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Iraj 4 years ago
parent
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100 changed files with 1857 additions and 603647 deletions
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MissingNodes_SrcCode2014/DumpDataset.mlx View File


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MissingNodes_SrcCode2014/MissingNodes_S8b.m View File

fprintf('testsalam%i', num_missing_nodes); fprintf('testsalam%i', num_missing_nodes);
[data, attData, missing_nodes_mapping] = RemoveRandomNodesWithImages( original_data, original_attData, totalAttNum, num_missing_nodes, missing_nodes_mapping, numImagesProfiles ); [data, attData, missing_nodes_mapping] = RemoveRandomNodesWithImages( original_data, original_attData, totalAttNum, num_missing_nodes, missing_nodes_mapping, numImagesProfiles );
else else
%Sigal 13.10.13 - TODO - add option to pre selected missing node %Sigal 13.10.13 - TODO - add option to pre selected missing node
%Sigal - 23.1.14 - %%%%TODO - add option for images %Sigal - 23.1.14 - %%%%TODO - add option for images

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MissingNodes_SrcCode2014/RemoveRandomNodesWithImages.m View File

for i=1:num_nodes_to_remove for i=1:num_nodes_to_remove
valid_nodes = find(missing_nodes_all_neighbors~=1); valid_nodes = find(missing_nodes_all_neighbors~=1);
<<<<<<< HEAD
if(size(valid_nodes,2) < 1) if(size(valid_nodes,2) < 1)
fprintf('Full Graph') fprintf('Full Graph')
end end
inx = ceil(rand(1)*size(valid_nodes,2)); inx = ceil(rand(1)*size(valid_nodes,2));
node = valid_nodes(inx); node = valid_nodes(inx);
=======
%inx = ceil(rand(1)*size(valid_nodes,2));
inx = size(data,2)-1;
%node = valid_nodes(inx);
node = size(data,2);
>>>>>>> 3750fcfc8ca443a312af79261f66978da7181c08
%sigal - 23.1.14 - choose image profile %sigal - 23.1.14 - choose image profile
profile = ceil(rand(1)*size(imagesProfiles,2)); profile = ceil(rand(1)*size(imagesProfiles,2));
newNode = [node;imagesProfiles(profile)]; newNode = [node;imagesProfiles(profile)];

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MissingNodes_SrcCode2014/RunExpSrv8s.m View File

% fprintf('RunExpSrv8s:Invalid netSize %d.\n',netSize); % fprintf('RunExpSrv8s:Invalid netSize %d.\n',netSize);
% return; % return;
% end % end
<<<<<<< HEAD
ds_str = 'in/'; ds_str = 'in/';
num_missing_nodes_arr = [2]; num_missing_nodes_arr = [2];
=======
ds_str = 'graph_production/produced_graphs/';
num_missing_nodes_arr = [1];
>>>>>>> 3750fcfc8ca443a312af79261f66978da7181c08
rootDir = '../'; rootDir = '../';
if(iter == 0) if(iter == 0)
copyfile('../output/graphed_0.mat',file_name); copyfile('../output/graphed_0.mat',file_name);
end end
<<<<<<< HEAD
LogMsg(sprintf('Results for file %s,iter %d at %s',file,iter,out_file)); LogMsg(sprintf('Results for file %s,iter %d at %s',file,iter,out_file));
%fprintf('Completed RunExperiment cycle - results at %s.\n',out_file); %fprintf('Completed RunExperiment cycle - results at %s.\n',out_file);
end end
catch catch
fprintf('An Error Occured!!!!!') fprintf('An Error Occured!!!!!')
=======
end
% run algorithm (file load is done internaly)
[rand_score,purity,p_triads,missing_nodes_mapping,removed_nodes] = MissingNodes_S8b(datasetDir, file, ...
attributes, attUpperRange, attWeight, addMissingAtt, normFactorVec, affinities, num_missing_nodes_arr, attAffinityThreshold, ...
imagesData, numImagesProfiles, imgMissProb, imgSimType, imgSimProbDiff, percentKnownPHsVec, dumpGED, dump_data_dir, iter);
%[rand_score,purity,p_triads,missing_nodes_mapping,removed_nodes] = MissingNodes_Sparse(datasetDir, file, affinities, 1);
% dump graph data for KronEM runs
if dumpKronEM == 1
DumpDataset(datasetDir, file, iter, removed_nodes, dumpFilePath);
end
% save results
out_file = sprintf('%sres_%s_%s.mat', results_dir, file, date_now);
save(out_file);
file_name = sprintf('%s%s','D:\Uni\sharif\Project\SAMI\Code\SAMI\output\mine\',file);
if(iter == 1)
copyfile('D:\Uni\sharif\Project\SAMI\Code\SAMI\output\graphed_1.mat',file_name);
end
LogMsg(sprintf('Results for file %s,iter %d at %s',file,iter,out_file));
%fprintf('Completed RunExperiment cycle - results at %s.\n',out_file);
>>>>>>> 3750fcfc8ca443a312af79261f66978da7181c08
end end
% beep; % beep;

