python类adjusted_rand_score()的实例源码

def test_GMM_n_components(*data):
    '''
    test the performance with different N_components
    :param data: data, target
    :return: None
    '''
    X,labels_true=data
    nums=range(1,50)
    ARIs=[]
    for num in nums:
        clst=mixture.GaussianMixture(n_components=num)
        clst.fit(X)
        predicted_labels=clst.predict(X)
        ARIs.append(adjusted_rand_score(labels_true,predicted_labels))

    ## graph
    fig=plt.figure()
    ax=fig.add_subplot(1,1,1)
    ax.plot(nums,ARIs,marker="+")
    ax.set_xlabel("n_components")
    ax.set_ylabel("ARI")
    fig.suptitle("GMM")
    plt.show()

def test_AgglomerativeClustering_nclusters(*data):
    '''
    test the performance with different n_clusters
    :param data:  data, target
    :return: None
    '''
    X,labels_true=data
    nums=range(1,50)
    ARIs=[]
    for num in nums:
        clst=cluster.AgglomerativeClustering(n_clusters=num)
        predicted_labels=clst.fit_predict(X)
        ARIs.append(adjusted_rand_score(labels_true,predicted_labels))

    ## graph
    fig=plt.figure()
    ax=fig.add_subplot(1,1,1)
    ax.plot(nums,ARIs,marker="+")
    ax.set_xlabel("n_clusters")
    ax.set_ylabel("ARI")
    fig.suptitle("AgglomerativeClustering")
    plt.show()

def test_discretize(seed=8):
    # Test the discretize using a noise assignment matrix
    random_state = np.random.RandomState(seed)
    for n_samples in [50, 100, 150, 500]:
        for n_class in range(2, 10):
            # random class labels
            y_true = random_state.random_integers(0, n_class, n_samples)
            y_true = np.array(y_true, np.float)
            # noise class assignment matrix
            y_indicator = sparse.coo_matrix((np.ones(n_samples),
                                             (np.arange(n_samples),
                                              y_true)),
                                            shape=(n_samples,
                                                   n_class + 1))
            y_true_noisy = (y_indicator.toarray()
                            + 0.1 * random_state.randn(n_samples,
                                                       n_class + 1))
            y_pred = discretize(y_true_noisy, random_state)
            assert_greater(adjusted_rand_score(y_true, y_pred), 0.8)

def bench_k_means(estimator, name, data):
    t0 = time()
    estimator.fit(data)
    print('% 9s   %.2fs    %i   %.3f   %.3f   %.3f   %.3f   %.3f    %.3f'
          % (name, (time() - t0), estimator.inertia_,
             metrics.homogeneity_score(labels, estimator.labels_),
             metrics.completeness_score(labels, estimator.labels_),
             metrics.v_measure_score(labels, estimator.labels_),
             metrics.adjusted_rand_score(labels, estimator.labels_),
             metrics.adjusted_mutual_info_score(labels,  estimator.labels_),
             metrics.silhouette_score(data, estimator.labels_,
                                      metric='euclidean',
                                      sample_size=sample_size)))

def bench_k_means(labels, labels_, name, data):
    print('%20s  %.3f   %.3f   %.3f   %.3f   %.3f'
          % ( name,
             metrics.homogeneity_score(labels,   labels_),
             metrics.completeness_score(labels,  labels_),
             metrics.v_measure_score(labels,     labels_),
             metrics.adjusted_rand_score(labels, labels_),
             metrics.adjusted_mutual_info_score(labels, labels_)))
    nbins=len(set(labels_))
    vals,bins=np.histogram(labels_,bins=nbins)
    print 20*' ','hist-min,max',np.min(vals),np.max(vals)

def computeAdjustedEvaluations(self, labels_families, predicted_clusters):
        if labels_families is None:
            self.adjusted_rand_score = 0
            self.adjusted_mutual_info_score = 0
            return
        self.adjusted_rand_score = metrics.adjusted_rand_score(labels_families, predicted_clusters)
        self.adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(labels_families, predicted_clusters)

