diff --git a/.gitignore b/.gitignore index 4f40673..4a80fb5 100644 --- a/.gitignore +++ b/.gitignore @@ -12,13 +12,13 @@ networks/weblinks LOCAL/ networks/example.py *old/ -sanity_checks.ipynb +*.ipynb nohup.out -undirect* -Summary/ +Summary/BackboneStats.tex # New stuff for now new_networks/ +Figures/ # Run scripts script* diff --git a/00-pre-process.py b/00-pre-process.py index fc6077a..bbe63cb 100644 --- a/00-pre-process.py +++ b/00-pre-process.py @@ -80,15 +80,16 @@ def read_gpickle(file_name): if weight_type in 'proximity': print('Prox -> Dist') - P_dict = nx.get_edge_attributes(G, weight_attr) + P_dict = dict(nx.get_edge_attributes(G, weight_attr)) D_dict = {key: prox2dist(value) for key, value in P_dict.items()} nx.set_edge_attributes(G, name='distance', values=D_dict) if weight_type == 'distance': - D_dict = nx.get_edge_attributes(G, name=weight_attr) + D_dict = dict(nx.get_edge_attributes(G, name=weight_attr)) P_dict = {key: dist2prox(value) for key, value in D_dict.items()} + print(P_dict.values()) if (min(P_dict.values()) < 0) or (max(P_dict.values()) > 1.0): raise TypeError("Proximity values not in [0,1]") diff --git a/01-calc-backbone.py b/01-calc-backbone.py index ee0e721..0468bd4 100644 --- a/01-calc-backbone.py +++ b/01-calc-backbone.py @@ -53,7 +53,7 @@ # Files wGgraphml = 'networks/{folder:s}/backbone.graphml'.format(folder=folder) wFdistortion = 'networks/{folder:s}/distortion.pickle'.format(folder=folder) - wFasymmetry = 'networks/{folder:s}/asymmetry.pickle'.format(folder=folder) + #wFasymmetry = 'networks/{folder:s}/asymmetry.pickle'.format(folder=folder) # Load Network rGfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) @@ -65,7 +65,7 @@ # # Asymmetry distribution # - alpha = get_asymmetry_distribution(G) + #alpha = get_asymmetry_distribution(G) # Dictionary of distortion distribution distortion_dist = dict() @@ -85,13 +85,13 @@ print('--- Exporting Formats ---') ensurePathExists(wGgraphml) ensurePathExists(wFdistortion) - ensurePathExists(wFasymmetry) + #ensurePathExists(wFasymmetry) print('> Backbone') nx.write_graphml(G, wGgraphml) print('> Distortion') pk.dump(distortion_dist, open(wFdistortion, 'wb')) - print('> Asymmetry') - pk.dump(alpha, open(wFasymmetry, 'wb')) + #print('> Asymmetry') + #pk.dump(alpha, open(wFasymmetry, 'wb')) print('\n\n') diff --git a/02-network-stats.py b/02-network-stats.py index 8d7c4ca..3ff554a 100644 --- a/02-network-stats.py +++ b/02-network-stats.py @@ -43,54 +43,67 @@ rGfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) rBfile = 'networks/{folder:s}/backbone.graphml'.format(folder=folder) wGstats = 'networks/{folder:s}/network-stats.csv'.format(folder=folder) - wFasymmetry = 'networks/{folder:s}/backbone_asymmetry.pickle'.format(folder=folder) + #wFasymmetry = 'networks/{folder:s}/backbone_asymmetry.pickle'.format(folder=folder) # Load graph G = nx.read_graphml(rGfile) # Calculate stats - n_nodes = G.number_of_nodes() - n_edges = G.number_of_edges() + wcc_nodes = G.number_of_nodes() + wcc_edges = G.number_of_edges() density = nx.density(G) + + LSCC = G.subgraph(max(nx.strongly_connected_components(G), key=len)) + + lscc_nodes = LSCC.number_of_nodes() + lscc_edges = LSCC.number_of_edges() # Load backbone - # Metric G = nx.read_graphml(rBfile) - n_edges_metric = G.number_of_edges() - - # New asymmetry dist - alpha = dict() - alpha['metric'] = get_asymmetry_distribution(G) - # Ultrametric - edges2remove = [(i, j) for i, j, d in G.edges(data=True) if 'ultrametric' not in d] - G.remove_edges_from(edges2remove) - n_edges_ultrametric = G.number_of_edges() - alpha['ultrametric'] = get_asymmetry_distribution(G) + # Metric + tau_wcc_metric = G.number_of_edges()/wcc_edges + # Ultrametric AND LSCC + tau_wcc_ultrametric = 0 #sum([int(d) for _, _, d in G.edges(data='ultrametric')])/wcc_edges + tau_lscc_metric = 0 + tau_lscc_ultrametric = 0 + for u, v, ultra in G.edges(data='ultrametric'): + if LSCC.has_edge(u, v): + tau_lscc_metric += 1 + if ultra: + tau_wcc_ultrametric += 1 + if LSCC.has_edge(u, v): + tau_lscc_ultrametric += 1 + + tau_wcc_ultrametric /= wcc_edges + if lscc_edges > 0.0: + tau_lscc_ultrametric /= lscc_edges + tau_lscc_metric /= lscc_edges # to Result Series sR = pd.Series({ - 'n-nodes': n_nodes, - 'n-edges': n_edges, + 'n-nodes': wcc_nodes, + 'n-edges': wcc_edges, # 'density': density, # - 'n-edges-metric': n_edges_metric, - 'n-edges-ultrametric': n_edges_ultrametric, + 'LSCC-nodes': lscc_nodes, + 'LSCC-edges': lscc_edges, # - '%-edges-metric': (n_edges_metric / n_edges), - '%-edges-ultrametric': (n_edges_ultrametric / n_edges), + 'tau-metric': tau_wcc_metric, + 'tau-ultrametric': tau_wcc_ultrametric, # - '%-redundancy-metric': 1 - (n_edges_metric / n_edges), - '%-redundancy-ultrametric': 1 - (n_edges_ultrametric / n_edges), + 'LSCC-tau-metric': tau_lscc_metric, + 'LSCC-tau-ultrametric': tau_lscc_ultrametric, # - '%-edges-ultrametric/metric': ((n_edges_ultrametric / n_edges) / (n_edges_metric / n_edges)), + 'ultrametric_metric_ratio': (tau_wcc_ultrametric/tau_wcc_metric), + 'LSCC-ultrametric_metric_ratio': (tau_lscc_ultrametric/tau_lscc_metric if tau_lscc_metric > 0 else 0), # }, name=network, dtype='object') # Print print(sR) sR.to_csv(wGstats) - print('> Asymmetry') - pk.dump(alpha, open(wFasymmetry, 'wb')) + #print('> Asymmetry') + #pk.dump(alpha, open(wFasymmetry, 'wb')) print("\n\n") diff --git a/20-undirected-version.py b/20-undirected-version.py index 8794bc8..b996473 100644 --- a/20-undirected-version.py +++ b/20-undirected-version.py @@ -47,32 +47,31 @@ print("Loading network: {network:s}".format(network=network)) G = nx.read_graphml(rGraphml) + # Select largest connected component + G = G.subgraph(max(nx.strongly_connected_components(G), key=len)) nx.set_edge_attributes(G, values=None, name='alpha') - U = {'min': nx.Graph(), 'max': nx.Graph(), 'avg': nx.Graph()} - for g in U.values(): - g.add_nodes_from(G.nodes()) + U = nx.Graph() + U.add_nodes_from(G.nodes()) for u, v, w in G.edges(data=True): if w['alpha'] == None: G[u][v]['alpha'] = 0.0 - pij = w['proximity'] if G.has_edge(v, u): G[v][u]['alpha'] = 0.0 - pji = G[v][u]['proximity'] - pmin = min(pij, pji) - U['min'].add_edge(u, v, distance=prox2dist(pmin)) - else: - pji = 0 - - pmax = max(pij, pji) - pavg = 0.5*(pij+pji) - - U['max'].add_edge(u, v, distance=prox2dist(pmax)) - U['avg'].add_edge(u, v, distance=prox2dist(pavg)) + + din = G[u][v]['distance'] + dout = G[v][u]['distance'] + + U.add_edge(u, v, avg_distance=0.5*(din + dout), max_distance=max(din, dout)) + + components = [] + for c in nx.connected_components(U): + if len(c) > 2: + components.append((G.subgraph(c).copy(), U.subgraph(c).copy())) #nx.write_graphml(U, wGraphml) - pk.dump(U, open(wGraphml, 'wb')) + pk.dump(components, open(wGraphml, 'wb')) print("Done") \ No newline at end of file diff --git a/21-calc-backbone.py b/21-calc-backbone.py index d7561cc..9577aa4 100644 --- a/21-calc-backbone.py +++ b/21-calc-backbone.py @@ -48,37 +48,41 @@ weight_attr = settings.get('weight-attr') # Files - wGgraphml = 'networks/{folder:s}/undirected_backbones.pickle'.format(folder=folder) + rGfile = 'networks/{folder:s}/undirected_networks.pickle'.format(folder=folder) wFdistortion = 'networks/{folder:s}/undirected_distortions.pickle'.format(folder=folder) + wGstats = 'networks/{folder:s}/undirected_networks-stats.csv'.format(folder=folder) # Load Network print("Loading network: {network:s}".format(network=network)) - rGfile = 'networks/{folder:s}/undirected_networks.pickle'.format(folder=folder) - G = pk.load(open(rGfile, 'rb')) + components = pk.load(open(rGfile, 'rb')) + - # Dictionary of distortion distribution - distortion_dist = {'min': dict(), 'max': dict(), 'avg': dict()} + df = pd.DataFrame(columns=['n-nodes', 'nd-edges', 'nu-edges', 'tau-metric', 'tau-ultrametric', + 'tau-avg-metric', 'tau-avg-ultrametric', 'tau-max-metric', 'tau-max-ultrametric'], index=range(len(components))) - for type in ['min', 'max', 'avg']: - print(type) - # - # Metric computation - # - G[type], s_values = dc.backbone(G[type], weight='distance', kind='metric', distortion=True) - distortion_dist[type]['metric'] = s_values - # - # Ultrametric computation - # - U, s_values = dc.backbone(G[type], weight='distance', kind='ultrametric', distortion=True) - distortion_dist[type]['ultrametric'] = s_values - nx.set_edge_attributes(G[type], name='ultrametric', values={(u, v): U.has_edge(u, v) for u, v in G[type].edges()}) + single_s = {'metric': dict(), 'ultrametric': dict(), 'avg-metric': dict(), + 'avg-ultrametric': dict(), 'max-metric': dict(), 'max-ultrametric': dict()} + + s_values = [single_s.copy() for _ in range(len(components))] + + for idx, (D, U) in enumerate(components): + df['n-nodes'][idx] = D.number_of_nodes() + df['nd-edges'][idx] = D.number_of_edges() + df['nu-edges'][idx] = U.number_of_edges() + + for kind in ['metric', 'ultrametric']: + B, s_values[idx][kind] = dc.backbone(D, weight='distance', kind=kind, distortion=True) + df[f'tau-{kind}'][idx] = B.number_of_edges()/df['nd-edges'][idx] + for utype in ['avg', 'max']: + B, s_values[idx][f'{utype}-{kind}'] = dc.backbone(U, weight=f'{utype}_distance', kind=kind, distortion=True) + df[f'tau-{utype}-{kind}'][idx] = B.number_of_edges()/df['nu-edges'][idx] + print('--- Exporting Formats ---') - ensurePathExists(wGgraphml) ensurePathExists(wFdistortion) - print('> Backbone') - pk.dump(G, open(wGgraphml, 'wb')) + print('> Backbone Statistics') + df.to_csv(wGstats) print('> Distortion') - pk.dump(distortion_dist, open(wFdistortion, 'wb')) + pk.dump(s_values, open(wFdistortion, 'wb')) print('\n') diff --git a/22-backbone-comparison.py b/22-backbone-comparison.py index ddccbd8..bb4c160 100644 --- a/22-backbone-comparison.py +++ b/22-backbone-comparison.py @@ -47,8 +47,7 @@ for idx, network in enumerate(networks): print(network) - settings = config[network] - folder = settings.get('folder') + folder = config[network].get('folder') dfM.loc[idx, 'name'] = network dfU.loc[idx, 'name'] = network diff --git a/22-network-stats.py b/22-network-stats.py new file mode 100644 index 0000000..e7b79c7 --- /dev/null +++ b/22-network-stats.py @@ -0,0 +1,93 @@ +# coding=utf-8 +# Author: Rion B Correia & Felipe Xavier Costa +# Date: Feb 22, 2023 +# +# Description: Reads a network and computes backbone size statistics. +# +# +import numpy as np +import pandas as pd +pd.set_option('display.max_rows', 100) +pd.set_option('display.max_columns', 500) +pd.set_option('display.width', 1000) +#pd.options.display.float_format = '{:.2%}'.format +import networkx as nx +import argparse +import configparser +from utils import get_asymmetry_distribution +import pickle as pk + + +if __name__ == '__main__': + + # + # Init + # + config = configparser.ConfigParser() + config.read('networks.ini') + networks = list(config.keys())[1:] + + # + # Args + # + parser = argparse.ArgumentParser() + parser.add_argument("--network", default='bike-sharing', type=str, choices=networks, help="Network name.") + args = parser.parse_args() + # + network = args.network + # + settings = config[network] + folder = settings.get('folder') + + # Files + rGfile = 'networks/{folder:s}/undirected_networks.pickle'.format(folder=folder) + rBfile = 'networks/{folder:s}/undirected_backbones.pickle'.format(folder=folder) + wGstats = 'networks/{folder:s}/undirected_networks-stats.csv'.format(folder=folder) + #wFasymmetry = 'networks/{folder:s}/backbone_asymmetry.pickle'.format(folder=folder) + + # Load graph + G = pk.load(open(rGfile, 'rb')) + B = pk.load(open(rBfile, 'rb')) + + df = pd.DataFrame(columns=['n-nodes', 'n-edges', 'density', 'tau-edges-metric','tau-edges-ultrametric'], + index=['min', 'max', 'avg', 'harm']) + + # Min and Harm can be done in entrie network + for type in ['min', 'harm']: + print(type) + df['n-nodes'][type] = G[type].number_of_nodes() + df['n-edges'][type] = G[type].number_of_edges() + df['density'][type] = nx.density(G[type]) + + if df['n-edges'][type] > 0: + df['tau-edges-metric'][type] = B[type].number_of_edges()/df['n-edges'][type] + df['tau-edges-ultrametric'][type] = sum([int(d) for _, _, d in B[type].edges(data='ultrametric')])/df['n-edges'][type] + else: + df['tau-edges-metric'][type] = 0.0 + df['tau-edges-ultrametric'][type] = 0.0 + + # Max and Avg Should be in a subset of the LSCC + rDfile = 'networks/{folder:s}/network.graphml'.format(folder=folder) + D = nx.read_graphml(rDfile) + lscc_nodes = max(nx.strongly_connected_components(D), key=len) + for type in ['max', 'avg']: + print(type) + g = G[type].subgraph(lscc_nodes) + + df['n-nodes'][type] = g.number_of_nodes() + df['n-edges'][type] = g.number_of_edges() + df['density'][type] = nx.density(g) + + if df['n-edges'][type] > 0: + b = B[type].subgraph(lscc_nodes) + df['tau-edges-metric'][type] = b.number_of_edges()/df['n-edges'][type] + df['tau-edges-ultrametric'][type] = sum([int(d) for _, _, d in b.edges(data='ultrametric')])/df['n-edges'][type] + else: + df['tau-edges-metric'][type] = 0.0 + df['tau-edges-ultrametric'][type] = 0.0 + + + # Print + print(df) + df.to_csv(wGstats) + print("\n\n") diff --git a/README.md