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MissingNodes_SrcCode2014/_Log/log.txt
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README.md View File

The "src" folder is the source code of SAMI paper which has seen some minor changes
The "MissingNodes_SrcCode2014" folder is the source code of SAMI paper which has seen some minor changes
from the original received version. from the original received version.
The "codes" folder is the folder containing the following files:
1.adjlisttext_tonxgraph.py: gets an adj. list as input file and gives out the visualized
graph
2.mat_tonxgraph.py: gets a .mat file as input file and gives out the visualized graph
3.mae.py: computes mae of two graphs given their .mat adj matrix file


For using the source code you must pay attention to two files: "RunExpSrv8s" and
"MissingNodes_S8b". The first one is the function which sets up the files and
calls the main function i.e. "MissingNodes_S8b".
**Running the project**
For running the source code you must use a command like "RunExpSrv8s('0','0','1')" where first parameter shows start of iteration,
second parameter shows end of iteration and last param is an arbitrary number.


**Input**
You must place all input files in a folder named "in" in root directory of project.


For having your own dataset run on this code you should know the below variables:

*RUNEXPSRV_8S.m
1. num_missing_nodes_arr: number of randomly removed nodes on each iteration
2. ds_*: array of node numbers of your input arr
3. ds_str: dataset path as a string
4. root_dir
5. file_prefix: file name prefix of the input files

*MISSINGNODES_S8B
1. k: filename postfix for saving
2. clusters_out: true and predicted graph saved as .mat file
3. graphs_out: 4 graphs including {original, predicted, predicted permuted,
original permuted} as .mat file


*grid dataset is run on the src code as an example
**Calcuating MAE**
For calculating the MEA you must first run the project to get the output then run the python code named "calc_mae.py"

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calc_mae.py View File

import numpy as np
import networkx as nx
import matplotlib.pyplot as plt
import scipy.io as sp
import os

path = 'output\mine'
missing_node_count = 2
mae_list = list()
for filename in os.listdir(path):
adj_matrix_orig = sp.loadmat(path + '\\' + filename)['remapped_data'].A
adj_matrix_p = sp.loadmat(path + '\\' + filename)['out_data'].A
mae = np.sum(abs(adj_matrix_orig - adj_matrix_p))
mae = mae / (adj_matrix_p.shape[0] * 2 * missing_node_count)
mae_list.append(mae)

print(np.mean(mae_list))

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7 9

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_113__.txt.mat_0_1_miss.txt View File

8 4

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_121__.txt.mat_0_1_miss.txt View File

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_150__.txt.mat_0_1_miss.txt View File

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3 2

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_180__.txt.mat_0_1_miss.txt View File

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_310__.txt.mat_0_1_miss.txt View File

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_330__.txt.mat_0_1_miss.txt View File

12 1

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_330__.txt.mat_0_orig_edges.txt View File

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in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_45__.txt.mat_0_1_miss.txt View File

12 1

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4 7
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4 9
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5 2
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5 7
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9 10
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10 3
10 4
10 8
10 9
10 11
11 3
11 4
11 8
11 9
11 10

+ 1
- 0
in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_48__.txt.mat_0_1_miss.txt View File

10 3

+ 60
- 0
in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_48__.txt.mat_0_1_part_edges.txt View File

0 1
0 3
0 4
0 5
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1 3
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4 8
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5 8
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6 8
6 10
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7 4
7 5
7 8
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8 1
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8 4
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8 7
8 10
8 11
10 0
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10 6
10 8
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11 3
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+ 84
- 0
in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_48__.txt.mat_0_orig_edges.txt View File

0 1
0 2
0 3
0 4
0 5
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10 3
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11 3
11 6
11 8
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11 10

+ 1
- 0
in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_4__.txt.mat_0_1_miss.txt View File

7 9

+ 54
- 0
in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_4__.txt.mat_0_1_part_edges.txt View File

0 1
0 2
0 3
0 4
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+ 76
- 0
in/testImg_noTh_/F922_I1P1M0_Iter_00/dumpKronEM_2019_12_10_736_2.178/testgraph_12_4__.txt.mat_0_orig_edges.txt View File

0 1
0 2
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