Merge pull request #7503 from alimate/BAEL-3070

BAEL-3070: K-Means Clustering Code Samples
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Eric Martin 2019-08-14 07:19:13 -05:00 committed by GitHub
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12 changed files with 4640 additions and 9 deletions

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@ -31,6 +31,17 @@
<version>${guava.version}</version> <version>${guava.version}</version>
</dependency> </dependency>
<dependency>
<groupId>com.squareup.retrofit2</groupId>
<artifactId>retrofit</artifactId>
<version>${retrofit.version}</version>
</dependency>
<dependency>
<groupId>com.squareup.retrofit2</groupId>
<artifactId>converter-jackson</artifactId>
<version>${retrofit.version}</version>
</dependency>
<dependency> <dependency>
<groupId>org.apache.commons</groupId> <groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId> <artifactId>commons-lang3</artifactId>
@ -61,5 +72,6 @@
<org.assertj.core.version>3.9.0</org.assertj.core.version> <org.assertj.core.version>3.9.0</org.assertj.core.version>
<commons-collections4.version>4.3</commons-collections4.version> <commons-collections4.version>4.3</commons-collections4.version>
<guava.version>28.0-jre</guava.version> <guava.version>28.0-jre</guava.version>
<retrofit.version>2.6.0</retrofit.version>
</properties> </properties>
</project> </project>

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@ -0,0 +1,45 @@
package com.baeldung.algorithms.kmeans;
import java.util.Map;
import java.util.Objects;
/**
* Encapsulates all coordinates for a particular cluster centroid.
*/
public class Centroid {
/**
* The centroid coordinates.
*/
private final Map<String, Double> coordinates;
public Centroid(Map<String, Double> coordinates) {
this.coordinates = coordinates;
}
public Map<String, Double> getCoordinates() {
return coordinates;
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
Centroid centroid = (Centroid) o;
return Objects.equals(getCoordinates(), centroid.getCoordinates());
}
@Override
public int hashCode() {
return Objects.hash(getCoordinates());
}
@Override
public String toString() {
return "Centroid " + coordinates;
}
}

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@ -0,0 +1,20 @@
package com.baeldung.algorithms.kmeans;
import java.util.Map;
/**
* Defines a contract to calculate distance between two feature vectors. The less the
* calculated distance, the more two items are similar to each other.
*/
public interface Distance {
/**
* Calculates the distance between two feature vectors.
*
* @param f1 The first set of features.
* @param f2 The second set of features.
* @return Calculated distance.
* @throws IllegalArgumentException If the given feature vectors are invalid.
*/
double calculate(Map<String, Double> f1, Map<String, Double> f2);
}

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@ -0,0 +1,23 @@
package com.baeldung.algorithms.kmeans;
import java.util.List;
import java.util.Map;
/**
* Encapsulates methods to calculates errors between centroid and the cluster members.
*/
public class Errors {
public static double sse(Map<Centroid, List<Record>> clustered, Distance distance) {
double sum = 0;
for (Map.Entry<Centroid, List<Record>> entry : clustered.entrySet()) {
Centroid centroid = entry.getKey();
for (Record record : entry.getValue()) {
double d = distance.calculate(centroid.getCoordinates(), record.getFeatures());
sum += Math.pow(d, 2);
}
}
return sum;
}
}

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@ -0,0 +1,26 @@
package com.baeldung.algorithms.kmeans;
import java.util.Map;
/**
* Calculates the distance between two items using the Euclidean formula.
*/
public class EuclideanDistance implements Distance {
@Override
public double calculate(Map<String, Double> f1, Map<String, Double> f2) {
if (f1 == null || f2 == null) {
throw new IllegalArgumentException("Feature vectors can't be null");
}
double sum = 0;
for (String key : f1.keySet()) {
Double v1 = f1.get(key);
Double v2 = f2.get(key);
if (v1 != null && v2 != null) sum += Math.pow(v1 - v2, 2);
}
return Math.sqrt(sum);
}
}

