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# Default ignored files | |||
/workspace.xml |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<module type="PYTHON_MODULE" version="4"> | |||
<component name="NewModuleRootManager"> | |||
<content url="file://$MODULE_DIR$" /> | |||
<orderEntry type="jdk" jdkName="Remote Python 3.7.3 (sftp://faez@192.168.207.78:22/home/faez/faez_venv/bin/python)" jdkType="Python SDK" /> | |||
<orderEntry type="sourceFolder" forTests="false" /> | |||
</component> | |||
<component name="TestRunnerService"> | |||
<option name="PROJECT_TEST_RUNNER" value="Unittests" /> | |||
</component> | |||
</module> |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
<component name="PublishConfigData" autoUpload="Always" serverName="faez@192.168.207.78"> | |||
<serverData> | |||
<paths name="faez@192.167.207.71"> | |||
<serverdata> | |||
<mappings> | |||
<mapping deploy="/home/faez/Codes/GraphCompletion2" local="$PROJECT_DIR$" web="/" /> | |||
</mappings> | |||
</serverdata> | |||
</paths> | |||
<paths name="faez@192.168.207.71:22"> | |||
<serverdata> | |||
<mappings> | |||
<mapping deploy="/home/faez/Codes/GraphCompletion2" local="$PROJECT_DIR$" /> | |||
</mappings> | |||
</serverdata> | |||
</paths> | |||
<paths name="faez@192.168.207.71:22 (1)"> | |||
<serverdata> | |||
<mappings> | |||
<mapping local="$PROJECT_DIR$" web="/" /> | |||
</mappings> | |||
</serverdata> | |||
</paths> | |||
<paths name="faez@192.168.207.78"> | |||
<serverdata> | |||
<mappings> | |||
<mapping deploy="/home/faez/Codes/GraphCompletion2" local="$PROJECT_DIR$" web="/" /> | |||
</mappings> | |||
</serverdata> | |||
</paths> | |||
<paths name="faez@192.168.207.78:22"> | |||
<serverdata> | |||
<mappings> | |||
<mapping local="$PROJECT_DIR$" web="/" /> | |||
</mappings> | |||
</serverdata> | |||
</paths> | |||
<paths name="faez@192.168.207.78:22 (1)"> | |||
<serverdata> | |||
<mappings> | |||
<mapping local="$PROJECT_DIR$" web="/" /> | |||
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</serverdata> | |||
</paths> | |||
</serverData> | |||
<option name="myAutoUpload" value="ALWAYS" /> | |||
</component> | |||
</project> |
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<component name="InspectionProjectProfileManager"> | |||
<settings> | |||
<option name="USE_PROJECT_PROFILE" value="false" /> | |||
<version value="1.0" /> | |||
</settings> | |||
</component> |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
<component name="JavaScriptSettings"> | |||
<option name="languageLevel" value="ES6" /> | |||
</component> | |||
<component name="ProjectRootManager" version="2" project-jdk-name="Remote Python 3.7.3 (sftp://faez@192.168.207.78:22/home/faez/faez_venv/bin/python)" project-jdk-type="Python SDK" /> | |||
</project> |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
<component name="ProjectModuleManager"> | |||
<modules> | |||
<module fileurl="file://$PROJECT_DIR$/.idea/GraphRNN.iml" filepath="$PROJECT_DIR$/.idea/GraphRNN.iml" /> | |||
</modules> | |||
</component> | |||
</project> |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
<component name="RemoteMappingsManager"> | |||
<list> | |||
<list> | |||
<remote-mappings server-id="python@sftp://faez@192.168.207.78:22/home/faez/faez_venv/bin/python"> | |||
<settings> | |||
<list> | |||
<mapping local-root="$PROJECT_DIR$" remote-root="/home/faez/Codes/GraphCompletion2" /> | |||
</list> | |||
</settings> | |||
</remote-mappings> | |||
</list> | |||
</list> | |||
</component> | |||
</project> |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
<component name="VcsDirectoryMappings"> | |||
<mapping directory="$PROJECT_DIR$" vcs="Git" /> | |||
</component> | |||
</project> |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
<component name="WebServers"> | |||
<option name="servers"> | |||
<webServer id="10e3317b-4e39-402a-b65f-af742f10f4b3" name="faez@192.167.207.71" url="http://192.168.207.71"> | |||
<fileTransfer host="192.168.207.71" port="22" accessType="SFTP"> | |||
<advancedOptions> | |||
<advancedOptions dataProtectionLevel="Private" passiveMode="true" shareSSLContext="true" /> | |||
</advancedOptions> | |||
<option name="port" value="22" /> | |||
</fileTransfer> | |||
</webServer> | |||
<webServer id="54e7a78c-4a67-4cb7-ad8a-005e3bcd92ca" name="faez@192.168.207.78" url="http://192.168.207.78"> | |||
<fileTransfer host="192.168.207.78" port="22" accessType="SFTP"> | |||
<advancedOptions> | |||
<advancedOptions dataProtectionLevel="Private" passiveMode="true" shareSSLContext="true" /> | |||
</advancedOptions> | |||
<option name="port" value="22" /> | |||
</fileTransfer> | |||
</webServer> | |||
</option> | |||
</component> | |||
</project> |
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<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
<component name="ChangeListManager"> | |||
<list default="true" id="62e08229-ef03-4c17-ab67-e9a8510f4a5f" name="Default Changelist" comment=""> | |||
<change beforePath="$PROJECT_DIR$/baselines/graphvae/args.py" beforeDir="false" afterPath="$PROJECT_DIR$/baselines/graphvae/args.py" afterDir="false" /> | |||
<change beforePath="$PROJECT_DIR$/baselines/graphvae/graphvae_model.py" beforeDir="false" afterPath="$PROJECT_DIR$/baselines/graphvae/graphvae_model.py" afterDir="false" /> | |||
<change beforePath="$PROJECT_DIR$/baselines/graphvae/graphvae_train.py" beforeDir="false" afterPath="$PROJECT_DIR$/baselines/graphvae/graphvae_train.py" afterDir="false" /> | |||
</list> | |||
<option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" /> | |||
<option name="SHOW_DIALOG" value="false" /> | |||
<option name="HIGHLIGHT_CONFLICTS" value="true" /> | |||
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" /> | |||
<option name="LAST_RESOLUTION" value="IGNORE" /> | |||
</component> | |||
<component name="Git.Settings"> | |||
<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" /> | |||
</component> | |||
<component name="ProjectId" id="1RasLsxZIGMCL2VPQnLdlf6CbR4" /> | |||
<component name="PropertiesComponent"> | |||
<property name="WebServerToolWindowFactoryState" value="true" /> | |||
<property name="settings.editor.selected.configurable" value="com.jetbrains.python.configuration.PyActiveSdkModuleConfigurable" /> | |||
</component> | |||
<component name="RunDashboard"> | |||
<option name="ruleStates"> | |||
<list> | |||