def toJson(self):
        obj = {}
        obj['homogeneity']                = self.homogeneity
        obj['completeness']               = self.completeness
        obj['v_measure']                  = self.v_measure
        obj['adjusted_rand_score']        = self.adjusted_rand_score
        obj['adjusted_mutual_info_score'] = self.adjusted_mutual_info_score
        return obj

def analyze_k_means(estimator, name, data):
    t0 = time()
    estimator.fit(data) 
    print(" %9s %.2fs %i %.3f %.3f %.3f %.3f %.3f %.3f"%( name, time()-t0, estimator.inertia_, metrics.homogeneity_score(labels,  estimator.labels_), metrics.completeness_score(labels, estimator.labels_), metrics.v_measure_score(labels, estimator.labels_), metrics.adjusted_rand_score(labels, estimator.labels_), metrics.adjusted_mutual_info_score(labels, estimator.labels_), metrics.silhouette_score(data, estimator.labels_, metric='euclidean', sample_size = samples) ))

def column_average_ari(Zv, Zc, cc_state_object):
    from sklearn.metrics import adjusted_rand_score
    ari = 0
    n_cols = len(Zv)
    for col in xrange(n_cols):
        view_t = Zv[col]
        Zc_true = Zc[view_t]

        view_i = cc_state_object.Zv[col]
        Zc_inferred = cc_state_object.views[view_i].Z.tolist()
        ari += adjusted_rand_score(Zc_true, Zc_inferred)

    return ari/float(n_cols)

def compute_cluster_scores(labels, pred_labels, path):
    assert len(labels) == len(pred_labels)
    rand_score = metrics.adjusted_rand_score(labels, pred_labels)
    nmi_score = metrics.normalized_mutual_info_score(labels, pred_labels)
    with open(path, 'a') as rr:
        rr.write("%4.4f %4.4f\n" % (rand_score, nmi_score))

def ARI(labels_true, labels_pred):
    return adjusted_rand_score(labels_true, labels_pred)

def measure( predicted,true ):
    NMI = normalized_mutual_info_score( true,predicted )
    print("NMI:"+str(NMI))
    RAND = adjusted_rand_score( true,predicted )
    print("RAND:"+str(RAND))
    HOMO = homogeneity_score( true,predicted )
    print("HOMOGENEITY:"+str(HOMO))
    COMPLETENESS = completeness_score( true,predicted )
    print("COMPLETENESS:"+str(COMPLETENESS))
    return {'NMI':NMI,'RAND':RAND,'HOMOGENEITY':HOMO,'COMPLETENESS':COMPLETENESS}

def performance(self, group_labels=None):
        """
        Computes performance metrics for clustering algorithm

        Parameters
        ----------
        group_labels : (optional) ndarray(shape=nsubjects)
            Labels for subject groups
        """
        n_samples = len(self.algorithm.labels_)

        if group_labels is None:
            truelab = np.zeros(n_samples)
            unique_labels = np.unique(group_labels)
            self.clusters["true_int"] = truelab
        else:
            truelab = np.zeros(n_samples)
            unique_labels = np.unique(group_labels)

            for i, label_i in enumerate(unique_labels):
                truelab[group_labels == label_i] = i

            self.clusters["true"] = group_labels
            self.clusters["true_int"] = truelab

        lab = self.algorithm.labels_
        self.results["homogeneity"] = homogeneity_score(truelab, lab)
        self.results["completeness"] = completeness_score(truelab, lab)
        self.results["v_measure"] = v_measure_score(truelab, lab)
        self.results["adj_rand"] = adjusted_rand_score(truelab, lab)
        self.results["adj_MI"] = adjusted_mutual_info_score(truelab, lab)

def test_GMM(*data):
    '''
    test the method of GMM
    :param data: data , target
    :return: None
    '''
    X,labels_true=data
    clst=mixture.GaussianMixture()
    clst.fit(X)
    predicted_labels=clst.predict(X)
    print("ARI:{0}".format(adjusted_rand_score(labels_true,predicted_labels)))

def test_GMM_cov_type(*data):
    '''
    test the performance with different cov_type
    :param data: data, target
    :return: None
    '''
    X,labels_true=data
    nums=range(1,50)