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@ -0,0 +1,236 @@
package com.baeldung.algorithms.kmeans;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Random;
import java.util.Set;
import static java.util.stream.Collectors.toList;
import static java.util.stream.Collectors.toSet;
/**
* Encapsulates an implementation of KMeans clustering algorithm.
*
* @author Ali Dehghani
*/
public class KMeans {
private KMeans() {
throw new IllegalAccessError("You shouldn't call this constructor");
}
/**
* Will be used to generate random numbers.
*/
private static final Random random = new Random();
/**
* Performs the K-Means clustering algorithm on the given dataset.
*
* @param records The dataset.
* @param k Number of Clusters.
* @param distance To calculate the distance between two items.
* @param maxIterations Upper bound for the number of iterations.
* @return K clusters along with their features.
*/
public static Map<Centroid, List<Record>> fit(List<Record> records, int k, Distance distance, int maxIterations) {
applyPreconditions(records, k, distance, maxIterations);
List<Centroid> centroids = randomCentroids(records, k);
Map<Centroid, List<Record>> clusters = new HashMap<>();
Map<Centroid, List<Record>> lastState = new HashMap<>();
// iterate for a pre-defined number of times
for (int i = 0; i < maxIterations; i++) {
boolean isLastIteration = i == maxIterations - 1;
// in each iteration we should find the nearest centroid for each record
for (Record record : records) {
Centroid centroid = nearestCentroid(record, centroids, distance);
assignToCluster(clusters, record, centroid);
}
// if the assignment does not change, then the algorithm terminates
boolean shouldTerminate = isLastIteration || clusters.equals(lastState);
lastState = clusters;
if (shouldTerminate) {
break;
}
// at the end of each iteration we should relocate the centroids
centroids = relocateCentroids(clusters);
clusters = new HashMap<>();
}
return lastState;
}
/**
* Move all cluster centroids to the average of all assigned features.
*
* @param clusters The current cluster configuration.
* @return Collection of new and relocated centroids.
*/
private static List<Centroid> relocateCentroids(Map<Centroid, List<Record>> clusters) {
return clusters
.entrySet()
.stream()
.map(e -> average(e.getKey(), e.getValue()))
.collect(toList());
}
/**
* Moves the given centroid to the average position of all assigned features. If
* the centroid has no feature in its cluster, then there would be no need for a
* relocation. Otherwise, for each entry we calculate the average of all records
* first by summing all the entries and then dividing the final summation value by
* the number of records.
*
* @param centroid The centroid to move.
* @param records The assigned features.
* @return The moved centroid.
*/
private static Centroid average(Centroid centroid, List<Record> records) {
// if this cluster is empty, then we shouldn't move the centroid
if (records == null || records.isEmpty()) {
return centroid;
}
// Since some records don't have all possible attributes, we initialize
// average coordinates equal to current centroid coordinates
Map<String, Double> average = centroid.getCoordinates();
// The average function works correctly if we clear all coordinates corresponding
// to present record attributes
records
.stream()
.flatMap(e -> e
.getFeatures()
.keySet()
.stream())
.forEach(k -> average.put(k, 0.0));
for (Record record : records) {
record
.getFeatures()
.forEach((k, v) -> average.compute(k, (k1, currentValue) -> v + currentValue));
}
average.forEach((k, v) -> average.put(k, v / records.size()));
return new Centroid(average);
}
/**
* Assigns a feature vector to the given centroid. If this is the first assignment for this centroid,
* first we should create the list.
*
* @param clusters The current cluster configuration.
* @param record The feature vector.
* @param centroid The centroid.
*/
private static void assignToCluster(Map<Centroid, List<Record>> clusters, Record record, Centroid centroid) {
clusters.compute(centroid, (key, list) -> {
if (list == null) {
list = new ArrayList<>();
}
list.add(record);
return list;
});
}
/**
* With the help of the given distance calculator, iterates through centroids and finds the
* nearest one to the given record.
*
* @param record The feature vector to find a centroid for.
* @param centroids Collection of all centroids.
* @param distance To calculate the distance between two items.
* @return The nearest centroid to the given feature vector.
*/
private static Centroid nearestCentroid(Record record, List<Centroid> centroids, Distance distance) {
double minimumDistance = Double.MAX_VALUE;
Centroid nearest = null;
for (Centroid centroid : centroids) {
double currentDistance = distance.calculate(record.getFeatures(), centroid.getCoordinates());
if (currentDistance < minimumDistance) {
minimumDistance = currentDistance;
nearest = centroid;
}
}
return nearest;
}
/**
* Generates k random centroids. Before kicking-off the centroid generation process,
* first we calculate the possible value range for each attribute. Then when
* we're going to generate the centroids, we generate random coordinates in
* the [min, max] range for each attribute.
*
* @param records The dataset which helps to calculate the [min, max] range for
* each attribute.
* @param k Number of clusters.
* @return Collections of randomly generated centroids.
*/
private static List<Centroid> randomCentroids(List<Record> records, int k) {
List<Centroid> centroids = new ArrayList<>();
Map<String, Double> maxs = new HashMap<>();
Map<String, Double> mins = new HashMap<>();
for (Record record : records) {
record
.getFeatures()
.forEach((key, value) -> {
// compares the value with the current max and choose the bigger value between them
maxs.compute(key, (k1, max) -> max == null || value > max ? value : max);
// compare the value with the current min and choose the smaller value between them
mins.compute(key, (k1, min) -> min == null || value < min ? value : min);
});
}
Set<String> attributes = records
.stream()
.flatMap(e -> e
.getFeatures()
.keySet()
.stream())
.collect(toSet());
for (int i = 0; i < k; i++) {
Map<String, Double> coordinates = new HashMap<>();
for (String attribute : attributes) {
double max = maxs.get(attribute);
double min = mins.get(attribute);
coordinates.put(attribute, random.nextDouble() * (max - min) + min);
}
centroids.add(new Centroid(coordinates));
}
return centroids;
}
private static void applyPreconditions(List<Record> records, int k, Distance distance, int maxIterations) {
if (records == null || records.isEmpty()) {
throw new IllegalArgumentException("The dataset can't be empty");
}
if (k <= 1) {
throw new IllegalArgumentException("It doesn't make sense to have less than or equal to 1 cluster");
}
if (distance == null) {
throw new IllegalArgumentException("The distance calculator is required");
}
if (maxIterations <= 0) {
throw new IllegalArgumentException("Max iterations should be a positive number");
}
}
}

