Here's something of mine that might actually be useful: a Python implementation of the K-means clustering algorithm. I wrote something similar last year in Java for a school project, and decided to rewrite it in Python this summer for practice.

The purpose of the algorithm is to discover internal structure in some set of data points - you supply the points and the number of clusters you expect to get, and the algorithm returns the same points, organized into clusters by proximity. Once you have the clusters, you can get their sample means, their variances, do a bunch of statistics, etc. This approach has become very popular among the bioinformatics crowd, and especially among analysts of gene expression (microarray) data.

The central idea behind K-means is the manipulation of things called "centroids." A centroid is an imaginary point specific to a cluster of points. It is an average point - that is, if you took all the points in the cluster, and averaged their coordinates, you'd have the centroid.

K-means starts by creating singleton clusters around k randomly sampled points from your input list. Then, it assigns each point in that list to the cluster with the closest centroid. This shift in the contents of the cluster causes a shift in the position of the centroid. You keep re-assigning points and shifting centroids again and again, until the largest centroid shift distance is smaller than the input cutoff.

But that's the abridged version - see if you can figure out what it's doing.

# clustering.py contains classes and functions that cluster data points import sys, math, random # -- The Point class represents points in n-dimensional space class Point: # Instance variables # self.coords is a list of coordinates for this Point # self.n is the number of dimensions this Point lives in (ie, its space) # self.reference is an object bound to this Point # Initialize new Points def __init__(self, coords, reference=None): self.coords = coords self.n = len(coords) self.reference = reference # Return a string representation of this Point def __repr__(self): return str(self.coords) # -- The Cluster class represents clusters of points in n-dimensional space class Cluster: # Instance variables # self.points is a list of Points associated with this Cluster # self.n is the number of dimensions this Cluster's Points live in # self.centroid is the sample mean Point of this Cluster def __init__(self, points): # We forbid empty Clusters (they don't make mathematical sense!) if len(points) == 0: raise Exception("ILLEGAL: EMPTY CLUSTER") self.points = points self.n = points[0].n # We also forbid Clusters containing Points in different spaces # Ie, no Clusters with 2D Points and 3D Points for p in points: if p.n != self.n: raise Exception("ILLEGAL: MULTISPACE CLUSTER") # Figure out what the centroid of this Cluster should be self.centroid = self.calculateCentroid() # Return a string representation of this Cluster def __repr__(self): return str(self.points) # Update function for the K-means algorithm # Assigns a new list of Points to this Cluster, returns centroid difference def update(self, points): old_centroid = self.centroid self.points = points self.centroid = self.calculateCentroid() return getDistance(old_centroid, self.centroid) # Calculates the centroid Point - the centroid is the sample mean Point # (in plain English, the average of all the Points in the Cluster) def calculateCentroid(self): centroid_coords = [] # For each coordinate: for i in range(self.n): # Take the average across all Points centroid_coords.append(0.0) for p in self.points: centroid_coords[i] = centroid_coords[i]+p.coords[i] centroid_coords[i] = centroid_coords[i]/len(self.points) # Return a Point object using the average coordinates return Point(centroid_coords) # -- Return Clusters of Points formed by K-means clustering def kmeans(points, k, cutoff): # Randomly sample k Points from the points list, build Clusters around them initial = random.sample(points, k) clusters = [] for p in initial: clusters.append(Cluster([p])) # Enter the program loop while True: # Make a list for each Cluster lists = [] for c in clusters: lists.append([]) # For each Point: for p in points: # Figure out which Cluster's centroid is the nearest smallest_distance = getDistance(p, clusters[0].centroid) index = 0 for i in range(len(clusters[1:])): distance = getDistance(p, clusters[i+1].centroid) if distance < smallest_distance: smallest_distance = distance index = i+1 # Add this Point to that Cluster's corresponding list lists[index].append(p) # Update each Cluster with the corresponding list # Record the biggest centroid shift for any Cluster biggest_shift = 0.0 for i in range(len(clusters)): shift = clusters[i].update(lists[i]) biggest_shift = max(biggest_shift, shift) # If the biggest centroid shift is less than the cutoff, stop if biggest_shift < cutoff: break # Return the list of Clusters return clusters # -- Get the Euclidean distance between two Points def getDistance(a, b): # Forbid measurements between Points in different spaces if a.n != b.n: raise Exception("ILLEGAL: NON-COMPARABLE POINTS") # Euclidean distance between a and b is sqrt(sum((a[i]-b[i])^2) for all i) ret = 0.0 for i in range(a.n): ret = ret+pow((a.coords[i]-b.coords[i]), 2) return math.sqrt(ret) # -- Create a random Point in n-dimensional space def makeRandomPoint(n, lower, upper): coords = [] for i in range(n): coords.append(random.uniform(lower, upper)) return Point(coords) # -- Main function def main(args): num_points, n, k, cutoff, lower, upper = 10, 2, 3, 0.5, -200, 200 # Create num_points random Points in n-dimensional space points = [] for i in range(num_points): points.append(makeRandomPoint(n, lower, upper)) # Cluster the points using the K-means algorithm clusters = kmeans(points, k, cutoff) # Print the results print "

POINTS:" for p in points: print "P:", p print "

CLUSTERS:" for c in clusters: print "C:", c # -- The following code executes upon command-line invocation if __name__ == "__main__": main(sys.argv)

:D