Status
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Terminal Output
| Builder file created | |
| Configuration file | |
| ProBound run | |
| Sequence logos |
Terminal output
Pipeline Output:
> Converts the configuration file to work on run server, checks input OK > Builds configuration file OK > Runs ProBound OK > Runs Model Viewer OK
Configuration Builder File
±
ProBound builder configuration file:
[{"function": "optimizerSetting", "nThreads": 20, "lambdaL2": 1e-06}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGTGGGCCTGG", "nColumns": 2, "transliterate": {"out": [], "in": []}, "modeledColumns": [0, 1], "countTableFile": "jobs/85fb9ae0757b/countTable.0.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGGCACCCTGG", "nColumns": 2, "transliterate": {"out": ["dh"], "in": ["CG"]}, "modeledColumns": [0, 1], "countTableFile": "jobs/85fb9ae0757b/countTable.1.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGCAGTCCTGG", "nColumns": 2, "transliterate": {"out": ["c"], "in": ["C"]}, "modeledColumns": [0, 1], "countTableFile": "jobs/85fb9ae0757b/countTable.2.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGAGTGCCTGG", "nColumns": 2, "transliterate": {"out": ["a"], "in": ["A"]}, "modeledColumns": [0, 1], "countTableFile": "jobs/85fb9ae0757b/countTable.3.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addSELEX"}, {"function": "addSELEX"}, {"function": "addSELEX"}, {"function": "addSELEX"}, {"function": "setAlphabet", "letterComplement": "C-G,A-T,a-t,c-g,d-h", "letterOrder": "ACGTacgtdh"}, {"function": "addNS"}, {"function": "addBindingMode", "flankLength": 3, "dinucleotideDistance": 1, "size": 12}, {"function": "bindingModeSeed", "index": 1, "mononucleotideIUPAC": "NNTTGCGCAANN"}, {"function": "bindingModeConstraints", "index": 1, "maxFlankLength": -1, "fittingStages": [{"optimizeFlankLength": true}]}, {"function": "symmetry", "index": 1, "symmetryString": "1:12:1"}, {"function": "output", "outputPath": "jobs/85fb9ae0757b", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]Configuration File
±
ProBound configuration file:
{
"modelSeeding": {"bindingModes": [
{"seedScale": 1},
{
"mononucleotideIUPAC": "NNTTGCGCAANN",
"seedScale": 1
}
]},
"optimizerSetting": {
"nThreads": 20,
"likelihoodThreshold": 0,
"lambdaL2": 1.0E-6,
"patternSearchSettings": {},
"pseudocount": 0,
"minimizerType": "lbfgs",
"nRetries": 3,
"hkSettings": {},
"output": {
"storeHessian": false,
"outputPath": "jobs/85fb9ae0757b",
"printTrajectory": false,
"baseName": "fit",
"printPSAM": false,
"verbose": true
},
"lbfgsSettings": {},
"sgdSettings": {},
"fixedLibrarySize": false,
"expBound": 40,
"slbfgs_plsSettings": {},
"slbfgsSettings": {}
},
"modelSettings": {
"enrichmentModel": [
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
}
],
"letterOrder": "ACGTacgtdh",
"countTable": [
{
"leftFlank": "GGTAGTGGAGGTGGGCCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/85fb9ae0757b/countTable.0.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGGCACCCTGG",
"transliterate": {
"in": ["CG"],
"out": ["dh"]
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/85fb9ae0757b/countTable.1.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGCAGTCCTGG",
"transliterate": {
"in": ["C"],
"out": ["c"]
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/85fb9ae0757b/countTable.2.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGAGTGCCTGG",
"transliterate": {
"in": ["A"],
"out": ["a"]
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/85fb9ae0757b/countTable.3.tsv.gz"
}
],
"bindingModeInteractions": [],
"bindingModes": [
{
"size": 0,
"fitLogActivity": true,
"flankLength": 0,
"dinucleotideDistance": 0,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 12,
"fitLogActivity": true,
"flankLength": 3,
"dinucleotideDistance": 1,
"positionBias": false,
"singleStrand": false,
"modifications": []
}
],
"letterComplement": "C-G,A-T,a-t,c-g,d-h"
},
"modelFittingConstraints": {
"enrichmentModel": [
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
}
],
"nShifts": 0,
"countTable": [
{},
{},
{},
{}
],
"addBindingModesSequentially": true,
"flankLengths": [0],
"bindingModeInteractions": [],
"singleModeLengthSweep": false,
"bindingModes": [
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
},
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"symmetryString": "1:12:1",
"optimizeFlankLength": false,
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [{"optimizeFlankLength": true}],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
}
]
}
}Probound Text Output
±
Output from ProBound:
> Reading configuration JSON object and validating general schema.