<RuleState> | |||
<option name="name" value="ConfigurationTypeDashboardGroupingRule" /> | |||
</RuleState> | |||
<RuleState> | |||
<option name="name" value="StatusDashboardGroupingRule" /> | |||
</RuleState> | |||
</list> | |||
</option> | |||
</component> | |||
<component name="RunManager" selected="Python.graphvae_model"> | |||
<configuration name="faez_test" type="PythonConfigurationType" factoryName="Python" temporary="true"> | |||
<module name="GraphRNN" /> | |||
<option name="INTERPRETER_OPTIONS" value="" /> | |||
<option name="PARENT_ENVS" value="true" /> | |||
<envs> | |||
<env name="PYTHONUNBUFFERED" value="1" /> | |||
</envs> | |||
<option name="SDK_HOME" value="" /> | |||
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/baselines/graphvae" /> | |||
<option name="IS_MODULE_SDK" value="true" /> | |||
<option name="ADD_CONTENT_ROOTS" value="true" /> | |||
<option name="ADD_SOURCE_ROOTS" value="true" /> | |||
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" /> | |||
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/baselines/graphvae/faez_test.py" /> | |||
<option name="PARAMETERS" value="" /> | |||
<option name="SHOW_COMMAND_LINE" value="false" /> | |||
<option name="EMULATE_TERMINAL" value="false" /> | |||
<option name="MODULE_MODE" value="false" /> | |||
<option name="REDIRECT_INPUT" value="false" /> | |||
<option name="INPUT_FILE" value="" /> | |||
<method v="2" /> | |||
</configuration> | |||
<configuration name="graphvae_model" type="PythonConfigurationType" factoryName="Python" temporary="true"> | |||
<module name="GraphRNN" /> | |||
<option name="INTERPRETER_OPTIONS" value="" /> | |||
<option name="PARENT_ENVS" value="true" /> | |||
<envs> | |||
<env name="PYTHONUNBUFFERED" value="1" /> | |||
</envs> | |||
<option name="SDK_HOME" value="" /> | |||
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/baselines/graphvae" /> | |||
<option name="IS_MODULE_SDK" value="true" /> | |||
<option name="ADD_CONTENT_ROOTS" value="true" /> | |||
<option name="ADD_SOURCE_ROOTS" value="true" /> | |||
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" /> | |||
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/baselines/graphvae/graphvae_model.py" /> | |||
<option name="PARAMETERS" value="" /> | |||
<option name="SHOW_COMMAND_LINE" value="false" /> | |||
<option name="EMULATE_TERMINAL" value="false" /> | |||
<option name="MODULE_MODE" value="false" /> | |||
<option name="REDIRECT_INPUT" value="false" /> | |||
<option name="INPUT_FILE" value="" /> | |||
<method v="2" /> | |||
</configuration> | |||
<configuration name="graphvae_t" type="PythonConfigurationType" factoryName="Python" temporary="true"> | |||
<module name="GraphRNN" /> | |||
<option name="INTERPRETER_OPTIONS" value="" /> | |||
<option name="PARENT_ENVS" value="true" /> | |||
<envs> | |||
<env name="PYTHONUNBUFFERED" value="1" /> | |||
</envs> | |||
<option name="SDK_HOME" value="" /> | |||
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/baselines/graphvae" /> | |||
<option name="IS_MODULE_SDK" value="true" /> | |||
<option name="ADD_CONTENT_ROOTS" value="true" /> | |||
<option name="ADD_SOURCE_ROOTS" value="true" /> | |||
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" /> | |||
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/baselines/graphvae/graphvae_t.py" /> | |||
<option name="PARAMETERS" value="" /> | |||
<option name="SHOW_COMMAND_LINE" value="false" /> | |||
<option name="EMULATE_TERMINAL" value="false" /> | |||
<option name="MODULE_MODE" value="false" /> | |||
<option name="REDIRECT_INPUT" value="false" /> | |||
<option name="INPUT_FILE" value="" /> | |||
<method v="2" /> | |||
</configuration> | |||
<configuration name="graphvae_train" type="PythonConfigurationType" factoryName="Python" temporary="true"> | |||
<module name="GraphRNN" /> | |||
<option name="INTERPRETER_OPTIONS" value="" /> | |||
<option name="PARENT_ENVS" value="true" /> | |||
<envs> | |||
<env name="PYTHONUNBUFFERED" value="1" /> | |||
</envs> | |||
<option name="SDK_HOME" value="" /> | |||
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/baselines/graphvae" /> | |||
<option name="IS_MODULE_SDK" value="true" /> | |||
<option name="ADD_CONTENT_ROOTS" value="true" /> | |||
<option name="ADD_SOURCE_ROOTS" value="true" /> | |||
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" /> | |||
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/baselines/graphvae/graphvae_train.py" /> | |||
<option name="PARAMETERS" value="" /> | |||
<option name="SHOW_COMMAND_LINE" value="false" /> | |||
<option name="EMULATE_TERMINAL" value="false" /> | |||
<option name="MODULE_MODE" value="false" /> | |||
<option name="REDIRECT_INPUT" value="false" /> | |||
<option name="INPUT_FILE" value="" /> | |||
<method v="2" /> | |||
</configuration> | |||
<recent_temporary> | |||
<list> | |||
<item itemvalue="Python.graphvae_model" /> | |||
<item itemvalue="Python.graphvae_train" /> | |||
<item itemvalue="Python.graphvae_t" /> | |||
<item itemvalue="Python.faez_test" /> | |||
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</recent_temporary> | |||
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<component name="SvnConfiguration"> | |||
<configuration /> | |||
</component> | |||
<component name="TaskManager"> | |||
<task active="true" id="Default" summary="Default task"> | |||
<changelist id="62e08229-ef03-4c17-ab67-e9a8510f4a5f" name="Default Changelist" comment="" /> | |||
<created>1569916488590</created> | |||
<option name="number" value="Default" /> | |||
<option name="presentableId" value="Default" /> | |||
<updated>1569916488590</updated> | |||
<workItem from="1569916489756" duration="9290000" /> | |||
<workItem from="1569999702915" duration="1928000" /> | |||
<workItem from="1570261001168" duration="9989000" /> | |||
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<servers /> | |||
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<component name="com.intellij.coverage.CoverageDataManagerImpl"> | |||
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</component> | |||
</project> |
@@ -0,0 +1,186 @@ | |||
<?xml version="1.0" encoding="UTF-8"?> | |||
<project version="4"> | |||
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<change beforePath="$PROJECT_DIR$/baselines/graphvae/graphvae_t.py" beforeDir="false" afterPath="$PROJECT_DIR$/baselines/graphvae/graphvae_t.py" afterDir="false" /> | |||
