"]) + + # Проверки + assert incidence_matrix.shape[0] == hypergraph["num_nodes"] + assert incidence_matrix.shape[1] == len(hypergraph["hyperedges"]) + assert incidence_matrix.sum() == sum(len(edge) for edge in hypergraph["hyperedges"]) + +@pytest.mark.parametrize("filename", [ + "biological_network.json", + "electric_network.json" +]) +def test_incidence_to_adjacency(filename): + # Загружаем гиперграф из JSON + with open(os.path.join(DATA_DIR, filename), "r") as f: + hypergraph = json.load(f) + + # Преобразуем гиперграф в матрицу инцидентности и затем в матрицу смежности + incidence_matrix = hypergraph_to_incidence_matrix(hypergraph["hyperedges"]) + adjacency_matrix = incidence_to_adjacency(incidence_matrix) + + # Проверки + assert adjacency_matrix.shape[0] == adjacency_matrix.shape[1] + assert adjacency_matrix.sum() > 0 + assert (adjacency_matrix.diagonal() == 0).all() diff --git a/hc/hypergraph_clustering/tests/test_visualization.py b/hc/hypergraph_clustering/tests/test_visualization.py new file mode 100644 index 0000000..a4c6983 --- /dev/null +++ b/hc/hypergraph_clustering/tests/test_visualization.py @@ -0,0 +1,44 @@ +import pytest +import os +import json +import numpy as np +from hypergraph_clustering.visualization.plot import plot_hypergraph, plot_clusters +from hypergraph_clustering.utils.graph_conversion import hypergraph_to_incidence_matrix, incidence_to_adjacency +from hypergraph_clustering.clustering.agglomerative import AgglomerativeHypergraphClustering + +DATA_DIR = "data" + +@pytest.mark.parametrize("filename", [ + "social_network.json", + "transport_network.json", +]) +def test_plot_hypergraph(filename): + """ + Тестирует построение гиперграфа. + """ + filepath = os.path.join(DATA_DIR, filename) + with open(filepath, "r") as f: + hypergraph = json.load(f) + + hyperedges = hypergraph["hyperedges"] + plot_hypergraph(hyperedges, title=f"Hypergraph: {filename}") + +@pytest.mark.parametrize("filename", [ + "social_network.json", + "transport_network.json", +]) +def test_plot_clusters(filename): + """ + Тестирует визуализацию кластеров. + """ + filepath = os.path.join(DATA_DIR, filename) + with open(filepath, "r") as f: + hypergraph = json.load(f) + + incidence_matrix = hypergraph_to_incidence_matrix(hypergraph["hyperedges"]) + adjacency_matrix = incidence_to_adjacency(incidence_matrix) + + clustering = AgglomerativeHypergraphClustering(n_clusters=2, linkage="ward") + labels = clustering.fit(adjacency_matrix) + + plot_clusters(adjacency_matrix, labels, title=f"Clusters: {filename}") diff --git a/hc/hypergraph_clustering/utils/__init__.py b/hc/hypergraph_clustering/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/hc/hypergraph_clustering/utils/examples.py b/hc/hypergraph_clustering/utils/examples.py new file mode 100644 index 0000000..2a256cd --- /dev/null +++ b/hc/hypergraph_clustering/utils/examples.py @@ -0,0 +1,6 @@ +import json + +def load_hypergraphs(file_path="data/sample_hypergraph.json"): + with open(file_path, "r") as f: + data = json.load(f) + return data diff --git a/hc/hypergraph_clustering/utils/graph_conversion.py b/hc/hypergraph_clustering/utils/graph_conversion.py new file mode 100644 index 0000000..78ee2d9 --- /dev/null +++ b/hc/hypergraph_clustering/utils/graph_conversion.py @@ -0,0 +1,30 @@ +import networkx as nx +import numpy as np + +def hypergraph_to_incidence_matrix(hyperedges): + """ + Преобразует гиперграф в матрицу инцидентности. + + :param hyperedges: Список гиперребер (каждое гиперребро — список вершин). + :return: np.ndarray, матрица инцидентности. + """ + nodes = sorted(set(node for edge in hyperedges for node in edge)) + node_index = {node: i for i, node in enumerate(nodes)} + incidence_matrix = np.zeros((len(nodes), len(hyperedges))) + + for j, edge in enumerate(hyperedges): + for node in edge: + incidence_matrix[node_index[node], j] = 1 + + return incidence_matrix + +def