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Chapter 8. Clustering Algorithms

Recommended Article: 【Algorithm】 Algorithm Index

1. Introduction

2. Type 1. unsupervised hierarchical clustering

3. Type 2. K-means clustering

4. Type 3. Density-based clustering

5. Type 4. Mixture distribution clustering

6. Type 5. Graph-based clustering

7. Other Clustering Algorithms

1. Introduction

⑴ Clustering is an optimization problem

① variability

○ variability can be defined as the sum of distance or distance squared

○ Types of distance functions

○ Reason: big and bad is worse than small and bad

② dissimilarity

○ Clustering is not about finding a global minimum for dissimilarity

○ Reason 1. A trivial solution exists where ∀variability = 0 with as many clusters as samples

○ Reason 2. It’s unfair to penalize large clusters per se: big is not necessarily worse than small

○ Constraints are needed: minimum distance between clusters, number of clusters, etc.

⑵ Clustering is an unsupervised algorithm

① Due to this, evaluating the performance of clustering algorithms is difficult, but it can be assessed as follows

② Method 1. NMI(normalized mutual information)

③ Method 2. ARI(adjusted rand index)

④ Method 3. ASW(average silhouette width)

⑤ Method 4. AMI

⑥ Method 5. Homo

⑦ Method 6. Relative distance between clusters

⑶ Types of Clustering

① Type 1. agglomerative: bottom-up approach. An approach that builds larger clusters

② Type 2. divisive: top-down approach. An approach that divides into smaller clusters

③ In practice, agglomerative is more commonly used

2. Type 1. Unsupervised hierarchical clustering

⑴ Overview

① Often used to draw a heatmap from an internal matrix (Example: RStudio’s heatmap function)

② A type of graph-based method

③ Unlike non-hierarchical clustering, hierarchical clustering does not pre-determine the number of clusters

⑵ Type 1. Divisive Analysis

① A technique that starts from the entire group and separates objects with decreasing similarity

② Stage 1: Initially assign N elements to N clusters

③ Stage 2: Merge the closest clusters into one

④ Stage 3: Repeat stage 2 until constraints such as the number of clusters are met

○ In this case, a dendrogram is used

⑶ Type 2. Agglomerative Analysis (agglomerative hierarchical clustering)

① Definition: A method that considers each entity as a subgroup and progressively merges similar subgroups to form new subgroups

⑷ Linkage metric: Defining distance between clusters

① Type 1. Single-linkage: The shortest distance between elements of one cluster and another

② Type 2. Complete-linkage: The farthest distance between elements of one cluster and another

③ Type 3. Average-linkage: The distance between the centers of two clusters

○ Can also mean the average distance between elements of one cluster and another

④ Type 4. Centroid-linkage: Measuring the distance between the centers of two clusters

⑤ Type 5. Ward-linkage: A method of measuring distance between clusters based on within-cluster sum of squares

Figure 1. Performance of clustering according to linkage metric]

⑸ Features

① One of the most frequently used clustering algorithms along with K-means clustering

② Advantage 1. Deterministic: can reach the same conclusion in any environment

③ Advantage 2. Can try various linkage criteria

④ Disadvantage 1. Slow naïve algorithm. Generally requires Ο(n3) time complexity

○ Reason: Ο(n²) is required to perform stage 2 and it has to be repeated Ο(n) times

○ In some cases, Ο(n²) time complexity is required depending on the linkage criteria

⑹ References

3. Type 2. K-means clustering

⑴ Overview

① Often used in clustering algorithms targeting images

⑵ Algorithm

Figure 2. How K-means clustering works

① Stage 1: Randomly select k initial centroids

② Stage 2: Assign clusters based on which centroid each element is closest to

③ Stage 3: Calculate the center of each cluster to define new centroids

④ Stage 4: Clustering ends when centroids no longer change

⑶ Features

① The most widely used clustering algorithm

② K-means clustering is one of the greedy algorithms for clustering

③ Determining K

○ Background knowledge

○ Example: Differentiating between cancerous and non-cancerous data in bio multi-omics data

○ Elbow Method

○ A method to determine the number of clusters in cluster analysis by plotting the total within-cluster sum of squares against the number of clusters and selecting the elbow point as the appropriate number of clusters

○ Choose the cluster corresponding to the elbow part where the slope is gentle when the number of clusters is on the x-axis and SSE value on the y-axis