b/README.md index 8d73826..b4788c3 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,11 @@ Source codes for the Directed Distance Backbone project. +The considered networks have edge attributes 'distance' by construction. + ### Scripts functionalities: | Starts with | Functionality | |-------------|-------------------------| | 0 | Specific model measures | | 1 | All models analysis | -| 2 | Undirected analysis | \ No newline at end of file +| 2 | Undirected analysis | diff --git a/Summary/BackboneCompareStats.csv b/Summary/BackboneCompareStats.csv new file mode 100644 index 0000000..f2a317b --- /dev/null +++ b/Summary/BackboneCompareStats.csv @@ -0,0 +1,21 @@ +,n-edges,n-min-edges,n-max-edges,%-metric,%-min-metric,%-max-metric,%-avg-metric,%-harm-metric,%-ultrametric,%-min-ultrametric,%-max-ultrametric,%-avg-ultrametric,%-harm-ultrametric +business-faculty,3432.0,2944,488,0.3508158508158508,0.1745923913043478,0.6290983606557377,0.6618852459016393,0.1864809782608695,0.0976107226107226,0.0431385869565217,0.1762295081967213,0.1721311475409836,0.0407608695652173 +cs-faculty,2929.0,2741,188,0.5148514851485149,0.3349142648668369,0.824468085106383,0.8776595744680851,0.3283473184968989,0.2266985319221577,0.1130974097044874,0.4787234042553192,0.4574468085106383,0.0981393651951842 +history-faculty,2428.0,2266,162,0.414332784184514,0.2436010591350397,0.7716049382716049,0.8148148148148148,0.2471315092674316,0.2199341021416803,0.1032656663724624,0.4259259259259259,0.3641975308641975,0.0966460723742277 +caviar-proj,295.0,205,90,0.7050847457627119,0.5902439024390244,0.7555555555555555,0.7444444444444445,0.5951219512195122,0.6474576271186441,0.5560975609756098,0.6888888888888889,0.6888888888888889,0.5317073170731708 +celegans-her,3500.0,2932,568,0.5568571428571428,0.3216234652114597,0.823943661971831,0.8433098591549296,0.3219645293315143,0.2677142857142857,0.114256480218281,0.4348591549295774,0.3943661971830985,0.1105047748976807 +celegans-male,3474.0,2832,642,0.5400115141047783,0.330861581920904,0.6947040498442367,0.7305295950155763,0.3343926553672316,0.2769142199194012,0.1228813559322034,0.397196261682243,0.381619937694704,0.1182909604519774 +colombia-calls,438484.0,238586,199898,0.026014632232875,0.0097994014736824,0.0157030085343525,0.0151177100321163,0.0097281483406402,0.0089011229600167,0.003638101145918,0.0043172017729041,0.004312199221603,0.0036129529813149 +colombia-mobility,173857.0,106707,67150,0.0170887568518955,0.0130544387903324,0.0181831720029784,0.0180938198064035,0.0128576382055535,0.0121651702261053,0.0080875668887701,0.0128369322412509,0.0128369322412509,0.0080781954323521 +mobility-manizales,2518.0,1281,1237,0.2664813343923749,0.1194379391100702,0.2651576394502829,0.2497978981406629,0.1498829039812646,0.0766481334392374,0.0437158469945355,0.0452708164915117,0.0452708164915117,0.0437158469945355 +mobility-medellin,33884.0,18381,15503,0.2467241175776177,0.1514607475110168,0.1897697219892924,0.205379603947623,0.1702301289374898,0.0544209656475032,0.0245906098688863,0.0271560343159388,0.0266400051602915,0.0224144497034981 +tennis-loss,101436.0,85084,16352,0.5961985882724082,0.1592073715387146,0.5377323874755382,0.6114848336594912,0.1604296930092614,0.2377656847667494,0.090863147007663,0.0912426614481409,0.077727495107632,0.0866202811339382 +yeast-grn,1666106.0,1613628,52478,0.0637174345449809,0.0093491188799401,0.0983840847593277,0.0939250733640763,0.0091105260939944,0.0137824364116088,0.0039104428034218,0.0251915088227447,0.0233240596059301,0.0038930906008076 +bike-sharing,53118.0,35063,18055,0.5953160887081592,0.5589367709551379,0.6353918582110218,0.6767654389365827,0.3849071670992214,0.0275236266425693,0.0207626272709123,0.0400443090556632,0.0399889227360841,0.0206485469012919 +giraffe,30.0,15,15,0.7666666666666667,0.7333333333333333,0.8,0.8666666666666667,0.8,0.3333333333333333,0.3333333333333333,0.3333333333333333,0.3333333333333333,0.3333333333333333 +comorbidity,8930.0,4465,4465,0.4743561030235162,0.3659574468085106,0.5117581187010078,0.5068309070548712,0.4665173572228443,0.0217245240761478,0.0210526315789473,0.0210526315789473,0.0210526315789473,0.0210526315789473 +phone-calls,609.0,430,179,0.916256157635468,0.8651162790697674,0.9497206703910616,0.9553072625698324,0.8511627906976744,0.8489326765188834,0.7465116279069768,0.9273743016759776,0.9273743016759776,0.7465116279069768 +us-airports,18906.0,11973,6933,0.2743044536126097,0.1382276789442913,0.2271743833838165,0.243473243905957,0.1440741668754698,0.1898339151592087,0.0900359141401486,0.1339968267705178,0.133852589066782,0.0897853503716695 +DDI,2966.0,1483,1483,0.5900202292650034,0.4895482130815913,0.4389750505731625,0.4598786244099798,0.4942683749157114,0.4049224544841537,0.2832097100472016,0.2784895482130816,0.2771409305461901,0.2771409305461901 +us-weblinks,505476.0,450539,54937,0.367809747643805,0.1606897516086287,0.5996141034275625,0.579208912026503,0.1607940711015028,0.2536678299266434,0.1127493957237886,0.4496059122267324,0.3865336658354115,0.1081992901835357 +host-pathogen,18529.0,18529,0,0.9985967942144746,0.6638242754600896,0.0,0.0,0.6638242754600896,0.9984348858546064,0.591451238598953,0.0,0.0,0.591451238598953 \ No newline at end of file diff --git a/Summary/BackboneCompareStats_Components.csv b/Summary/BackboneCompareStats_Components.csv new file mode 100644 index 0000000..e25691c --- /dev/null +++ b/Summary/BackboneCompareStats_Components.csv @@ -0,0 +1,148 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +business-faculty-0,84.0,2558.0,488.0,0.3924941360437842,0.0965598123534011,0.6618852459016393,0.1721311475409836,0.6290983606557377,0.1762295081967213 +cs-faculty-0,78.0,1180.0,179.0,0.5830508474576271,0.1932203389830508,0.8715083798882681,0.4301675977653631,0.8156424581005587,0.4525139664804469 +history-faculty-0,56.0,905.0,158.0,0.5348066298342542,0.2154696132596685,0.810126582278481,0.3481012658227848,0.7658227848101266,0.4113924050632911 +caviar-proj-0,63.0,232.0,90.0,0.6594827586206896,0.5948275862068966,0.7444444444444445,0.6888888888888889,0.7555555555555555,0.6888888888888889 +celegans-her-0,215.0,2748.0,558.0,0.5673216885007278,0.2536390101892285,0.8405017921146953,0.3835125448028674,0.8207885304659498,0.4247311827956989 +celegans-her-1,3.0,5.0,2.0,1.0,0.8,1.0,1.0,1.0,1.0 +celegans-her-3,4.0,8.0,3.0,0.875,0.875,1.0,1.0,1.0,1.0 +celegans-male-0,238.0,2852.0,634.0,0.5157784011220197,0.2457924263674614,0.7271293375394322,0.3738170347003154,0.6908517350157729,0.389589905362776 +colombia-calls-0,863.0,438484.0,199898.0,0.026014632232875,0.0089011229600167,0.0151177100321163,0.004312199221603,0.0157030085343525,0.0043172017729041 +colombia-mobility-0,863.0,173857.0,67150.0,0.0170887568518955,0.0121651702261053,0.0180938198064035,0.0128369322412509,0.0181831720029784,0.0128369322412509 +mobility-manizales-0,57.0,2518.0,1237.0,0.2664813343923749,0.0766481334392374,0.2497978981406629,0.0452708164915117,0.2651576394502829,0.0452708164915117 +mobility-medellin-0,413.0,33884.0,15503.0,0.2467241175776177,0.0544209656475032,0.205379603947623,0.0266400051602915,0.1897697219892924,0.0271560343159388 +tennis-loss-0,1263.0,85842.0,16349.0,0.5327345588406608,0.1286549707602339,0.6114135421126674,0.0775582604440638,0.5376475625420515,0.0910759067832895 +yeast-grn-0,1225.0,366239.0,52478.0,0.0662518191672651,0.0154953459353045,0.0939250733640763,0.0233240596059301,0.0983840847593277,0.0251915088227447 +bike-sharing-0,723.0,53115.0,18055.0,0.5952932316671373,0.0274875270639179,0.6767654389365827,0.0399889227360841,0.6353918582110218,0.0400443090556632 +giraffe-0,6.0,30.0,15.0,0.7666666666666667,0.3333333333333333,0.8666666666666667,0.3333333333333333,0.8,0.3333333333333333 +comorbidity-0,95.0,8930.0,4465.0,0.4743561030235162,0.0217245240761478,0.5068309070548712,0.0210526315789473,0.5117581187010078,0.0210526315789473 +phone-calls-1,30.0,75.0,33.0,0.84,0.7466666666666667,0.9393939393939394,0.8787878787878788,0.9393939393939394,0.8787878787878788 +phone-calls-2,9.0,19.0,9.0,1.0,0.8421052631578947,1.0,0.8888888888888888,1.0,0.8888888888888888 +phone-calls-3,24.0,64.0,26.0,0.8125,0.75,0.9615384615384616,0.8846153846153846,0.9230769230769232,0.8846153846153846 +phone-calls-4,6.0,12.0,6.0,0.8333333333333334,0.75,0.8333333333333334,0.8333333333333334,0.8333333333333334,0.8333333333333334 +phone-calls-6,8.0,16.0,7.0,0.9375,0.875,1.0,1.0,1.0,1.0 +phone-calls-7,7.0,14.0,6.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-airports-0,926.0,18593.0,6930.0,0.2654224708223525,0.1797988490292045,0.2431457431457431,0.1334776334776334,0.2268398268398268,0.1336219336219336 +DDI-0,412.0,2966.0,1483.0,0.5900202292650034,0.4049224544841537,0.4598786244099798,0.2771409305461901,0.4389750505731625,0.2784895482130816 +us-weblinks-0,18112.0,288838.0,49855.0,0.3465160401332234,0.2233743482505764,0.5658008223849162,0.3718583893290542,0.5850165479891686,0.43654598335172 +us-weblinks-1,273.0,1720.0,374.0,0.55,0.4860465116279069,0.7834224598930482,0.7272727272727273,0.8048128342245989,0.732620320855615 +us-weblinks-2,31.0,107.0,44.0,0.6074766355140186,0.5981308411214953,0.6818181818181818,0.6818181818181818,0.7045454545454546,0.6818181818181818 +us-weblinks-3,21.0,385.0,175.0,0.9974025974025974,0.8701298701298701,1.0,0.5257142857142857,1.0,0.8685714285714285 +us-weblinks-6,262.0,3343.0,551.0,0.3885731379000897,0.3281483697277894,0.515426497277677,0.4736842105263157,0.5172413793103449,0.4900181488203267 +us-weblinks-7,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-9,88.0,956.0,226.0,0.3085774058577405,0.256276150627615,0.4734513274336283,0.3849557522123893,0.4690265486725664,0.3849557522123893 +us-weblinks-10,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-13,278.0,3860.0,837.0,0.2821243523316062,0.2152849740932642,0.3691756272401433,0.3309438470728793,0.3703703703703703,0.3333333333333333 +us-weblinks-14,18.0,70.0,34.0,0.4857142857142857,0.4857142857142857,0.5,0.5,0.5,0.5 +us-weblinks-15,9.0,70.0,34.0,1.0,1.0,1.0,0.2647058823529412,1.0,1.0 +us-weblinks-16,30.0,191.0,44.0,0.5968586387434555,0.450261780104712,0.8863636363636364,0.6590909090909091,0.8636363636363636,0.75 +us-weblinks-17,12.0,125.0,59.0,0.192,0.184,0.1864406779661017,0.1864406779661017,0.288135593220339,0.1864406779661017 +us-weblinks-18,9.0,44.0,14.0,0.8636363636363636,0.8409090909090909,0.8571428571428571,0.7142857142857143,0.8571428571428571,0.7857142857142857 +us-weblinks-22,19.0,325.0,154.0,0.9907692307692308,0.3015384615384615,1.0,0.1168831168831168,0.9935064935064936,0.1753246753246753 +us-weblinks-24,3.0,5.0,2.0,1.0,0.8,1.0,1.0,1.0,1.0 +us-weblinks-25,6.0,26.0,11.0,0.3846153846153846,0.3846153846153846,0.4545454545454545,0.4545454545454545,0.4545454545454545,0.4545454545454545 +us-weblinks-26,4.0,9.0,3.0,0.7777777777777778,0.7777777777777778,1.0,1.0,1.0,1.0 +us-weblinks-27,4.0,8.0,3.0,0.75,0.75,1.0,1.0,1.0,1.0 +us-weblinks-28,10.0,75.0,30.0,0.9866666666666668,0.4266666666666667,0.9666666666666668,0.3,1.0,0.3 +us-weblinks-30,4.0,8.0,4.0,0.75,0.75,0.75,0.75,0.75,0.75 +us-weblinks-34,3.0,5.0,2.0,0.6,0.6,1.0,1.0,1.0,1.0 +us-weblinks-36,3.0,6.0,3.0,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-40,3.0,6.0,3.0,1.0,1.0,1.0,0.6666666666666666,1.0,1.0 +us-weblinks-41,4.0,8.0,4.0,0.875,0.875,0.75,0.75,0.75,0.75 +us-weblinks-42,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-46,4.0,12.0,6.0,1.0,1.0,1.0,0.8333333333333334,1.0,1.0 +us-weblinks-47,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-50,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-51,14.0,54.0,21.0,0.7777777777777778,0.5370370370370371,0.9523809523809524,0.6190476190476191,0.9523809523809524,0.6666666666666666 +us-weblinks-52,4.0,9.0,4.0,0.7777777777777778,0.7777777777777778,0.75,0.75,0.75,0.75 +us-weblinks-57,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-58,12.0,27.0,11.0,0.8518518518518519,0.8518518518518519,1.0,1.0,1.0,1.0 +us-weblinks-61,6.0,11.0,5.0,0.9090909090909092,0.9090909090909092,1.0,1.0,1.0,1.0 +us-weblinks-62,5.0,9.0,4.0,0.8888888888888888,0.8888888888888888,1.0,1.0,1.0,1.0 +us-weblinks-64,4.0,7.0,3.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-65,3.0,6.0,3.0,1.0,1.0,1.0,0.6666666666666666,1.0,1.0 +us-weblinks-68,4.0,11.0,5.0,0.5454545454545454,0.5454545454545454,0.6,0.6,0.6,0.6 +us-weblinks-69,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-70,30.0,715.0,290.0,0.558041958041958,0.2489510489510489,0.4206896551724138,0.1,0.7793103448275862,0.1689655172413793 +us-weblinks-74,4.0,10.0,4.0,0.6,0.6,0.75,0.75,0.75,0.75 +us-weblinks-75,8.0,56.0,28.0,0.25,0.25,0.25,0.25,0.3571428571428571,0.25 +us-weblinks-76,5.0,14.0,4.0,0.7142857142857143,0.6428571428571429,1.0,1.0,1.0,1.0 +us-weblinks-77,7.0,31.0,10.0,0.8709677419354839,0.4516129032258064,1.0,0.6,1.0,0.6 +us-weblinks-78,4.0,10.0,4.0,1.0,1.0,1.0,0.75,1.0,1.0 +us-weblinks-79,4.0,10.0,4.0,0.9,0.9,1.0,0.75,1.0,0.75 +us-weblinks-82,4.0,7.0,3.