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<option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" /> | |||
<option name="SHOW_DIALOG" value="false" /> | |||
<option name="HIGHLIGHT_CONFLICTS" value="true" /> | |||
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" /> | |||
<option name="LAST_RESOLUTION" value="IGNORE" /> | |||
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<component name="FileTemplateManagerImpl"> | |||
<option name="RECENT_TEMPLATES"> | |||
<list> | |||
<option value="Python Script" /> | |||
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<component name="Git.Settings"> | |||
<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" /> | |||
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<component name="ProjectId" id="1RuXmB9p05mUz58ntQQQWlgP5D5" /> | |||
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<property name="WebServerToolWindowFactoryState" value="true" /> | |||
<property name="last_opened_file_path" value="$PROJECT_DIR$/../diffpool" /> | |||
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<configuration name="faez_test_2" type="PythonConfigurationType" factoryName="Python" temporary="true"> | |||
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<configuration name="graphvae_t" type="PythonConfigurationType" factoryName="Python" temporary="true"> | |||
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<option name="INTERPRETER_OPTIONS" value="" /> | |||
<option name="PARENT_ENVS" value="true" /> | |||
<envs> | |||
<env name="PYTHONUNBUFFERED" value="1" /> | |||
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<option name="SDK_HOME" value="" /> | |||
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/baselines/graphvae" /> | |||
<option name="IS_MODULE_SDK" value="true" /> | |||
<option name="ADD_CONTENT_ROOTS" value="true" /> | |||
<option name="ADD_SOURCE_ROOTS" value="true" /> | |||
<EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" /> | |||
<option name="SCRIPT_NAME" value="$PROJECT_DIR$/baselines/graphvae/graphvae_t.py" /> | |||
<option name="PARAMETERS" value="" /> | |||
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<option name="EMULATE_TERMINAL" value="false" /> | |||
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<option name="REDIRECT_INPUT" value="false" /> | |||
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<configuration name="graphvae_train" type="PythonConfigurationType" factoryName="Python" temporary="true"> | |||
<module name="GraphRNN" /> | |||
<option name="INTERPRETER_OPTIONS" value="" /> | |||
<option name="PARENT_ENVS" value="true" /> | |||
<envs> | |||
<env name="PYTHONUNBUFFERED" value="1" /> | |||
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<option name="SDK_HOME" value="" /> | |||
<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/baselines/graphvae" /> | |||
<option name="IS_MODULE_SDK" value="true" /> | |||
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from sklearn.metrics import mean_absolute_error | |||
import sys | |||
sys.path.append('../') | |||
from train import * | |||
from args import Args | |||
from GraphCompletion.graph_completion_with_training import graph_show | |||
from GraphCompletion.graph_show import graph_save | |||
def test_completion(x_batch, y_len_unsorted, args, rnn, output, test_batch_size=32, sample_time=1): | |||
rnn.hidden = rnn.init_hidden(1) | |||
rnn.eval() | |||
output.eval() | |||
# generate graphs | |||
max_num_node = int(args.max_num_node) | |||
y_pred = Variable( | |||
torch.zeros(test_batch_size, max_num_node, args.max_prev_node)).cuda() # normalized prediction score | |||
y_pred_long = Variable(torch.zeros(test_batch_size, max_num_node, args.max_prev_node)).cuda() # discrete prediction | |||
x_step = Variable(torch.ones(1, 1, args.max_prev_node)).cuda() | |||
# number_of_missing_nodes = args.number_of_missing_nodes | |||
number_of_missing_nodes = 2 | |||
for j in range(test_batch_size): | |||
incomplete_graph_size = y_len_unsorted.data[j] - number_of_missing_nodes | |||
for i in range(y_len_unsorted.data[j]-1): | |||
h = rnn(x_step) | |||
y_pred_step = output(h) | |||
y_pred[j:j+1, i:i + 1, :] = F.sigmoid(y_pred_step) | |||
if(i<incomplete_graph_size): | |||
x_step = (x_batch[j:j+1, i+1:i+2, :]).cuda() | |||
else: | |||
x_step = sample_sigmoid(y_pred_step, sample=True, sample_time=sample_time) | |||
y_pred_long[j:j+1, i:i + 1, :] = x_step | |||
rnn.hidden = Variable(rnn.hidden.data).cuda() | |||
y_pred_long_data = y_pred_long.data.long() | |||
adj_true_list = [] | |||
graph_true_list = [] | |||
adj_incomplete_list = [] | |||
graph_incomplete_list = [] | |||
adj_pred_list = [] | |||
graph_pred_list = [] | |||
for i in range(test_batch_size): | |||
adj_true = decode_adj(x_batch[i, 1:y_len_unsorted.data[i], :].cpu().numpy()) | |||
adj_true_list.append(adj_true) | |||
graph_true_list.append(nx.from_numpy_matrix(adj_true)) | |||
adj_incomplete = decode_adj(x_batch[i, 1:y_len_unsorted.data[i] - number_of_missing_nodes, :].cpu().numpy()) | |||
adj_incomplete_list.append(adj_incomplete) | |||
graph_incomplete_list.append(nx.from_numpy_matrix(adj_incomplete)) | |||
adj_pred = decode_adj(y_pred_long_data[i, 0:y_len_unsorted.data[i]-1, :].cpu().numpy()) | |||
adj_pred_list.append(adj_pred) | |||
graph_pred_list.append(nx.from_numpy_matrix(adj_pred)) | |||
return adj_true_list, graph_true_list, adj_incomplete_list, graph_incomplete_list, adj_pred_list, graph_pred_list | |||
if __name__ == '__main__': | |||
# All necessary arguments are defined in args.py | |||
args = Args() | |||
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.cuda) | |||
# check if necessary directories exist | |||
if not os.path.isdir(args.model_save_path): | |||
os.makedirs(args.model_save_path) | |||
if not os.path.isdir(args.graph_save_path): | |||
os.makedirs(args.graph_save_path) | |||
if not os.path.isdir(args.figure_save_path): | |||
os.makedirs(args.figure_save_path) | |||
if not os.path.isdir(args.timing_save_path): | |||
os.makedirs(args.timing_save_path) | |||
if not os.path.isdir(args.figure_prediction_save_path): | |||
os.makedirs(args.figure_prediction_save_path) | |||
if not os.path.isdir(args.nll_save_path): | |||
os.makedirs(args.nll_save_path) | |||
graphs = create_graphs.create(args) | |||
# split datasets | |||
random.seed(123) | |||
