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Update exps.
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‎gklearn/experiments/papers/PRL_2020/runtimes_28cores.py

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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Mon Sep 21 10:34:26 2020
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@author: ljia
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"""
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from utils import Graph_Kernel_List, Dataset_List, compute_graph_kernel
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from gklearn.utils.graphdataset import load_predefined_dataset
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import logging
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# def get_graphs(ds_name):
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# from gklearn.utils.graph_synthesizer import GraphSynthesizer
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# gsyzer = GraphSynthesizer()
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# graphs = gsyzer.unified_graphs(num_graphs=100, num_nodes=num_nodes, num_edges=int(num_nodes*2), num_node_labels=0, num_edge_labels=0, seed=None, directed=False)
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# return graphs
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def xp_runtimes_of_all_7cores():
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# Run and save.
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import pickle
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import os
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save_dir = 'outputs/runtimes_of_all_7cores/'
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if not os.path.exists(save_dir):
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os.makedirs(save_dir)
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run_times = {}
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for kernel_name in Graph_Kernel_List:
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print()
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print('Kernel:', kernel_name)
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run_times[kernel_name] = []
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for ds_name in Dataset_List:
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print()
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print('Dataset:', ds_name)
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# get graphs.
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graphs, _ = load_predefined_dataset(ds_name)
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# Compute Gram matrix.
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try:
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name, n_jobs=28)
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run_times[kernel_name].append(run_time)
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except Exception as exp:
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run_times[kernel_name].append('error')
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print('An exception occured when running this experiment:')
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LOG_FILENAME = save_dir + 'error.txt'
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logging.basicConfig(filename=LOG_FILENAME, level=logging.DEBUG)
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logging.exception('')
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print(repr(exp))
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pickle.dump(run_time, open(save_dir + 'run_time.' + kernel_name + '.' + ds_name + '.pkl', 'wb'))
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# Save all.
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pickle.dump(run_times, open(save_dir + 'run_times.pkl', 'wb'))
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return
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if __name__ == '__main__':
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xp_runtimes_of_all_7cores()

‎gklearn/experiments/papers/PRL_2020/synthesized_graphs_N.py

Lines changed: 13 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
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@author: ljia
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"""
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from utils import Graph_Kernel_List, compute_graph_kernel
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import logging
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def generate_graphs():
@@ -39,10 +40,19 @@ def xp_synthesied_graphs_dataset_size():
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print('Number of graphs:', num_graphs)
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sub_graphs = [g.copy() for g in graphs[0:num_graphs]]
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gram_matrix, run_time = compute_graph_kernel(sub_graphs, kernel_name)
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run_times[kernel_name].append(run_time)
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pickle.dump(run_times, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_graphs) + '.pkl', 'wb'))
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try:
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gram_matrix, run_time = compute_graph_kernel(sub_graphs, kernel_name, n_jobs=1)
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run_times[kernel_name].append(run_time)
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except Exception as exp:
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run_times[kernel_name].append('error')
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print('An exception occured when running this experiment:')
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LOG_FILENAME = save_dir + 'error.txt'
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logging.basicConfig(filename=LOG_FILENAME, level=logging.DEBUG)
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logging.exception('')
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print(repr(exp))
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pickle.dump(run_time, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_graphs) + '.pkl', 'wb'))
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# Save all.
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pickle.dump(run_times, open(save_dir + 'run_times.pkl', 'wb'))

‎gklearn/experiments/papers/PRL_2020/synthesized_graphs_degrees.py

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
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@author: ljia
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"""
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from utils import Graph_Kernel_List, compute_graph_kernel
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import logging
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def generate_graphs(degree):
@@ -39,10 +40,18 @@ def xp_synthesied_graphs_degrees():
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graphs = generate_graphs(degree)
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# Compute Gram matrix.
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name)
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run_times[kernel_name].append(run_time)
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try:
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name, n_jobs=1)
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run_times[kernel_name].append(run_time)
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except Exception as exp:
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run_times[kernel_name].append('error')
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print('An exception occured when running this experiment:')
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LOG_FILENAME = save_dir + 'error.txt'
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logging.basicConfig(filename=LOG_FILENAME, level=logging.DEBUG)
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logging.exception('')
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print(repr(exp))
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45-
pickle.dump(run_times, open(save_dir + 'run_time.' + kernel_name + '.' + str(degree) + '.pkl', 'wb'))
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pickle.dump(run_time, open(save_dir + 'run_time.' + kernel_name + '.' + str(degree) + '.pkl', 'wb'))
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# Save all.
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pickle.dump(run_times, open(save_dir + 'run_times.pkl', 'wb'))