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package com.baeldung.algorithms.kmeans;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import com.fasterxml.jackson.databind.ObjectMapper;
import okhttp3.OkHttpClient;
import retrofit2.Retrofit;
import retrofit2.converter.jackson.JacksonConverterFactory;
import static java.util.stream.Collectors.toSet;
public class LastFm {
private static OkHttpClient okHttp = new OkHttpClient.Builder()
.addInterceptor(new LastFmService.Authenticator("put your API key here"))
.build();
private static Retrofit retrofit = new Retrofit.Builder()
.client(okHttp)
.addConverterFactory(JacksonConverterFactory.create())
.baseUrl("http://ws.audioscrobbler.com/")
.build();
private static LastFmService lastFm = retrofit.create(LastFmService.class);
private static ObjectMapper mapper = new ObjectMapper();
public static void main(String[] args) throws IOException {
List<String> artists = getTop100Artists();
Set<String> tags = getTop100Tags();
List<Record> records = datasetWithTaggedArtists(artists, tags);
Map<Centroid, List<Record>> clusters = KMeans.fit(records, 7, new EuclideanDistance(), 1000);
// Print the cluster configuration
clusters.forEach((key, value) -> {
System.out.println("------------------------------ CLUSTER -----------------------------------");
System.out.println(sortedCentroid(key));
String members = String.join(", ", value
.stream()
.map(Record::getDescription)
.collect(toSet()));
System.out.print(members);
System.out.println();
System.out.println();
});
Map<String, Object> json = convertToD3CompatibleMap(clusters);
System.out.println(mapper.writeValueAsString(json));
}
private static Map<String, Object> convertToD3CompatibleMap(Map<Centroid, List<Record>> clusters) {
Map<String, Object> json = new HashMap<>();
json.put("name", "Musicians");
List<Map<String, Object>> children = new ArrayList<>();
clusters.forEach((key, value) -> {
Map<String, Object> child = new HashMap<>();
child.put("name", dominantGenre(sortedCentroid(key)));
List<Map<String, String>> nested = new ArrayList<>();
for (Record record : value) {
nested.add(Collections.singletonMap("name", record.getDescription()));
}
child.put("children", nested);
children.add(child);
});
json.put("children", children);
return json;
}
private static String dominantGenre(Centroid centroid) {
return centroid
.getCoordinates()
.keySet()
.stream()
.limit(2)
.collect(Collectors.joining(", "));
}
private static Centroid sortedCentroid(Centroid key) {
List<Map.Entry<String, Double>> entries = new ArrayList<>(key
.getCoordinates()
.entrySet());
entries.sort((e1, e2) -> e2
.getValue()
.compareTo(e1.getValue()));
Map<String, Double> sorted = new LinkedHashMap<>();
for (Map.Entry<String, Double> entry : entries) {
sorted.put(entry.getKey(), entry.getValue());
}
return new Centroid(sorted);
}
private static List<Record> datasetWithTaggedArtists(List<String> artists, Set<String> topTags) throws IOException {
List<Record> records = new ArrayList<>();
for (String artist : artists) {
Map<String, Double> tags = lastFm
.topTagsFor(artist)
.execute()
.body()
.all();
// Only keep popular tags.
tags
.entrySet()
.removeIf(e -> !topTags.contains(e.getKey()));
records.add(new Record(artist, tags));
}
return records;
}
private static Set<String> getTop100Tags() throws IOException {
return lastFm
.topTags()
.execute()
.body()
.all();
}
private static List<String> getTop100Artists() throws IOException {
List<String> artists = new ArrayList<>();
for (int i = 1; i <= 2; i++) {
artists.addAll(lastFm
.topArtists(i)
.execute()
.body()
.all());
}
return artists;
}
}