shuffle(graphs) | |||
graphs_len = len(graphs) | |||
args.max_num_node = max([graphs[i].number_of_nodes() for i in range(len(graphs))]) | |||
max_num_edge = max([graphs[i].number_of_edges() for i in range(len(graphs))]) | |||
min_num_edge = min([graphs[i].number_of_edges() for i in range(len(graphs))]) | |||
# show graphs statistics | |||
print('total graph num: {}'.format(len(graphs))) | |||
print('max number node: {}'.format(args.max_num_node)) | |||
print('max/min number edge: {}; {}'.format(max_num_edge, min_num_edge)) | |||
print('max previous node: {}'.format(args.max_prev_node)) | |||
if 'nobfs' in args.note: | |||
args.max_prev_node = args.max_num_node-1 | |||
dataset = Graph_sequence_sampler_pytorch_nobfs_for_completion(graphs, | |||
max_num_node=args.max_num_node) | |||
sample_strategy = torch.utils.data.sampler.WeightedRandomSampler([1.0 / len(dataset) for i in range(len(dataset))], | |||
num_samples=args.batch_size * args.batch_ratio, | |||
replacement=True) | |||
dataset_loader = torch.utils.data.DataLoader(dataset, batch_size=args.batch_size, num_workers=args.num_workers, | |||
sampler=sample_strategy) | |||
rnn_GraphRNN = GRU_plain(input_size=args.max_prev_node, embedding_size=args.embedding_size_rnn, | |||
hidden_size=args.hidden_size_rnn, num_layers=args.num_layers, has_input=True, | |||
has_output=False).cuda() | |||
output_GraphRNN = MLP_plain(h_size=args.hidden_size_rnn, embedding_size=args.embedding_size_output, | |||
y_size=args.max_prev_node).cuda() | |||
fname = args.model_save_path + args.fname_GraphRNN + 'lstm_' + str(args.load_epoch) + '.dat' | |||
rnn_GraphRNN.load_state_dict(torch.load(fname)) | |||
fname = args.model_save_path + args.fname_GraphRNN + 'output_' + str(args.load_epoch) + '.dat' | |||
output_GraphRNN.load_state_dict(torch.load(fname)) | |||
# ****************************************************************** | |||
rnn_GraphCompletion = GRU_plain(input_size=args.max_prev_node, embedding_size=args.embedding_size_rnn, | |||
hidden_size=args.hidden_size_rnn, num_layers=args.num_layers, has_input=True, | |||
has_output=False).cuda() | |||
output_GraphCompletion = MLP_plain(h_size=args.hidden_size_rnn, embedding_size=args.embedding_size_output, | |||
y_size=args.max_prev_node).cuda() | |||
fname = args.model_save_path + args.fname + 'lstm_' + args.graph_completion_string + str(args.epochs) + '.dat' | |||
rnn_GraphCompletion.load_state_dict(torch.load(fname)) | |||
fname = args.model_save_path + args.fname + 'output_' + args.graph_completion_string + str(args.epochs) + '.dat' | |||
output_GraphCompletion.load_state_dict(torch.load(fname)) | |||
# ****************************************************************** | |||
MAE_GraphRNN = [] | |||
MAE_GraphCompletion = [] | |||
for batch_idx, data in enumerate(dataset_loader): | |||
if True: | |||
x_unsorted = data['x'].float() | |||
y_unsorted = data['y'].float() | |||
y_len_unsorted = data['len'] | |||
# ********************************* | |||
adj_true_list, graph_true_list, adj_incomplete_list, graph_incomplete_list, adj_pred_list, graph_pred_list\ | |||
= test_completion(x_unsorted, y_len_unsorted, args, rnn_GraphRNN, output_GraphRNN) | |||
adj_true_list, graph_true_list, adj_incomplete_list, graph_incomplete_list, adj_pred_list_completion_model\ | |||
, graph_pred_list_completion_model \ | |||
= test_completion(x_unsorted, y_len_unsorted, args, rnn_GraphCompletion, output_GraphCompletion) | |||
mae = np.sum(np.absolute((adj_pred_list[0].astype("float") - adj_true_list[0].astype("float")))) | |||
# print("adj_true: ") | |||
# print(adj_true_list[0]) | |||
# graph_show(nx.from_numpy_matrix(adj_true_list[0]),"adj_true" ) | |||
# graph_show(nx.from_numpy_matrix(adj_incomplete_list[0]), "adj_incomplete") | |||
# print("my error") | |||
# print(mae) | |||
# print(mean_absolute_error(adj_pred_list[0], adj_true_list[0])) | |||
# print("adj_pred_list:") | |||
# print(adj_pred_list[0]) | |||
# graph_show(nx.from_numpy_matrix(adj_pred_list[0]), "pred_true") | |||
for i in range(len(graph_true_list)): | |||
# graph_save(graph_true_list[i], graph_incomplete_list[i], | |||
# graph_pred_list[i], graph_pred_list_completion_model[i], i, args.graph_save_path) | |||
mae = mean_absolute_error(adj_pred_list[i], adj_true_list[i]) | |||
MAE_GraphRNN.append(mae) | |||
mae = mean_absolute_error(adj_pred_list_completion_model[i], adj_true_list[i]) | |||
MAE_GraphCompletion.append(mae) | |||
# ********************************* | |||
# print(MAE_GraphCompletion) | |||
# G_pred_step = test_mlp(x_unsorted, y_len_unsorted, epoch, args, rnn_for_graph_completion, | |||
# output_for_graph_completion) | |||
# nx.write_gpickle(G_pred_step, "completed_graphs_with_training.dat") | |||
print("MAE_GraphRNN:") | |||
print(np.mean(MAE_GraphRNN)) | |||
# print(MAE_GraphRNN) | |||
print("MAE_GraphCompletion:") | |||
print(np.mean(MAE_GraphCompletion)) |
@@ -0,0 +1,213 @@ | |||
import torch | |||
import torch.nn.functional as F | |||
from torch.autograd import Variable | |||
from sklearn.metrics import mean_absolute_error | |||
import sys | |||
sys.path.append('../') | |||
from data import * | |||
from train import * | |||
from args import Args | |||
def test_mlp(x_batch, y_len_unsorted, epoch, args, rnn, output, test_batch_size=32, save_histogram=False,sample_time=1): | |||
rnn.hidden = rnn.init_hidden(1) | |||
rnn.eval() | |||
output.eval() | |||
# generate graphs | |||
max_num_node = int(args.max_num_node) | |||
y_pred = Variable( | |||
torch.zeros(test_batch_size, max_num_node, args.max_prev_node)).cuda() # normalized prediction score | |||
y_pred_long = Variable(torch.zeros(test_batch_size, max_num_node, args.max_prev_node)).cuda() # discrete prediction | |||
x_step = Variable(torch.ones(1, 1, args.max_prev_node)).cuda() | |||
incompleteness_ratio = 0.96 | |||
for j in range(test_batch_size): | |||
incomplete_graph_size = int(int(y_len_unsorted.data[j]) * incompleteness_ratio) | |||
# print(y_len_unsorted.data[j]) | |||
for i in range(y_len_unsorted.data[j]-1): | |||
h = rnn(x_step) | |||
y_pred_step = output(h) | |||
y_pred[j:j+1, i:i + 1, :] = F.sigmoid(y_pred_step) | |||
if (i<incomplete_graph_size): | |||
x_step = (x_batch[j:j+1, i+1:i+2, :]).cuda() | |||
else: | |||
x_step = sample_sigmoid(y_pred_step, sample=True, sample_time=sample_time) | |||
y_pred_long[j:j+1, i:i + 1, :] = x_step | |||