    cov_types=['spherical','tied','diag','full']
    markers="+o*s"
    fig=plt.figure()
    ax=fig.add_subplot(1,1,1)

    for i ,cov_type in enumerate(cov_types):
        ARIs=[]
        for num in nums:
            clst=mixture.GaussianMixture(n_components=num,covariance_type=cov_type)
            clst.fit(X)
            predicted_labels=clst.predict(X)
            ARIs.append(adjusted_rand_score(labels_true,predicted_labels))
        ax.plot(nums,ARIs,marker=markers[i],label="covariance_type:{0}".format(cov_type))

    ax.set_xlabel("n_components")
    ax.legend(loc="best")
    ax.set_ylabel("ARI")
    fig.suptitle("GMM")
    plt.show()

def test_DBSCAN(*data):
    '''
    test the DBSCAN method
    :param data:  train, target
    :return: None
    '''
    X,labels_true=data
    clst=cluster.DBSCAN()
    predicted_labels=clst.fit_predict(X)
    print("ARI:%s"% adjusted_rand_score(labels_true,predicted_labels))
    print("Core sample num:{0}".format(len(clst.core_sample_indices_)))

def test_DBSCAN_epsilon(*data):
    '''
    test the score with different eps
    :param data:  train, target
    :return: None
    '''
    X,labels_true=data
    epsilons=np.logspace(-1,1.5)
    ARIs=[]
    Core_nums=[]
    for epsilon in epsilons:
        clst=cluster.DBSCAN(eps=epsilon)
        predicted_labels=clst.fit_predict(X)
        ARIs.append( adjusted_rand_score(labels_true,predicted_labels))
        Core_nums.append(len(clst.core_sample_indices_))

    ## graph
    fig=plt.figure()
    ax=fig.add_subplot(1,2,1)
    ax.plot(epsilons,ARIs,marker='+')
    ax.set_xscale('log')
    ax.set_xlabel(r"$\epsilon$")
    ax.set_ylim(0,1)
    ax.set_ylabel('ARI')

    ax=fig.add_subplot(1,2,2)
    ax.plot(epsilons,Core_nums,marker='o')
    ax.set_xscale('log')
    ax.set_xlabel(r"$\epsilon$")
    ax.set_ylabel('Core_Nums')

    fig.suptitle("DBSCAN")
    plt.show()

def test_Kmeans(*data):
    '''
    test the Kmeans
    :param data: data, target
    :return: None
    '''
    X,labels_true=data
    clst=cluster.KMeans()
    clst.fit(X)
    predicted_labels=clst.predict(X)
    print("ARI:{0}".format( adjusted_rand_score(labels_true,predicted_labels)))
    print("Sum center distance {0}".format(clst.inertia_))

def test_Kmeans_nclusters(*data):
    '''
    test the performance with different n_clusters
    :param data: data, target
    :return: None
    '''
    X,labels_true=data
    nums=range(1,50)
    ARIs=[]
    Distances=[]
    for num in nums:
        clst=cluster.KMeans(n_clusters=num)
        clst.fit(X)
        predicted_labels=clst.predict(X)
        ARIs.append(adjusted_rand_score(labels_true,predicted_labels))
        Distances.append(clst.inertia_)

    ## graph
    fig=plt.figure()
    ax=fig.add_subplot(1,2,1)
    ax.plot(nums,ARIs,marker="+")
    ax.set_xlabel("n_clusters")
    ax.set_ylabel("ARI")
    ax=fig.add_subplot(1,2,2)
    ax.plot(nums,Distances,marker='o')
    ax.set_xlabel("n_clusters")
    ax.set_ylabel("inertia_")
    fig.suptitle("KMeans")
    plt.show()

def test_AgglomerativeClustering(*data):
    '''
    test AGG method
    :param data: data, target
    :return: None
    '''
    X,labels_true=data
    clst=cluster.AgglomerativeClustering()
    predicted_labels=clst.fit_predict(X)
    print("ARI:{0}".format(adjusted_rand_score(labels_true,predicted_labels)))

def evaluate(path):
    system = systems[path]