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package com.baeldung.algorithms.kmeans;
import java.io.IOException;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonProperty;
import okhttp3.HttpUrl;
import okhttp3.Interceptor;
import okhttp3.Request;
import okhttp3.Response;
import retrofit2.Call;
import retrofit2.http.GET;
import retrofit2.http.Query;
import static com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility.ANY;
import static java.util.stream.Collectors.toList;
public interface LastFmService {
@GET("/2.0/?method=chart.gettopartists&format=json&limit=50")
Call<Artists> topArtists(@Query("page") int page);
@GET("/2.0/?method=artist.gettoptags&format=json&limit=20&autocorrect=1")
Call<Tags> topTagsFor(@Query("artist") String artist);
@GET("/2.0/?method=chart.gettoptags&format=json&limit=100")
Call<TopTags> topTags();
/**
* HTTP interceptor to intercept all HTTP requests and add the API key to them.
*/
class Authenticator implements Interceptor {
private final String apiKey;
Authenticator(String apiKey) {
this.apiKey = apiKey;
}
@Override
public Response intercept(Chain chain) throws IOException {
HttpUrl url = chain
.request()
.url()
.newBuilder()
.addQueryParameter("api_key", apiKey)
.build();
Request request = chain
.request()
.newBuilder()
.url(url)
.build();
return chain.proceed(request);
}
}
@JsonAutoDetect(fieldVisibility = ANY)
class TopTags {
private Map<String, Object> tags;
@SuppressWarnings("unchecked")
public Set<String> all() {
List<Map<String, Object>> topTags = (List<Map<String, Object>>) tags.get("tag");
return topTags
.stream()
.map(e -> ((String) e.get("name")))
.collect(Collectors.toSet());
}
}
@JsonAutoDetect(fieldVisibility = ANY)
class Tags {
@JsonProperty("toptags") private Map<String, Object> topTags;
@SuppressWarnings("unchecked")
public Map<String, Double> all() {
try {
Map<String, Double> all = new HashMap<>();
List<Map<String, Object>> tags = (List<Map<String, Object>>) topTags.get("tag");
for (Map<String, Object> tag : tags) {
all.put(((String) tag.get("name")), ((Integer) tag.get("count")).doubleValue());
}
return all;
} catch (Exception e) {
return Collections.emptyMap();
}
}
}
@JsonAutoDetect(fieldVisibility = ANY)
class Artists {
private Map<String, Object> artists;
@SuppressWarnings("unchecked")
public List<String> all() {
try {
List<Map<String, Object>> artists = (List<Map<String, Object>>) this.artists.get("artist");
return artists
.stream()
.map(e -> ((String) e.get("name")))
.collect(toList());
} catch (Exception e) {
return Collections.emptyList();
}
}
}
}

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package com.baeldung.algorithms.kmeans;
import java.util.Map;
import java.util.Objects;
/**
* Encapsulates all feature values for a few attributes. Optionally each record
* can be described with the {@link #description} field.
*/
public class Record {
/**
* The record description. For example, this can be the artist name for the famous musician
* example.
*/
private final String description;
/**
* Encapsulates all attributes and their corresponding values, i.e. features.
*/
private final Map<String, Double> features;
public Record(String description, Map<String, Double> features) {
this.description = description;
this.features = features;
}
public Record(Map<String, Double> features) {
this("", features);
}
public String getDescription() {
return description;
}
public Map<String, Double> getFeatures() {
return features;
}
@Override
public String toString() {
String prefix = description == null || description
.trim()
.isEmpty() ? "Record" : description;
return prefix + ": " + features;
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
Record record = (Record) o;
return Objects.equals(getDescription(), record.getDescription()) && Objects.equals(getFeatures(), record.getFeatures());
}
@Override
public int hashCode() {
return Objects.hash(getDescription(), getFeatures());
}
}

