adding optimization code

BrentLab · Sep 26, 2020 · 833dc0a · 833dc0a
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diff --git a/TFA_Optimization/README.md b/TFA_Optimization/README.md
@@ -47,6 +47,7 @@ python TFAinference.py -e hkMatrixE_optimize.csv -c hkSignedBinaryCS.csv -i 20 -
 
 
 Expected printed output:
+
 **the numbers won't be exactly the same because a new random set of starting CS values is generated with each execution**
 
     Variance explained and error from random CS values:  -2369.709 3293052.697 
@@ -70,41 +71,21 @@ Expected printed output:
 Expected file outputs:
 
 logFiles/ExampleCSiteration0.csv - ExampleCSiteration19.csv
-
-    these are the CS values inferred across 20 iterations
-
 logFiles/ExampleTFAiteration0.csv - ExampleTFAiteration19.csv
 
-    these are the TFA values inferred across 20 iterations
+    these are the CS/TFA values inferred across 20 iterations
 
 logFiles/ExampleCS.log
-
-    this is the gurobi output when optimizing CS values
-    logged output from each iteration is appended to the end of this file
-
 logFiles/ExampleTFA.log
 
-    this is the gurobi output when optimizing TFA values
-    logged output from each iteration is appended to the end of this file
-
-logFiles/ExampleCrossCheck.log
-
-    this is the gurobi output when optimizing TFA values for the optional second expression dataset
+    this is the gurobi output when optimizing CS values / TFA values / TFA values for the optional -v input
     logged output from each iteration is appended to the end of this file
 
 modelFiles/ExampleCS.lp
-
-    this is the model file created for gurobi to optimize CS values
-    at each iteration, the entire file is updated to match the current model
-
 modelFiles/ExampleTFA.lp
-
-    this is the model file created for gurobi to optimize TFA values
-    at each iteration, the entire file is updated to match the current model
-
 modelFiles/ExampleCrossCheck.lp
 
-    this is the model file created for gurobi to optimize TFA values for the optional dataset
+    this is the model file created for gurobi to optimize CS values / TFA values / TFA values for the optional -v input
     at each iteration, the entire file is updated to match the current model
 
 
diff --git a/TFA_Optimization/logFiles/ExampleCS.log b/TFA_Optimization/logFiles/ExampleCS.log
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration0.csv b/TFA_Optimization/logFiles/ExampleCSiteration0.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration1.csv b/TFA_Optimization/logFiles/ExampleCSiteration1.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration10.csv b/TFA_Optimization/logFiles/ExampleCSiteration10.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration11.csv b/TFA_Optimization/logFiles/ExampleCSiteration11.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration12.csv b/TFA_Optimization/logFiles/ExampleCSiteration12.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration13.csv b/TFA_Optimization/logFiles/ExampleCSiteration13.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration14.csv b/TFA_Optimization/logFiles/ExampleCSiteration14.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration15.csv b/TFA_Optimization/logFiles/ExampleCSiteration15.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration16.csv b/TFA_Optimization/logFiles/ExampleCSiteration16.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration17.csv b/TFA_Optimization/logFiles/ExampleCSiteration17.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration2.csv b/TFA_Optimization/logFiles/ExampleCSiteration2.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration3.csv b/TFA_Optimization/logFiles/ExampleCSiteration3.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration4.csv b/TFA_Optimization/logFiles/ExampleCSiteration4.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration5.csv b/TFA_Optimization/logFiles/ExampleCSiteration5.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration6.csv b/TFA_Optimization/logFiles/ExampleCSiteration6.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration7.csv b/TFA_Optimization/logFiles/ExampleCSiteration7.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration8.csv b/TFA_Optimization/logFiles/ExampleCSiteration8.csv
diff --git a/TFA_Optimization/logFiles/ExampleCSiteration9.csv b/TFA_Optimization/logFiles/ExampleCSiteration9.csv