    measure, scores, clusters_gold, clusters_system = 0., OrderedDict(), [], []

    for lemma in lemmas:
        instances = sorted(gold[lemma].keys())

        senses_gold   = {sid: i for i, sid in enumerate(sorted(set(gold[lemma].values())))}
        senses_system = {sid: i for i, sid in enumerate(sorted(set(system[lemma].values())))}

        clusters_gold   = [senses_gold[gold[lemma][instance]]     for instance in instances]
        clusters_system = [senses_system[system[lemma][instance]] for instance in instances]

        if 'vmeasure' == args.measure:
            if 'instances' == args.average:
                measure += v_measure_score(clusters_gold, clusters_system) * len(instances) / total
            else:
                measure += v_measure_score(clusters_gold, clusters_system)

            scores[lemma] = (
                homogeneity_score(clusters_gold, clusters_system),
                completeness_score(clusters_gold, clusters_system),
                v_measure_score(clusters_gold, clusters_system)
            )
        else:
            scores[lemma] = adjusted_rand_score(clusters_gold, clusters_system)

            if 'instances' == args.average:
                measure += scores[lemma] * len(instances) / total
            else:
                measure += scores[lemma]

    if 'words' == args.average:
        measure /= len(lemmas)

    return measure, scores

def bench_k_means(estimator, name, data):
    t0 = time()
    estimator.fit(data)
    print('% 9s   %.2fs    %i   %.3f   %.3f   %.3f   %.3f   %.3f    %.3f'
          % (name, (time() - t0), estimator.inertia_,
             metrics.homogeneity_score(labels, estimator.labels_),
             metrics.completeness_score(labels, estimator.labels_),
             metrics.v_measure_score(labels, estimator.labels_),
             metrics.adjusted_rand_score(labels, estimator.labels_),
             metrics.adjusted_mutual_info_score(labels,  estimator.labels_),
             metrics.silhouette_score(data, estimator.labels_,
                                      metric='euclidean',
                                      sample_size=sample_size)))

def check_clustering(name, Alg):
    X, y = make_blobs(n_samples=50, random_state=1)
    X, y = shuffle(X, y, random_state=7)
    X = StandardScaler().fit_transform(X)
    n_samples, n_features = X.shape
    # catch deprecation and neighbors warnings
    with warnings.catch_warnings(record=True):
        alg = Alg()
    set_testing_parameters(alg)
    if hasattr(alg, "n_clusters"):
        alg.set_params(n_clusters=3)
    set_random_state(alg)
    if name == 'AffinityPropagation':
        alg.set_params(preference=-100)
        alg.set_params(max_iter=100)

    # fit
    alg.fit(X)
    # with lists
    alg.fit(X.tolist())

    assert_equal(alg.labels_.shape, (n_samples,))
    pred = alg.labels_
    assert_greater(adjusted_rand_score(pred, y), 0.4)
    # fit another time with ``fit_predict`` and compare results
    if name is 'SpectralClustering':
        # there is no way to make Spectral clustering deterministic :(
        return
    set_random_state(alg)
    with warnings.catch_warnings(record=True):
        pred2 = alg.fit_predict(X)
    assert_array_equal(pred, pred2)

def test_spectral_clustering_sparse():
    X, y = make_blobs(n_samples=20, random_state=0,
                      centers=[[1, 1], [-1, -1]], cluster_std=0.01)

    S = rbf_kernel(X, gamma=1)
    S = np.maximum(S - 1e-4, 0)
    S = sparse.coo_matrix(S)

    labels = SpectralClustering(random_state=0, n_clusters=2,
                                affinity='precomputed').fit(S).labels_
    assert_equal(adjusted_rand_score(y, labels), 1)

def ARI(y_true,y_pred):
    return metrics.adjusted_rand_score(y_true, y_pred)