‎gklearn/experiments/papers/PRL_2020/synthesized_graphs_num_el.py

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
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@author: ljia
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"""
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from utils import Graph_Kernel_List_ESym, compute_graph_kernel
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import logging
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def generate_graphs(num_el_alp):
@@ -39,10 +40,18 @@ def xp_synthesied_graphs_num_edge_label_alphabet():
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graphs = generate_graphs(num_el_alp)
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4142
# Compute Gram matrix.
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name)
43-
run_times[kernel_name].append(run_time)
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try:
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name, n_jobs=1)
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run_times[kernel_name].append(run_time)
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except Exception as exp:
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run_times[kernel_name].append('error')
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print('An exception occured when running this experiment:')
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LOG_FILENAME = save_dir + 'error.txt'
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logging.basicConfig(filename=LOG_FILENAME, level=logging.DEBUG)
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logging.exception('')
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print(repr(exp))
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pickle.dump(run_times, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_el_alp) + '.pkl', 'wb'))
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pickle.dump(run_time, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_el_alp) + '.pkl', 'wb'))
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# Save all.
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pickle.dump(run_times, open(save_dir + 'run_times.pkl', 'wb'))

‎gklearn/experiments/papers/PRL_2020/synthesized_graphs_num_nl.py

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
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@author: ljia
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"""
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from utils import Graph_Kernel_List_VSym, compute_graph_kernel
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import logging
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1112
def generate_graphs(num_nl_alp):
@@ -39,10 +40,18 @@ def xp_synthesied_graphs_num_node_label_alphabet():
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graphs = generate_graphs(num_nl_alp)
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4142
# Compute Gram matrix.
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name)
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run_times[kernel_name].append(run_time)
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try:
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name, n_jobs=1)
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run_times[kernel_name].append(run_time)
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except Exception as exp:
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run_times[kernel_name].append('error')
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print('An exception occured when running this experiment:')
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LOG_FILENAME = save_dir + 'error.txt'
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logging.basicConfig(filename=LOG_FILENAME, level=logging.DEBUG)
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logging.exception('')
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print(repr(exp))
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45-
pickle.dump(run_times, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_nl_alp) + '.pkl', 'wb'))
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pickle.dump(run_time, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_nl_alp) + '.pkl', 'wb'))
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# Save all.
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pickle.dump(run_times, open(save_dir + 'run_times.pkl', 'wb'))

‎gklearn/experiments/papers/PRL_2020/synthesized_graphs_num_nodes.py

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
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@author: ljia
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"""
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from utils import Graph_Kernel_List, compute_graph_kernel
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import logging
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1011

1112
def generate_graphs(num_nodes):
@@ -39,10 +40,18 @@ def xp_synthesied_graphs_num_nodes():
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graphs = generate_graphs(num_nodes)
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4142
# Compute Gram matrix.
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name)
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run_times[kernel_name].append(run_time)
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try:
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gram_matrix, run_time = compute_graph_kernel(graphs, kernel_name, n_jobs=1)
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run_times[kernel_name].append(run_time)
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except Exception as exp:
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run_times[kernel_name].append('error')
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print('An exception occured when running this experiment:')
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LOG_FILENAME = save_dir + 'error.txt'
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logging.basicConfig(filename=LOG_FILENAME, level=logging.DEBUG)
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logging.exception('')
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print(repr(exp))
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45-
pickle.dump(run_times, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_nodes) + '.pkl', 'wb'))
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pickle.dump(run_time, open(save_dir + 'run_time.' + kernel_name + '.' + str(num_nodes) + '.pkl', 'wb'))
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# Save all.
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pickle.dump(run_times, open(save_dir + 'run_times.pkl', 'wb'))

‎gklearn/experiments/papers/PRL_2020/utils.py

Lines changed: 8 additions & 3 deletions
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@@ -5,6 +5,9 @@
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@author: ljia
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"""
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import multiprocessing
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Graph_Kernel_List = ['PathUpToH', 'WLSubtree', 'SylvesterEquation', 'Marginalized', 'ShortestPath', 'Treelet', 'ConjugateGradient', 'FixedPoint', 'SpectralDecomposition', 'StructuralSP', 'CommonWalk']
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# Graph_Kernel_List = ['CommonWalk', 'Marginalized', 'SylvesterEquation', 'ConjugateGradient', 'FixedPoint', 'SpectralDecomposition', 'ShortestPath', 'StructuralSP', 'PathUpToH', 'Treelet', 'WLSubtree']
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Graph_Kernel_List_ECon = ['ConjugateGradient', 'FixedPoint', 'StructuralSP']
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2326

24-
def compute_graph_kernel(graphs, kernel_name):
25-
import multiprocessing
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Dataset_List = ['Alkane', 'Acyclic', 'MAO', 'PAH', 'MUTAG', 'Letter-med', 'ENZYMES', 'AIDS', 'NCI1', 'NCI109', 'DD']
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def compute_graph_kernel(graphs, kernel_name, n_jobs=multiprocessing.cpu_count()):
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2732
if kernel_name == 'CommonWalk':
2833
from gklearn.kernels.commonWalkKernel import commonwalkkernel
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99104
params = {'base_kernel': 'subtree', 'height': 5}
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101106
# params['parallel'] = None
102-
params['n_jobs'] = multiprocessing.cpu_count()
107+
params['n_jobs'] = n_jobs
103108
params['verbose'] = True
104109
results = estimator(graphs, **params)
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