Esempio n. 1
0
def evaluate_embeddings(embeddings,
                        edges,
                        cda=True,
                        greedy_routing=False,
                        cda_max_vertices=1000,
                        gr_max_pairs=10000,
                        eval_core=False,
                        core_exponent=0.5):
    "evaluate quality of embeddings compared with real elge set"
    report = []

    # get connected component
    true_graph = nx.Graph()
    true_graph.add_edges_from(edges)
    Gcc = sorted(nx.connected_component_subgraphs(true_graph),
                 key=len,
                 reverse=True)
    true_graph = Gcc[0]

    # use BallTree for efficient graph construction
    print "construct BallTree"
    vertices = list(true_graph.nodes())
    edges = list(true_graph.edges())
    n = len(vertices)
    if eval_core:
        vertices = [
            v for v in vertices if true_graph.degree(v) >= n**core_exponent
        ]
        true_graph = true_graph.subgraph(vertices)
        edges = list(true_graph.edges())

    embeddings_array = np.array([embeddings[v] for v in vertices])
    bt = BallTree(embeddings_array, metric=distance)

    degrees = defaultdict(int)
    print "compute number of correct directed arcs"
    for v1, v2 in edges:
        degrees[v1] += 1
        degrees[v2] += 1

    # compute number of correct DIRECTED arcs assuming that degrees are known
    if cda:
        all_correct_arcs = set()
        cda_vertices = vertices[:]
        if len(cda_vertices) > cda_max_vertices:
            np.random.shuffle(cda_vertices)
            cda_vertices = cda_vertices[:cda_max_vertices]
        for v_i, v in enumerate(cda_vertices):
            start = time.time()
            degree = degrees[v]
            dist, ind = bt.query(np.array(embeddings[v]).reshape(1, -1),
                                 k=degree +
                                 1)  # one of neighbors is vertex inself
            neigh = [vertices[i] for i in ind[0].tolist() if vertices[i] != v]
            for ne in neigh:
                if make_edge(v, ne) in edges:
                    all_correct_arcs.add((v, ne))
            finish = time.time()
            #print "DEBUG: {} / {}, time={}s".format(v_i + 1, len(cda_vertices), datetime.timedelta(seconds=finish-start))
        report.append([
            'ratio of correct arcs for known degrees',
            float(len(all_correct_arcs)) / (2 * len(edges))
        ])

    if greedy_routing:
        print "compute greedy routing efficiency"
        random_pairs = set()
        if n * (n - 1) / 2 <= gr_max_pairs:
            random_pairs = set(combinations(vertices, 2))
        else:
            while (len(random_pairs) < gr_max_pairs):
                v1 = np.random.choice(vertices)
                v2 = np.random.choice(vertices)
                if v1 != v2:
                    random_pairs.add((v1, v2))

        total_distribution = defaultdict(int)
        success_distribution = defaultdict(int)
        complete_fails_distribution = defaultdict(int)
        all_path_length_pairs = defaultdict(int)
        for i, pair in enumerate(random_pairs):
            src, dst = pair
            # best path
            best_path_length = nx.shortest_path_length(true_graph,
                                                       source=src,
                                                       target=dst)
            total_distribution[0] += 1
            total_distribution[best_path_length] += 1

            # greedy path
            curr_src = src
            path_length = 0
            seen = set()
            while curr_src != dst:
                seen.add(curr_src)
                # find neighbor closest to destination
                unseen_neighbors = filter(lambda x: x not in seen,
                                          true_graph.neighbors(curr_src))
                if not len(unseen_neighbors):
                    # greedy algorithm stuck in 'leaf'
                    path_length = np.nan
                    break

                def curr_distance(v):
                    return distance(embeddings[dst], embeddings[v])

                closest_neigh = min(unseen_neighbors, key=curr_distance)
                path_length += 1
                curr_src = closest_neigh