rnn.hidden = Variable(rnn.hidden.data).cuda() | |||
y_pred_long_data = y_pred_long.data.long() | |||
G_pred_list = [] | |||
adj_true_list = [] | |||
adj_pred_list = [] | |||
for i in range(test_batch_size): | |||
adj_pred = decode_adj(y_pred_long_data[i].cpu().numpy()) | |||
adj_pred_list.append(adj_pred) | |||
adj_true_list.append(decode_adj(x_batch[i].cpu().numpy())) | |||
G_pred = get_graph(adj_pred) # get a graph from zero-padded adj | |||
G_pred_list.append(G_pred) | |||
return G_pred_list, adj_true_list, adj_pred_list | |||
def save_graph(graph, name): | |||
adj_pred = decode_adj(graph.cpu().numpy()) | |||
G_pred = get_graph(adj_pred) # get a graph from zero-padded adj | |||
G = np.asarray(nx.to_numpy_matrix(G_pred)) | |||
np.savetxt(name + '.txt', G, fmt='%d') | |||
def data_to_graph_converter(data): | |||
G_list = [] | |||
for i in range(len(data)): | |||
x = data[i].numpy() | |||
x = x.astype(int) | |||
adj_pred = decode_adj(x) | |||
G = get_graph(adj_pred) # get a graph from zero-padded adj | |||
G_list.append(G) | |||
return G_list | |||
def get_incomplete_graph(x_batch, y_len_unsorted, incompleteness_ratio = 0.96): | |||
batch_size = len(x_batch) | |||
max_prev_node = len(x_batch[0][0]) | |||
max_incomplete_num_node = int(int(max(y_len_unsorted)) * incompleteness_ratio) | |||
incomplete_graph = Variable(torch.zeros(batch_size, max_incomplete_num_node, max_prev_node)) | |||
for i in range(len(y_len_unsorted)): | |||
incomplete_graph_size = int(int(y_len_unsorted.data[i])*incompleteness_ratio) | |||
incomplete_graph[i] = torch.cat((x_batch[i,:incomplete_graph_size], | |||
torch.zeros([max_incomplete_num_node - incomplete_graph_size, | |||
max_prev_node])), dim=0) | |||
return incomplete_graph | |||
if __name__ == '__main__': | |||
# All necessary arguments are defined in args.py | |||
args = Args() | |||
os.environ['CUDA_VISIBLE_DEVICES'] = str(args.cuda) | |||
print('CUDA', args.cuda) | |||
print('File name prefix', args.fname) | |||
# check if necessary directories exist | |||
if not os.path.isdir(args.model_save_path): | |||
os.makedirs(args.model_save_path) | |||
if not os.path.isdir(args.graph_save_path): | |||
os.makedirs(args.graph_save_path) | |||
if not os.path.isdir(args.figure_save_path): | |||
os.makedirs(args.figure_save_path) | |||
if not os.path.isdir(args.timing_save_path): | |||
os.makedirs(args.timing_save_path) | |||
if not os.path.isdir(args.figure_prediction_save_path): | |||
os.makedirs(args.figure_prediction_save_path) | |||
if not os.path.isdir(args.nll_save_path): | |||
os.makedirs(args.nll_save_path) | |||
graphs = create_graphs.create(args) | |||
# split datasets | |||
random.seed(123) | |||
shuffle(graphs) | |||
graphs_len = len(graphs) | |||
graphs_test = graphs[int(0.8 * graphs_len):] | |||
graphs_train = graphs[0:int(0.8 * graphs_len)] | |||
graphs_validate = graphs[0:int(0.2 * graphs_len)] | |||
graph_validate_len = 0 | |||
for graph in graphs_validate: | |||
graph_validate_len += graph.number_of_nodes() | |||
graph_validate_len /= len(graphs_validate) | |||
print('graph_validate_len', graph_validate_len) | |||
graph_test_len = 0 | |||
for graph in graphs_test: | |||
graph_test_len += graph.number_of_nodes() | |||
graph_test_len /= len(graphs_test) | |||
print('graph_test_len', graph_test_len) | |||
args.max_num_node = max([graphs[i].number_of_nodes() for i in range(len(graphs))]) | |||
max_num_edge = max([graphs[i].number_of_edges() for i in range(len(graphs))]) | |||
min_num_edge = min([graphs[i].number_of_edges() for i in range(len(graphs))]) | |||
# args.max_num_node = 2000 | |||
# show graphs statistics | |||
print('total graph num: {}, training set: {}'.format(len(graphs), len(graphs_train))) | |||
print('max number node: {}'.format(args.max_num_node)) | |||
print('max/min number edge: {}; {}'.format(max_num_edge, min_num_edge)) | |||
print('max previous node: {}'.format(args.max_prev_node)) | |||
# save ground truth graphs | |||
## To get train and test set, after loading you need to manually slice | |||
save_graph_list(graphs, args.graph_save_path + args.fname_train + '0.dat') | |||
save_graph_list(graphs, args.graph_save_path + args.fname_test + '0.dat') | |||
print('train and test graphs saved at: ', args.graph_save_path + args.fname_test + '0.dat') | |||
if 'nobfs' in args.note: | |||
args.max_prev_node = args.max_num_node-1 | |||
dataset = Graph_sequence_sampler_pytorch_nobfs_for_completion(graphs_train, | |||
max_num_node=args.max_num_node) | |||
# dataset = Graph_sequence_sampler_pytorch(graphs_train, max_prev_node=args.max_prev_node, | |||
# max_num_node=args.max_num_node) | |||
sample_strategy = torch.utils.data.sampler.WeightedRandomSampler([1.0 / len(dataset) for i in range(len(dataset))], | |||
num_samples=args.batch_size * args.batch_ratio, | |||
replacement=True) | |||
dataset_loader = torch.utils.data.DataLoader(dataset, batch_size=args.batch_size, num_workers=args.num_workers, | |||
sampler=sample_strategy) | |||
rnn = GRU_plain(input_size=args.max_prev_node, embedding_size=args.embedding_size_rnn, | |||
hidden_size=args.hidden_size_rnn, num_layers=args.num_layers, has_input=True, | |||
has_output=False).cuda() | |||
output = MLP_plain(h_size=args.hidden_size_rnn, embedding_size=args.embedding_size_output, | |||
y_size=args.max_prev_node).cuda() | |||
name = "GraphRNN_MLP" + '_' + args.graph_type + '_' + str(args.num_layers) + '_' + str(args.hidden_size_rnn) + '_' | |||
fname = args.model_save_path + name + 'lstm_' + str(args.load_epoch) + '.dat' | |||
rnn.load_state_dict(torch.load(fname)) | |||
fname = args.model_save_path + name + 'output_' + str(args.load_epoch) + '.dat' | |||
output.load_state_dict(torch.load(fname)) | |||
# ****************************************************************** | |||
rnn_for_graph_completion = GRU_plain(input_size=args.max_prev_node, embedding_size=args.embedding_size_rnn, | |||
hidden_size=args.hidden_size_rnn, num_layers=args.num_layers, has_input=True, | |||
has_output=False).cuda() | |||
output_for_graph_completion = MLP_plain(h_size=args.hidden_size_rnn, embedding_size=args.embedding_size_output, | |||
y_size=args.max_prev_node).cuda() | |||
graph_completion_string = 'graph_completion_one_node_' | |||