def compute_affinity_propagation(preference_, X):
    # DATA FILLING
    #text = io.Input.local_read_text_file(inputFilePath)
    #input_array = text.split('\n')
    centers = [[1, 1], [-1, -1], [1, -1]]
    n_samples = 300
    #Make Blobs used for generating of labels_true array
    if (X == None):
        X, labels_true = make_blobs(n_samples = n_samples, centers=centers, cluster_std=1, random_state=0)
        print("Data is none!!!")
        print("Generating " + str(n_samples) + " samples")
    else :
        data, labels_true = make_blobs(n_samples=len(X), centers=centers, cluster_std=1, random_state=0)
    #slist = list()
    #for line in X:
    #    slist.append(line)
    #io.Output.write_array_to_txt_file("clustering\\Affinity_Propagation\\input_data1.txt", slist)
    #float_array = []
    #for line in input_array:
    #    float_line = [float(i) for i in line.split(' ')]
    #    float_array.append(float_line)
    #X = array(float_array)

    af = AffinityPropagation(preference=preference_).fit(X)
    cluster_centers_indices = af.cluster_centers_indices_
    labels = af.labels_
    n_clusters_ = len(cluster_centers_indices)
    print('Estimated number of clusters: %d' % n_clusters_)
    print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels_true, labels))
    print("Completeness: %0.3f" % metrics.completeness_score(labels_true, labels))
    print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
    print("Adjusted Rand Index: %0.3f" % metrics.adjusted_rand_score(labels_true, labels))
    print("Adjusted Mutual Information: %0.3f" % metrics.adjusted_mutual_info_score(labels_true, labels))
#    print("Silhouette Coefficient: %0.3f" % metrics.silhouette_score(X, labels, metric='sqeuclidean'))
    print("Fowlkes Mallows Score: %0.3f" % metrics.fowlkes_mallows_score(labels_true, labels))

    plt.close('all')
    plt.figure(1)
    plt.clf()
    colors = cycle('bgrcmykbgrcmykbgrcmykbgrcmyk')
    for k, col in zip(range(n_clusters_), colors):
        class_members = labels == k
        cluster_center = X[cluster_centers_indices[k]]
        plt.plot(X[class_members, 0], X[class_members, 1], col + '.')
        plt.plot(cluster_center[0], cluster_center[1], 'o', markerfacecolor=col, markeredgecolor='k', markersize=14)
        for x in X[class_members]:
            plt.plot([cluster_center[0], x[0]], [cluster_center[1], x[1]], col)

    plt.title('Estimated number of clusters: %d' % n_clusters_)
    plt.show()

def test_Kmeans_n_init(*data):
    '''
    test the performance with different n_init and init paramter
    :param data: data, target
    :return: None
    '''
    X,labels_true=data
    nums=range(1,50)
    ## graph
    fig=plt.figure()

    ARIs_k=[]
    Distances_k=[]
    ARIs_r=[]
    Distances_r=[]
    for num in nums:
            clst=cluster.KMeans(n_init=num,init='k-means++')
            clst.fit(X)
            predicted_labels=clst.predict(X)
            ARIs_k.append(adjusted_rand_score(labels_true,predicted_labels))
            Distances_k.append(clst.inertia_)

            clst=cluster.KMeans(n_init=num,init='random')
            clst.fit(X)
            predicted_labels=clst.predict(X)
            ARIs_r.append(adjusted_rand_score(labels_true,predicted_labels))
            Distances_r.append(clst.inertia_)

    ax=fig.add_subplot(1,2,1)
    ax.plot(nums,ARIs_k,marker="+",label="k-means++")
    ax.plot(nums,ARIs_r,marker="+",label="random")
    ax.set_xlabel("n_init")
    ax.set_ylabel("ARI")
    ax.set_ylim(0,1)
    ax.legend(loc='best')
    ax=fig.add_subplot(1,2,2)
    ax.plot(nums,Distances_k,marker='o',label="k-means++")
    ax.plot(nums,Distances_r,marker='o',label="random")
    ax.set_xlabel("n_init")
    ax.set_ylabel("inertia_")
    ax.legend(loc='best')

    fig.suptitle("KMeans")
    plt.show()

def test_affinities():
    # Note: in the following, random_state has been selected to have
    # a dataset that yields a stable eigen decomposition both when built
    # on OSX and Linux
    X, y = make_blobs(n_samples=20, random_state=0,
                      centers=[[1, 1], [-1, -1]], cluster_std=0.01
                     )
    # nearest neighbors affinity
    sp = SpectralClustering(n_clusters=2, affinity='nearest_neighbors',
                            random_state=0)
    assert_warns_message(UserWarning, 'not fully connected', sp.fit, X)
    assert_equal(adjusted_rand_score(y, sp.labels_), 1)

    sp = SpectralClustering(n_clusters=2, gamma=2, random_state=0)
    labels = sp.fit(X).labels_
    assert_equal(adjusted_rand_score(y, labels), 1)

