K-means Clustering

The K-means algorithm is the first unsupervised method we encounter in the course. The previous supervised methods worked with a set of observations and labels $\mathcal{T} = \{(\mathbf{x}_1, y_1), \ldots, (\mathbf{x}_n, y_n)\}$. The unsupervised methods use unlabeled observations $\mathcal{T} = \{\mathbf{x}_1, \ldots, \mathbf{x}_n\}$. The goal is to infer properties of a probability distribution $p_X(\mathbf{x})$.

In low-dimensional problems ($dim(\mathbf{x}) \leq 3$), we can estimate the probability density directly using variety of techniques (e.g. histograms, Parzen window). And when we have a prior information about the type of a particular probability distribution, we can directly estimate the distribution parameters.

Due to curse of dimensionality these methods fail in higher dimensions. When the dimensionality increases, the volume grows exponentially and the data becomes exponentially sparser. In such cases we use techniques that do not find the full underlying distribution $p_X(\mathbf{x})$, but instead describe the data in a more relaxed way.

The main groups of unsupervised methods are:

• dimensionality reduction methods
• clustering methods

The dimensionality reduction methods map data onto a lower-dimensional manifold while minimizing the lost information. The clustering methods partition the observations into groups with small difference between the group samples.

The unsupervised methods have many applications including smart feature selection, data visualization, efficient data encoding, adaptive classification and image segmentation. Last but not least example is Google's PageRank algorithm.

The K-means algorithm is a popular clustering approach. The goal is to find a clustering $\{\mathcal{T}_k\}^K_{k=1}$ of the observations that minimizes the within-cluster sum of squares (WCSS): $$\{\mathbf{c}_1, \ldots, \mathbf{c}_K; \mathcal{T}_1, \ldots, \mathcal{T}_K\} = \underset{\text{all }\mathbf{c}^{'}_k, \mathcal{T}^{'}_k} {\operatorname{arg\,min}} \sum_{k=1}^{K} \sum_{\mathbf{x} \in \mathcal{T}^{'}_k} \| \mathbf{x} - \mathbf{c}^{'}_k \|^2_2,$$ where $K$ is a user specified number of clusters, $\mathcal{T}_1,\ldots,\mathcal{T}_K$ are sets of observations belonging to clusters $1,\ldots,K$ and each cluster is represented by its prototype $\mathbf{c}_k$.

The solution that K-means reaches often depends on the initialization of the means and there is no guarantee that it reaches the global optimum. As you can see in the two examples below, the solution is not unique and it can happen that the algorithm reaches a local minimum (as in the lower example), where reassigning any point to some other cluster would increase WCSS, but where a better solution does exist.

The chance of getting trapped in a local minimum can be reduced by performing more trials of the K-means clustering and choosing the result that minimizes WCSS.

K-Means++ is the K-means with clever initialization of cluster centers. The motivation is to make initializations which make K-means more likely to end up in a better local minima (a minima with a lower WCSS).

Your task is to implement the basic K-means algorithm as described in the box above. See the template for details.

# In order to obtain the same results, use this initialization of the random number generator
# (don't put this into functions submitted to the upload system).
np.random.seed(0) 
 
x = np.array([[16, 12, 50, 96, 34, 59, 22, 75, 26, 51]])
cluster_labels, centroids, sq_dists = k_means(x, 3, np.inf)
print('cluster_labels: ', cluster_labels, '\ncentroids: ', centroids, '\nsq_dists: ', sq_dists)
# -> cluster_labels:  [1 1 0 0 2 0 1 0 1 0] 
# -> centroids:       [[66 19 34]] 
# -> sq_dists:        [  9.  49. 256. 900.   0.  49.   9.  81.  49. 225.]

Limited number of iterations:

np.random.seed(0) 
images = np.load("data_kmeans.npz", allow_pickle=True)["images"]
x = compute_measurements(images)
_, centroids, _ = k_means(x, 3, 4)
print('centroids:\n', centroids)
# -> centroids:
# -> [[  330.84821429  -115.04545455 -4566.76      ]
# ->  [-2348.99107143   658.20454545  2375.78      ]]

Test the algorithm on the measurements extracted from the unlabelled data:

• data_kmeans.npz, which consists of images of three letters - H, L, T (here K = 3)
• the MNIST dataset data_mnist_kmeans.npz of hand written numbers, K = 10

Inspect the results.

Implement the function k_means_multiple_trials(x, k, n_trials, max_iter)]] which tries to avoid being trapped in local minimum by performing K-means several times and selecting the solution that minimizes the WCSS.

Implement clever K-means initialization: K-means++. The function centroids = k_meanspp(x, k) returns initial cluster prototypes for use in the already implemented K-means algorithm. You will first need to prepare idx = random_sample(weights) function that picks randomly a sample based on the sample weights. See the following recipe and figure to illustrate the sampling process:

1. normalize the sample weights
2. generate a random number in the interval (0, 1)
3. select corresponding sample

Note: use random_sample() with all weights set to 1 for choosing the first centroid.

Your implementation should return the same results:

np.random.seed(0)
distances = np.array([10, 2, 4, 8, 3])
idx_1 = random_sample(distances)
idx_2 = random_sample(distances)
print('idx_1: ', idx_1, '\nidx_2: ', idx_2)
# -> idx_1:  2 
# -> idx_2:  3

K-means++ favors initialization with cluster prototypes far from each other:

np.random.seed(0)
x = np.atleast_2d(np.array(range(100)))
centroids = k_meanspp(x, 3)
print('centroids: ', centroids)
# centroids:  [[54 82 15]]

Inspect the K-means++ initialization for the data generated by gen_kmeanspp_data and compare it to a uniform random initialization of vanilla K-means. Save the figures of initializations to random_initialization.png and kmeanspp_initialization.png. Use your random_sample function to generate ALL kmeans++ output indexes.

Apply K-means algorithm to the color quantization problem. The aim is to reduce the number of distinct colors in an image such that the resulting image is visually close to the source image. The algorithm is as

1. Reshape the input image to (N, 3) and convert it to np.float64
2. Randomly select 1000 pixels from the reshaped image (inds = np.random.randint(0, N-1, 1000)).
3. Perform K-means clustering of the selected pixels in the three-dimensional RGB space (using k_means function with max_iter=float('inf'), without k_meanspp initialization).
4. Assign all image pixels to the found means.
5. convert the result to np.uint8 without rounding it first.

You are supposed to implement a function im_q = quantize_colors(im, k) which performs the described color quantization. Run this function on geeks.png image and save the resulting quantized version as geeks_quantized.png. The right image below is a sample result (for k=8):

Important (for automatic evaluation): To generate indices of the 1000 random pixels, use this code: inds = np.random.randint(0, (h_image * w_image)-1, 1000).