○ Silhouette Method

○ A method that quantitatively calculates the quality of clustering using silhouette coefficients

○ Shows how well clusters are separated from each other

○ A silhouette coefficient close to 1 indicates well-optimized, well-separated clusters

○ A silhouette coefficient close to 0 indicates poorly optimized, closely spaced clusters

○ Dendrogram: Use dendrogram visualization in hierarchical cluster analysis to determine the number of clusters

④ Advantage 1. Fast. Ο(Kn) time is required to perform stage 2 (K is the number of clusters, n is the number of data points)

⑤ Advantage 2. Mathematically converges after a finite number of iterations as the objective function decreases with each iteration

⑤ Disadvantage 1. Choosing the wrong K can lead to incorrect results

⑥ Disadvantage 2. Results can vary depending on initial centroid position, so it’s not deterministic

⑷ Python code

from sklearn.cluster import KMeans

X = [[1, 2, 3],[1, 2, 3.1],[2, 2, 4],[2, 2, 4.1]]
kmeans = KMeans(n_clusters=2, random_state=0)
kmeans.fit(X)
cluster_labels = kmeans.labels_

print(cluster_labels)
# [1 1 0 0]

⑸ unsupervised hierarchical clustering vs K-means clustering

Table. 1. Comparison of unsupervised hierarchical clustering and K-means clustering

⑹ K-NN vs K-means clustering

Table. 2. K-NN vs K-means clustering

⑺ Type 2-1. K-medoid clustering

⑻ Type 2-2. Lloyd’s K-means clustering algorithm

4. Type 3. Density-Based Clustering (DBSCAN, density-based spatial clustering of applications with noise)

⑴ Overview: One of the non-hierarchical clustering analyses like K-means clustering

① An algorithm that groups closely distributed entities based on the calculation of their densities

② No need to pre-specify the number of clusters

③ Clusters are connected based on cluster density, allowing for clustering of geometric shapes

⑵ Components

① Core point

○ A data point that has a minimum number(min_samples) of other data points within a certain radius(epsilon)

○ The minimum number of data points required within the radius is set as a hyperparameter

② Neighbor point

○ Other data existing within a certain radius around a specific data point

③ Border point

○ Not a core point but exists within the radius of a core point

○ Included in the cluster centered around the core point and typically forms the outskirts of the cluster

④ Noise point

○ Neither a core point nor satisfies the border point condition

○ Also considered as an outlier

⑶ Procedure

① Stage 1. Identify core points with a minimum number(min_samples) of points within a certain radius(epsilon).

② Stage 2. Explore connected components in the adjacency graph using only core points.

③ Stage 3. Assign non-core points as noise.

⑷ Features

① Advantage 1. No need to predefine the number of clusters, unlike k-means clustering

② Advantage 2. Can identify clusters with geometric shapes due to clustering based on cluster density

③ Disadvantage 1. Difficult to determine hyperparameters, sensitive to parameter choices

④ Disadvantage 2. Challenges in computation when clusters have varying densities or in higher dimensions

⑸ Python example

Figure 3. DBSCAN Python example

import pandas as pd
from sklearn.datasets import make_blobs
from sklearn.cluster import DBSCAN
import matplotlib.pyplot as plt

# Step 1: Generate sample data
X, _ = make_blobs(n_samples=300, centers=4, cluster_std=0.60, random_state=0)

# Step 2: Convert to DataFrame
df = pd.DataFrame(X, columns=['x', 'y'])

# DBSCAN parameters
epsilon = 0.5  
min_samples = 5 

# Step 3: Perform DBSCAN clustering
db = DBSCAN(eps=epsilon, min_samples=min_samples)
df['cluster_label'] = db.fit_predict(df[['x', 'y']])

# Step 4: Visualize the clustering results
plt.figure(figsize=(12, 8))
plt.scatter(df['x'], df['y'], c=df['cluster_label'], cmap='viridis', marker='o')
plt.title('DBSCAN Clustering')
plt.xlabel('X')
plt.ylabel('Y')
plt.show()

⑹ Application

① OPTICS

(skip)

from sklearn.cluster import OPTICS

# OPTICS parameters
min_samples = 5
xi = 0.05
min_cluster_size = 0.05

# Perform OPTICS clustering
optics = OPTICS(min_samples=min_samples, xi=xi, min_cluster_size=min_cluster_size)
df['cluster_label'] = optics.fit_predict(df[['x', 'y']])

(skip)