# fname = args.model_save_path + args.fname + 'lstm_' + graph_completion_string + str(args.load_epoch) + '.dat' | |||
# rnn_for_graph_completion.load_state_dict(torch.load(fname)) | |||
# fname = args.model_save_path + args.fname + 'output_' + graph_completion_string + str(args.load_epoch) + '.dat' | |||
# output_for_graph_completion.load_state_dict(torch.load(fname)) | |||
# ****************************************************************** | |||
args.lr = 0.00001 | |||
epoch = args.load_epoch | |||
print('model loaded!, lr: {}'.format(args.lr)) | |||
for batch_idx, data in enumerate(dataset_loader): | |||
if batch_idx==0: | |||
rnn.zero_grad() | |||
output.zero_grad() | |||
x_unsorted = data['x'].float() | |||
G = data_to_graph_converter(x_unsorted[:,1:,:]) | |||
nx.write_gpickle(G, "main_graphs.dat") | |||
y_unsorted = data['y'].float() | |||
y_len_unsorted = data['len'] | |||
# ********************************* | |||
G = get_incomplete_graph(x_unsorted, y_len_unsorted) | |||
G = data_to_graph_converter(G[:, 1:, :]) | |||
nx.write_gpickle(G, "incomplete_graphs.dat") | |||
# ********************************* | |||
G_pred_step, adj_true_list, adj_pred_list = test_mlp(x_unsorted, y_len_unsorted, epoch, args, rnn, output) | |||
nx.write_gpickle(G_pred_step, "completed_graphs.dat") | |||
mae = np.sum(np.absolute((adj_pred_list[0].astype("float") - adj_true_list[0].astype("float")))) | |||
print("adj_true: ") | |||
print(adj_true_list[0]) | |||
print("my err") | |||
print(mae) | |||
print(mean_absolute_error(adj_pred_list[0], adj_true_list[0])) | |||
print("adj_pred_list:") | |||
print(adj_pred_list[0]) | |||
# ********************************* | |||
# G_pred_step = test_mlp(x_unsorted, y_len_unsorted, epoch, args, rnn_for_graph_completion, | |||
# output_for_graph_completion) | |||
# nx.write_gpickle(G_pred_step, "completed_graphs_with_training.dat") |
@@ -0,0 +1,675 @@ | |||
import torch | |||
import torch.nn.functional as F | |||
from torch.autograd import Variable | |||
import sys | |||
sys.path.append('../') | |||
from train import * | |||
from args import Args | |||
from torch import optim | |||
from torch.optim.lr_scheduler import MultiStepLR | |||
from torch.nn.utils.rnn import pad_packed_sequence, pack_padded_sequence | |||
from torch.nn.init import * | |||
import matplotlib.pyplot as plt | |||
import networkx as nx | |||
from tensorboard_logger import configure, log_value | |||
from baselines.graphvae.graphvae_model import GraphVAE | |||
import itertools | |||
device = torch.device("cuda:0") | |||
def plot_grad_flow(named_parameters): | |||
ave_grads = [] | |||
layers = [] | |||
for n, p in named_parameters: | |||
if(p.requires_grad) and ("bias" not in n): | |||
layers.append(n) | |||
print(p.grad) | |||
print("**********************************") | |||
print(p.grad.abs()) | |||
print("**********************************") | |||
print(p.grad.abs().mean()) | |||
print("**********************************") | |||
ave_grads.append(p.grad.abs().mean()) | |||
plt.plot(ave_grads, alpha=0.3, color="b") | |||
plt.hlines(0, 0, len(ave_grads)+1, linewidth=1, color="k" ) | |||
plt.xticks(range(0,len(ave_grads), 1), layers, rotation="vertical") | |||
plt.xlim(xmin=0, xmax=len(ave_grads)) | |||
plt.xlabel("Layers") | |||
plt.ylabel("average gradient") | |||
plt.title("Gradient flow") | |||
plt.grid(True) | |||
plt.show() | |||
def graph_show(G, title): | |||
pos = nx.spring_layout(G, scale=2) | |||
nx.draw(G, pos, font_size=8) | |||
fig = plt.gcf() | |||
fig.canvas.set_window_title(title) | |||
plt.show() | |||
def decode_adj(adj_output): | |||
''' | |||
recover to adj from adj_output | |||
note: here adj_output have shape (n-1)*m | |||
''' | |||
max_prev_node = adj_output.shape[1] | |||
adj = np.zeros((adj_output.shape[0], adj_output.shape[0])) | |||
for i in range(adj_output.shape[0]): | |||
input_start = max(0, i - max_prev_node + 1) | |||
input_end = i + 1 | |||
output_start = max_prev_node + max(0, i - max_prev_node + 1) - (i + 1) | |||
output_end = max_prev_node | |||
adj[i, input_start:input_end] = adj_output[i,::-1][output_start:output_end] # reverse order | |||
adj_full = np.zeros((adj_output.shape[0]+1, adj_output.shape[0]+1)) | |||
n = adj_full.shape[0] | |||
adj_full[1:n, 0:n-1] = np.tril(adj, 0) | |||
adj_full = adj_full + adj_full.T | |||
return adj_full | |||
def tensor_to_graph_converter(tensor, title): | |||
adj_matrix = decode_adj(tensor.numpy()) | |||
G = nx.from_numpy_matrix(adj_matrix) | |||
graph_show(G, title) | |||
return | |||
def get_indices(number_of_missing_nodes, row_size): | |||
# print("$$$$$$$$") | |||
# print(row_size) | |||
row_index = [] | |||
column_index = [] | |||
start_index = 0 | |||
for i in range(number_of_missing_nodes): | |||
for j in range(row_size): | |||
row_index.append(i) | |||
column_index.append(j + start_index) | |||
start_index+=1 | |||
return row_index, column_index | |||
def GraphRNN_loss2(true_adj_batch, predicted_adj_batch, y_pred, y, batch_size, number_of_missing_nodes): | |||
row_list = list(range(number_of_missing_nodes)) | |||
permutation_indices = list(itertools.permutations(row_list)) | |||
loss_sum = 0 | |||
for data_index in range(batch_size): | |||
row_size = len(true_adj_batch[data_index])-number_of_missing_nodes | |||
row_index, column_index = get_indices(number_of_missing_nodes, row_size) | |||
# print("true_adj_batch: ") | |||
# print(true_adj_batch[data_index]) | |||
# print("y: ") | |||
# print(y[data_index]) | |||
# print("predicted_adj_batch: ") | |||
# print(predicted_adj_batch[data_index]) | |||
# print("y_pred:") | |||
# print(y_pred[data_index]+0) | |||
# print("selected_y_pred:") | |||
# print(y_pred[data_index][row_index, column_index]) | |||
# print("selected_y:") | |||
# print(y[data_index][row_index, column_index]) | |||
loss_list = [] | |||
for row_order in permutation_indices: | |||
permuted_y_pred = y_pred[data_index][list(row_order)] | |||
loss_list.append(F.binary_cross_entropy(permuted_y_pred[row_index, column_index], | |||
y[data_index][row_index, column_index])) | |||
loss_sum+=min(loss_list) | |||
loss_sum/=batch_size | |||
return loss_sum | |||
def GraphRNN_loss(true_adj_batch, predicted_adj_batch, batch_size, number_of_missing_nodes): | |||
# loss_sum = 0 | |||
for data_index in range(batch_size): | |||
loss_sum= F.binary_cross_entropy(predicted_adj_batch[data_index], | |||
true_adj_batch[data_index]) | |||
break | |||
# loss_sum/=batch_size | |||
# loss_sum.requires_grad = True | |||
return loss_sum | |||
