From 05b6db09b8a81d84e885136b3ae7dba39f41732d Mon Sep 17 00:00:00 2001 From: Pierre LOTTE <pierre.lotte@irit.fr> Date: Mon, 3 Feb 2025 07:39:57 +0000 Subject: [PATCH] Add soft/fuzzy clustering splitting --- paradise/main.py | 6 +- paradise/split/__init__.py | 1 + paradise/split/base.py | 39 +- paradise/split/soft.py | 89 +++ poetry.lock | 1062 +++++++++++++++++++----------------- pyproject.toml | 1 + 6 files changed, 676 insertions(+), 522 deletions(-) create mode 100644 paradise/split/soft.py diff --git a/paradise/main.py b/paradise/main.py index cfd8077..c6c08e9 100755 --- a/paradise/main.py +++ b/paradise/main.py @@ -13,7 +13,7 @@ import numpy as np import pandas as pd from generator import DatasetGenerator -from split import BaseSplitter +from split import SoftSplitter from trainers import BaseTrainer from results import ResultExtractor, ROCResults @@ -160,8 +160,8 @@ if __name__ == "__main__": # Split data # ================================================================================================================= - if args.split and args.task in ["train", "all"]: - splitter = BaseSplitter(f"{INPUT_DIR}/{config_name}") + if args.split and args.task in ["generate", "train", "all"]: + splitter = SoftSplitter(f"{INPUT_DIR}/{config_name}") splitter.split_data(method=args.method, merge=args.merge) # ================================================================================================================= diff --git a/paradise/split/__init__.py b/paradise/split/__init__.py index 8061bd0..7bd362f 100644 --- a/paradise/split/__init__.py +++ b/paradise/split/__init__.py @@ -2,3 +2,4 @@ This module provides the necessary code to split data. """ from .base import BaseSplitter +from .soft import SoftSplitter diff --git a/paradise/split/base.py b/paradise/split/base.py index f22698a..326485d 100644 --- a/paradise/split/base.py +++ b/paradise/split/base.py @@ -31,31 +31,33 @@ class BaseSplitter: self.output_path = f"{path}/splitting" os.makedirs(f"{path}/splitting", exist_ok=True) + self.w_df = pd.read_csv(f"{self.data_path}/dataset_train.csv", index_col="Timestamp") + self.df = pd.read_csv(f"{self.data_path}/dataset.csv", index_col="Timestamp") + self.train_df = pd.read_csv(f"{self.data_path}/dataset_train.csv", index_col="Timestamp") + self.labels_df = pd.read_csv(f"{self.data_path}/dataset_variables_labels.csv") + + # Remove the categorial variables from the correlation computation + self.w_df.drop(columns=self.df.select_dtypes(include="int64").columns, inplace=True) + self.w_df.drop(columns=["Timestamp", "is_anomaly"], errors="ignore", inplace=True) + self.w_df.drop(columns=self.w_df.columns[self.w_df.nunique() <= 1], inplace=True) + def split_data(self, method="HDBSCAN", merge=False): """ This method will be in charge of splitting data into subsystems. """ - w_df = pd.read_csv(f"{self.data_path}/dataset_train.csv", index_col="Timestamp") - df = pd.read_csv(f"{self.data_path}/dataset.csv", index_col="Timestamp") - train_df = pd.read_csv(f"{self.data_path}/dataset_train.csv", index_col="Timestamp") - labels_df = pd.read_csv(f"{self.data_path}/dataset_variables_labels.csv") - - # Remove the categorial variables from the correlation computation - w_df.drop(columns=df.select_dtypes(include="int64").columns, inplace=True) - w_df.drop(columns=["Timestamp", "is_anomaly"], errors="ignore", inplace=True) - w_df.drop(columns=w_df.columns[w_df.nunique() <= 1], inplace=True) + x = self._compute_correlations(merge=merge) + self._split_data(x, method=method) + def _split_data(self, x, method="HDBSCAN"): # Compute all the correlations for the dataset and find the coefficient that produces the best # cluters from its coefficient max_silhouette = 0 best_clusters = None - x = self._compute_correlations(w_df, merge=merge) - if "HDBSCAN" == method: model = HDBSCAN(min_cluster_size=2, allow_single_cluster=True, n_jobs=-1) best_clusters = model.fit_predict(x) elif "kmeans" == method: - for i in range(1, len(w_df.columns)): + for i in range(1, len(self.w_df.columns)): model = KMeans(n_clusters=i, n_init="auto") # Compute clusters and their silhouette score @@ -75,18 +77,19 @@ class BaseSplitter: # Split the dataset for i in range(-1 if -1 in best_clusters else 0, max(best_clusters)+1): - drop = [col for idx, col in enumerate(w_df.columns) if best_clusters[idx] != i] - df.drop(columns=drop)\ + drop = [col for idx, col in enumerate(self.w_df.columns) if best_clusters[idx] != i] + self.df.drop(columns=drop)\ .to_csv(f"{self.data_path}/dataset_{i}_auto_split.csv", index_label="Timestamp") - train_df.drop(columns=drop)\ + self.train_df.drop(columns=drop)\ .to_csv(f"{self.data_path}/dataset_{i}_auto_split_train.csv", index_label="Timestamp") - labels = np.bitwise_or.reduce(labels_df.drop(columns=drop).to_numpy(), axis=1, dtype=np.int32) + labels = np.bitwise_or.reduce(self.labels_df.drop(columns=drop).to_numpy(), axis=1, dtype=np.int32) pd.DataFrame(labels).to_csv(f"{self.data_path}/dataset_{i}_auto_split_labels.csv", index=False) - def _compute_correlations(self, data, merge=False): + def _compute_correlations(self, merge=False): """ Compute the vector of correlation coefficients for each of the variable of the dataset. """ + sns.set(font_scale=3.0) with open(f"{self.output_path}/split_time.csv", "a", encoding="utf-8") as f: f.write("Algorithm,duration\n") x = [] @@ -94,7 +97,7 @@ class BaseSplitter: coeff_name = coeff.__name__[:-11] start_time = time() - correlation_matrix = coeff().compute(data) + correlation_matrix = coeff().compute(self.w_df) duration = time() - start_time f.write(f"{coeff_name},{duration}\n") diff --git a/paradise/split/soft.py b/paradise/split/soft.py new file mode 100644 index 0000000..7ef30db --- /dev/null +++ b/paradise/split/soft.py @@ -0,0 +1,89 @@ +""" +This module contains the basic splitter algorithm based on the correlation coefficients computing and +soft clustering. +""" +import json +import os + +from time import time +from warnings import simplefilter + +import matplotlib.pyplot as plt +import numpy as np +import pandas as pd +import seaborn as sns + +from scipy.spatial.distance import euclidean +from skfuzzy.cluster import cmeans +from sklearn.exceptions import ConvergenceWarning +from sklearn.metrics import silhouette_score + +from .correlations import CORRELATION_CLASSES +from .base import BaseSplitter + +simplefilter("ignore", category=ConvergenceWarning) + + +class SoftSplitter(BaseSplitter): + """ + Class in charge of doing basic splitting using correlation coefficients + """ + def _fuzzy_silhouette(self, fuzzy_matrix, points, distances_matrix): + s = np.zeros(len(points)) + ranked_scores = [] + + for i in range(len(points)): + la = [euclidean(points[i], points[x]) for x in range(len(points)) if x != i and np.argmax(fuzzy_matrix[:, i]) == np.argmax(fuzzy_matrix[:, x])] + if la: + a = np.mean(la) + b = np.sort(distances_matrix[:, i])[1] + s[i] = (b-a)/max(a,b) + + ranked_scores.append(-np.sort(-fuzzy_matrix[:, i])) + + alpha = 1 + non_summed = np.array([((ranked_scores[i][0] - ranked_scores[i][1])**alpha) for i in range(len(points))]) + denom = sum(non_summed) + num = sum(non_summed * s) + + return num/denom + + + def _split_data(self, x, method=""): + # Compute all the correlations for the dataset and find the coefficient that produces the best + # cluters from its coefficient + best_clusters = None + best_fs = 0 + all_fs = [] + k = 1 + + for i in range(2, len(self.w_df.columns)): + # Compute fuzzy clusters. The third argument has been taken from the tutorial of skfuzzy + # and might not be the best choice. + _, scores, _, d, _, _, _ = cmeans(x.T, i, 2, error=0.005, maxiter=1000) + score = self._fuzzy_silhouette(scores, x, d) + all_fs.append(score) + + # Check if the proposed clustering is better than already proposed solutions + if score > best_fs: + best_fs = score + best_clusters = scores.T + k = i + + + # Save choosen clustering + with open(f"{self.output_path}/dataset_split_clusters.txt", "w", encoding="utf-8") as f: + f.write(f"{best_clusters.tolist()}\n\n") + f.write(f"All silhouette: {all_fs}\n\n") + + # Split the dataset + for i in range(k): + drop = [col for idx, col in enumerate(self.w_df.columns) if np.argmax(best_clusters[idx]) != i and best_clusters[idx, i] < best_clusters[idx, np.argmax(best_clusters[idx])] /2] + f.write(f"Cluster {i} -> {[col for col in self.w_df.columns if col not in drop]}\n") + self.df.drop(columns=drop)\ + 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GitLab