            if path_length == best_path_length:
                success_distribution[0] += 1
                success_distribution[best_path_length] += 1
            if np.isnan(path_length):
                complete_fails_distribution[0] += 1
                complete_fails_distribution[best_path_length] += 1
            all_path_length_pairs[(best_path_length, path_length)] += 1
        all_success = success_distribution[0]
        all_complete_fails = complete_fails_distribution[0]
        all_total = total_distribution[0]
        all_ratio = float(all_success) / all_total * 100
        print "Complete fails: {} / {} ({:.2f} %)".format(
            all_complete_fails, all_total,
            float(all_complete_fails) / all_total * 100)
        print "Success: {} / {} ({:.2f} %)".format(all_success, all_total,
                                                   all_ratio)
        for pl in sorted(
                set(total_distribution.keys())
                | set(success_distribution.keys())):
            if pl == 0:
                continue
            total = total_distribution.get(pl, 0)
            success = success_distribution.get(pl, 0)
            ratio = float(success) / total * 100
            print "Success at path length = {}: {} / {} ({:.2f} %)".format(
                pl, success, total, ratio)
    if False:
        # depends on R, bad for subgraphs -- not used
        n = len(vertices)
        R = 2 * np.log(n)
        coshR = np.cosh(R)

        predicted_edges = set()
        print "predict edges"
        for v in vertices:
            coords = embeddings[v]
            neigh_idx = bt.query_radius(coords, R)
            neigh = [
                vertices[i] for i in neigh_idx[0].tolist() if vertices[i] != v
            ]
            predicted_edges.update([make_edge(v, ne) for ne in neigh])
        report.append(['total_predicted_edges', len(predicted_edges)])

        # contingency matrix
        print "compute contingency matrix"
        report.append(['true positive', len(edges & predicted_edges)])
        report.append(['false positive', len(predicted_edges - edges)])
        report.append(['false negative', len(edges - predicted_edges)])
        report.append(
            ['true negative', n * (n - 1) / 2 - len(edges | predicted_edges)])

    return report
Esempio n. 2
0
def evaluate_embeddings(embeddings, edges, cda=True, greedy_routing=False, cda_max_vertices=1000, gr_max_pairs=10000):
    "evaluate quality of embeddings compared with real elge set"
    report = []

    # get connected component
    true_graph = nx.Graph()
    true_graph.add_edges_from(edges)
    Gcc=sorted(nx.connected_component_subgraphs(true_graph), key=len, reverse=True)
    true_graph=Gcc[0]

    # use BallTree for efficient graph construction
    print "construct BallTree"
    vertices = list(true_graph.nodes())
    n = len(vertices)
    embeddings_array = np.array([embeddings[v] for v in vertices])
    bt = BallTree(embeddings_array, metric=distance)

    degrees = defaultdict(int)
    print "compute number of correct directed arcs"
    for v1, v2 in edges:
        degrees[v1] += 1
        degrees[v2] += 1

    # compute number of correct DIRECTED arcs assuming that degrees are known
    if cda:
        all_correct_arcs = set()
        cda_vertices = vertices[:]
        if len(cda_vertices) > cda_max_vertices:
            np.random.shuffle(cda_vertices)
            cda_vertices = cda_vertices[:cda_max_vertices]
        for v_i, v in enumerate(cda_vertices):
            start = time.time()
            degree = degrees[v]
            dist, ind = bt.query(embeddings[v], k=degree+1)  # one of neighbors is vertex inself
            neigh = [vertices[i] for i in ind[0].tolist() if vertices[i] != v]
            for ne in neigh:
                if make_edge(v, ne) in edges:
                    all_correct_arcs.add((v, ne))
            finish = time.time()
            #print "DEBUG: {} / {}, time={}s".format(v_i + 1, len(cda_vertices), datetime.timedelta(seconds=finish-start))
        report.append(['ratio of correct arcs for known degrees', float(len(all_correct_arcs)) / (2 * len(edges))])

    if greedy_routing:
        print "compute greedy routing efficiency"
        random_pairs = set()
        if n * (n-1) / 2 <= gr_max_pairs:
            random_pairs = set(combinations(vertices, 2))
        else:
            while(len(random_pairs) < gr_max_pairs):
                v1 = np.random.choice(vertices)
                v2 = np.random.choice(vertices)
                if v1 != v2:
                    random_pairs.add((v1, v2))

        total_distribution = defaultdict(int)
        success_distribution = defaultdict(int)
        for i, pair in enumerate(random_pairs):
            src, dst = pair
            # best path
            best_path_length = nx.shortest_path_length(true_graph, source=src, target=dst)
            total_distribution[0] += 1
            total_distribution[best_path_length] += 1