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-83,6.0,11.0,5.0,0.9090909090909092,0.9090909090909092,1.0,1.0,1.0,1.0 +us-weblinks-84,4.0,12.0,6.0,0.5,0.5,0.5,0.5,0.5,0.5 +us-weblinks-86,3.0,6.0,3.0,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,1.0,1.0 +us-weblinks-87,10.0,70.0,32.0,0.4,0.3285714285714285,0.59375,0.28125,0.59375,0.375 +us-weblinks-89,13.0,156.0,78.0,1.0,0.2243589743589743,1.0,0.1538461538461538,1.0,0.1538461538461538 +us-weblinks-90,6.0,30.0,15.0,0.6333333333333333,0.4,0.7333333333333333,0.3333333333333333,1.0,0.3333333333333333 +us-weblinks-91,3.0,6.0,3.0,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-93,4.0,7.0,3.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-95,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-96,4.0,9.0,3.0,0.7777777777777778,0.6666666666666666,1.0,1.0,1.0,1.0 +us-weblinks-97,3.0,6.0,3.0,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-98,3.0,5.0,2.0,1.0,0.8,1.0,1.0,1.0,1.0 +us-weblinks-99,5.0,20.0,10.0,0.4,0.4,0.4,0.4,0.4,0.4 +us-weblinks-100,4.0,8.0,3.0,0.75,0.75,1.0,1.0,1.0,1.0 +us-weblinks-104,5.0,12.0,6.0,0.75,0.75,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-105,6.0,14.0,5.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-108,5.0,10.0,4.0,0.9,0.9,1.0,1.0,1.0,1.0 +us-weblinks-109,13.0,146.0,68.0,0.1712328767123287,0.1643835616438356,0.1911764705882352,0.1764705882352941,0.1911764705882352,0.1764705882352941 +us-weblinks-110,5.0,9.0,4.0,0.8888888888888888,0.8888888888888888,1.0,1.0,1.0,1.0 +us-weblinks-111,4.0,12.0,6.0,1.0,1.0,1.0,0.5,1.0,1.0 +us-weblinks-112,6.0,30.0,15.0,1.0,0.8666666666666667,1.0,0.3333333333333333,1.0,0.7333333333333333 +us-weblinks-120,5.0,20.0,10.0,0.45,0.4,0.5,0.4,0.5,0.4 +us-weblinks-121,4.0,8.0,3.0,0.75,0.75,1.0,1.0,1.0,1.0 +us-weblinks-122,6.0,30.0,15.0,1.0,0.5333333333333333,1.0,0.3333333333333333,1.0,0.4666666666666667 +us-weblinks-124,17.0,44.0,22.0,1.0,0.9545454545454546,1.0,0.9090909090909092,1.0,0.9090909090909092 +us-weblinks-126,6.0,14.0,5.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-127,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-130,5.0,10.0,4.0,0.9,0.9,1.0,1.0,1.0,1.0 +us-weblinks-132,3.0,6.0,3.0,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-133,10.0,25.0,9.0,1.0,0.88,1.0,1.0,1.0,1.0 +us-weblinks-136,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-137,3.0,6.0,3.0,0.8333333333333334,0.8333333333333334,1.0,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-138,4.0,12.0,6.0,0.5,0.5,0.5,0.5,0.5,0.5 +us-weblinks-139,10.0,74.0,30.0,1.0,1.0,1.0,0.3,1.0,1.0 +us-weblinks-141,3.0,6.0,3.0,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-143,7.0,15.0,6.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-144,8.0,56.0,28.0,1.0,1.0,1.0,0.6428571428571429,1.0,1.0 +us-weblinks-146,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-147,3.0,5.0,2.0,1.0,0.8,1.0,1.0,1.0,1.0 +us-weblinks-148,6.0,20.0,7.0,0.55,0.55,0.7142857142857143,0.7142857142857143,0.7142857142857143,0.7142857142857143 +us-weblinks-149,8.0,16.0,7.0,1.0,0.875,1.0,1.0,1.0,1.0 +us-weblinks-150,8.0,20.0,8.0,0.95,0.95,0.875,0.875,0.875,0.875 +us-weblinks-152,8.0,16.0,7.0,0.9375,0.9375,1.0,1.0,1.0,1.0 +us-weblinks-153,4.0,7.0,3.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-154,7.0,42.0,21.0,1.0,0.7619047619047619,1.0,0.5714285714285714,1.0,0.5714285714285714 +us-weblinks-156,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-159,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-161,8.0,27.0,8.0,0.9629629629629628,0.925925925925926,1.0,0.875,1.0,0.875 +us-weblinks-162,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-166,3.0,6.0,3.0,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-168,9.0,72.0,36.0,1.0,0.2222222222222222,1.0,0.2222222222222222,1.0,0.2222222222222222 +us-weblinks-170,8.0,56.0,28.0,1.0,0.4642857142857143,1.0,0.4642857142857143,1.0,0.4642857142857143 +us-weblinks-171,3.0,6.0,3.0,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-173,4.0,8.0,3.0,0.75,0.75,1.0,1.0,1.0,1.0 +us-weblinks-174,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-176,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-179,3.0,5.0,2.0,1.0,0.8,1.0,1.0,1.0,1.0 +us-weblinks-182,4.0,7.0,3.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-185,4.0,11.0,5.0,0.9090909090909092,0.7272727272727273,0.8,0.6,0.8,0.6 +us-weblinks-187,4.0,7.0,3.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +us-weblinks-190,5.0,11.0,5.0,0.7272727272727273,0.7272727272727273,0.8,0.8,0.8,0.8 +us-weblinks-195,6.0,13.0,5.0,0.9230769230769232,0.7692307692307693,1.0,1.0,1.0,1.0 +us-weblinks-196,3.0,6.0,3.0,1.0,1.0,1.0,0.6666666666666666,1.0,1.0 +us-weblinks-199,5.0,12.0,5.0,0.6666666666666666,0.6666666666666666,0.8,0.8,0.8,0.8 +us-weblinks-200,6.0,30.0,15.0,0.8666666666666667,0.6,1.0,0.3333333333333333,1.0,0.5333333333333333 +us-weblinks-201,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-202,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-204,4.0,10.0,4.0,1.0,1.0,1.0,0.75,1.0,1.0 +us-weblinks-205,3.0,6.0,3.0,1.0,0.6666666666666666,1.0,0.6666666666666666,1.0,0.6666666666666666 +us-weblinks-206,5.0,17.0,7.0,0.5882352941176471,0.5294117647058824,0.8571428571428571,0.5714285714285714,1.0,0.5714285714285714 +us-weblinks-209,3.0,6.0,3.0,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +us-weblinks-211,4.0,8.0,4.0,0.75,0.75,0.75,0.75,0.75,0.75 +us-weblinks-212,3.0,5.0,2.0,0.8,0.8,1.0,1.0,1.0,1.0 +us-weblinks-213,5.0,13.0,5.0,0.9230769230769232,0.9230769230769232,1.0,0.8,1.0,1.0 +us-weblinks-214,4.0,7.0,3.0,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 diff --git a/Summary/BackboneCompareStats_LSCC.csv b/Summary/BackboneCompareStats_LSCC.csv new file mode 100644 index 0000000..9a12889 --- /dev/null +++ b/Summary/BackboneCompareStats_LSCC.csv @@ -0,0 +1,20 @@ +,n-nodes,n-edges,n-max-edges,tau-metric,tau-max-metric,tau-avg-metric,tau-ultrametric,tau-max-ultrametric,tau-avg-ultrametric +business-faculty,94.0,2842.0,488,0.3652357494722026,0.6290983606557377,0.6618852459016393,0.0946516537649542,0.1762295081967213,0.1721311475409836 +cs-faculty,167.0,2384.0,188,0.5285234899328859,0.824468085106383,0.8776595744680851,0.2202181208053691,0.4787234042553192,0.4574468085106383 +history-faculty,116.0,1897.0,162,0.430152872957301,0.7716049382716049,0.8148148148148148,0.2087506589351608,0.4259259259259259,0.3641975308641975 +caviar-proj,66.0,242.0,90,0.6611570247933884,0.7555555555555555,0.7444444444444445,0.5991735537190083,0.6888888888888889,0.6888888888888889 +celegans-her,249.0,3046.0,568,0.5531845042678923,0.823943661971831,0.8433098591549296,0.2567301378857518,0.4348591549295774,0.3943661971830985 +celegans-male,289.0,3206.0,642,0.5343106674984405,0.6947040498442367,0.7305295950155763,0.2682470368059887,0.397196261682243,0.381619937694704 +colombia-calls,863.0,438484.0,199898,0.026014632232875,0.0157030085343525,0.0151177100321163,0.0089011229600167,0.0043172017729041,0.004312199221603 +colombia-mobility,863.0,173857.0,67150,0.0170887568518955,0.0181831720029784,0.0180938198064035,0.0121651702261053,0.0128369322412509,0.0128369322412509 +mobility-manizales,57.0,2518.0,1237,0.2664813343923749,0.2651576394502829,0.2497978981406629,0.0766481334392374,0.0452708164915117,0.0452708164915117 +mobility-medellin,413.0,33884.0,15503,0.2467241175776177,0.1897697219892924,0.205379603947623,0.0544209656475032,0.0271560343159388,0.0266400051602915 +tennis-loss,2428.0,98102.0,16352,0.5824753827648774,0.5377323874755382,0.6114848336594912,0.2118611241361032,0.0912426614481409,0.077727495107632 +yeast-grn,1229.0,367432.0,52478,0.0662244986827494,0.0983840847593277,0.0939250733640763,0.0154913017918961,0.0251915088227447,0.0233240596059301 +bike-sharing,723.0,53115.0,18055,0.5952932316671373,0.6353918582110218,0.6767654389365827,0.0274875270639179,0.0400443090556632,0.0399889227360841 +giraffe,6.0,30.0,15,0.7666666666666667,0.8,0.8666666666666667,0.3333333333333333,0.3333333333333333,0.3333333333333333 +comorbidity,95.0,8930.0,4465,0.4743561030235162,0.5117581187010078,0.5068309070548712,0.0217245240761478,0.0210526315789473,0.0210526315789473 +phone-calls,114.0,274.0,97,0.8832116788321168,0.9484536082474226,0.9587628865979382,0.7737226277372263,0.9072164948453608,0.9072164948453608 +us-airports,995.0,18820.0,6932,0.2710945802337938,0.2270628967109059,0.2433641084824004,0.1862911795961742,0.133871898442008,0.1337276399307559 +DDI,412.0,2966.0,1483,0.5900202292650034,0.4389750505731625,0.4598786244099798,0.4049224544841537,0.2784895482130816,0.2771409305461901 +us-weblinks,27725.0,372626.0,54259,0.3800352095666969,0.5953850974031958,0.5753884148251903,0.2562837805198778,0.44735435595938,0.3844339187968816 diff --git a/Summary/BackboneCompareStats_LargestComponent.csv b/Summary/BackboneCompareStats_LargestComponent.csv new file mode 100644 index 0000000..3d6cded --- /dev/null +++ b/Summary/BackboneCompareStats_LargestComponent.csv @@ -0,0 +1,20 @@ +Network,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +business-faculty,84.0,2558.0,488.0,0.3924941360437842,0.0965598123534011,0.6618852459016393,0.1721311475409836,0.6290983606557377,0.1762295081967213 +cs-faculty,78.0,1180.0,179.0,0.5830508474576271,0.1932203389830508,0.8715083798882681,0.4301675977653631,0.8156424581005587,0.4525139664804469 +history-faculty,56.0,905.0,158.0,0.5348066298342542,0.2154696132596685,0.810126582278481,0.3481012658227848,0.7658227848101266,0.4113924050632911 +caviar-proj,63.0,232.0,90.0,0.6594827586206896,0.5948275862068966,0.7444444444444445,0.6888888888888889,0.7555555555555555,0.6888888888888889 +celegans-her,215.0,2748.0,558.0,0.5673216885007278,0.2536390101892285,0.8405017921146953,0.3835125448028674,0.8207885304659498,0.4247311827956989 +celegans-male,238.0,2852.0,634.0,0.5157784011220197,0.2457924263674614,0.7271293375394322,0.3738170347003154,0.6908517350157729,0.389589905362776 +colombia-calls,863.0,438484.0,199898.0,0.026014632232875,0.0089011229600167,0.0151177100321163,0.004312199221603,0.0157030085343525,0.0043172017729041 +colombia-mobility,863.0,173857.0,67150.0,0.0170887568518955,0.0121651702261053,0.0180938198064035,0.0128369322412509,0.0181831720029784,0.0128369322412509 +mobility-manizales,57.0,2518.0,1237.0,0.2664813343923749,0.0766481334392374,0.2497978981406629,0.0452708164915117,0.2651576394502829,0.0452708164915117 +mobility-medellin,413.0,33884.0,15503.0,0.2467241175776177,0.0544209656475032,0.205379603947623,0.0266400051602915,0.1897697219892924,0.0271560343159388 +tennis-loss,1263.0,85842.0,16349.0,0.5327345588406608,0.1286549707602339,0.6114135421126674,0.0775582604440638,0.5376475625420515,0.0910759067832895 +yeast-grn,1225.0,366239.0,52478.0,0.0662518191672651,0.0154953459353045,0.0939250733640763,0.0233240596059301,0.0983840847593277,0.0251915088227447 +bike-sharing,723.0,53115.0,18055.0,0.5952932316671373,0.0274875270639179,0.6767654389365827,0.0399889227360841,0.6353918582110218,0.0400443090556632 +giraffe,6.0,30.0,15.0,0.7666666666666667,0.3333333333333333,0.8666666666666667,0.3333333333333333,0.8,0.3333333333333333 +comorbidity,95.0,8930.0,4465.0,0.4743561030235162,0.0217245240761478,0.5068309070548712,0.0210526315789473,0.5117581187010078,0.0210526315789473 +phone-calls,30.0,75.0,33.0,0.84,0.7466666666666667,0.9393939393939394,0.8787878787878788,0.9393939393939394,0.8787878787878788 +us-airports,926.0,18593.0,6930.0,0.2654224708223525,0.1797988490292045,0.2431457431457431,0.1334776334776334,0.2268398268398268,0.1336219336219336 +DDI,412.0,2966.0,1483.0,0.5900202292650034,0.4049224544841537,0.4598786244099798,0.2771409305461901,0.4389750505731625,0.2784895482130816 +us-weblinks,18112.0,288838.0,49855.0,0.3465160401332234,0.2233743482505764,0.5658008223849162,0.3718583893290542,0.5850165479891686,0.43654598335172 diff --git a/Summary/BackboneCompareStats_WCC.csv b/Summary/BackboneCompareStats_WCC.csv new file mode 100644 index 0000000..0c8b853 --- /dev/null +++ b/Summary/BackboneCompareStats_WCC.csv @@ -0,0 +1,21 @@ +,n-nodes,n-edges,n-min-edges,tau-metric,tau-min-metric,tau-harm-metric,tau-ultrametric,tau-min-ultrametric,tau-harm-ultrametric +business-faculty,113.0,3432.0,2944,0.3508158508158508,0.1745923913043478,0.1864809782608695,0.0976107226107226,0.0431385869565217,0.0407608695652173 +cs-faculty,206.0,2929.0,2741,0.5148514851485149,0.3349142648668369,0.3283473184968989,0.2266985319221577,0.1130974097044874,0.0981393651951842 +history-faculty,145.0,2428.0,2266,0.414332784184514,0.2436010591350397,0.2471315092674316,0.2199341021416803,0.1032656663724624,0.0966460723742277 +caviar-proj,110.0,295.0,205,0.7050847457627119,0.5902439024390244,0.5951219512195122,0.6474576271186441,0.5560975609756098,0.5317073170731708 +celegans-her,313.0,3500.0,2932,0.5568571428571428,0.3216234652114597,0.3219645293315143,0.2677142857142857,0.114256480218281,0.1105047748976807 +celegans-male,328.0,3474.0,2832,0.5400115141047783,0.330861581920904,0.3343926553672316,0.2769142199194012,0.1228813559322034,0.1182909604519774 +colombia-calls,863.0,438484.0,238586,0.026014632232875,0.0097994014736824,0.0097281483406402,0.0089011229600167,0.003638101145918,0.0036129529813149 +colombia-mobility,863.0,173857.0,106707,0.0170887568518955,0.0130544387903324,0.0128576382055535,0.0121651702261053,0.0080875668887701,0.0080781954323521 +mobility-manizales,57.0,2518.0,1281,0.2664813343923749,0.1194379391100702,0.1498829039812646,0.0766481334392374,0.0437158469945355,0.0437158469945355 +mobility-medellin,413.0,33884.0,18381,0.2467241175776177,0.1514607475110168,0.1702301289374898,0.0544209656475032,0.0245906098688863,0.0224144497034981 +tennis-loss,4245.0,101436.0,85084,0.5961985882724082,0.1592073715387146,0.1604296930092614,0.2377656847667494,0.090863147007663,0.0866202811339382 +yeast-grn,6216.0,1666106.0,1613628,0.0637174345449809,0.0093491188799401,0.0091105260939944,0.0137824364116088,0.0039104428034218,0.0038930906008076 +bike-sharing,725.0,53118.0,35063,0.5953160887081592,0.5589367709551379,0.3849071670992214,0.0275236266425693,0.0207626272709123,0.0206485469012919 +giraffe,6.0,30.0,15,0.7666666666666667,0.7333333333333333,0.8,0.3333333333333333,0.3333333333333333,0.3333333333333333 +comorbidity,95.0,8930.0,4465,0.4743561030235162,0.3659574468085106,0.4665173572228443,0.0217245240761478,0.0210526315789473,0.0210526315789473 +phone-calls,322.0,609.0,430,0.916256157635468,0.8651162790697674,0.8511627906976744,0.8489326765188834,0.7465116279069768,0.7465116279069768 +us-airports,1075.0,18906.0,11973,0.2743044536126097,0.1382276789442913,0.1440741668754698,0.1898339151592087,0.0900359141401486,0.0897853503716695 +DDI,412.0,2966.0,1483,0.5900202292650034,0.4895482130815913,0.4942683749157114,0.4049224544841537,0.2832097100472016,0.2771409305461901 +us-weblinks,42800.0,505476.0,450539,0.367809747643805,0.1606897516086287,0.1607940711015028,0.2536678299266434,0.1127493957237886,0.1081992901835357 +host-pathogen,10578.0,18529.0,18529,0.9985967942144746,0.6638242754600896,0.6638242754600896,0.9984348858546064,0.591451238598953,0.591451238598953 diff --git a/Summary/BackboneStats.csv b/Summary/BackboneStats.csv new file mode 100644 index 0000000..21015ff --- /dev/null +++ b/Summary/BackboneStats.csv @@ -0,0 +1,21 @@ +,n-nodes,n-edges,density,tau-metric,tau-ultrametric,ultrametric_metric_ratio,LSCC-nodes,LSCC-edges,LSCC-tau-metric,LSCC-tau-ultrametric,LSCC-ultrametric_metric_ratio +business-faculty,113.0,3432.0,0.2711757269279393,0.3508158508158508,0.0976107226107226,0.2782392026578073,94.0,2842.0,0.3652357494722026,0.0946516537649542,0.2591522157996146 +cs-faculty,206.0,2929.0,0.0693582761070329,0.5148514851485149,0.2266985319221577,0.4403183023872679,167.0,2384.0,0.5285234899328859,0.2202181208053691,0.4166666666666667 +history-faculty,145.0,2428.0,0.1162835249042145,0.414332784184514,0.2199341021416803,0.5308151093439363,116.0,1897.0,0.430152872957301,0.2087506589351608,0.4852941176470589 +caviar-proj,110.0,295.0,0.024603836530442,0.7050847457627119,0.6474576271186441,0.9182692307692308,66.0,242.0,0.6611570247933884,0.5991735537190083,0.90625 +celegans-her,313.0,3500.0,0.0358400917506348,0.5568571428571428,0.2677142857142857,0.4807593637762956,249.0,3046.0,0.5531845042678923,0.2567301378857518,0.4640949554896142 +celegans-male,328.0,3474.0,0.0323897963750279,0.5400115141047783,0.2769142199194012,0.5127931769722814,289.0,3206.0,0.5343106674984405,0.2682470368059887,0.5020431990659661 +colombia-calls,863.0,438484.0,0.5894346866405165,0.026014632232875,0.0089011229600167,0.3421583238362409,863.0,438484.0,0.026014632232875,0.0089011229600167,0.3421583238362409 +colombia-mobility,863.0,173857.0,0.233708291101295,0.0170887568518955,0.0121651702261053,0.7118815213732751,863.0,173857.0,0.0170887568518955,0.0121651702261053,0.7118815213732751 +mobility-manizales,57.0,2518.0,0.7888471177944862,0.2664813343923749,0.0766481334392374,0.2876304023845007,57.0,2518.0,0.2664813343923749,0.0766481334392374,0.2876304023845007 +mobility-medellin,413.0,33884.0,0.1991349114929829,0.2467241175776177,0.0544209656475032,0.2205741626794258,413.0,33884.0,0.2467241175776177,0.0544209656475032,0.2205741626794258 +tennis-loss,4245.0,101436.0,0.005630397351655,0.5961985882724082,0.2377656847667494,0.3988028308750578,2428.0,98102.0,0.5824753827648774,0.2118611241361032,0.3637254558818382 +yeast-grn,6216.0,1666106.0,0.0431271232156187,0.0637174345449809,0.0137824364116088,0.2163055764883195,1229.0,367432.0,0.0662244986827494,0.0154913017918961,0.2339210126166112 +bike-sharing,725.0,53118.0,0.1011964183654029,0.5953160887081592,0.0275236266425693,0.0462336348112073,723.0,53115.0,0.5952932316671373,0.0274875270639179,0.0461747683354944 +giraffe,6.0,30.0,1.0,0.7666666666666667,0.3333333333333333,0.4347826086956521,6.0,30.0,0.7666666666666667,0.3333333333333333,0.4347826086956521 +comorbidity,95.0,8930.0,1.0,0.4743561030235162,0.0217245240761478,0.0457979225684608,95.0,8930.0,0.4743561030235162,0.0217245240761478,0.0457979225684608 +phone-calls,322.0,609.0,0.005891913856156,0.916256157635468,0.8489326765188834,0.9265232974910392,114.0,274.0,0.8832116788321168,0.7737226277372263,0.8760330578512397 +us-airports,1075.0,18906.0,0.016375211121216,0.2743044536126097,0.1898339151592087,0.692055534130351,995.0,18820.0,0.2710945802337938,0.1862911795961742,0.6871814974519795 +DDI,412.0,2966.0,0.0175158859518578,0.5900202292650034,0.4049224544841537,0.6862857142857143,412.0,2966.0,0.5900202292650034,0.4049224544841537,0.6862857142857143 +us-weblinks,42800.0,505476.0,0.0002759453939551,0.367809747643805,0.2536678299266434,0.6896713084730447,27725.0,372626.0,0.3800352095666969,0.2562837805198778,0.6743685165700404 +host-pathogen,10578.0,18529.0,0.0001656097548462,0.9985967942144746,0.9984348858546064,0.9998378641301412,1.0,0.0,0.0,0.0,0.0 diff --git a/Summary/CompareSize_LSCC_WCC.csv b/Summary/CompareSize_LSCC_WCC.csv new file mode 100644 index 0000000..2bfd37f --- /dev/null +++ b/Summary/CompareSize_LSCC_WCC.csv @@ -0,0 +1,20 @@ +Network,N_WCC,N_LSCC,Percent +bike-sharing,725,723,0.997241379310345 +business-faculty,113,84,0.743362831858407 +caviar-proj,110,63,0.572727272727273 +celegans-her,313,215,0.686900958466454 +celegans-male,328,238,0.725609756097561 +colombia-calls,863,863,1 +colombia-mobility,863,863,1 +comorbidity,95,95,1 +cs-faculty,206,78,0.378640776699029 +DDI,412,412,1 +giraffe,6,6,1 +history-faculty,145,56,0.386206896551724 +mobility-manizales,57,57,1 +mobility-medellin,413,413,1 +phone-calls,322,30,0.093167701863354 +tennis-loss,4245,1263,0.297526501766784 +us-airports,1075,926,0.861395348837209 +us-weblinks,42800,18112,0.423177570093458 +yeast-grn,6216,1225,0.197072072072072 diff --git a/combining_data.html b/combining_data.html new file mode 100644 index 0000000..557e674 --- /dev/null +++ b/combining_data.html @@ -0,0 +1,15984 @@ + + + + + +combining_data + + + + + + + + + + + + + + + + + + + + + +
+
+ + +
+
+
+ + +
+ +
+
+ + +
+ +
+
+ + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+ + +
+ +
+ + + + + +
+ +
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+
+ + +
+
+
+ + +
+ +
+ + + + + +
+ +
+
+ + +
+ +
+ + + + + + + + + diff --git a/networks.ini b/networks.ini index 01bf385..4de991a 100644 --- a/networks.ini +++ b/networks.ini @@ -2,80 +2,80 @@ [business-faculty] folder = academic_hiring/business -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [cs-faculty] folder = academic_hiring/computer_science -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [history-faculty] folder = academic_hiring/history -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [caviar-proj] folder = caviar_proj -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [celegans-her] folder = celegans/hermaphrodite -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [celegans-male] folder = celegans/male -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [colombia-calls] folder = colombia_social/calls -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [colombia-mobility] folder = colombia_social/mobility -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [mobility-manizales] folder = mobility/manizales -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [mobility-medellin] folder = mobility/medellin -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [tennis-loss] folder = tennis_losses -weight-type = proximity -weight-attr = proximity +weight-type = distance +weight-attr = distance [yeast-grn] folder = yeast_grn -weight-type = proximity -weight-attr = weight +weight-type = distance +weight-attr = distance [bike-sharing] folder = bike-sharing weight-type = distance -weight-attr = avg-trip-duration +weight-attr = distance [giraffe] @@ -93,7 +93,7 @@ weight-attr = distance [phone-calls] folder = phone-calls weight-type = distance -weight-attr = avg-call-duration +weight-attr = distance [us-airports] @@ -108,13 +108,13 @@ weight-type = distance weight-attr = distance -[host-pathogen] -folder = host-pathogen +[us-weblinks] +folder = weblinks_us weight-type = distance weight-attr = distance -[water-pipes] -folder = water-pipes +[host-pathogen] +folder = host-pathogen weight-type = distance weight-attr = distance \ No newline at end of file diff --git a/networks/academic_hiring/business/distortion-stats.csv b/networks/academic_hiring/business/distortion-stats.csv index 9b104f2..2ca9168 100644 --- a/networks/academic_hiring/business/distortion-stats.csv +++ b/networks/academic_hiring/business/distortion-stats.csv @@ -1,7 +1,7 @@ ,business-faculty -avg-metric-distrotion,1.8417604162738177 -std-metric-distrotion,0.8701525542567358 -med-metric-distrotion,1.5559188690842038 -avg-ultrametric-distrotion,1.8421666977235764 -std-ultrametric-distrotion,0.49975154308446146 -med-ultrametric-distrotion,1.7505810736026564 +avg-metric-distrotion,2.4711172793382956 +std-metric-distrotion,1.580389775275598 +med-metric-distrotion,1.9847995251912423 +avg-ultrametric-distrotion,1.8372344580535185 +std-ultrametric-distrotion,0.5361094982557445 +med-ultrametric-distrotion,1.7977272727272724 diff --git a/networks/academic_hiring/business/network-stats.csv b/networks/academic_hiring/business/network-stats.csv index ae7445d..3643107 100644 --- a/networks/academic_hiring/business/network-stats.csv +++ b/networks/academic_hiring/business/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,113 n-edges,3432 density,0.27117572692793934 -n-edges-metric,1565 -n-edges-ultrametric,638 -%-edges-metric,0.456002331002331 -%-edges-ultrametric,0.1858974358974359 -%-redundancy-metric,0.543997668997669 -%-redundancy-ultrametric,0.8141025641025641 -%-edges-ultrametric/metric,0.40766773162939296 +LSCC-nodes,94 +LSCC-edges,2842 +tau-metric,0.3508158508158508 +tau-ultrametric,0.09761072261072261 +LSCC-tau-metric,0.36523574947220266 +LSCC-tau-ultrametric,0.09465165376495425 +ultrametric_metric_ratio,0.2782392026578073 +LSCC-ultrametric_metric_ratio,0.2591522157996146 diff --git a/networks/academic_hiring/business/undirected_networks-stats.csv b/networks/academic_hiring/business/undirected_networks-stats.csv new file mode 100644 index 0000000..9281c69 --- /dev/null +++ b/networks/academic_hiring/business/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,84,2558,488,0.3924941360437842,0.0965598123534011,0.6618852459016393,0.1721311475409836,0.6290983606557377,0.1762295081967213 diff --git a/networks/academic_hiring/computer_science/distortion-stats.csv b/networks/academic_hiring/computer_science/distortion-stats.csv index 4135c63..3aebe35 100644 --- a/networks/academic_hiring/computer_science/distortion-stats.csv +++ b/networks/academic_hiring/computer_science/distortion-stats.csv @@ -1,7 +1,7 @@ ,cs-faculty -avg-metric-distrotion,1.4313423583624842 -std-metric-distrotion,0.5212111045943651 -med-metric-distrotion,1.2773205382146027 -avg-ultrametric-distrotion,1.919797245410675 -std-ultrametric-distrotion,0.3434775101932094 -med-ultrametric-distrotion,2.0004011231448056 +avg-metric-distrotion,2.2202344040987034 +std-metric-distrotion,1.4373428666614874 +med-metric-distrotion,1.74375 +avg-ultrametric-distrotion,1.9527656123892012 +std-ultrametric-distrotion,0.6084173541593506 +med-ultrametric-distrotion,1.9529346622369879 diff --git a/networks/academic_hiring/computer_science/network-stats.csv b/networks/academic_hiring/computer_science/network-stats.csv index 22a7653..407ff18 100644 --- a/networks/academic_hiring/computer_science/network-stats.csv +++ b/networks/academic_hiring/computer_science/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,206 n-edges,2929 density,0.06935827610703292 -n-edges-metric,2149 -n-edges-ultrametric,1554 -%-edges-metric,0.7336975076818026 -%-edges-ultrametric,0.5305565039262546 -%-redundancy-metric,0.26630249231819736 -%-redundancy-ultrametric,0.46944349607374536 -%-edges-ultrametric/metric,0.7231270358306189 +LSCC-nodes,167 +LSCC-edges,2384 +tau-metric,0.5148514851485149 +tau-ultrametric,0.22669853192215772 +LSCC-tau-metric,0.5285234899328859 +LSCC-tau-ultrametric,0.22021812080536912 +ultrametric_metric_ratio,0.4403183023872679 +LSCC-ultrametric_metric_ratio,0.4166666666666667 diff --git a/networks/academic_hiring/computer_science/undirected_networks-stats.csv b/networks/academic_hiring/computer_science/undirected_networks-stats.csv new file mode 100644 index 0000000..91b74f9 --- /dev/null +++ b/networks/academic_hiring/computer_science/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,78,1180,179,0.5830508474576271,0.19322033898305085,0.8715083798882681,0.4301675977653631,0.8156424581005587,0.45251396648044695 +1,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +2,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +3,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 diff --git a/networks/academic_hiring/history/distortion-stats.csv b/networks/academic_hiring/history/distortion-stats.csv index 3b079be..945d967 100644 --- a/networks/academic_hiring/history/distortion-stats.csv +++ b/networks/academic_hiring/history/distortion-stats.csv @@ -1,7 +1,7 @@ ,history-faculty -avg-metric-distrotion,1.5559455725216669 -std-metric-distrotion,0.5811976176560245 -med-metric-distrotion,1.364675678928156 -avg-ultrametric-distrotion,1.701464140510005 -std-ultrametric-distrotion,0.36609771219019227 -med-ultrametric-distrotion,1.5003307607497243 +avg-metric-distrotion,2.47750378353155 +std-metric-distrotion,1.4141477302762964 +med-metric-distrotion,1.9434998587677366 +avg-ultrametric-distrotion,1.832526494252117 +std-ultrametric-distrotion,0.5194322232735079 +med-ultrametric-distrotion,1.7207792207792207 diff --git a/networks/academic_hiring/history/network-stats.csv b/networks/academic_hiring/history/network-stats.csv index 0e3ad35..eb46f57 100644 --- a/networks/academic_hiring/history/network-stats.csv +++ b/networks/academic_hiring/history/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,145 n-edges,2428 density,0.11628352490421456 -n-edges-metric,1473 -n-edges-ultrametric,1120 -%-edges-metric,0.60667215815486 -%-edges-ultrametric,0.4612850082372323 -%-redundancy-metric,0.39332784184514 -%-redundancy-ultrametric,0.5387149917627677 -%-edges-ultrametric/metric,0.7603530210454854 +LSCC-nodes,116 +LSCC-edges,1897 +tau-metric,0.414332784184514 +tau-ultrametric,0.21993410214168038 +LSCC-tau-metric,0.430152872957301 +LSCC-tau-ultrametric,0.2087506589351608 +ultrametric_metric_ratio,0.5308151093439363 +LSCC-ultrametric_metric_ratio,0.4852941176470589 diff --git a/networks/academic_hiring/history/undirected_networks-stats.csv b/networks/academic_hiring/history/undirected_networks-stats.csv new file mode 100644 index 0000000..cb0dd7b --- /dev/null +++ b/networks/academic_hiring/history/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,56,905,158,0.5348066298342542,0.2154696132596685,0.810126582278481,0.34810126582278483,0.7658227848101266,0.41139240506329117 diff --git a/networks/bike-sharing/distortion-stats.csv b/networks/bike-sharing/distortion-stats.csv index 9aa70a1..58936ae 100644 --- a/networks/bike-sharing/distortion-stats.csv +++ b/networks/bike-sharing/distortion-stats.csv @@ -3,5 +3,5 @@ avg-metric-distrotion,2.0641451556224766 std-metric-distrotion,5.746482376572031 med-metric-distrotion,1.2679001386170317 avg-ultrametric-distrotion,2.2656642639793887 -std-ultrametric-distrotion,0.8443258962297594 +std-ultrametric-distrotion,0.8443258962297593 med-ultrametric-distrotion,2.101589239008594 diff --git a/networks/bike-sharing/network-stats.csv b/networks/bike-sharing/network-stats.csv index 7beb8f8..855e272 100644 --- a/networks/bike-sharing/network-stats.csv +++ b/networks/bike-sharing/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,725 n-edges,53118 density,0.10119641836540294 -n-edges-metric,31622 -n-edges-ultrametric,1462 -%-edges-metric,0.5953160887081592 -%-edges-ultrametric,0.027523626642569375 -%-redundancy-metric,0.4046839112918408 -%-redundancy-ultrametric,0.9724763733574306 -%-edges-ultrametric/metric,0.04623363481120739 +LSCC-nodes,723 +LSCC-edges,53115 +tau-metric,0.5953160887081592 +tau-ultrametric,0.027523626642569375 +LSCC-tau-metric,0.5952932316671373 +LSCC-tau-ultrametric,0.027487527063917914 +ultrametric_metric_ratio,0.04623363481120739 +LSCC-ultrametric_metric_ratio,0.046174768335494484 diff --git a/networks/bike-sharing/undirected_networks-stats.csv b/networks/bike-sharing/undirected_networks-stats.csv new file mode 100644 index 0000000..1b3eba8 --- /dev/null +++ b/networks/bike-sharing/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,723,53115,18055,0.5952932316671373,0.027487527063917914,0.6767654389365827,0.03998892273608419,0.6353918582110218,0.04004430905566325 diff --git a/networks/caviar_proj/distortion-stats.csv b/networks/caviar_proj/distortion-stats.csv index 3326164..0572657 100644 --- a/networks/caviar_proj/distortion-stats.csv +++ b/networks/caviar_proj/distortion-stats.csv @@ -1,7 +1,7 @@ ,caviar-proj -avg-metric-distrotion,12.303903201374151 -std-metric-distrotion,24.08885358639796 -med-metric-distrotion,5.1201119171412195 -avg-ultrametric-distrotion,1.1769867110300105 -std-ultrametric-distrotion,0.09952798505297794 -med-ultrametric-distrotion,1.1463308727746417 +avg-metric-distrotion,9.15718196706913 +std-metric-distrotion,11.72213843956718 +med-metric-distrotion,4.067175572519084 +avg-ultrametric-distrotion,1.4989875047551156 +std-ultrametric-distrotion,0.43815551328962954 +med-ultrametric-distrotion,1.4417112299465242 diff --git a/networks/caviar_proj/network-stats.csv b/networks/caviar_proj/network-stats.csv index 7295c80..284545c 100644 --- a/networks/caviar_proj/network-stats.csv +++ b/networks/caviar_proj/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,110 n-edges,295 density,0.024603836530442035 -n-edges-metric,197 -n-edges-ultrametric,192 -%-edges-metric,0.6677966101694915 -%-edges-ultrametric,0.6508474576271186 -%-redundancy-metric,0.33220338983050846 -%-redundancy-ultrametric,0.3491525423728814 -%-edges-ultrametric/metric,0.9746192893401014 +LSCC-nodes,66 +LSCC-edges,242 +tau-metric,0.7050847457627119 +tau-ultrametric,0.6474576271186441 +LSCC-tau-metric,0.6611570247933884 +LSCC-tau-ultrametric,0.5991735537190083 +ultrametric_metric_ratio,0.9182692307692308 +LSCC-ultrametric_metric_ratio,0.90625 diff --git a/networks/caviar_proj/undirected_networks-stats.csv b/networks/caviar_proj/undirected_networks-stats.csv new file mode 100644 index 0000000..bdd22c9 --- /dev/null +++ b/networks/caviar_proj/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,63,232,90,0.6594827586206896,0.5948275862068966,0.7444444444444445,0.6888888888888889,0.7555555555555555,0.6888888888888889 diff --git a/networks/celegans/README.md b/networks/celegans/README.md index fc9433b..49dba63 100644 --- a/networks/celegans/README.md +++ b/networks/celegans/README.md @@ -6,7 +6,6 @@ Reference: Cook et al., "Whole-animal connectomes of both Caenorhabditis elegans Files used: - `SI 2 Synapse adjacency matrices.xlsx`: data - The C. elegans connectome has two different types of connections. The gap junctions, which are symmetric, and the pre-post synapitc cell interactions, which are assymetric. Here we consider the former, and also distinguish the hermaphrodite and the male sex. Edge weight is the number of synapses between cells relative to the total number of synapses. Both networks contains multiple weakly connected components with the largest one comparising approximately 69% (64%) of the network in the case of the hermaphrodite (male) sex. diff --git a/networks/celegans/hermaphrodite/distortion-stats.csv b/networks/celegans/hermaphrodite/distortion-stats.csv index 22c4491..43efb30 100644 --- a/networks/celegans/hermaphrodite/distortion-stats.csv +++ b/networks/celegans/hermaphrodite/distortion-stats.csv @@ -1,7 +1,7 @@ ,celegans-her -avg-metric-distrotion,1.95588063043959 -std-metric-distrotion,1.1414160337694403 -med-metric-distrotion,1.614539364744017 -avg-ultrametric-distrotion,1.9689462272175715 -std-ultrametric-distrotion,0.6678309885158372 -med-ultrametric-distrotion,1.7150153217568949 +avg-metric-distrotion,2.1778130554853674 +std-metric-distrotion,1.488375519695493 +med-metric-distrotion,1.7408695652173913 +avg-ultrametric-distrotion,1.8737551458224337 +std-ultrametric-distrotion,0.7352574076141358 +med-ultrametric-distrotion,1.6490740740740741 diff --git a/networks/celegans/hermaphrodite/network-stats.csv b/networks/celegans/hermaphrodite/network-stats.csv index 083b61d..299e8c2 100644 --- a/networks/celegans/hermaphrodite/network-stats.csv +++ b/networks/celegans/hermaphrodite/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,313 n-edges,3500 density,0.03584009175063488 -n-edges-metric,2036 -n-edges-ultrametric,1153 -%-edges-metric,0.5817142857142857 -%-edges-ultrametric,0.3294285714285714 -%-redundancy-metric,0.41828571428571426 -%-redundancy-ultrametric,0.6705714285714286 -%-edges-ultrametric/metric,0.5663064833005893 +LSCC-nodes,249 +LSCC-edges,3046 +tau-metric,0.5568571428571428 +tau-ultrametric,0.26771428571428574 +LSCC-tau-metric,0.5531845042678923 +LSCC-tau-ultrametric,0.25673013788575183 +ultrametric_metric_ratio,0.4807593637762956 +LSCC-ultrametric_metric_ratio,0.46409495548961427 diff --git a/networks/celegans/hermaphrodite/undirected_networks-stats.csv b/networks/celegans/hermaphrodite/undirected_networks-stats.csv new file mode 100644 index 0000000..84910e7 --- /dev/null +++ b/networks/celegans/hermaphrodite/undirected_networks-stats.csv @@ -0,0 +1,5 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,215,2748,558,0.5673216885007278,0.2536390101892285,0.8405017921146953,0.3835125448028674,0.8207885304659498,0.42473118279569894 +1,3,5,2,1.0,0.8,1.0,1.0,1.0,1.0 +2,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +3,4,8,3,0.875,0.875,1.0,1.0,1.0,1.0 diff --git a/networks/celegans/male/distortion-stats.csv b/networks/celegans/male/distortion-stats.csv index 768bcb9..39fac76 100644 --- a/networks/celegans/male/distortion-stats.csv +++ b/networks/celegans/male/distortion-stats.csv @@ -1,7 +1,7 @@ ,celegans-male -avg-metric-distrotion,2.174823586114673 -std-metric-distrotion,1.2577969506447333 -med-metric-distrotion,1.7830454326057597 -avg-ultrametric-distrotion,2.0103309980406845 -std-ultrametric-distrotion,0.7861492489681112 -med-ultrametric-distrotion,2.0001587301587302 +avg-metric-distrotion,2.679056669037608 +std-metric-distrotion,1.977359626463165 +med-metric-distrotion,2.0560125342734037 +avg-ultrametric-distrotion,1.836252580334619 +std-ultrametric-distrotion,0.692744013193066 +med-ultrametric-distrotion,1.652475845410628 diff --git a/networks/celegans/male/network-stats.csv b/networks/celegans/male/network-stats.csv index 2bf9daa..a266b58 100644 --- a/networks/celegans/male/network-stats.csv +++ b/networks/celegans/male/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,328 n-edges,3474 density,0.03238979637502797 -n-edges-metric,1908 -n-edges-ultrametric,1058 -%-edges-metric,0.5492227979274611 -%-edges-ultrametric,0.3045480713874496 -%-redundancy-metric,0.4507772020725389 -%-redundancy-ultrametric,0.6954519286125505 -%-edges-ultrametric/metric,0.5545073375262055 +LSCC-nodes,289 +LSCC-edges,3206 +tau-metric,0.5400115141047783 +tau-ultrametric,0.27691421991940124 +LSCC-tau-metric,0.5343106674984405 +LSCC-tau-ultrametric,0.26824703680598877 +ultrametric_metric_ratio,0.5127931769722814 +LSCC-ultrametric_metric_ratio,0.5020431990659661 diff --git a/networks/celegans/male/undirected_networks-stats.csv b/networks/celegans/male/undirected_networks-stats.csv new file mode 100644 index 0000000..9fef9a0 --- /dev/null +++ b/networks/celegans/male/undirected_networks-stats.csv @@ -0,0 +1,4 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,238,2852,634,0.5157784011220197,0.24579242636746143,0.7271293375394322,0.37381703470031546,0.6908517350157729,0.38958990536277605 +1,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +2,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 diff --git a/networks/colombia_social/calls/distortion-stats.csv b/networks/colombia_social/calls/distortion-stats.csv index 01742de..828f3ef 100644 --- a/networks/colombia_social/calls/distortion-stats.csv +++ b/networks/colombia_social/calls/distortion-stats.csv @@ -1,7 +1,7 @@ ,colombia-calls -avg-metric-distrotion,301.0222927319763 -std-metric-distrotion,530.7021003980509 -med-metric-distrotion,120.82286357924608 -avg-ultrametric-distrotion,1.2770780163452997 -std-ultrametric-distrotion,0.2497648607723491 -med-ultrametric-distrotion,1.205631261877681 +avg-metric-distrotion,57.47057510114324 +std-metric-distrotion,145.37774293019044 +med-metric-distrotion,18.612675345787377 +avg-ultrametric-distrotion,1.6447399544714127 +std-ultrametric-distrotion,0.6065223885636564 +med-ultrametric-distrotion,1.472898064394248 diff --git a/networks/colombia_social/calls/network-stats.csv b/networks/colombia_social/calls/network-stats.csv index a561974..d30453c 100644 --- a/networks/colombia_social/calls/network-stats.csv +++ b/networks/colombia_social/calls/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,863 n-edges,438484 density,0.5894346866405165 -n-edges-metric,2259 -n-edges-ultrametric,1746 -%-edges-metric,0.005151841344267978 -%-edges-ultrametric,0.003981901278039792 -%-redundancy-metric,0.9948481586557321 -%-redundancy-ultrametric,0.9960180987219602 -%-edges-ultrametric/metric,0.7729083665338646 +LSCC-nodes,863 +LSCC-edges,438484 +tau-metric,0.026014632232875087 +tau-ultrametric,0.008901122960016786 +LSCC-tau-metric,0.026014632232875087 +LSCC-tau-ultrametric,0.008901122960016786 +ultrametric_metric_ratio,0.34215832383624095 +LSCC-ultrametric_metric_ratio,0.34215832383624095 