    X = check_random_state(10).rand(10, 5) * 10

    kernels_available = kernel_metrics()
    for kern in kernels_available:
        # Additive chi^2 gives a negative similarity matrix which
        # doesn't make sense for spectral clustering
        if kern != 'additive_chi2':
            sp = SpectralClustering(n_clusters=2, affinity=kern,
                                    random_state=0)
            labels = sp.fit(X).labels_
            assert_equal((X.shape[0],), labels.shape)

    sp = SpectralClustering(n_clusters=2, affinity=lambda x, y: 1,
                            random_state=0)
    labels = sp.fit(X).labels_
    assert_equal((X.shape[0],), labels.shape)

    def histogram(x, y, **kwargs):
        # Histogram kernel implemented as a callable.
        assert_equal(kwargs, {})    # no kernel_params that we didn't ask for
        return np.minimum(x, y).sum()

    sp = SpectralClustering(n_clusters=2, affinity=histogram, random_state=0)
    labels = sp.fit(X).labels_
    assert_equal((X.shape[0],), labels.shape)

    # raise error on unknown affinity
    sp = SpectralClustering(n_clusters=2, affinity='<unknown>')
    assert_raises(ValueError, sp.fit, X)

def compare_with_children(
            self, idea_id, post_ids, post_clusters, remainder, labels):
        # Compare to children classification
        compare_with_ideas = None
        all_idea_scores = []
        ideas_of_post = defaultdict(list)
        children_remainder = set(post_ids)
        children_ids = self.idea_children[idea_id]
        if len(children_ids):
            posts_of_children = {
                child_id: self.get_posts_of_idea(child_id)
                for child_id in children_ids}
            for idea_id, c_post_ids in posts_of_children.items():
                for post_id in c_post_ids:
                    ideas_of_post[post_id].append(idea_id)
                children_remainder -= set(c_post_ids)
            for post_id in children_remainder:
                ideas_of_post[post_id] = [idea_id]
            # if many ideas to a post, choose one with the most ideas in same cluster.
            # A bit arbitrary but I need a single idea.
            for cluster in chain(post_clusters, (remainder,)):
                idea_score = defaultdict(int)
                all_idea_scores.append(idea_score)
                for post_id in cluster:
                    for idea_id in ideas_of_post[post_id]:
                        idea_score[idea_id] += 1
                for post_id in cluster:
                    if len(ideas_of_post[post_id]) > 1:
                        scores = [(idea_score[idea_id], idea_id)
                                  for idea_id in ideas_of_post[post_id]]
                        scores.sort(reverse=True)
                        ideas_of_post[post_id] = [score[1] for score in scores]
            # index_by_post_id = {v: k for (k, v) in post_id_by_index.iteritems()}
            idea_of_index = [ideas_of_post[post_id][0] for post_id in post_ids]
            compare_with_ideas = {
                "Homogeneity": metrics.homogeneity_score(idea_of_index, labels),
                "Completeness": metrics.completeness_score(idea_of_index, labels),
                "V-measure": metrics.v_measure_score(idea_of_index, labels),
                "Adjusted Rand Index": metrics.adjusted_rand_score(
                    idea_of_index, labels),
                "Adjusted Mutual Information": metrics.adjusted_mutual_info_score(
                    idea_of_index, labels)}
        else:
            for post_id in children_remainder:
                ideas_of_post[post_id] = [idea_id]
            for cluster in chain(post_clusters, (remainder,)):
                all_idea_scores.append({idea_id: len(cluster)})
        return (compare_with_ideas, all_idea_scores, ideas_of_post,
                children_remainder)