            # greedy path
            curr_src = src
            path_length = 0
            seen = set()
            while curr_src != dst:
                seen.add(curr_src)
                # find neighbor closest to destination
                unseen_neighbors = filter(lambda x: x not in seen, true_graph.neighbors(curr_src))
                if not len(unseen_neighbors):
                    # greedy algorithm stuck in 'leaf'
                    path_length = np.nan
                    break

                def curr_distance(v):
                    return distance(embeddings[dst], embeddings[v])
                closest_neigh = min(unseen_neighbors, key=curr_distance)
                path_length += 1
                curr_src = closest_neigh

            if path_length == best_path_length:
                success_distribution[0] += 1
                success_distribution[best_path_length] += 1
        all_success = success_distribution[0]
        all_total = total_distribution[0]
        all_ratio = float(all_success) / all_total * 100
        print "Total: {} / {} ({:.2f} %)".format(all_success, all_total, all_ratio)
        for pl in sorted(set(total_distribution.keys()) | set(success_distribution.keys())):
            if pl == 0:
                continue
            total = total_distribution.get(pl, 0)
            success = success_distribution.get(pl, 0)
            ratio = float(success) / total * 100
            print "Path length = {}: {} / {} ({:.2f} %)".format(pl, success, total, ratio)

    if False:
        # depends on R, bad for subgraphs -- not used
        n = len(vertices)
        R = 2 * np.log(n)
        coshR = np.cosh(R)

        predicted_edges = set()
        print "predict edges"
        for v in vertices:
            coords = embeddings[v]
            neigh_idx = bt.query_radius(coords, R)
            neigh = [vertices[i] for i in neigh_idx[0].tolist() if vertices[i] != v]
            predicted_edges.update([make_edge(v, ne) for ne in neigh])
        report.append(['total_predicted_edges', len(predicted_edges)])

        # contingency matrix
        print "compute contingency matrix"
        report.append(['true positive', len(edges & predicted_edges)])
        report.append(['false positive', len(predicted_edges - edges)])
        report.append(['false negative', len(edges - predicted_edges)])
        report.append(['true negative', n*(n-1)/2 - len(edges | predicted_edges)])

    return report
Esempio n. 3
0
def find_embeddings(
    vertices,
    edges,
    mode,
    learning_rate=0.1,
    n_epoch=100,
    ratio_to_second=2.0,
    ratio_between_first=1.0,
    ratio_random=1.0,
    silent=False,
):
    "find (r, phi) for each vertex"
    vertices = list(vertices)
    n = len(vertices)
    R = 2 * np.log(n)

    print "mode: {}".format(mode)
    np.random.seed(0)
    degrees = defaultdict(int)
    print "count degrees"
    for v1, v2 in edges:
        degrees[v1] += 1
        degrees[v2] += 1
    if mode == "random":
        # phi=rand(0, 2pi), r = rand(0,R)
        return {v: (np.random.uniform(0.0, R), np.random.uniform(0.0, 2 * np.pi)) for v in vertices}
    elif mode == "degrees":
        # phi=rand(0,2pi), r = 2log(n/k)
        return {v: (2 * np.log(n / degrees[v]), np.random.uniform(0.0, 2 * np.pi)) for v in vertices}
    elif mode.startswith("fit"):
        x0 = []
        for (r, phi) in zip(
            [2 * np.log(n / degrees[v]) for v in vertices], [np.random.uniform(0.0, 2 * np.pi) for v in vertices]
        ):
            x0.append(r)
            x0.append(phi)
        x0 = np.array(x0)

        nedges = set()
        all_nedges = set()
        for (v1, v2) in combinations(vertices, 2):
            # if (v1, v2) not in edges and (v2, v1) not in edges:
            e = make_edge(v1, v2)
            if e not in edges:
                all_nedges.add(e)

        if mode == "fit_random":
            a = list(all_nedges)
            random.shuffle(a)
            nedges = set(a[: len(edges)])
        elif mode == "fit_degrees":
            K = float(ratio_to_second)  # ratio of nedges to second neighbour
            L = float(ratio_between_first)  # ratio of nedges between first neighbours
            M = float(ratio_random)  # ratio of random nedges
            # free_nedges = all_nedges.copy()

            G = nx.Graph()
            G.add_edges_from(edges)
            srt_vertices = sorted(degrees.keys(), key=lambda v: -degrees[v])
            shuf_vertices = srt_vertices[:]
            random.shuffle(shuf_vertices)
            for v in srt_vertices:
                # get first neighbours
                first_neigh = set(G.neighbors(v))
                # get second neighbours
                second_neigh = set()
                for neigh in first_neigh:
                    second_neigh.update(G.neighbors(neigh))
                second_neigh.remove(v)

                n_vertex_nedges = 0
                # from v to second neighbours
                for i, sec_n in enumerate(second_neigh):
                    # print "i: {}".format(i)
                    if i + 1 > degrees[v] * K:
                        continue
                    e = make_edge(v, sec_n)
                    if e not in nedges:
                        nedges.add(e)
                        n_vertex_nedges += 1