diff --git a/networks/colombia_social/calls/undirected_networks-stats.csv b/networks/colombia_social/calls/undirected_networks-stats.csv new file mode 100644 index 0000000..6f4e4a8 --- /dev/null +++ b/networks/colombia_social/calls/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,863,438484,199898,0.026014632232875087,0.008901122960016786,0.01511771003211638,0.004312199221603017,0.01570300853435252,0.004317201772904181 diff --git a/networks/colombia_social/mobility/distortion-stats.csv b/networks/colombia_social/mobility/distortion-stats.csv index 4c42db3..ba0972f 100644 --- a/networks/colombia_social/mobility/distortion-stats.csv +++ b/networks/colombia_social/mobility/distortion-stats.csv @@ -1,7 +1,7 @@ ,colombia-mobility -avg-metric-distrotion,1820.2025896150562 -std-metric-distrotion,2472.0253138745315 -med-metric-distrotion,885.8200616884867 -avg-ultrametric-distrotion,1.4622926742178406 -std-ultrametric-distrotion,0.43348096030316424 -med-ultrametric-distrotion,1.325643948313469 +avg-metric-distrotion,893.4523910433584 +std-metric-distrotion,2534.0900110208036 +med-metric-distrotion,272.9416451435882 +avg-ultrametric-distrotion,1.6838892414737063 +std-ultrametric-distrotion,0.8659094276832128 +med-ultrametric-distrotion,1.408221397357254 diff --git a/networks/colombia_social/mobility/network-stats.csv b/networks/colombia_social/mobility/network-stats.csv index ff0de70..1e78cad 100644 --- a/networks/colombia_social/mobility/network-stats.csv +++ b/networks/colombia_social/mobility/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,863 n-edges,173857 density,0.23370829110129507 -n-edges-metric,2535 -n-edges-ultrametric,1727 -%-edges-metric,0.01458094871072203 -%-edges-ultrametric,0.009933451054602346 -%-redundancy-metric,0.985419051289278 -%-redundancy-ultrametric,0.9900665489453977 -%-edges-ultrametric/metric,0.6812623274161737 +LSCC-nodes,863 +LSCC-edges,173857 +tau-metric,0.017088756851895523 +tau-ultrametric,0.012165170226105363 +LSCC-tau-metric,0.017088756851895523 +LSCC-tau-ultrametric,0.012165170226105363 +ultrametric_metric_ratio,0.7118815213732751 +LSCC-ultrametric_metric_ratio,0.7118815213732751 diff --git a/networks/colombia_social/mobility/undirected_networks-stats.csv b/networks/colombia_social/mobility/undirected_networks-stats.csv new file mode 100644 index 0000000..db0acb1 --- /dev/null +++ b/networks/colombia_social/mobility/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,863,173857,67150,0.017088756851895523,0.012165170226105363,0.018093819806403573,0.012836932241250931,0.018183172002978407,0.012836932241250931 diff --git a/networks/comorbidity/network-stats.csv b/networks/comorbidity/network-stats.csv index dedffba..c1dd436 100644 --- a/networks/comorbidity/network-stats.csv +++ b/networks/comorbidity/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,95 n-edges,8930 density,1.0 -n-edges-metric,4236 -n-edges-ultrametric,194 -%-edges-metric,0.4743561030235162 -%-edges-ultrametric,0.021724524076147816 -%-redundancy-metric,0.5256438969764838 -%-redundancy-ultrametric,0.9782754759238522 -%-edges-ultrametric/metric,0.04579792256846081 +LSCC-nodes,95 +LSCC-edges,8930 +tau-metric,0.4743561030235162 +tau-ultrametric,0.021724524076147816 +LSCC-tau-metric,0.4743561030235162 +LSCC-tau-ultrametric,0.021724524076147816 +ultrametric_metric_ratio,0.04579792256846081 +LSCC-ultrametric_metric_ratio,0.04579792256846081 diff --git a/networks/comorbidity/undirected_networks-stats.csv b/networks/comorbidity/undirected_networks-stats.csv new file mode 100644 index 0000000..30b21fa --- /dev/null +++ b/networks/comorbidity/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,95,8930,4465,0.4743561030235162,0.021724524076147816,0.5068309070548712,0.021052631578947368,0.5117581187010078,0.021052631578947368 diff --git a/networks/giraffe/distortion-stats.csv b/networks/giraffe/distortion-stats.csv index 93298cf..c8c3ffa 100644 --- a/networks/giraffe/distortion-stats.csv +++ b/networks/giraffe/distortion-stats.csv @@ -1,7 +1,7 @@ ,giraffe -avg-metric-distrotion,1.465337597719577 -std-metric-distrotion,0.4390612512920237 -med-metric-distrotion,1.367236742904062 -avg-ultrametric-distrotion,1.3714221225553633 -std-ultrametric-distrotion,0.24759731942029223 -med-ultrametric-distrotion,1.3013617145913456 +avg-metric-distrotion,1.2960057452108402 +std-metric-distrotion,0.37148902016580027 +med-metric-distrotion,1.1218918698130869 +avg-ultrametric-distrotion,1.4646474300944707 +std-ultrametric-distrotion,0.3341136697792818 +med-ultrametric-distrotion,1.4018752160387138 diff --git a/networks/giraffe/network-stats.csv b/networks/giraffe/network-stats.csv index ab960ef..c0e8a3a 100644 --- a/networks/giraffe/network-stats.csv +++ b/networks/giraffe/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,6 n-edges,30 density,1.0 -n-edges-metric,23 -n-edges-ultrametric,9 -%-edges-metric,0.7666666666666667 -%-edges-ultrametric,0.3 -%-redundancy-metric,0.23333333333333328 -%-redundancy-ultrametric,0.7 -%-edges-ultrametric/metric,0.3913043478260869 +LSCC-nodes,6 +LSCC-edges,30 +tau-metric,0.7666666666666667 +tau-ultrametric,0.3333333333333333 +LSCC-tau-metric,0.7666666666666667 +LSCC-tau-ultrametric,0.3333333333333333 +ultrametric_metric_ratio,0.4347826086956521 +LSCC-ultrametric_metric_ratio,0.4347826086956521 diff --git a/networks/giraffe/undirected_networks-stats.csv b/networks/giraffe/undirected_networks-stats.csv new file mode 100644 index 0000000..995bb78 --- /dev/null +++ b/networks/giraffe/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,6,30,15,0.7666666666666667,0.3333333333333333,0.8666666666666667,0.3333333333333333,0.8,0.3333333333333333 diff --git a/networks/host-pathogen/components-stats.csv b/networks/host-pathogen/components-stats.csv new file mode 100644 index 0000000..2480824 --- /dev/null +++ b/networks/host-pathogen/components-stats.csv @@ -0,0 +1,7 @@ +,host-pathogen +n-nodes,10578 +n-edges,18529 +n-edges-metric,18503 +n-nodes-lscc,1 +n-edges-lscc,0 +n-edges-metric-lscc,0 diff --git a/networks/host-pathogen/distortion-stats.csv b/networks/host-pathogen/distortion-stats.csv index 596638c..7843f84 100644 --- a/networks/host-pathogen/distortion-stats.csv +++ b/networks/host-pathogen/distortion-stats.csv @@ -1,7 +1,7 @@ ,host-pathogen -avg-metric-distrotion,15.746708631086898 -std-metric-distrotion,52.66714613659394 -med-metric-distrotion,3.754556157267433 -avg-ultrametric-distrotion,1.1836126570978225 -std-ultrametric-distrotion,0.21355185024850043 -med-ultrametric-distrotion,1.1836126570978225 +avg-metric-distrotion,7.006620804856615 +std-metric-distrotion,17.476809458728397 +med-metric-distrotion,2.044827586206897 +avg-ultrametric-distrotion,1.5556756756756756 +std-ultrametric-distrotion,0.2216555309882 +med-ultrametric-distrotion,1.6733333333333333 diff --git a/networks/host-pathogen/network-stats.csv b/networks/host-pathogen/network-stats.csv index a0bc58d..42be838 100644 --- a/networks/host-pathogen/network-stats.csv +++ b/networks/host-pathogen/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,10578 n-edges,18529 density,0.00016560975484625947 -n-edges-metric,18431 -n-edges-ultrametric,18429 -%-edges-metric,0.994710993577635 -%-edges-ultrametric,0.9946030546710561 -%-redundancy-metric,0.005289006422364961 -%-redundancy-ultrametric,0.0053969453289438585 -%-edges-ultrametric/metric,0.9998914871683576 +LSCC-nodes,1 +LSCC-edges,0 +tau-metric,0.9985967942144746 +tau-ultrametric,0.9984348858546063 +LSCC-tau-metric,0 +LSCC-tau-ultrametric,0 +ultrametric_metric_ratio,0.9998378641301411 +LSCC-ultrametric_metric_ratio,0 diff --git a/networks/host-pathogen/undirected_networks-stats.csv b/networks/host-pathogen/undirected_networks-stats.csv new file mode 100644 index 0000000..7b8af53 --- /dev/null +++ b/networks/host-pathogen/undirected_networks-stats.csv @@ -0,0 +1 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric diff --git a/networks/mobility/manizales/distortion-stats.csv b/networks/mobility/manizales/distortion-stats.csv index 842963f..31ec7ef 100644 --- a/networks/mobility/manizales/distortion-stats.csv +++ b/networks/mobility/manizales/distortion-stats.csv @@ -1,7 +1,7 @@ ,mobility-manizales -avg-metric-distrotion,7.382533330580546 -std-metric-distrotion,6.4066607030629985 -med-metric-distrotion,5.044764455351957 -avg-ultrametric-distrotion,1.5196327721286316 -std-ultrametric-distrotion,0.39041882955255497 -med-ultrametric-distrotion,1.4449410090766284 +avg-metric-distrotion,3.10404732532493 +std-metric-distrotion,2.431873629408389 +med-metric-distrotion,2.285196874838309 +avg-ultrametric-distrotion,1.711458126647016 +std-ultrametric-distrotion,0.44409418888326574 +med-ultrametric-distrotion,1.6395005675368899 diff --git a/networks/mobility/manizales/network-stats.csv b/networks/mobility/manizales/network-stats.csv index 0fb288e..c8a56f8 100644 --- a/networks/mobility/manizales/network-stats.csv +++ b/networks/mobility/manizales/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,57 n-edges,2518 density,0.7888471177944862 -n-edges-metric,213 -n-edges-ultrametric,118 -%-edges-metric,0.0845909451945989 -%-edges-ultrametric,0.04686258935663225 -%-redundancy-metric,0.9154090548054011 -%-redundancy-ultrametric,0.9531374106433678 -%-edges-ultrametric/metric,0.5539906103286385 +LSCC-nodes,57 +LSCC-edges,2518 +tau-metric,0.2664813343923749 +tau-ultrametric,0.07664813343923749 +LSCC-tau-metric,0.2664813343923749 +LSCC-tau-ultrametric,0.07664813343923749 +ultrametric_metric_ratio,0.2876304023845007 +LSCC-ultrametric_metric_ratio,0.2876304023845007 diff --git a/networks/mobility/manizales/undirected_networks-stats.csv b/networks/mobility/manizales/undirected_networks-stats.csv new file mode 100644 index 0000000..307062d --- /dev/null +++ b/networks/mobility/manizales/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,57,2518,1237,0.2664813343923749,0.07664813343923749,0.2497978981406629,0.04527081649151172,0.2651576394502829,0.04527081649151172 diff --git a/networks/mobility/medellin/distortion-stats.csv b/networks/mobility/medellin/distortion-stats.csv index 3d0605e..46b43ad 100644 --- a/networks/mobility/medellin/distortion-stats.csv +++ b/networks/mobility/medellin/distortion-stats.csv @@ -1,7 +1,7 @@ ,mobility-medellin -avg-metric-distrotion,3.7732374159991826 -std-metric-distrotion,2.58633322574124 -med-metric-distrotion,3.1537910562769813 -avg-ultrametric-distrotion,1.7624647721526723 -std-ultrametric-distrotion,0.5033429769462727 -med-ultrametric-distrotion,1.666692580988735 +avg-metric-distrotion,3.1622965882933673 +std-metric-distrotion,2.9929298281800114 +med-metric-distrotion,2.3756772882352553 +avg-ultrametric-distrotion,2.193308219577776 +std-ultrametric-distrotion,0.8543245553926707 +med-ultrametric-distrotion,2.0317460317460316 diff --git a/networks/mobility/medellin/network-stats.csv b/networks/mobility/medellin/network-stats.csv index e6f2a33..872a869 100644 --- a/networks/mobility/medellin/network-stats.csv +++ b/networks/mobility/medellin/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,413 n-edges,33884 density,0.1991349114929829 -n-edges-metric,3362 -n-edges-ultrametric,1048 -%-edges-metric,0.09922087120764962 -%-edges-ultrametric,0.030929052059969306 -%-redundancy-metric,0.9007791287923503 -%-redundancy-ultrametric,0.9690709479400307 -%-edges-ultrametric/metric,0.31171921475312314 +LSCC-nodes,413 +LSCC-edges,33884 +tau-metric,0.24672411757761775 +tau-ultrametric,0.05442096564750325 +LSCC-tau-metric,0.24672411757761775 +LSCC-tau-ultrametric,0.05442096564750325 +ultrametric_metric_ratio,0.22057416267942584 +LSCC-ultrametric_metric_ratio,0.22057416267942584 diff --git a/networks/mobility/medellin/undirected_networks-stats.csv b/networks/mobility/medellin/undirected_networks-stats.csv new file mode 100644 index 0000000..1989b0c --- /dev/null +++ b/networks/mobility/medellin/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,413,33884,15503,0.24672411757761775,0.05442096564750325,0.20537960394762303,0.026640005160291556,0.1897697219892924,0.02715603431593885 diff --git a/networks/phone-calls/README.md b/networks/phone-calls/README.md index 298044c..a9e917a 100644 --- a/networks/phone-calls/README.md +++ b/networks/phone-calls/README.md @@ -5,4 +5,5 @@ Source: 0) and calculate the average call duration between users, from the caller to the callee. +This network measures the duration (in seconds) of phone calls collected during the Copenhagen Networks Study. +We consider only answered calls (duration >0) and calculate the average call duration between users, from the caller to the callee. diff --git a/networks/phone-calls/network-stats.csv b/networks/phone-calls/network-stats.csv index 087dcf6..18a1848 100644 --- a/networks/phone-calls/network-stats.csv +++ b/networks/phone-calls/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,322 n-edges,609 density,0.0058919138561560344 -n-edges-metric,558 -n-edges-ultrametric,517 -%-edges-metric,0.916256157635468 -%-edges-ultrametric,0.8489326765188834 -%-redundancy-metric,0.08374384236453203 -%-redundancy-ultrametric,0.15106732348111662 -%-edges-ultrametric/metric,0.9265232974910393 +LSCC-nodes,114 +LSCC-edges,274 +tau-metric,0.916256157635468 +tau-ultrametric,0.8489326765188834 +LSCC-tau-metric,0.8832116788321168 +LSCC-tau-ultrametric,0.7737226277372263 +ultrametric_metric_ratio,0.9265232974910393 +LSCC-ultrametric_metric_ratio,0.8760330578512397 diff --git a/networks/phone-calls/undirected_networks-stats.csv b/networks/phone-calls/undirected_networks-stats.csv new file mode 100644 index 0000000..207d0fc --- /dev/null +++ b/networks/phone-calls/undirected_networks-stats.csv @@ -0,0 +1,9 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,5,8,4,1.0,1.0,1.0,1.0,1.0,1.0 +1,30,75,33,0.84,0.7466666666666667,0.9393939393939394,0.8787878787878788,0.9393939393939394,0.8787878787878788 +2,9,19,9,1.0,0.8421052631578947,1.0,0.8888888888888888,1.0,0.8888888888888888 +3,24,64,26,0.8125,0.75,0.9615384615384616,0.8846153846153846,0.9230769230769231,0.8846153846153846 +4,6,12,6,0.8333333333333334,0.75,0.8333333333333334,0.8333333333333334,0.8333333333333334,0.8333333333333334 +5,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +6,8,16,7,0.9375,0.875,1.0,1.0,1.0,1.0 +7,7,14,6,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 diff --git a/networks/tennis_losses/distortion-stats.csv b/networks/tennis_losses/distortion-stats.csv index c3063be..8fe8eb3 100644 --- a/networks/tennis_losses/distortion-stats.csv +++ b/networks/tennis_losses/distortion-stats.csv @@ -1,7 +1,7 @@ ,tennis-loss -avg-metric-distrotion,1.603511869278301 -std-metric-distrotion,0.578379999534823 -med-metric-distrotion,1.440031508667256 -avg-ultrametric-distrotion,1.9112777254084488 -std-ultrametric-distrotion,0.41291702874323766 -med-ultrametric-distrotion,2.0000131811351594 +avg-metric-distrotion,1.657660299187473 +std-metric-distrotion,0.6365112324316072 +med-metric-distrotion,1.4749599996284433 +avg-ultrametric-distrotion,1.9961172719622648 +std-ultrametric-distrotion,0.7705697671646052 +med-ultrametric-distrotion,1.8181818181818181 diff --git a/networks/tennis_losses/network-stats.csv b/networks/tennis_losses/network-stats.csv index 90ffe84..963c2db 100644 --- a/networks/tennis_losses/network-stats.csv +++ b/networks/tennis_losses/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,4245 n-edges,101436 density,0.005630397351655049 -n-edges-metric,44772 -n-edges-ultrametric,21033 -%-edges-metric,0.44138175795575535 -%-edges-ultrametric,0.2073524192594345 -%-redundancy-metric,0.5586182420442447 -%-redundancy-ultrametric,0.7926475807405655 -%-edges-ultrametric/metric,0.4697802197802198 +LSCC-nodes,2428 +LSCC-edges,98102 +tau-metric,0.5961985882724082 +tau-ultrametric,0.23776568476674947 +LSCC-tau-metric,0.5824753827648774 +LSCC-tau-ultrametric,0.21186112413610325 +ultrametric_metric_ratio,0.39880283087505786 +LSCC-ultrametric_metric_ratio,0.3637254558818382 diff --git a/networks/tennis_losses/undirected_networks-stats.csv b/networks/tennis_losses/undirected_networks-stats.csv new file mode 100644 index 0000000..c735a70 --- /dev/null +++ b/networks/tennis_losses/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,1263,85842,16349,0.5327345588406608,0.1286549707602339,0.6114135421126674,0.07755826044406386,0.5376475625420515,0.0910759067832895 diff --git a/networks/us-airports-2006/distortion-stats.csv b/networks/us-airports-2006/distortion-stats.csv index eef3e69..36069ca 100644 --- a/networks/us-airports-2006/distortion-stats.csv +++ b/networks/us-airports-2006/distortion-stats.csv @@ -1,7 +1,7 @@ ,us-airports -avg-metric-distrotion,279.62369536587715 -std-metric-distrotion,2089.5648450053404 -med-metric-distrotion,17.74398880165022 -avg-ultrametric-distrotion,1.5860719422697427 -std-ultrametric-distrotion,0.48867596020871645 -med-ultrametric-distrotion,1.4736143472021324 +avg-metric-distrotion,325.7879369492816 +std-metric-distrotion,2785.479453072874 +med-metric-distrotion,24.801390651294934 +avg-ultrametric-distrotion,1.5869752815140707 +std-ultrametric-distrotion,0.5025409384862389 +med-ultrametric-distrotion,1.4674968591560829 diff --git a/networks/us-airports-2006/network-stats.csv b/networks/us-airports-2006/network-stats.csv index a40c518..ef83c30 100644 --- a/networks/us-airports-2006/network-stats.csv +++ b/networks/us-airports-2006/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,1075 n-edges,18906 density,0.01637521112121606 -n-edges-metric,5217 -n-edges-ultrametric,3592 -%-edges-metric,0.2759441447159632 -%-edges-ultrametric,0.1899925949434042 -%-redundancy-metric,0.7240558552840368 -%-redundancy-ultrametric,0.8100074050565957 -%-edges-ultrametric/metric,0.6885183055395822 +LSCC-nodes,995 +LSCC-edges,18820 +tau-metric,0.27430445361260974 +tau-ultrametric,0.18983391515920872 +LSCC-tau-metric,0.27109458023379385 +LSCC-tau-ultrametric,0.18629117959617428 +ultrametric_metric_ratio,0.692055534130351 +LSCC-ultrametric_metric_ratio,0.6871814974519795 diff --git a/networks/us-airports-2006/undirected_networks-stats.csv b/networks/us-airports-2006/undirected_networks-stats.csv new file mode 100644 index 0000000..d5ef0ee --- /dev/null +++ b/networks/us-airports-2006/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,926,18593,6930,0.2654224708223525,0.17979884902920454,0.24314574314574314,0.13347763347763347,0.22683982683982684,0.13362193362193361 diff --git a/networks/water-pipes/README.md b/networks/water-pipes/README.md deleted file mode 100644 index 0e45e5f..0000000 --- a/networks/water-pipes/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Water Pipes Network - -Source: Farmani, R., Savic, D.A., Walters, G.A.: Exnet benchmark problem for multi-objective optimization of large water systems. Modelling and control for participatory planning and managing water systems (2004) - -Files used: -- `exnet_pipes.txt`: data -- `exnet_junct.txt`: metadata - -A graph with nodes being pipe junctions and edge weights are the pipe length $d_{ij}$ connecting the junctions. diff --git a/networks/water-pipes/distortion-stats.csv b/networks/water-pipes/distortion-stats.csv deleted file mode 100644 index 323a151..0000000 --- a/networks/water-pipes/distortion-stats.csv +++ /dev/null @@ -1,7 +0,0 @@ -,water-pipes -avg-metric-distrotion,1.1686634712062107 -std-metric-distrotion,0.19395754201687038 -med-metric-distrotion,1.075268817204301 -avg-ultrametric-distrotion,1.4523543941158101 -std-ultrametric-distrotion,0.45166392882915574 -med-ultrametric-distrotion,1.3461538461538463 diff --git a/networks/water-pipes/network-stats.csv b/networks/water-pipes/network-stats.csv deleted file mode 100644 index 8854ec2..0000000 --- a/networks/water-pipes/network-stats.csv +++ /dev/null @@ -1,11 +0,0 @@ -,water-pipes -n-nodes,1836 -n-edges,2351 -density,0.0006978207571251328 -n-edges-metric,2342 -n-edges-ultrametric,2253 -%-edges-metric,0.9961718417694598 -%-edges-ultrametric,0.9583156103785623 -%-redundancy-metric,0.0038281582305401685 -%-redundancy-ultrametric,0.04168438962143772 -%-edges-ultrametric/metric,0.96199829205807 diff --git a/networks/weblinks_us/network-stats.csv b/networks/weblinks_us/network-stats.csv new file mode 100644 index 0000000..30e91f1 --- /dev/null +++ b/networks/weblinks_us/network-stats.csv @@ -0,0 +1,12 @@ +,us-weblinks +n-nodes,42800 +n-edges,505476 +density,0.0002759453939551824 +LSCC-nodes,27725 +LSCC-edges,372626 +tau-metric,0.36780974764380503 +tau-ultrametric,0.2536678299266434 +LSCC-tau-metric,0.3800352095666969 +LSCC-tau-ultrametric,0.2562837805198778 +ultrametric_metric_ratio,0.6896713084730447 +LSCC-ultrametric_metric_ratio,0.6743685165700404 diff --git a/networks/weblinks_us/undirected_networks-stats.csv b/networks/weblinks_us/undirected_networks-stats.csv new file mode 100644 index 0000000..d3dfa00 --- /dev/null +++ b/networks/weblinks_us/undirected_networks-stats.csv @@ -0,0 +1,216 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,18112,288838,49855,0.34651604013322346,0.22337434825057645,0.5658008223849162,0.37185838932905424,0.5850165479891686,0.43654598335172 +1,273,1720,374,0.55,0.48604651162790696,0.7834224598930482,0.7272727272727273,0.8048128342245989,0.732620320855615 +2,31,107,44,0.6074766355140186,0.5981308411214953,0.6818181818181818,0.6818181818181818,0.7045454545454546,0.6818181818181818 +3,21,385,175,0.9974025974025974,0.8701298701298701,1.0,0.5257142857142857,1.0,0.8685714285714285 +4,6,14,5,1.0,1.0,1.0,1.0,1.0,1.0 +5,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +6,262,3343,551,0.38857313790008974,0.32814836972778944,0.515426497277677,0.47368421052631576,0.5172413793103449,0.4900181488203267 +7,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +8,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +9,88,956,226,0.30857740585774057,0.25627615062761505,0.47345132743362833,0.38495575221238937,0.4690265486725664,0.38495575221238937 +10,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +11,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +12,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +13,278,3860,837,0.2821243523316062,0.21528497409326425,0.36917562724014336,0.3309438470728793,0.37037037037037035,0.3333333333333333 +14,18,70,34,0.4857142857142857,0.4857142857142857,0.5,0.5,0.5,0.5 +15,9,70,34,1.0,1.0,1.0,0.2647058823529412,1.0,1.0 +16,30,191,44,0.5968586387434555,0.450261780104712,0.8863636363636364,0.6590909090909091,0.8636363636363636,0.75 +17,12,125,59,0.192,0.184,0.1864406779661017,0.1864406779661017,0.288135593220339,0.1864406779661017 +18,9,44,14,0.8636363636363636,0.8409090909090909,0.8571428571428571,0.7142857142857143,0.8571428571428571,0.7857142857142857 +19,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +20,8,14,7,1.0,1.0,1.0,1.0,1.0,1.0 +21,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +22,19,325,154,0.9907692307692307,0.30153846153846153,1.0,0.11688311688311688,0.9935064935064936,0.17532467532467533 +23,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +24,3,5,2,1.0,0.8,1.0,1.0,1.0,1.0 +25,6,26,11,0.38461538461538464,0.38461538461538464,0.45454545454545453,0.45454545454545453,0.45454545454545453,0.45454545454545453 +26,4,9,3,0.7777777777777778,0.7777777777777778,1.0,1.0,1.0,1.0 +27,4,8,3,0.75,0.75,1.0,1.0,1.0,1.0 +28,10,75,30,0.9866666666666667,0.4266666666666667,0.9666666666666667,0.3,1.0,0.3 +29,8,14,7,1.0,1.0,1.0,1.0,1.0,1.0 +30,4,8,4,0.75,0.75,0.75,0.75,0.75,0.75 +31,4,7,3,1.0,1.0,1.0,1.0,1.0,1.0 +32,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +33,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +34,3,5,2,0.6,0.6,1.0,1.0,1.0,1.0 +35,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +36,3,6,3,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +37,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +38,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +39,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +40,3,6,3,1.0,1.0,1.0,0.6666666666666666,1.0,1.0 +41,4,8,4,0.875,0.875,0.75,0.75,0.75,0.75 +42,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +43,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +44,4,7,3,1.0,1.0,1.0,1.0,1.0,1.0 +45,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +46,4,12,6,1.0,1.0,1.0,0.8333333333333334,1.0,1.0 +47,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +48,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +49,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +50,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +51,14,54,21,0.7777777777777778,0.5370370370370371,0.9523809523809523,0.6190476190476191,0.9523809523809523,0.6666666666666666 +52,4,9,4,0.7777777777777778,0.7777777777777778,0.75,0.75,0.75,0.75 +53,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +54,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +55,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +56,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +57,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +58,12,27,11,0.8518518518518519,0.8518518518518519,1.0,1.0,1.0,1.0 +59,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +60,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +61,6,11,5,0.9090909090909091,0.9090909090909091,1.0,1.0,1.0,1.0 +62,5,9,4,0.8888888888888888,0.8888888888888888,1.0,1.0,1.0,1.0 +63,12,22,11,1.0,1.0,1.0,1.0,1.0,1.0 +64,4,7,3,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +65,3,6,3,1.0,1.0,1.0,0.6666666666666666,1.0,1.0 +66,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +67,4,8,3,1.0,1.0,1.0,1.0,1.0,1.0 +68,4,11,5,0.5454545454545454,0.5454545454545454,0.6,0.6,0.6,0.6 +69,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +70,30,715,290,0.558041958041958,0.24895104895104894,0.4206896551724138,0.1,0.7793103448275862,0.16896551724137931 +71,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +72,7,15,6,1.0,1.0,1.0,1.0,1.0,1.0 +73,7,12,6,1.0,1.0,1.0,1.0,1.0,1.0 +74,4,10,4,0.6,0.6,0.75,0.75,0.75,0.75 +75,8,56,28,0.25,0.25,0.25,0.25,0.35714285714285715,0.25 +76,5,14,4,0.7142857142857143,0.6428571428571429,1.0,1.0,1.0,1.0 +77,7,31,10,0.8709677419354839,0.45161290322580644,1.0,0.6,1.0,0.6 +78,4,10,4,1.0,1.0,1.0,0.75,1.0,1.0 +79,4,10,4,0.9,0.9,1.0,0.75,1.0,0.75 +80,6,11,5,1.0,1.0,1.0,1.0,1.0,1.0 +81,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +82,4,7,3,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +83,6,11,5,0.9090909090909091,0.9090909090909091,1.0,1.0,1.0,1.0 +84,4,12,6,0.5,0.5,0.5,0.5,0.5,0.5 +85,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +86,3,6,3,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,1.0,1.0 +87,10,70,32,0.4,0.32857142857142857,0.59375,0.28125,0.59375,0.375 +88,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +89,13,156,78,1.0,0.22435897435897437,1.0,0.15384615384615385,1.0,0.15384615384615385 +90,6,30,15,0.6333333333333333,0.4,0.7333333333333333,0.3333333333333333,1.0,0.3333333333333333 +91,3,6,3,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +92,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +93,4,7,3,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +94,4,7,3,1.0,1.0,1.0,1.0,1.0,1.0 +95,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +96,4,9,3,0.7777777777777778,0.6666666666666666,1.0,1.0,1.0,1.0 +97,3,6,3,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +98,3,5,2,1.0,0.8,1.0,1.0,1.0,1.0 +99,5,20,10,0.4,0.4,0.4,0.4,0.4,0.4 +100,4,8,3,0.75,0.75,1.0,1.0,1.0,1.0 +101,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +102,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +103,8,14,7,1.0,1.0,1.0,1.0,1.0,1.0 +104,5,12,6,0.75,0.75,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +105,6,14,5,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +106,5,8,4,1.0,1.0,1.0,1.0,1.0,1.0 +107,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +108,5,10,4,0.9,0.9,1.0,1.0,1.0,1.0 +109,13,146,68,0.17123287671232876,0.1643835616438356,0.19117647058823528,0.17647058823529413,0.19117647058823528,0.17647058823529413 +110,5,9,4,0.8888888888888888,0.8888888888888888,1.0,1.0,1.0,1.0 +111,4,12,6,1.0,1.0,1.0,0.5,1.0,1.0 +112,6,30,15,1.0,0.8666666666666667,1.0,0.3333333333333333,1.0,0.7333333333333333 +113,5,8,4,1.0,1.0,1.0,1.0,1.0,1.0 +114,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +115,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +116,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +117,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +118,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +119,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +120,5,20,10,0.45,0.4,0.5,0.4,0.5,0.4 +121,4,8,3,0.75,0.75,1.0,1.0,1.0,1.0 +122,6,30,15,1.0,0.5333333333333333,1.0,0.3333333333333333,1.0,0.4666666666666667 +123,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +124,17,44,22,1.0,0.9545454545454546,1.0,0.9090909090909091,1.0,0.9090909090909091 +125,4,7,3,1.0,1.0,1.0,1.0,1.0,1.0 +126,6,14,5,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +127,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +128,4,7,3,1.0,1.0,1.0,1.0,1.0,1.0 +129,12,24,11,1.0,1.0,1.0,1.0,1.0,1.0 +130,5,10,4,0.9,0.9,1.0,1.0,1.0,1.0 +131,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +132,3,6,3,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +133,10,25,9,1.0,0.88,1.0,1.0,1.0,1.0 +134,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +135,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +136,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +137,3,6,3,0.8333333333333334,0.8333333333333334,1.0,0.6666666666666666,0.6666666666666666,0.6666666666666666 +138,4,12,6,0.5,0.5,0.5,0.5,0.5,0.5 +139,10,74,30,1.0,1.0,1.0,0.3,1.0,1.0 +140,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +141,3,6,3,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +142,4,7,3,1.0,1.0,1.0,1.0,1.0,1.0 +143,7,15,6,0.8,0.8,1.0,1.0,1.0,1.0 +144,8,56,28,1.0,1.0,1.0,0.6428571428571429,1.0,1.0 +145,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +146,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +147,3,5,2,1.0,0.8,1.0,1.0,1.0,1.0 +148,6,20,7,0.55,0.55,0.7142857142857143,0.7142857142857143,0.7142857142857143,0.7142857142857143 +149,8,16,7,1.0,0.875,1.0,1.0,1.0,1.0 +150,8,20,8,0.95,0.95,0.875,0.875,0.875,0.875 +151,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +152,8,16,7,0.9375,0.9375,1.0,1.0,1.0,1.0 +153,4,7,3,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +154,7,42,21,1.0,0.7619047619047619,1.0,0.5714285714285714,1.0,0.5714285714285714 +155,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +156,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +157,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +158,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +159,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +160,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +161,8,27,8,0.9629629629629629,0.9259259259259259,1.0,0.875,1.0,0.875 +162,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +163,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +164,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +165,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +166,3,6,3,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +167,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +168,9,72,36,1.0,0.2222222222222222,1.0,0.2222222222222222,1.0,0.2222222222222222 +169,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +170,8,56,28,1.0,0.4642857142857143,1.0,0.4642857142857143,1.0,0.4642857142857143 +171,3,6,3,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +172,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +173,4,8,3,0.75,0.75,1.0,1.0,1.0,1.0 +174,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +175,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +176,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +177,3,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +178,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +179,3,5,2,1.0,0.8,1.0,1.0,1.0,1.0 +180,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +181,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +182,4,7,3,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +183,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +184,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +185,4,11,5,0.9090909090909091,0.7272727272727273,0.8,0.6,0.8,0.6 +186,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +187,4,7,3,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 +188,7,12,6,1.0,1.0,1.0,1.0,1.0,1.0 +189,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +190,5,11,5,0.7272727272727273,0.7272727272727273,0.8,0.8,0.8,0.8 +191,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +192,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +193,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +194,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +195,6,13,5,0.9230769230769231,0.7692307692307693,1.0,1.0,1.0,1.0 +196,3,6,3,1.0,1.0,1.0,0.6666666666666666,1.0,1.0 +197,3,5,2,1.0,1.0,1.0,1.0,1.0,1.0 +198,4,6,3,1.0,1.0,1.0,1.0,1.0,1.0 +199,5,12,5,0.6666666666666666,0.6666666666666666,0.8,0.8,0.8,0.8 +200,6,30,15,0.8666666666666667,0.6,1.0,0.3333333333333333,1.0,0.5333333333333333 +201,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +202,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +203,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +204,4,10,4,1.0,1.0,1.0,0.75,1.0,1.0 +205,3,6,3,1.0,0.6666666666666666,1.0,0.6666666666666666,1.0,0.6666666666666666 +206,5,17,7,0.5882352941176471,0.5294117647058824,0.8571428571428571,0.5714285714285714,1.0,0.5714285714285714 +207,11,20,10,1.0,1.0,1.0,1.0,1.0,1.0 +208,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +209,3,6,3,0.8333333333333334,0.8333333333333334,0.6666666666666666,0.6666666666666666,0.6666666666666666,0.6666666666666666 +210,3,4,2,1.0,1.0,1.0,1.0,1.0,1.0 +211,4,8,4,0.75,0.75,0.75,0.75,0.75,0.75 +212,3,5,2,0.8,0.8,1.0,1.0,1.0,1.0 +213,5,13,5,0.9230769230769231,0.9230769230769231,1.0,0.8,1.0,1.0 +214,4,7,3,0.8571428571428571,0.8571428571428571,1.0,1.0,1.0,1.0 diff --git a/networks/yeast_grn/network-stats.csv b/networks/yeast_grn/network-stats.csv index 286d7c1..3fba1c4 100644 --- a/networks/yeast_grn/network-stats.csv +++ b/networks/yeast_grn/network-stats.csv @@ -2,10 +2,11 @@ n-nodes,6216 n-edges,1666106 density,0.04312712321561879 -n-edges-metric,106160 -n-edges-ultrametric,22963 -%-edges-metric,0.06371743454498092 -%-edges-ultrametric,0.013782436411608865 -%-redundancy-metric,0.9362825654550191 -%-redundancy-ultrametric,0.9862175635883912 -%-edges-ultrametric/metric,0.21630557648831955 +LSCC-nodes,1229 +LSCC-edges,367432 +tau-metric,0.06371743454498092 +tau-ultrametric,0.013782436411608865 +LSCC-tau-metric,0.06622449868274946 +LSCC-tau-ultrametric,0.015491301791896188 +ultrametric_metric_ratio,0.21630557648831955 +LSCC-ultrametric_metric_ratio,0.2339210126166112 diff --git a/networks/yeast_grn/undirected_networks-stats.csv b/networks/yeast_grn/undirected_networks-stats.csv new file mode 100644 index 0000000..a88ba58 --- /dev/null +++ b/networks/yeast_grn/undirected_networks-stats.csv @@ -0,0 +1,2 @@ +,n-nodes,nd-edges,nu-edges,tau-metric,tau-ultrametric,tau-avg-metric,tau-avg-ultrametric,tau-max-metric,tau-max-ultrametric +0,1225,366239,52478,0.0662518191672651,0.015495345935304541,0.09392507336407638,0.023324059605930102,0.09838408475932772,0.02519150882274477 diff --git a/utils.py b/utils.py index acb51bb..97c46ff 100644 --- a/utils.py +++ b/utils.py @@ -95,4 +95,103 @@ def fuzzy_reciprocity(G, weight='proximity'): cov -= pbar*(G[u][v][weight] - pbar) stdev += (G[u][v][weight] - pbar)*(G[u][v][weight] - pbar) - return cov/stdev \ No newline at end of file + return cov/stdev + +def venn3_sqr_diagram(Ne, Nb, Nc, Nbc, width=0.1, title=None): + + import matplotlib.patches as mpatches + import matplotlib.pyplot as plt + import numpy as np + + fig, ax = plt.subplots(figsize=(5, 10)) + fig.set_facecolor('tab:gray') + ax.set_facecolor('tab:gray') + + L1 = Nb/Ne + L2 = Nc/Ne + L3 = Nbc/Ne + + artist = [mpatches.Rectangle((0.0, 0.0), width, 1.0, color='b'), + mpatches.Rectangle((0.0, 0.0), width, L1, color='g'), + mpatches.Rectangle((0.0, L1-L3), width, L2, color='r', alpha=0.5)] + + for art in artist: + ax.add_artist(art) + + ax.text(0.5*width, 0.5*(L1-L3), Nb-Nbc, verticalalignment='center', horizontalalignment='center', color='w') + ax.text(0.5*width, (L1-L3)+0.5*L3, Nbc, verticalalignment='center', horizontalalignment='center', color='w') + ax.text(0.5*width, L1+0.5*(L2-L3), Nc-Nbc, verticalalignment='center', horizontalalignment='center', color='w') + ax.text(0.5*width, 0.5*(1+L1+L2-L3), Ne-(Nb+Nc-Nbc), verticalalignment='center', horizontalalignment='center', color='w') + + ax.text(1.01*width, 0.5*(L1-L3), 'Backbone WCC', verticalalignment='center', horizontalalignment='left', color='k') + ax.text(1.01*width, (L1-L3)+0.5*L3, 'Backbone LSCC', verticalalignment='center', horizontalalignment='left', color='k') + ax.text(1.01*width, L1+0.5*(L2-L3), 'Semi-metric LSCC', verticalalignment='center', horizontalalignment='left', color='k') + ax.text(1.01*width, 0.5*(1+L1+L2-L3), 'Semi-Metric WCC', verticalalignment='center', horizontalalignment='left', color='k') + + ax.set_title(title) + ax.set_xlim((0.0, 1.3*width)) + #ax.set_ylim((-pad, 0.5+pad)) + ax.set_axis_off() + + #plt.show() + plt.savefig(f'Figures/Components/{title}.png') + + +def plot_s_dist(data, folder): + + import matplotlib.pyplot as plt + import powerlaw + import pandas as pd + + ss = pd.Series(list(data), name='s-value') + + # Select only s-values + dfs = ss.loc[(ss > 1.0)].sort_values(ascending=False).to_frame() + xmin = dfs['s-value'].min() + xmin = 1 + fit = powerlaw.Fit(dfs['s-value'], xmin=xmin, estimate_discrete=False) + + alpha = fit.power_law.alpha + sigma = fit.power_law.sigma + print('Powerlaw: alpha:', alpha) + print('sigma:', sigma) + + # Compare + R, p = fit.distribution_compare('power_law', 'lognormal_positive') + print("R:", R, 'p-value', p) + + fig, ax = plt.subplots(figsize=(5, 4)) + + fit.plot_pdf(color='#d62728', linewidth=2, label='Empirical data', ax=ax) + + # + Rp = '$R = {R:.2f}$; $p = {p:.3f}$'.format(R=R, p=p) + ax.annotate(Rp, xy=(.03, .13), xycoords='axes fraction', color='black') + + if R > 0: + pw_goodness = '$\sigma = {sigma:.3f}$'.format(sigma=fit.power_law.sigma) + ax.annotate(pw_goodness, xy=(.03, .05), xycoords='axes fraction', color='#1f77b4') + else: + ln_goodness = '$\mu = {mu:.2f}; \sigma = {sigma:.3f}$'.format(mu=fit.lognormal_positive.mu, sigma=fit.lognormal_positive.sigma) + ax.annotate(ln_goodness, xy=(.03, .05), xycoords='axes fraction', color='#2ca02c') + # + pw_label = r'Power law fit' + ln_label = r'Lognormal fit' + + fit.power_law.plot_pdf(color='#aec7e8', linewidth=1, linestyle='--', label=pw_label, ax=ax) + fit.lognormal_positive.plot_pdf(color='#98df8a', linewidth=1, linestyle='--', label=ln_label, ax=ax) + + # + ax.set_title(r'Semi-metric edges ($s_{{ij}}>1)$' '\n' '{source:s}'.format(source=folder)) + ax.set_ylabel(r'$P(s_{ij} \geq x)$') + ax.set_xlabel(r'$s_{ij}$ frequency') + + ax.grid() + + ax.legend(loc='best') + + plt.tight_layout() + # plt.subplots_adjust(left=0.09, right=0.98, bottom=0.07, top=0.90, wspace=0, hspace=0.0) + #plt.savefig(wImgFile, dpi=150, bbox_inches='tight') # , pad_inches=0.05) + plt.savefig(f'{folder}.pdf', dpi=150, bbox_inches='tight') + #plt.show() \ No newline at end of file