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{
"children": [
{
"children": [
{
"name": "Radiohead"
},
{
"name": "Red Hot Chili Peppers"
},
{
"name": "Coldplay"
},
{
"name": "Nirvana"
},
{
"name": "Panic! at the Disco"
},
{
"name": "The Cure"
},
{
"name": "Linkin Park"
},
{
"name": "Radiohead"
},
{
"name": "Red Hot Chili Peppers"
},
{
"name": "Coldplay"
},
{
"name": "Nirvana"
},
{
"name": "Panic! at the Disco"
},
{
"name": "The Cure"
},
{
"name": "Linkin Park"
},
{
"name": "Muse"
},
{
"name": "Maroon 5"
},
{
"name": "Foo Fighters"
},
{
"name": "Paramore"
},
{
"name": "Oasis"
},
{
"name": "Fall Out Boy"
},
{
"name": "OneRepublic"
},
{
"name": "Weezer"
},
{
"name": "System of a Down"
},
{
"name": "The White Stripes"
}
],
"name": "rock, alternative"
},
{
"children": [
{
"name": "Lil Nas X"
},
{
"name": "Post Malone"
},
{
"name": "Drake"
},
{
"name": "Kanye West"
},
{
"name": "Kendrick Lamar"
},
{
"name": "Tyler, the Creator"
},
{
"name": "Eminem"
},
{
"name": "Childish Gambino"
},
{
"name": "Frank Ocean"
},
{
"name": "Lil Nas X"
},
{
"name": "Post Malone"
},
{
"name": "Drake"
},
{
"name": "Kanye West"
},
{
"name": "Kendrick Lamar"
},
{
"name": "Tyler, the Creator"
},
{
"name": "Eminem"
},
{
"name": "Childish Gambino"
},
{
"name": "Frank Ocean"
},
{
"name": "Lizzo"
},
{
"name": "Travi$ Scott"
},
{
"name": "A$AP Rocky"
},
{
"name": "Nicki Minaj"
},
{
"name": "xxxtentacion"
}
],
"name": "Hip-Hop, rap"
},
{
"children": [
{
"name": "Arctic Monkeys"
},
{
"name": "Imagine Dragons"
},
{
"name": "The Killers"
},
{
"name": "Gorillaz"
},
{
"name": "The Black Keys"
},
{
"name": "Arctic Monkeys"
},
{
"name": "Imagine Dragons"
},
{
"name": "The Killers"
},
{
"name": "Gorillaz"
},
{
"name": "The Black Keys"
},
{
"name": "Twenty One Pilots"
},
{
"name": "Ellie Goulding"
},
{
"name": "Florence + the Machine"
},
{
"name": "Vampire Weekend"
},
{
"name": "The Smiths"
},
{
"name": "The Strokes"
},
{
"name": "MGMT"
},
{
"name": "Foster the People"
},
{
"name": "Two Door Cinema Club"
},
{
"name": "Cage the Elephant"
},
{
"name": "Arcade Fire"
},
{
"name": "The 1975"
}
],
"name": "indie, alternative"
},
{
"children": [
{
"name": "Ed Sheeran"
},
{
"name": "Tame Impala"
},
{
"name": "Ed Sheeran"
},
{
"name": "Tame Impala"
},
{
"name": "Green Day"
},
{
"name": "Metallica"
},
{
"name": "blink-182"
},
{
"name": "Bon Iver"
},
{
"name": "The Clash"
}
],
"name": "rock, punk rock"
},
{
"children": [
{
"name": "Calvin Harris"
},
{
"name": "The Weeknd"
},
{
"name": "The Chainsmokers"
},
{
"name": "Daft Punk"
},
{
"name": "Marshmello"
},
{
"name": "David Guetta"
},
{
"name": "Calvin Harris"
},
{
"name": "The Weeknd"
},
{
"name": "The Chainsmokers"
},
{
"name": "Daft Punk"
},
{
"name": "Marshmello"
},
{
"name": "David Guetta"
},
{
"name": "Avicii"
},
{
"name": "Kygo"
},
{
"name": "Martin Garrix"
},
{
"name": "Major Lazer"
},
{
"name": "Depeche Mode"
}
],
"name": "electronic, dance"
},
{
"children": [
{
"name": "Queen"
},
{
"name": "The Beatles"
},
{
"name": "David Bowie"
},
{
"name": "Fleetwood Mac"
},
{
"name": "Pink Floyd"
},
{
"name": "The Rolling Stones"
},
{
"name": "Led Zeppelin"
},
{
"name": "Queen"
},
{
"name": "The Beatles"
},
{
"name": "David Bowie"
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View File

@ -0,0 +1,68 @@
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