                # between first neighbours
                for j, pair in enumerate(combinations(first_neigh, 2)):
                    # print "j: {}".format(j)
                    if j + 1 > degrees[v] * L:
                        continue
                    v1, v2 = pair
                    e = make_edge(v1, v2)
                    if e not in nedges:
                        nedges.add(e)

                # random edges
                max_n_random_vertices = int(degrees[v] * M)
                n_random_vertices = 0
                for rand_v in shuf_vertices:
                    if n_random_vertices >= max_n_random_vertices:
                        break
                    e = make_edge(v, rand_v)
                    if e not in nedges and e not in edges:
                        nedges.add(e)
                        n_random_vertices += 1
        else:
            nedges = all_nedges.copy()
        print "number of nedges={}".format(len(nedges))
        q = Q(vertices, edges, nedges)
        grad_q = GradQ(vertices, edges, nedges)
        if mode == "fit_degrees_sgd":
            print "Learning rate: {}".format(learning_rate)
            print "Ratio to second: {}".format(ratio_to_second)
            print "Ratio between first: {}".format(ratio_between_first)
            print "Ratio random: {}".format(ratio_random)

            G = nx.Graph()
            G.add_edges_from(edges)

            # construct connected(!) core
            core_exponent = 0.4
            core_vertices, fringe_vertices = [], []
            # one-pass split by condition
            for v in vertices:
                core_vertices.append(v) if degrees[v] >= n ** core_exponent else fringe_vertices.append(v)
            # add vertices to ensure connectivity of core
            fringe_vertices.sort(key=lambda v: -degrees[v])
            while not nx.is_connected(G.subgraph(core_vertices)):
                core_vertices.append(fringe_vertices.pop(0))

            print "Core size: {}".format(len(core_vertices))
            G_core = G.subgraph(core_vertices)
            print "Is core connected:", nx.is_connected(G_core)

            # loss_function = MSE(binary_edges=True)
            loss_function = LogLoss(binary_edges=True)
            optimizer = SGD(n_epoch=n_epoch, learning_rate=learning_rate, verbose=not silent)

            FRINGE_FRACTION = 0.1
            max_fringe_size = int(G.number_of_nodes() * FRINGE_FRACTION)
            curr_graph = G.subgraph(core_vertices)
            curr_core_vertices = set(core_vertices)
            curr_embedding_model = PoincareModel(curr_graph, fit_radius=False)
            curr_pair_generator = BinaryPairGenerator(curr_graph, batch_size=1)
            optimizer.optimize_embedding(curr_embedding_model, loss_function, curr_pair_generator)
            for i in range(int(1 / FRINGE_FRACTION) + 1):
                total_fringe = fringe(G, curr_core_vertices)
                # print "DEBUG:", curr_graph. number_of_nodes(), len(curr_core_vertices), len(total_fringe)
                fringe_vertices = set(sorted(total_fringe, key=lambda v: -G.degree(v))[:max_fringe_size])
                # print "DEBUG:", i+1, fringe_vertices
                if not fringe_vertices:
                    break
                curr_graph = G.subgraph(curr_core_vertices | fringe_vertices)
                curr_embedding_model = PoincareModel(curr_graph, fit_radius=False, init_embedding=curr_embedding_model)
                curr_pair_generator = BinaryPairGenerator(curr_graph, batch_size=1)
                optimizer.optimize_embedding(
                    curr_embedding_model, loss_function, curr_pair_generator, fixed_vertices=curr_core_vertices
                )

                curr_core_vertices |= fringe_vertices

            embedding_model = curr_embedding_model
            """
            core_embedding_model = PoincareModel(G_core, fit_radius=False)
            core_pair_generator = BinaryPairGenerator(G_core, batch_size=1)
            optimizer.optimize_embedding(core_embedding_model, loss_function, core_pair_generator)
            #optimizer = SGD(n_epoch=n_epoch, learning_rate=learning_rate, verbose=not silent)
            embedding_model = PoincareModel(G, fit_radius=False, init_embedding=core_embedding_model)
            pair_generator = BinaryPairGenerator(G, batch_size=1)
            optimizer.optimize_embedding(embedding_model, loss_function, pair_generator, fixed_vertices=core_vertices)

