fixed minor issues

WGS-TB · Apr 13, 2021 · 53ddfe7 · 53ddfe7
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commit 53ddfe7
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Showing 26 changed files with 6,443 additions and 16 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,7 +6,6 @@ test.py
 .idea
 *.m~
 temp_for_test.py
-Results
 gurobi.log
 log.txt
 PaperPlotTable.py

diff --git a/Results/Apr_12_2021_01_10_28/CM.csv b/Results/Apr_12_2021_01_10_28/CM.csv
@@ -0,0 +1,3 @@
+,N,m,s,group_size,seed,max_tests_per_individual,tn,fp,fn,tp,balanced_accuracy,Status,solver_time,time
+0,1000,500,50,8,10,16,950,0,2,48,0.98,101,8.84,9.22
+1,1000,500,50,16,10,16,950,0,1,49,0.99,101,10.11,10.47
diff --git a/Results/Apr_12_2021_01_10_28/Logs/log_1000_16_500_50_10.txt b/Results/Apr_12_2021_01_10_28/Logs/log_1000_16_500_50_10.txt
@@ -0,0 +1,86 @@
+Version identifier: 12.10.0.0 | 2019-11-26 | 843d4de
+CPXPARAM_Read_DataCheck                          1
+CPXPARAM_TimeLimit                               1800
+Found incumbent of value 3000.000000 after 0.00 sec. (0.08 ticks)
+Tried aggregator 1 time.
+MIP Presolve eliminated 0 rows and 274 columns.
+MIP Presolve modified 65 coefficients.
+Reduced MIP has 500 rows, 1226 columns, and 8149 nonzeros.
+Reduced MIP has 1226 binaries, 0 generals, 0 SOSs, and 0 indicators.
+Presolve time = 0.01 sec. (7.14 ticks)
+Probing time = 0.00 sec. (1.26 ticks)
+Tried aggregator 1 time.
+Detecting symmetries...
+Reduced MIP has 500 rows, 1226 columns, and 8149 nonzeros.
+Reduced MIP has 1226 binaries, 0 generals, 0 SOSs, and 0 indicators.
+Presolve time = 0.00 sec. (4.11 ticks)
+Probing time = 0.00 sec. (1.26 ticks)
+Clique table members: 3493.
+MIP emphasis: balance optimality and feasibility.
+MIP search method: dynamic search.
+Parallel mode: deterministic, using up to 8 threads.
+Root relaxation solution time = 0.42 sec. (20.28 ticks)
+
+        Nodes                                         Cuts/
+   Node  Left     Objective  IInf  Best Integer    Best Bound    ItCnt     Gap
+
+*     0+    0                         1937.0000        0.0000           100.00%
+*     0+    0                          737.0000        0.0000           100.00%
+*     0+    0                          701.0000        0.0000           100.00%
+*     0+    0                          680.0000        0.0000           100.00%
+*     0+    0                          653.0000        0.0000           100.00%
+*     0+    0                          601.0000        0.0000           100.00%
+*     0+    0                          577.0000        0.0000           100.00%
+*     0+    0                          547.0000        0.0000           100.00%
+*     0+    0                          528.0000        0.0000           100.00%
+      0     0       51.8279   270      528.0000       51.8279      466   90.18%
+*     0+    0                           73.0000       51.8279            29.00%
+      0     0       60.3981   270       73.0000     Cuts: 195     1110   17.26%
+      0     0       64.3190   270       73.0000     Cuts: 225     1478   11.89%
+      0     0       65.5196   270       73.0000    Covers: 13     1854   10.25%
+      0     0       67.8895   270       73.0000     Cuts: 205     2644    7.00%
+      0     0       71.0209   270       73.0000     Cuts: 210     3479    2.71%
+Detecting symmetries...
+
+Repeating presolve.
+Tried aggregator 1 time.
+MIP Presolve eliminated 2 rows and 343 columns.
+MIP Presolve modified 221 coefficients.
+Reduced MIP has 498 rows, 883 columns, and 5489 nonzeros.
+Reduced MIP has 883 binaries, 0 generals, 0 SOSs, and 0 indicators.
