Python SpectralCoclustering.get_indices方法代码示例

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
    def find_disjoint_biclusters(self, biclusters_number=50):
        data = np.asarray_chkfinite(self.matrix)
        data[data == 0] = 0.000001
        coclustering = SpectralCoclustering(n_clusters=biclusters_number, random_state=0)
        coclustering.fit(data)

        biclusters = set()
        for i in range(biclusters_number):
            rows, columns = coclustering.get_indices(i)
            row_set = set(rows)
            columns_set = set(columns)
            if len(row_set) > 0 and len(columns_set) > 0:
                density = self._calculate_box_cluster_density(row_set, columns_set)
                odd_columns = set()
                for column in columns_set:
                    col_density = self._calculate_column_density(column, row_set)
                    if col_density < density / 4:
                        odd_columns.add(column)
                columns_set.difference_update(odd_columns)
                if len(columns_set) == 0:
                    continue

                odd_rows = set()
                for row in row_set:
                    row_density = self._calculate_row_density(row, columns_set)
                    if row_density < density / 4:
                        odd_rows.add(row)
                row_set.difference_update(odd_rows)

                if len(row_set) > 0 and len(columns_set) > 0:
                    density = self._calculate_box_cluster_density(row_set, columns_set)
                    biclusters.add(Bicluster(row_set, columns_set, density))

        return biclusters

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
def print_similarity_matrix(sphns, model, model2=None):
    print "      ",
    for phn1 in sphns:
        print phn1, " ",
    print ""
    m = np.ndarray((len(sphns), len(sphns)), dtype=np.float32)
    for i, phn1 in enumerate(sphns):
        print phn1.ljust(4) + ":",
        for j, phn2 in enumerate(sphns):
            sim = model.similarity(phn1, phn2)
            if model2 != None:
                sim -= model2.similarity(phn1, phn2)
            print "%0.2f" % sim,
            m[i][j] = sim
        print ""
    phn_order = [phn for phn in sphns]

    if BICLUSTER:
        #model = SpectralBiclustering(n_clusters=4, method='log',
        model = SpectralCoclustering(n_clusters=n_clusters,
                                             random_state=0)
        model.fit(m)
        print "INDICES:",
        indices = [model.get_indices(i) for i in xrange(n_clusters)]
        print indices
        tmp = []
        for i in xrange(n_clusters):
            tmp.extend([phn_order[indices[i][0][j]] for j in xrange(len(indices[i][0]))])
        phn_order = tmp
        fit_data = m[np.argsort(model.row_labels_)]
        fit_data = fit_data[:, np.argsort(model.column_labels_)]
        m = fit_data

    return phn_order, m

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
def biclustering(input,num_clusters):
	global agent1_dict
	data = np.matrix(input)
	model = SpectralCoclustering(n_clusters=num_clusters,random_state=0) 
	model.fit(data)
	#create agent 1 dictionary
	agent1_dict = {}
	for c in range(num_clusters): 	
		agent1_dict[c] = model.get_indices(c)[0].tolist() #0 row indices, 1 column indices
	return agent1_dict

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
def biclustering(data,num_clusters):
	clusters = {}
	data = np.asmatrix(data)
	model = SpectralCoclustering(n_clusters=num_clusters,random_state=0)
	#model = SpectralBiclustering(n_clusters=num_clusters)
	model.fit(data)
	for c in range(num_clusters):
		clusters[c] = model.get_indices(c)[0].tolist() #0 row indices, 1 column indices
	#fit_data = data[np.argsort(model.row_labels_)]
	#fit_data = fit_data[:, np.argsort(model.column_labels_)]
	#plot(fit_data)
	return clusters