            #print "Radius before: {}".format(embedding_model.embedding['radius'])
            #print "Radius after: {}".format(embedding_model.embedding['radius'])
            """
            return (embedding_model.embedding["vertices"], {"core": list(G.edges())})
        else:
            print "Check gradient: ", check_grad(q, grad_q, x0)
            res = minimize(q, x0, method="BFGS", jac=grad_q)
            # print res
            x = res.x
        retval = {}
        for i in range(len(vertices)):
            r = x[2 * i]
            phi = x[2 * i + 1]
            retval[vertices[i]] = (r, phi)

        return retval
    else:
        raise Exception("unknown mode")
Esempio n. 4
0
def find_embeddings(vertices,
                    edges,
                    mode,
                    learning_rate=0.1,
                    n_epoch=100,
                    ratio_to_second=2.,
                    ratio_between_first=1.,
                    ratio_random=1.,
                    silent=False):
    "find (r, phi) for each vertex"
    vertices = list(vertices)
    n = len(vertices)
    R = 2 * np.log(n)

    print "mode: {}".format(mode)
    np.random.seed(0)
    degrees = defaultdict(int)
    print "count degrees"
    for v1, v2 in edges:
        degrees[v1] += 1
        degrees[v2] += 1
    if mode == 'random':
        # phi=rand(0, 2pi), r = rand(0,R)
        return {
            v: (np.random.uniform(0.0, R), np.random.uniform(0.0, 2 * np.pi))
            for v in vertices
        }
    elif mode == 'degrees':
        # phi=rand(0,2pi), r = 2log(n/k)
        return {
            v: (2 * np.log(n / degrees[v]), np.random.uniform(0.0, 2 * np.pi))
            for v in vertices
        }
    elif mode.startswith('fit'):
        x0 = []
        for (r,
             phi) in zip([2 * np.log(n / degrees[v]) for v in vertices],
                         [np.random.uniform(0.0, 2 * np.pi)
                          for v in vertices]):
            x0.append(r)
            x0.append(phi)
        x0 = np.array(x0)

        nedges = set()
        all_nedges = set()
        for (v1, v2) in combinations(vertices, 2):
            #if (v1, v2) not in edges and (v2, v1) not in edges:
            e = make_edge(v1, v2)
            if e not in edges:
                all_nedges.add(e)

        if mode == 'fit_random':
            a = list(all_nedges)
            random.shuffle(a)
            nedges = set(a[:len(edges)])
        elif mode == 'fit_degrees':
            K = float(ratio_to_second)  # ratio of nedges to second neighbour
            L = float(ratio_between_first
                      )  # ratio of nedges between first neighbours
            M = float(ratio_random)  # ratio of random nedges
            #free_nedges = all_nedges.copy()

            G = nx.Graph()
            G.add_edges_from(edges)
            srt_vertices = sorted(degrees.keys(), key=lambda v: -degrees[v])
            shuf_vertices = srt_vertices[:]
            random.shuffle(shuf_vertices)
            for v in srt_vertices:
                # get first neighbours
                first_neigh = set(G.neighbors(v))
                # get second neighbours
                second_neigh = set()
                for neigh in first_neigh:
                    second_neigh.update(G.neighbors(neigh))
                second_neigh.remove(v)

                n_vertex_nedges = 0
                # from v to second neighbours
                for i, sec_n in enumerate(second_neigh):
                    #print "i: {}".format(i)
                    if i + 1 > degrees[v] * K:
                        continue
                    e = make_edge(v, sec_n)
                    if e not in nedges:
                        nedges.add(e)
                        n_vertex_nedges += 1

                # between first neighbours
                for j, pair in enumerate(combinations(first_neigh, 2)):
                    #print "j: {}".format(j)
                    if j + 1 > degrees[v] * L:
                        continue
                    v1, v2 = pair
                    e = make_edge(v1, v2)
                    if e not in nedges:
                        nedges.add(e)