def matrix_completion_loss(true_adj_batch, predicted_adj_batch, batch_size, number_of_missing_nodes): | |||
# graph_show(nx.from_numpy_matrix(true_adj[0]), "true_adj") | |||
# graph_show(nx.from_numpy_matrix(predicted_adj[0]), "predicted_adj") | |||
loss_sum=F.binary_cross_entropy(torch.from_numpy(predicted_adj_batch[0]), | |||
torch.from_numpy(true_adj_batch[0])) | |||
# loss_sum = 0 | |||
# for data_index in range(batch_size): | |||
# # print("########## data_len: ") | |||
# # print(data_len[data_index].item()) | |||
# # print("^^^^ data_index: " + str(data_index)) | |||
# adj_matrix = true_adj_batch[data_index] | |||
# predicted_adj_matrix = predicted_adj_batch[data_index] | |||
# number_of_nodes = np.shape(adj_matrix)[1] | |||
# # loss_sum+=F.binary_cross_entropy(torch.from_numpy(predicted_adj_matrix), | |||
# # torch.from_numpy(adj_matrix)) | |||
# sub_matrix = adj_matrix[number_of_nodes - number_of_missing_nodes:][:, | |||
# :number_of_nodes - number_of_missing_nodes] | |||
# predicted_sub_matrix = predicted_adj_matrix[number_of_nodes - number_of_missing_nodes:][:, | |||
# :number_of_nodes - number_of_missing_nodes] | |||
# min_permutation_loss = float("inf") | |||
# row_list = list(range(number_of_missing_nodes)) | |||
# permutation_indices = list(itertools.permutations(row_list)) | |||
# number_of_rows = np.shape(predicted_sub_matrix)[0] | |||
# number_of_columns = np.shape(predicted_sub_matrix)[1] | |||
# matrix_size = number_of_rows*number_of_columns | |||
# # print(str(number_of_rows) + " ### " + str(number_of_columns) + " @@@ " + str(matrix_size)) | |||
# | |||
# for row_order in permutation_indices: | |||
# permuted_sub_matrix = sub_matrix[list(row_order)] | |||
# # print("***** permuted_sub_matrix ") | |||
# # print(permuted_sub_matrix) | |||
# # print("***** predicted_sub_matrix ") | |||
# # print(predicted_sub_matrix) | |||
# adj_recon_loss = F.binary_cross_entropy(torch.from_numpy(predicted_sub_matrix), | |||
# torch.from_numpy(permuted_sub_matrix)) | |||
# # print(adj_recon_loss) | |||
# min_permutation_loss = np.minimum(min_permutation_loss, adj_recon_loss.item()) | |||
# # print(adj_recon_loss) | |||
# loss_sum += min_permutation_loss/matrix_size | |||
# # print("^^^^^ ") | |||
# # print(loss_sum) | |||
# loss_sum = torch.autograd.Variable(torch.from_numpy(np.array(loss_sum))) | |||
# # print(loss_sum) | |||
# loss_sum.requires_grad = True | |||
# print(loss_sum) | |||
# print(loss_sum/batch_size) | |||
return loss_sum/batch_size | |||
def graph_matching_loss(true_adj_batch, predicted_adj_batch, data_len, batch_size): | |||
# graph_show(nx.from_numpy_matrix(true_adj[0]), "true_adj") | |||
# graph_show(nx.from_numpy_matrix(predicted_adj[0]), "predicted_adj") | |||
loss_sum = 0 | |||
for data_index in range(batch_size): | |||
features = torch.zeros(data_len[data_index]) | |||
number_of_nodes = data_len[data_index].item() | |||
# print("########## data_len: ") | |||
# print(data_len[data_index].item()) | |||
if data_len[data_index].item()>14: | |||
continue | |||
graphvae = GraphVAE(1, 64, 256, data_len[data_index].item()) | |||
# print("^^^^ data_index: " + str(data_index)) | |||
current_true_adj = true_adj_batch[data_index] | |||
current_predicted_adj = predicted_adj_batch[data_index] | |||
current_features = features | |||
S = graphvae.edge_similarity_matrix(current_true_adj, current_predicted_adj, current_features, current_features, | |||
graphvae.deg_feature_similarity) | |||
init_corr = 1 / number_of_nodes | |||
init_assignment = torch.ones(number_of_nodes, number_of_nodes) * init_corr | |||
assignment = graphvae.mpm(init_assignment, S) | |||
row_ind, col_ind = scipy.optimize.linear_sum_assignment(-assignment.numpy()) | |||
permuted_adj = graphvae.permute_adj(torch.from_numpy(current_true_adj).float(), row_ind, col_ind) | |||
# print("***** permuted_adj ") | |||
# print(permuted_adj) | |||
# print("***** current_predicted_adj ") | |||
# print(torch.from_numpy(current_predicted_adj).float()) | |||
adj_recon_loss = graphvae.adj_recon_loss(permuted_adj, torch.from_numpy(current_predicted_adj).float()) | |||
# print(adj_recon_loss) | |||
loss_sum += adj_recon_loss.data | |||
loss_sum.requires_grad = True | |||
# print(loss_sum/batch_size) | |||
# print("^^^^^ ") | |||
# print(loss_sum) | |||
return loss_sum/batch_size | |||
def make_batch_of_matrices(initial_y, initial_y_len, y_train, y_pred, batch_size): | |||
true_adj_batch = [] | |||
predicted_adj_batch = [] | |||
for data_index in range(batch_size): | |||
a = initial_y[data_index][:initial_y_len[data_index] - 1].cpu() | |||
b = y_train[data_index] | |||
true_adj = torch.cat((a, b), dim=0) | |||
true_adj = decode_adj(true_adj.numpy()) | |||
true_adj_tensor = torch.from_numpy(true_adj + np.identity(len(true_adj[0]))).float().to(device) | |||
true_adj_batch.append(true_adj_tensor) | |||
b = y_pred[data_index].data | |||
# print("bbbbbbbbbbbbbbbbbbbbbbb :") | |||
# print(b) | |||
# print("b.data :") | |||
# print(b.data) | |||
# print("**********************************************************************************") | |||
predicted_adj = torch.cat((a, b.cpu()), dim=0) | |||
predicted_adj = decode_adj(predicted_adj.numpy()) | |||
predicted_adj_tensor = torch.from_numpy(predicted_adj + np.identity(len(predicted_adj[0]))).float().to(device) | |||
predicted_adj_tensor.requires_grad = True | |||
# predicted_adj_tensor = predicted_adj_tensor + 1 | |||
# print("*********** predicted_adj_tensor *******") | |||
# print(predicted_adj_tensor+0) | |||
predicted_adj_batch.append(predicted_adj_tensor+0) | |||
return true_adj_batch, predicted_adj_batch | |||
def train_mlp_epoch_for_completion(epoch, args, rnn, output, rnn_for_initialization, | |||
output_for_initialization, data_loader, | |||
optimizer_rnn, optimizer_output, | |||
scheduler_rnn, scheduler_output, number_of_missing_nodes): | |||
rnn.train() | |||
output.train() | |||
loss_sum = 0 | |||
for batch_idx, data in enumerate(data_loader): | |||
rnn.zero_grad() | |||
output.zero_grad() | |||
x_unsorted = data['x'].float() | |||
y_unsorted = data['y'].float() | |||
data_len = y_len_unsorted = data['len'] | |||
# data_index = 0 | |||
# b = y_unsorted[data_index][:y_len_unsorted[data_index] - 1].cpu() | |||
# tensor_to_graph_converter(b, "Complete Graph") | |||
# **** | |||
x_unsorted, y_unsorted, y_len_unsorted, hidden, initial_y, initial_y_len = \ | |||