② HDBSCAN

(skip)

import hdbscan

# HDBSCAN parameters
min_cluster_size = 5
min_samples = 5

# Perform HDBSCAN clustering
hdb = hdbscan.HDBSCAN(min_cluster_size=min_cluster_size, min_samples=min_samples)
df['cluster_label'] = db.fit_predict(df[['x', 'y']])

(skip)

③ DBSCAN++

5. Type 4. Mixture Distribution Clustering

⑴ Mixture Distribution Clustering: One of the non-hierarchical clustering analyses, like K-means clustering

① Assumes data comes from a population model represented as a weighted sum of k parametric models, estimates parameters and weights from the data

② Each of the k models represents a cluster, and each data point is classified into a cluster based on which model it most likely came from

③ Definition of Mixture Model: A mixture model represented as a weighted sum of M distributions (components)

p(x | θ) = Σ p(x | Ci, θ_i) p(C_i)

○ p(x

Ci, θi): The individual probability density function in the mixture model

○ θ_i: The parameter vector of the i-th distribution

○ C_i: The i-th cluster (class)

○ p(C_i): The importance or weight (αi) of the i-th cluster in the mixture model

④ Estimating parameters of the mixture model is complex compared to single models, often using the EM algorithm instead of differentiation

⑤ Accuracy of estimation may decrease or become challenging if the size of clusters is too small

⑥ Sensitive to outliers, hence preprocessing such as outlier removal is necessary

⑵ Gaussian Mixture Model (GMM)

Figure 4. Gaussian Mixture Model

① Overview

○ Assumes the overall data probability distribution is a linear combination of k Gaussian distributions.

○ Clusters are formed based on the probability of belonging to each distribution.

② Formula

○ In GMM, estimates the weights, means, and covariances of the appropriate k Gaussian distributions for the given data X = {x₁, x₂, …, x_N}

○ Simplification: When x is one-dimensional data

○ Matrix Representation: When x is multi-dimensional data, for the mean μ_k and covariance matrix ∑_k of the k-th cluster

③ EM algorithm (MLE estimation)

○ EM algorithm can be used to estimate the optimal Gaussian distribution each data point belongs to

○ Objective function: Expressed as log likelihood

○ Step 1: Assign random values to γ_i,k

○ Step 2: E-step: Estimate γ_i,k

○ Step 3: M-step: Calculate a_k, μ_k, ∑_k from γ_i,k

○ Step 4: If γ_i,k converges, stop; otherwise, move to Step 2: Convergence is guaranteed due to the characteristics of the Gaussian function.

④ Comparison between K means clustering and Gaussian mixture model

Figure 5. Comparison of K means clustering and Gaussian mixture model

6. Type 5. Graph-Based Clustering (SOM, Self-Organizing Maps)

⑴ Overview: One of the non-hierarchical clustering analyses, like K-means clustering

① SOM, developed by Kohonen, also known as Kohonen maps

② SOM is an artificial neural network modeled on the learning processes of the cerebral cortex and visual cortex

③ Clustering by autonomous learning methods

④ A type of unsupervised neural network that maps high-dimensional data into an easy-to-understand low-dimensional arrangement of neurons

⑤ The mapping preserves the positional relationships of input variables

⑥ In the actual space, if input variables are close, they are mapped close to each other on the map

⑦ Very fast due to using only one forward pass

⑵ Type 1. SOM

① Component 1. Input Layer

○ Receives the input vector, contains neurons equal to the number of input variables

○ The input layer data is aligned in the competitive layer through learning, referred to as the map

○ Each neuron in the input layer is fully connected to every neuron in the competitive layer

② Component 2. Competitive Layer

○ A layer arranged in a 2D grid, where input vectors cluster into a single point based on their characteristics

○ SOM uses competitive learning, where each neuron calculates its closeness to the input vector, repeatedly adjusting connection strengths

○ Through the learning process, the connection strength makes the neuron most similar to the input pattern the winner

○ Due to the winner-take-all structure, only the winning neuron appears in the competitive layer, with similar input patterns arranged in the same competitive neuron

③ Learning Algorithm

○ Step 1. Initialization: Initialize connection strengths for nodes in the SOM map

○ Step 2. Input Vector: Present the input vector

○ Step 3. Similarity Calculation: Calculate similarity between the input vector and prototype vectors using Euclidean distance

○ Step 4. Prototype Vector Search: Find the prototype vector (BMU) closest to the input vector

○ Step 5. Strength Readjustment: Readjust the connection strengths of the BMU and its neighbors

○ Step 6. Repeat: Return to step 2 and repeat

⑶ Type 2. Spectral Clustering

① Step 1: Calculate the distance between the given n data points to create an n × n adjacency matrix A.