+Presolve time = 0.00 sec. (2.44 ticks)
+Probing time = 0.00 sec. (0.72 ticks)
+Tried aggregator 1 time.
+Detecting symmetries...
+Reduced MIP has 498 rows, 883 columns, and 5489 nonzeros.
+Reduced MIP has 883 binaries, 0 generals, 0 SOSs, and 0 indicators.
+Presolve time = 0.00 sec. (2.85 ticks)
+Represolve time = 0.03 sec. (16.00 ticks)
+Probing time = 0.00 sec. (0.72 ticks)
+Clique table members: 2003.
+MIP emphasis: balance optimality and feasibility.
+MIP search method: dynamic search.
+Parallel mode: deterministic, using up to 8 threads.
+Root relaxation solution time = 0.06 sec. (83.87 ticks)
+
+        Nodes                                         Cuts/
+   Node  Left     Objective  IInf  Best Integer    Best Bound    ItCnt     Gap
+
+*     0+    0                           73.0000       71.0209             2.71%
+      0     0       71.9937    30       73.0000       71.9937     4822    1.38%
+      0     0        cutoff             73.0000                   4827    0.00%
+Elapsed time = 1.23 sec. (584.62 ticks, tree = 0.01 MB, solutions = 11)
+
+Clique cuts applied:  10
+Cover cuts applied:  71
+Mixed integer rounding cuts applied:  118
+Zero-half cuts applied:  4
+
+Root node processing (before b&c):
+  Real time             =    1.23 sec. (584.79 ticks)
+Parallel b&c, 8 threads:
+  Real time             =    0.00 sec. (0.00 ticks)
+  Sync time (average)   =    0.00 sec.
+  Wait time (average)   =    0.00 sec.
+                          ------------
+Total (root+branch&cut) =    1.23 sec. (584.79 ticks)
diff --git a/Results/Apr_12_2021_01_10_28/Logs/log_1000_8_500_50_10.txt b/Results/Apr_12_2021_01_10_28/Logs/log_1000_8_500_50_10.txt
@@ -0,0 +1,49 @@
+Version identifier: 12.10.0.0 | 2019-11-26 | 843d4de
+CPXPARAM_Read_DataCheck                          1
+CPXPARAM_TimeLimit                               1800
+Found incumbent of value 3000.000000 after 0.00 sec. (0.07 ticks)
+Tried aggregator 3 times.
+MIP Presolve eliminated 170 rows and 800 columns.
+MIP Presolve added 230 rows and 0 columns.
+MIP Presolve modified 603 coefficients.
+Aggregator did 83 substitutions.
+Reduced MIP has 477 rows, 612 columns, and 1844 nonzeros.
+Reduced MIP has 612 binaries, 0 generals, 0 SOSs, and 0 indicators.
+Presolve time = 0.01 sec. (9.39 ticks)
+Probing time = 0.00 sec. (0.22 ticks)
+Tried aggregator 1 time.
+Detecting symmetries...
+Reduced MIP has 477 rows, 612 columns, and 1844 nonzeros.
+Reduced MIP has 612 binaries, 0 generals, 0 SOSs, and 0 indicators.
+Presolve time = 0.00 sec. (1.25 ticks)
+Probing time = 0.00 sec. (0.22 ticks)
+Clique table members: 543.
+MIP emphasis: balance optimality and feasibility.
+MIP search method: dynamic search.
+Parallel mode: deterministic, using up to 8 threads.
+Root relaxation solution time = 0.00 sec. (0.94 ticks)
+
+        Nodes                                         Cuts/
+   Node  Left     Objective  IInf  Best Integer    Best Bound    ItCnt     Gap
+
+*     0+    0                         1567.0000        0.0000           100.00%
+*     0+    0                          197.0000        0.0000           100.00%
+      0     0       60.3333     2      197.0000       60.3333      112   69.37%
+*     0+    0                           64.0000       60.3333             5.73%
+      0     0       62.0000     2       64.0000       Cuts: 3      115    3.12%
+      0     0        cutoff             64.0000                    116    0.00%
+Elapsed time = 0.03 sec. (17.03 ticks, tree = 0.01 MB, solutions = 3)
+
+Clique cuts applied:  1
+Cover cuts applied:  1
+Implied bound cuts applied:  2
+Gomory fractional cuts applied:  1
+
+Root node processing (before b&c):
+  Real time             =    0.03 sec. (17.11 ticks)
+Parallel b&c, 8 threads:
+  Real time             =    0.00 sec. (0.00 ticks)
+  Sync time (average)   =    0.00 sec.