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
def biclustering(input,num_clusters):
	global agent1_dict
	data = np.matrix(input)
	model = SpectralCoclustering(n_clusters=num_clusters,random_state=0) 
	model.fit(data)
	#create agent 1 dictionary
	agent1_dict = {}
	for c in range(num_clusters): 	
		agent1_dict[c] = model.get_indices(c)[0].tolist() #0 row indices, 1 column indices
	fit_data = data[np.argsort(model.row_labels_)]
	fit_data = fit_data[:, np.argsort(model.column_labels_)]
	plot(fit_data)
	return agent1_dict

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
def biclustering(input_list,num_clusters):
	global agent1_dict
	#clustering agent 1
	data = np.matrix(input_list)
	#plot(data)#original data
	
	#model = SpectralBiclustering(n_clusters=num_clusters) #Biclustering refer http://scikit-learn.org/stable/auto_examples/bicluster/plot_spectral_biclustering.html#example-bicluster-plot-spectral-biclustering-py

	model = SpectralCoclustering(n_clusters=num_clusters,random_state=0) #Coclustering refer http://scikit-learn.org/stable/auto_examples/bicluster/plot_spectral_coclustering.html

	model.fit(data)
	#create agent 1 dictionary
	agent1_dict = {}
	for c in range(num_clusters): 	
		agent1_dict[c] = model.get_indices(c)[0].tolist() #0 row indices, 1 column indices
	fit_data = data[np.argsort(model.row_labels_)]
	fit_data = fit_data[:, np.argsort(model.column_labels_)]
	plot(fit_data)
	return agent1_dict

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
    weight = X[rows[:, np.newaxis], cols].sum()
    cut = (X[row_complement[:, np.newaxis], cols].sum() +
           X[rows[:, np.newaxis], col_complement].sum())
    return cut / weight


bicluster_ncuts = list(bicluster_ncut(i)
                       for i in xrange(len(newsgroups.target_names)))
best_idx = np.argsort(bicluster_ncuts)[:5]

print()
print("Best biclusters:")
print("----------------")
for idx, cluster in enumerate(best_idx):
    n_rows, n_cols = cocluster.get_shape(cluster)
    cluster_docs, cluster_words = cocluster.get_indices(cluster)
    if not len(cluster_docs) or not len(cluster_words):
        continue

    # categories
    cluster_categories = list(document_names[i] for i in cluster_docs)
    counter = Counter(cluster_categories)
    cat_string = ", ".join("{:.0f}% {}".format(float(c) / n_rows * 100,
                                               name)
                           for name, c in counter.most_common()[:3])

    # words
    out_of_cluster_docs = cocluster.row_labels_ != cluster
    out_of_cluster_docs = np.where(out_of_cluster_docs)[0]
    word_col = X[:, cluster_words]
    word_scores = np.array(word_col[cluster_docs, :].sum(axis=0) -

# 需要导入模块: from sklearn.cluster.bicluster import SpectralCoclustering [as 别名]
# 或者: from sklearn.cluster.bicluster.SpectralCoclustering import get_indices [as 别名]
        avg_data[row_sel, col_sel] = np.average(data[row_sel, col_sel])

avg_data = avg_data[np.argsort(model.row_labels_)]
avg_data = avg_data[:, np.argsort(model.column_labels_)]

plt.matshow(avg_data, cmap=plt.cm.Blues)
plt.title("Average cluster intensity")

plt.savefig('%s_averaged.png' % (identifier), bbox_inches='tight')

if args.write:
    print "Writing clusters to database."
    # No need to clean up here, just overwrite by _id.
    for c in range(n_clusters):
        (nr, nc) = model.get_shape(c)
        (row_ind, col_ind) = model.get_indices(c)
        
        cluster_val = None
        if nr > 25 or nc > 50:
            print "Nulling cluster %d: shape (%d, %d)" % (c, nr, nc)
        else:
            cluster_val = c
            
        for ri in row_ind:
            data_list[ri]['cluster'] = cluster_val
            datastream.save(data_list[ri])
        for ci in col_ind:
            events_list[ci]['cluster'] = cluster_val
            events.save(events_list[ci])            

# plt.show()