data_initializer_for_training(x_unsorted, y_unsorted, y_len_unsorted, | |||
args, rnn_for_initialization, output_for_initialization, | |||
number_of_missing_nodes, False, 0.96) | |||
# ____________________________________________________________________________________________ | |||
# x_unsorted1, y_unsorted1, y_len_unsorted1, hidden, initial_y1, initial_y_len1 = \ | |||
# data_initializer_for_training(x_unsorted, y_unsorted, y_len_unsorted, | |||
# args, rnn_for_initialization, output_for_initialization, | |||
# number_of_missing_nodes, False, 0.96) | |||
# ____________________________________________________________________________________________ | |||
# a = initial_y[data_index][:initial_y_len[data_index]-1].cpu() | |||
# tensor_to_graph_converter(a, "Incomplete Graph") | |||
# b = y_unsorted[data_index][:-1] | |||
# recons = torch.cat((a, b), dim=0) | |||
# tensor_to_graph_converter(recons, "Merged Complete Graph") | |||
# **** | |||
y_len_max = max(y_len_unsorted) | |||
x_unsorted = x_unsorted[:, 0:y_len_max, :] | |||
y_unsorted = y_unsorted[:, 0:y_len_max, :] | |||
# initialize lstm hidden state according to batch size | |||
# rnn.hidden = rnn.init_hidden(batch_size=x_unsorted.size(0)) | |||
# **** | |||
rnn.hidden = hidden | |||
# **** | |||
# sort input | |||
y_len,sort_index = torch.sort(y_len_unsorted,0,descending=True) | |||
y_len = y_len.numpy().tolist() | |||
x = torch.index_select(x_unsorted,0,sort_index) | |||
y = torch.index_select(y_unsorted,0,sort_index) | |||
x = Variable(x).cuda() | |||
y = Variable(y).cuda() | |||
h = rnn(x, pack=True, input_len=y_len) | |||
y_pred = output(h) | |||
y_pred = F.sigmoid(y_pred) | |||
# clean | |||
y_pred = pack_padded_sequence(y_pred, y_len, batch_first=True) | |||
y_pred = pad_packed_sequence(y_pred, batch_first=True)[0] | |||
# use cross entropy loss | |||
# print("y_unsorted: ") | |||
# print(y_unsorted[0]) | |||
# print("y: ") | |||
# print(y[0].cpu()) | |||
true_adj_batch, predicted_adj_batch = make_batch_of_matrices(initial_y, initial_y_len, y.cpu(),y_pred, len(y_pred)) | |||
# graph_show(nx.from_numpy_matrix(true_adj_batch[data_index]), "Complete2") | |||
# import time | |||
# start = time.time() | |||
# print("@@@@@@@@@@@@@@@@@@@@@@@@@") | |||
# print(args.loss) | |||
if args.loss == "graph_matching_loss": | |||
print(graph_matching_loss) | |||
# loss = graph_matching_loss(true_adj_batch, predicted_adj_batch, data_len, len(data_len)) | |||
elif args.loss == "matrix_completion_loss": | |||
print(matrix_completion_loss) | |||
# loss = matrix_completion_loss(true_adj_batch, predicted_adj_batch, len(data_len), | |||
# args.number_of_missing_nodes) | |||
elif args.loss =="GraphRNN_loss": | |||
# print("GraphRNN_loss") | |||
# print(y) | |||
# print(y_pred) | |||
# loss = F.binary_cross_entropy(torch.from_numpy(predicted_adj_batch[0]), torch.from_numpy(true_adj_batch[0])) | |||
# loss.requires_grad = True | |||
# print("true_adj_batch: ") | |||
# print(true_adj_batch[0]) | |||
# print("y: ") | |||
# print(y[0]) | |||
# print("predicted_adj_batch: ") | |||
# print(predicted_adj_batch[0]) | |||
# print("y_pred:") | |||
# print(y_pred[0]+0) | |||
# print("**************************************************************") | |||
# loss = GraphRNN_loss(true_adj_batch, predicted_adj_batch, len(data_len), args.number_of_missing_nodes); | |||
# loss = binary_cross_entropy_weight(predicted_adj_batch[0], true_adj_batch[0]) | |||
# print("**** GraphRNN_loss: ") | |||
# print(loss) | |||
# row_index = [0, 2] | |||
# col_index = [1, 3] | |||
# print("**************************") | |||
# print(y_pred[0][row_index, col_index]) | |||
# print(np.shape(y_pred[0])[1]) | |||
loss = GraphRNN_loss2(true_adj_batch, predicted_adj_batch, y_pred, y, len(y_pred), args.number_of_missing_nodes) | |||
# loss = binary_cross_entropy_weight(y_pred[0][row_index, col_index], y[0][row_index, col_index]) | |||
# print("**** main_loss: ") | |||
# print(loss) | |||
# print("*** epoch : " + str(epoch) + "*** loss: " + str(loss.data)) | |||
# break | |||
# end = time.time() | |||
# print(end - start) | |||
# print("y_pred") | |||
# print(y_pred[0]) | |||
# print("y") | |||
# print(y[0]) | |||
# print("***************************************************") | |||
# loss = binary_cross_entropy_weight(y_pred, y) | |||
loss.backward() | |||
# update deterministic and lstm | |||
optimizer_output.step() | |||
optimizer_rnn.step() | |||
scheduler_output.step() | |||
scheduler_rnn.step() | |||
# for p in rnn.parameters(): | |||
# print(p) | |||
# print(p.grad) | |||
# if p.grad is not None: | |||
# print("________________________________________________________") | |||
# print(p.grad.data) | |||
# plot_grad_flow(rnn.named_parameters()) | |||
if epoch % args.epochs_log==0 and batch_idx==0: # only output first batch's statistics | |||
print('Epoch: {}/{}, train loss: {:.6f}, graph type: {}, num_layer: {}, hidden: {}'.format( | |||
epoch, args.epochs,loss.data, args.graph_type, args.num_layers, args.hidden_size_rnn)) | |||
log_value(args.loss + args.fname + args.training_mode + "_ " | |||
"number_of_missing_nodes_" + | |||
str(number_of_missing_nodes), loss.data, epoch * args.batch_ratio + batch_idx) | |||
loss_sum += loss.data | |||
return loss_sum/(batch_idx+1) | |||
def train_for_completion(args, dataset_train, rnn, output, rnn_for_initialization,output_for_initialization): | |||
# check if load existing model | |||
if args.load: | |||
fname = args.model_save_path + args.fname + 'lstm_' + args.graph_completion_string + str(args.load_epoch) + '.dat' | |||
rnn.load_state_dict(torch.load(fname)) | |||
fname = args.model_save_path + args.fname + 'output_' + args.graph_completion_string + str(args.load_epoch) + '.dat' | |||
output.load_state_dict(torch.load(fname)) | |||
args.lr = 0.00001 | |||
epoch = args.load_epoch | |||
print('model loaded!, lr: {}'.format(args.lr)) | |||
else: | |||
epoch = 1 | |||
# initialize optimizer | |||
optimizer_rnn = optim.Adam(list(rnn.parameters()), lr=args.lr) | |||
optimizer_output = optim.Adam(list(output.parameters()), lr=args.lr) | |||
scheduler_rnn = MultiStepLR(optimizer_rnn, milestones=args.milestones, gamma=args.lr_rate) | |||
scheduler_output = MultiStepLR(optimizer_output, milestones=args.milestones, gamma=args.lr_rate) | |||