+  Wait time (average)   =    0.00 sec.
+                          ------------
+Total (root+branch&cut) =    0.03 sec. (17.11 ticks)
diff --git a/Results/Apr_12_2021_01_10_28/config.yml b/Results/Apr_12_2021_01_10_28/config.yml
@@ -0,0 +1,68 @@
+---
+design:
+  groups:
+    #input: 'design_matrix.csv'
+    #alternative_module: ['generate_groups_alt','gen_measurement_matrix_alt']
+    params:
+      seed: 10
+      N: 1000
+      'm': 500
+      'verbose': False
+      'run_ID': 'debugging'
+      'plotting': False
+      'saving': True
+      'graph_gen_method': 'no_multiple'
+      'group_size':
+        'mode': 'list'
+        'values': [8,16]
+      'max_tests_per_individual':
+        'mode': 'list'
+        'values': [16]
+      'save_to_file': False
+  'individual_status':
+    #input: 'individual_status.csv'
+    params:
+      seed: 10
+      'verbose': False
+      's':
+        'mode': 'list'
+        'values': [50]
+  'test_results':
+    #'input': 'test_results.csv'
+    'params':
+      'test_noise_methods': ['permutation']
+      'permutation_noise_prob':
+        'mode': 'list'
+        'values': [0.01]
+      'theta_l':
+        'mode': 'list'
+        'values': [0.00]
+      'theta_u':
+        'mode': 'list'
+        'values': [0.0625]
+      'binary_symmetric_noise_prob':
+        'mode': 'list'
+        'values': [0.26]
+
+decode:
+  'decoder':
+    #alternative_module: ['group_testing_decoder','GroupTestingDecoder']
+    params:
+      'lambda_w': 1
+      'lambda_e': 4
+      'defective_num_lower_bound': null
+      'sensitivity_threshold': null
+      'specificity_threshold': null
+      'is_it_noiseless': False
+      'lp_relaxation': False
+      'solver_name': 'CPLEX_PY'
+      'solver_options':
+        'timeLimit': 1800
+      'lambda_selection': False
+      'number_of_folds': 2
+      'cv_param':
+        'lambda_e': [0.125,0.25,0.5,1,2,4,8]
+    #'mip':True
+  'evaluation':
+    #'eval_metric': 'recall'
+    'eval_metric': 'balanced_accuracy'
diff --git a/Results/Apr_12_2021_01_10_28/opts.csv b/Results/Apr_12_2021_01_10_28/opts.csv
@@ -0,0 +1,3 @@
+,generate_groups,generate_individual_status,generate_test_results,test_results,seed,N,m,verbose,run_ID,plotting,saving,graph_gen_method,group_size,max_tests_per_individual,save_to_file,s,test_noise_methods,permutation_noise_prob,theta_l,theta_u,binary_symmetric_noise_prob
+0,generate,generate,generate,True,10,1000,500,False,debugging,False,True,no_multiple,8,16,False,50,['permutation'],0.01,0.0,0.0625,0.26
+1,generate,generate,generate,True,10,1000,500,False,debugging,False,True,no_multiple,16,16,False,50,['permutation'],0.01,0.0,0.0625,0.26
diff --git a/Results/Apr_12_2021_01_10_56/CM.csv b/Results/Apr_12_2021_01_10_56/CM.csv
@@ -0,0 +1,3 @@
+,N,m,s,group_size,seed,max_tests_per_individual,tn,fp,fn,tp,balanced_accuracy,Status,solver_time,time
+0,1000,500,50,8,10,16,950,0,2,48,0.98,101,49.42,49.88
+1,1000,500,50,16,10,16,950,0,1,49,0.99,101,69.11,69.56
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,7 +6,6 @@ test.py @@
     .idea
     *.m~
     temp_for_test.py
-    Results
     gurobi.log
     log.txt
     PaperPlotTable.py
@@ Expand Down @@