○ The Gaussian kernel is often used.

② Step 2: Based on the adjacency matrix, calculate the Laplacian matrix L: L_n or L_r can also be used.

○ L = D - A, where D_ii = ∑_j A_ij

○ L_n = D^-1/2LD^-1/2 = I - D^-1/2AD^-1/2

○ L_t = D^-1A

○ L_r = D^-1L = I - L^t = D^-1/2L_nD^1/2

③ Step 3: Calculate the matrix of eigenvectors W = [ω₂, ···, ω_k] ∈ ℝ^n×k corresponding to the k smallest eigenvalues of the Laplacian matrix.

○ The closer the eigenvalue is to 0, the more connected the graph is.

○ Exclude ω₁ = 1, which corresponds to λ₁ = 0, as it is trivial.

④ Step 4: The n data points are naturally embedded into k dimensions: Y = W^T = [y₁, ⋯, y_n], with each column vector representing the embedded data points.

⑤ Step 5: Perform clustering, such as K-means clustering, on the column vectors of Y.

7. Other Clustering Algorithms

⑴ SNN (Shared Nearest Neighbor) Modularity Optimization Based Clustering Algorithm

① Step 1. Search for K-nearest neighbors

② Step 2. Construct the SNN graph

③ Step 3. Optimize the modularity function to define clusters

④ Reference Paper: Waltman and van Eck (2013) The European Physical Journal B

⑵ Leiden Clustering

① The Leiden algorithm used in the scanpy pipeline

import scanpy as sc
import numpy as np

# Load your AnnData object
adata = sc.read_h5ad('my_h5ad.h5ad')

# Run PCA to reduce dimensionality
sc.pp.pca(adata, n_comps=20) 

# Compute the neighborhood graph
sc.pp.neighbors(adata)

# Run clustering using the Leiden algorithm (HERE!)
sc.tl.leiden(adata, resolution = 0.5)

# Optionally, compute UMAP for visualization
sc.tl.umap(adata)

# Plotting the results
sc.pl.umap(adata, color='leiden', title='Leiden Clustering')
sc.pl.spatial(adata, color = 'leiden')

⑶ Louvain Clustering

① Louvain Modularity Optimization: A type of graph-based method

⑷ Mean-Shift Clustering

⑸ NMF (Non-Negative Matrix Factorization)

① Algorithm for decomposing known matrix A into the product of matrices W and H: A ~ W × H

○ A Matrix: Sample-feature matrix, known from samples

○ H Matrix: Variable-feature matrix

○ This helps in extracting metagenes

○ Similar to K means clustering, PCA algorithms

② Application 1. Cell Type Classification

○ For determining cell type proportion from scRNA-seq obtained from tissue

○ Important to reduce the confounding effect of cell type heterogeneity

○ 3-1. Constrained linear regression

○ 3-2. Reference-based approach

○ 3-2-1. CIBERSORT(cell-type identification by estimating relative subsets of RNA transcript): Allows checking cell type proportion, p value per sample

③ Application 2. Joint NMF: Extends to multi-omics

⑹ Watershed Algorithm

① **An algorithm to identify ROI in images based on threshold values like certain brightness levels

⑺ Thresholding Method

① Definition: A technique to create a binary image based on a threshold

② Example :Otsu Thresholding Method

⑻ MST (Minimum Spanning Tree)

⑼ Curve Evolution

⑽ Sparse Neighboring Graph: A type of graph-based method

⑾ SC3

⑿ SIMLR

⒀ FICT

⒁ Fuzzy Clustering

⒂ C-means clustering

⒃ Faiss

① A similarity-based search and dense vector clustering algorithm developed by Meta in 2023.

② Fast search algorithm: capable of obtaining the nearest neighbor and the k-th nearest neighbor.

③ Allows for the search of multiple vectors at once (batch processing).

④ There is a trade-off between accuracy and speed.

⑤ Instead of minimizing Euclidean distance, it calculates by maximizing the maximum inner product.

⑥ Returns all elements contained within a given radius.

⒄ mclust

⒅ PAM clustering

Entered: 2021.11.16 13:17

Edited: 2023.09.22 00:20