light-size-constrained-clustering 0.0.7

Size Constrained Clustering Solver

Implementation of Deterministic Annealing Size Constrained Clustering. Size constrained clustering can be treated as an optimization problem. Details could be found in a set of reference paper.

This is a fork of https://github.com/jingw2/size_constrained_clustering that solves installation issues. And mantains only the Determinstic Annealing clustering.

Installation

Requirement Python >= 3.6, Numpy >= 1.13

• install from PyPI

pip install light-size-constrained-clustering

Methods

• Deterministic Annealling Algorithm: Input target cluster distribution, return correspondent clusters

Usage:

Deterministic Annealing

# setup
from light_size_constrained_clustering import da
import numpy as np

n_samples = 40 # number cells in spot
n_clusters = 4 # distinct number of cell types
distribution= [0.4,0.3,0.2,0.1] # distribution of each cell type (form deconv)
seed = 17

print(np.sum(distribution))
np.random.seed(seed)

X = np.random.rand(n_samples, 2)
# distribution is the distribution of cluster sizes
model = da.DeterministicAnnealing(n_clusters, distribution= distribution, random_state=seed)

model.fit(X)
centers = model.cluster_centers_
labels = model.labels_
print("Labels:")
print(labels)
print("Elements in cluster 0: ", np.count_nonzero(labels == 0))
print("Elements in cluster 1: ", np.count_nonzero(labels == 1))
print("Elements in cluster 2: ", np.count_nonzero(labels == 2))
print("Elements in cluster 3: ", np.count_nonzero(labels == 3))

In case of provided distributions not being respected due to lack of convergence, distribution can be nforced by using the parameter enforce_cluster_distribution

model.fit(X, enforce_cluster_distribution=True)

Cluster size: 16, 12, 8 and 4 in the figure above, corresponding to distribution [0.4, 0.3, 0.2, 0.1]

Copyright

Copyright (c) 2023 Jing Wang & Albert Pla. Released under the MIT License.

Third-party copyright in this distribution is noted where applicable.

Reference

• Clustering with Capacity and Size Constraints: A Deterministic Approach
• Deterministic Annealing, Clustering and Optimization
• Deterministic Annealing, Constrained Clustering, and Opthiieation
• Shrinkage Clustering
• Clustering with size constraints
• Data Clustering with Cluster Size Constraints Using a Modified k-means Algorithm
• KMeans Constrained Clustering Inspired by Minimum Cost Flow Problem
• Same Size Kmeans Heuristics Methods
• Google's Operations Research tools's SimpleMinCostFlow
• Cluster KMeans Constrained