climb-astro 0.2.1

A versatile two-phase clustering algorithm designed for datasets with both known and exploratory components.

CLustering In Multiphase Boundaries (CLiMB)

A versatile two-phase clustering algorithm designed for datasets with both known and exploratory components.

Features

• Two-Phase Clustering: Combines constrained clustering with exploratory clustering to identify both known and novel patterns.
• Density-Aware: Uses local density estimation to intelligently filter and assign points.
• Flexible Exploratory Phase: Supports multiple clustering algorithms (DBSCAN, HDBSCAN, OPTICS) through a strategy pattern.
• Visualization Tools: Built-in 2D and 3D visualization capabilities for cluster analysis.
• Parameter Tuning: Builder pattern for flexible parameter adjustment.
• Customizable Distance Metrics: Now supports various distance metrics such as Euclidean, Mahalanobis, and custom metrics, offering greater flexibility in distance calculation.
• Advanced Seed Points: Ability to initialize clustering with known seed points provided in a dictionary structure, allowing for more precise control over centroid initialization.

Installation

pip install climb-astro

Or install from source:

git clone https://github.com/LorenzoMonti/CLiMB.git
cd CLiMB
pip install -e .

Quick Start

import numpy as np
from sklearn.datasets import make_blobs
from sklearn.preprocessing import StandardScaler
from CLiMB.core.CLiMB import CLiMB
from CLiMB.exploratory.DBSCANExploratory import DBSCANExploratory

# The number of centers to generate
centers = 4

# Generate synthetic data with 5 dimensions
X, y = make_blobs(n_samples=500, centers=centers, n_features=5, random_state=42)

# Scale the data
scaler = StandardScaler()
X_scaled = scaler.fit_transform(X)

# Create seed points (optional)
seed_points = np.array([
    X[y == i].mean(axis=0) for i in range(centers)
])
seed_points_scaled = scaler.transform(seed_points)

# Example of seed points as a dictionary for more precise control
seed_dict_scaled = {
    tuple(seed_points_scaled[0]): [tuple(X_scaled[y == 0][0]), tuple(X_scaled[y == 0][1])], # Centroid 1 and associated seed points
    tuple(seed_points_scaled[1]): [tuple(X_scaled[y == 1][0])],                             # Centroid 2 and associated seed points
    tuple(seed_points_scaled[2]): [],                                                         # Centroid 3 with no specific seed points
    tuple(seed_points_scaled[3]): [tuple(X_scaled[y == 3][0]), tuple(X_scaled[y == 3][1]), tuple(X_scaled[y == 3][2])] # Centroid 4 and seed points
}

# Initialize and fit CLiMB with Mahalanobis metric and dictionary seed points
climb = CLiMB(
    constrained_clusters=4,
    seed_points=seed_dict_scaled, # Use the dictionary of seed points
    density_threshold=0.15,
    distance_threshold=2.5,
    radial_threshold=1.2,
    convergence_tolerance=0.05,
    distance_metric='euclidean',
    metric_params=None,
    exploratory_algorithm=DBSCANExploratory(0.5)
)
climb.fit(X_scaled)

# Get cluster labels
labels = climb.get_labels()

# Visualize results (only possible in lower dimensions)
climb.inverse_transform(scaler)
fig = climb.plot_comprehensive_3d(save_path="./3d")
fig2 = climb.plot_comprehensive_2d(save_path="./2d")

Examples

See the examples/ directory for detailed usage examples:

• simple_example.py: Basic usage with well-defined clusters
• complex_mixed.py: Handling mixed data with both convex and non-convex clusters
• mixed_seeds.py: Handling mixed data with both convex and non-convex clusters with seeds
• compare_methods.py: Comparing different exploratory clustering methods

How It Works

CLiMB operates in two phases:

1. Constrained Phase (KBound): A modified K-means that:

   • Uses seed points to guide initial clustering
   • Applies density and distance constraints
   • Prevents centroids from drifting too far using radial thresholds
   • Supports customizable distance metrics through the distance_metric and metric_params parameters.
   • Handles advanced seed points via a dictionary structure for more controlled initialization.

2. Exploratory Phase: Uses density-based clustering methods to discover patterns in points not assigned during the first phase.

Use Cases

CLiMB is particularly useful for:

• Datasets with partially known structure
• Astronomical data analysis
• Particle physics clustering
• Pattern discovery in scientific datasets
• Data exploration with prior knowledge

Advanced Usage

Using Different Exploratory Algorithms

from CLiMB.core.CLiMB import CLiMB
from CLiMB.exploratory.HDBSCANExploratory import HDBSCANExploratory

# Create HDBSCAN exploratory algorithm
hdbscan = HDBSCANExploratory(min_cluster_size=5, min_samples=3)

# Use it with CLIMB
climb = CLiMB(
    constrained_clusters=3,
    exploratory_algorithm=hdbscan
)

Parameter Tuning with Builder Pattern

climb = CLiMB()
climb.set_density(0.3) \
     .set_distance(2.5) \
     .set_radial(1.0) \
     .set_convergence(0.1)

Using Custom Distance Metrics

To use distance metrics other than Euclidean, you can use the distance_metric and metric_params parameters in the KBound class.

Example with Mahalanobis Metric:

import numpy as np
from CLiMB.core.KBound import KBound

# ... (Load or generate your data X) ...

# Calculate the inverse covariance matrix (VI) for Mahalanobis
covariance_matrix = np.cov(X.T)
inv_covariance_matrix = np.linalg.inv(covariance_matrix)

# Initialize KBound with the Mahalanobis metric and parameters
kbound = KBound(
    n_clusters=3,
    distance_metric='mahalanobis',
    metric_params={'VI': inv_covariance_matrix}
)
kbound.fit(X)

If you do not provide metric_params for the Mahalanobis metric, the inverse covariance matrix will be automatically calculated on the input data X during fit.

Example with Custom Metric:

import numpy as np
from CLiMB.core.KBound import KBound
from scipy.spatial.distance import euclidean

# Define your custom distance metric
def custom_distance(u, v):
    # Example: weighted Euclidean distance, where the first dimension counts double
    weight = np.array([2, 1, 1]) # Weights for each dimension
    return euclidean(u * weight, v * weight)

# Initialize KBound with the custom metric
kbound = KBound(
    n_clusters=3,
    distance_metric='custom',
    metric_params={'func': custom_distance}
)
kbound.fit(X)

Advanced Usage of Seed Points with Dictionary

In addition to the list of seed points, you can now provide a dictionary to initialize centroids and associate specific seed points with each centroid. This offers more granular control over the initialization of constrained clustering.

Example of Seed Point Dictionary:

import numpy as np
from CLiMB.core.KBound import KBound

# ... (Load or generate your data X and define initial centroids and seed points) ...

# Define a dictionary of seed points
# Keys are initial centroids (points), values are lists of seed points associated with that centroid
seed_dict = {
    tuple(initial_centroids[0]): [tuple(seed_point_cluster1_1), tuple(seed_point_cluster1_2)],
    tuple(initial_centroids[1]): [tuple(seed_point_cluster2_1)],
    tuple(initial_centroids[2]): [], # No specific seed points for this centroid
    # ... and so on for all centroids ...
}

# Initialize KBound with the seed point dictionary
kbound = KBound(
    n_clusters=len(initial_centroids),
    seeds=seed_dict
    # ... and so on for the other parameters
)
kbound.fit(X)

License

MIT

Tests Status

Citation