incidence_to_adjacency(incidence_matrix): + """ + Преобразует матрицу инцидентности в матрицу смежности графа. + + :param incidence_matrix: np.ndarray, матрица инцидентности. + :return: np.ndarray, матрица смежности. + """ + adjacency_matrix = np.dot(incidence_matrix, incidence_matrix.T) + np.fill_diagonal(adjacency_matrix, 0) # Убираем петли + return adjacency_matrix diff --git a/hc/hypergraph_clustering/visualization/plot.py b/hc/hypergraph_clustering/visualization/plot.py new file mode 100644 index 0000000..a858f23 --- /dev/null +++ b/hc/hypergraph_clustering/visualization/plot.py @@ -0,0 +1,60 @@ +import matplotlib.pyplot as plt +import networkx as nx +import numpy as np + +def plot_hypergraph(hyperedges, node_colors=None, title="Hypergraph Visualization"): + """ + Визуализирует гиперграф. + + :param hyperedges: list of lists, гиперребра гиперграфа. + :param node_colors: dict, цвета для узлов (по умолчанию одинаковые для всех). + :param title: str, заголовок графика. + """ + G = nx.Graph() + + # Добавляем узлы и гиперребра + for idx, edge in enumerate(hyperedges): + for node in edge: + G.add_node(node) + G.add_edges_from([(edge[i], edge[j]) for i in range(len(edge)) for j in range(i + 1, len(edge))]) + + # Определяем цвета узлов + if node_colors is None: + node_colors = {node: "blue" for node in G.nodes} + colors = [node_colors.get(node, "blue") for node in G.nodes] + + # Рисуем график + plt.figure(figsize=(8, 6)) + pos = nx.spring_layout(G) + nx.draw(G, pos, with_labels=True, node_color=colors, edge_color="gray", node_size=500, font_size=10) + plt.title(title) + plt.show() + +def plot_clusters(adjacency_matrix, labels, title="Cluster Visualization"): + """ + Визуализирует кластеры, полученные из кластеризации. + + :param adjacency_matrix: np.ndarray, матрица смежности графа. + :param labels: list, метки кластеров. + :param title: str, заголовок графика. + """ + G = nx.Graph() + nodes = range(adjacency_matrix.shape[0]) + + # Добавляем узлы и ребра + for i in nodes: + for j in nodes: + if adjacency_matrix[i, j] > 0: + G.add_edge(i, j, weight=adjacency_matrix[i, j]) + + # Определяем цвета кластеров + cluster_colors = plt.cm.rainbow(np.linspace(0, 1, len(set(labels)))) + node_colors = {node: cluster_colors[label] for node, label in enumerate(labels)} + colors = [node_colors[node] for node in G.nodes] + + # Рисуем график + plt.figure(figsize=(8, 6)) + pos = nx.spring_layout(G) + nx.draw(G, pos, with_labels=True, node_color=colors, edge_color="gray", node_size=500, font_size=10) + plt.title(title) + plt.show() diff --git a/hc/requirements.txt b/hc/requirements.txt new file mode 100644 index 0000000..78f2607 --- /dev/null +++ b/hc/requirements.txt @@ -0,0 +1,5 @@ +numpy +scikit-learn +networkx +pytest +matplotlib \ No newline at end of file diff --git a/hc/setup.py b/hc/setup.py new file mode 100644 index 0000000..84ca1b9 --- /dev/null +++ b/hc/setup.py @@ -0,0 +1,15 @@ +from setuptools import setup, find_packages + +setup( + name="hypergraph_clustering", + version="0.1.0", + description="Модуль для агломеративной кластеризации гиперграфов", + author="nosignalx2k", + packages=find_packages(), + install_requires=[ + "numpy", + "scikit-learn", + "networkx", + "matplotlib" + ], +) diff --git a/hc/test.py b/hc/test.py new file mode 100644 index 0000000..9dcfce5 --- /dev/null +++ b/hc/test.py @@ -0,0 +1,21 @@ +from hypergraph_clustering.clustering.agglomerative import AgglomerativeHypergraphClustering +import numpy as np + +# Пример графа +adjacency_matrix = np.array([ + [0, 1, 1, 0], + [1, 0, 1, 0], + [1, 1, 0, 1], + [0, 0, 1, 0] +]) + +# Кластеризация +clustering = AgglomerativeHypergraphClustering(n_clusters=2, linkage="average") +labels = clustering.fit(adjacency_matrix) + +# Оценка +metrics = clustering.evaluate(adjacency_matrix) +print("Metrics:", metrics) + +# Визуализация +clustering.plot_clusters(adjacency_matrix)