                # random edges
                max_n_random_vertices = int(degrees[v] * M)
                n_random_vertices = 0
                for rand_v in shuf_vertices:
                    if n_random_vertices >= max_n_random_vertices:
                        break
                    e = make_edge(v, rand_v)
                    if e not in nedges and e not in edges:
                        nedges.add(e)
                        n_random_vertices += 1
        else:
            nedges = all_nedges.copy()
        print "number of nedges={}".format(len(nedges))
        q = Q(vertices, edges, nedges)
        grad_q = GradQ(vertices, edges, nedges)
        if mode == 'fit_degrees_sgd':
            print "Learning rate: {}".format(learning_rate)
            print "Ratio to second: {}".format(ratio_to_second)
            print "Ratio between first: {}".format(ratio_between_first)
            print "Ratio random: {}".format(ratio_random)

            G = nx.Graph()
            G.add_edges_from(edges)

            # construct connected(!) core
            core_exponent = 0.4
            core_vertices, fringe_vertices = [], []
            # one-pass split by condition
            for v in vertices:
                core_vertices.append(v) if degrees[
                    v] >= n**core_exponent else fringe_vertices.append(v)
            # add vertices to ensure connectivity of core
            fringe_vertices.sort(key=lambda v: -degrees[v])
            while not nx.is_connected(G.subgraph(core_vertices)):
                core_vertices.append(fringe_vertices.pop(0))

            print "Core size: {}".format(len(core_vertices))
            G_core = G.subgraph(core_vertices)
            print "Is core connected:", nx.is_connected(G_core)

            #loss_function = MSE(binary_edges=True)
            loss_function = LogLoss(binary_edges=True)
            optimizer = SGD(n_epoch=n_epoch,
                            learning_rate=learning_rate,
                            verbose=not silent)

            FRINGE_FRACTION = 0.1
            max_fringe_size = int(G.number_of_nodes() * FRINGE_FRACTION)
            curr_graph = G.subgraph(core_vertices)
            curr_core_vertices = set(core_vertices)
            curr_embedding_model = PoincareModel(curr_graph, fit_radius=False)
            curr_pair_generator = BinaryPairGenerator(curr_graph, batch_size=1)
            optimizer.optimize_embedding(curr_embedding_model, loss_function,
                                         curr_pair_generator)
            for i in range(int(1 / FRINGE_FRACTION) + 1):
                total_fringe = fringe(G, curr_core_vertices)
                #print "DEBUG:", curr_graph. number_of_nodes(), len(curr_core_vertices), len(total_fringe)
                fringe_vertices = set(
                    sorted(total_fringe,
                           key=lambda v: -G.degree(v))[:max_fringe_size])
                #print "DEBUG:", i+1, fringe_vertices
                if not fringe_vertices:
                    break
                curr_graph = G.subgraph(curr_core_vertices | fringe_vertices)
                curr_embedding_model = PoincareModel(
                    curr_graph,
                    fit_radius=False,
                    init_embedding=curr_embedding_model)
                curr_pair_generator = BinaryPairGenerator(curr_graph,
                                                          batch_size=1)
                optimizer.optimize_embedding(curr_embedding_model,
                                             loss_function,
                                             curr_pair_generator,
                                             fixed_vertices=curr_core_vertices)

                curr_core_vertices |= fringe_vertices

            embedding_model = curr_embedding_model
            '''
            core_embedding_model = PoincareModel(G_core, fit_radius=False)
            core_pair_generator = BinaryPairGenerator(G_core, batch_size=1)
            optimizer.optimize_embedding(core_embedding_model, loss_function, core_pair_generator)
            #optimizer = SGD(n_epoch=n_epoch, learning_rate=learning_rate, verbose=not silent)
            embedding_model = PoincareModel(G, fit_radius=False, init_embedding=core_embedding_model)
            pair_generator = BinaryPairGenerator(G, batch_size=1)
            optimizer.optimize_embedding(embedding_model, loss_function, pair_generator, fixed_vertices=core_vertices)

            #print "Radius before: {}".format(embedding_model.embedding['radius'])
            #print "Radius after: {}".format(embedding_model.embedding['radius'])
            '''
            return (embedding_model.embedding['vertices'], {
                'core': list(G.edges())
            })
        else:
            print "Check gradient: ", check_grad(q, grad_q, x0)
            res = minimize(q, x0, method='BFGS', jac=grad_q)
            #print res
            x = res.x
        retval = {}
        for i in range(len(vertices)):
            r = x[2 * i]
            phi = x[2 * i + 1]
            retval[vertices[i]] = (r, phi)

        return retval
    else:
        raise Exception('unknown mode')