# From kmeans_pytorch import numpy as np import torch from tqdm import tqdm def initialize(X, num_clusters): """ initialize cluster centers :param X: (torch.tensor) matrix :param num_clusters: (int) number of clusters :return: (np.array) initial state """ num_samples = len(X) indices = np.random.choice(num_samples, num_clusters, replace=False) initial_state = X[indices] return initial_state def kmeans( X, num_clusters, distance='euclidean', tol=1e-4, device=torch.device('cuda') ): """ perform kmeans :param X: (torch.tensor) matrix :param num_clusters: (int) number of clusters :param distance: (str) distance [options: 'euclidean', 'cosine'] [default: 'euclidean'] :param tol: (float) threshold [default: 0.0001] :param device: (torch.device) device [default: cpu] :return: (torch.tensor, torch.tensor) cluster ids, cluster centers """ print(f'running k-means on {device}..') if distance == 'euclidean': pairwise_distance_function = pairwise_distance elif distance == 'cosine': pairwise_distance_function = pairwise_cosine else: raise NotImplementedError # convert to float X = X.float() # transfer to device X = X.to(device) # initialize initial_state = initialize(X, num_clusters) iteration = 0 tqdm_meter = tqdm(desc='[running kmeans]') while True: dis = pairwise_distance_function(X, initial_state) choice_cluster = torch.argmin(dis, dim=1) initial_state_pre = initial_state.clone() for index in range(num_clusters): selected = torch.nonzero(choice_cluster == index).squeeze().to(device) selected = torch.index_select(X, 0, selected) initial_state[index] = selected.mean(dim=0) center_shift = torch.sum( torch.sqrt( torch.sum((initial_state - initial_state_pre) ** 2, dim=1) )) # increment iteration iteration = iteration + 1 # update tqdm meter tqdm_meter.set_postfix( iteration=f'{iteration}', center_shift=f'{center_shift ** 2:0.6f}', tol=f'{tol:0.6f}' ) tqdm_meter.update() if center_shift ** 2 < tol: break return choice_cluster, initial_state def kmeans_predict( X, cluster_centers, distance='euclidean', device=torch.device('cpu') ): """ predict using cluster centers :param X: (torch.tensor) matrix :param cluster_centers: (torch.tensor) cluster centers :param distance: (str) distance [options: 'euclidean', 'cosine'] [default: 'euclidean'] :param device: (torch.device) device [default: 'cpu'] :return: (torch.tensor) cluster ids """ print(f'predicting on {device}..') if distance == 'euclidean': pairwise_distance_function = pairwise_distance elif distance == 'cosine': pairwise_distance_function = pairwise_cosine else: raise NotImplementedError # convert to float X = X.float() # transfer to device X = X.to(device) dis = pairwise_distance_function(X, cluster_centers) choice_cluster = torch.argmin(dis, dim=1) return choice_cluster.cpu() def pairwise_distance(data1, data2): return torch.cdist(data1[None, :, :], data2[None, :, :])[0] def pairwise_cosine(data1, data2): # N*1*M A = data1.unsqueeze(dim=1) # 1*N*M B = data2.unsqueeze(dim=0) # normalize the points | [0.3, 0.4] -> [0.3/sqrt(0.09 + 0.16), 0.4/sqrt(0.09 + 0.16)] = [0.3/0.5, 0.4/0.5] A_normalized = A / A.norm(dim=-1, keepdim=True) B_normalized = B / B.norm(dim=-1, keepdim=True) cosine = A_normalized * B_normalized # return N*N matrix for pairwise distance cosine_dis = 1 - cosine.sum(dim=-1).squeeze() return cosine_dis