> Validating configuration schema.
{"enrichmentModel":[{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}],"nShifts":0,"countTable":[{},{},{},{}],"addBindingModesSequentially":true,"flankLengths":[0],"bindingModeInteractions":[],"singleModeLengthSweep":false,"bindingModes":[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"1:12:1","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false}]}
Entry=bindingModes, aEntry=[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"1:12:1","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false}]
Entry=bindingModeInteractions, aEntry=[]
Entry=countTable, aEntry=[{},{},{},{}]
Entry=enrichmentModel, aEntry=[{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}]
> Builds likelihood object.
>> Creating CombinedLikelihood object.
Alphabet
========
Letter Complement: C-G,A-T,a-t,c-g,d-h
Letter Order: ACGTacgtdh
Optimizer settings:
===================
lambdaL2 = 1.0E-6
pseudocount = 0.0
expBound = 40.0
fixedLibrarySize = false
>> Determining fitting order.
Summary of experiments
======================
Experiment 0:
-------------
Count table: Count table 0
Enrichment model: SELEX enrichment model 0
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 1:
-------------
Count table: Count table 1
Enrichment model: SELEX enrichment model 1
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 2:
-------------
Count table: Count table 2
Enrichment model: SELEX enrichment model 2
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 3:
-------------
Count table: Count table 3
Enrichment model: SELEX enrichment model 3
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
> Builds optimizer.
> Using LBFGS.
> Starting optimization.
==================================
== Starts fiting Binding mode 0 ==
==================================
> Optimizing h (component0-0-h).
>> Starting new optimization: component0-0-h. (2021-05-21 21:19:09.34).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 13.050499929814006
gradient = {0.4985,-0.4985,0.4985,-0.4985,0.4985,-0.4985,0.4985,-0.4985}
gradient norm = 1.4100602185777915
Starting Function Value: 13.050499929814006
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 6.170494707327713 5.000000000000000 3.545947849690474 1.278334961008242
2 5 5.031019873074111 7.517917534531883 0.154935858570556 1.163311226104668
3 6 2.793746661962761 3.581877632807754 1.000000000000000 0.143284710075567
4 7 2.775878479997686 0.392798021126114 1.000000000000000 0.052597328107552
5 8 2.773110112018768 0.105472286222861 1.000000000000000 0.000114780068703
6 9 2.773110098844394 0.105472286222861 1.000000000000000 0.000000052794758
Convergence criteria met.
After: gradient norm = 5.279475816993409E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {-3.2610,3.2610}
Count Table 1:
---------------
h: {-3.2610,3.2610}
Count Table 2:
---------------
h: {-3.2610,3.2610}
Count Table 3:
---------------
h: {-3.2610,3.2610}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-6.5221,-6.5221}
Activity(exp=1): {-6.5221,-6.5221}
Activity(exp=2): {-6.5221,-6.5221}
Activity(exp=3): {-6.5221,-6.5221}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000}
Dinucleotide(d=1): 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Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
> Initial optimization (component0-1-f0).
>> Starting new optimization: component0-1-f0. (2021-05-21 21:19:11.189).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[8,9]},{"h":[10,11]},{"h":[12,13]},{"h":[14,15]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.7731100988444175
gradient = {-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 4.700040924393198E-5
Starting Function Value: 2.7731100988444175
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.773110092434357 0.000270851001064 5.762737078698412 0.000085455608652
2 8 2.773106768121861 0.082199213008199 341.00000000000000 0.000310774209718
3 9 2.772941435826315 5.832078915517512 1.000000000000000 0.007777418643765
4 10 2.772809160829440 6.647970811524455 1.000000000000000 0.009442407825165
5 11 2.772705872154199 7.140759714578853 1.000000000000000 0.005518268571886
6 12 2.772686246294128 1.426838342995848 1.000000000000000 0.001379466106936
7 13 2.772684747883667 0.357887055490941 1.000000000000000 0.000076284004272
8 14 2.772684722382377 0.136218290172200 1.000000000000000 0.000004658915009
9 15 2.772684722239776 0.011131578210290 1.000000000000000 0.000000449571246
Gradient = {1.1264e-10,-1.2947e-07,1.1264e-10,-1.2972e-07,1.1264e-10,-1.2991e-07,1.1264e-10,-1.2956e-07,1.2964e-07,-1.2964e-07,1.2989e-07,-1.2989e-07,1.3008e-07,-1.3008e-07,1.2973e-07,-1.2973e-07}
pCurr = {-5.7043e-05,-5.6877e-05,-5.7043e-05,-5.6873e-05,-5.7043e-05,-5.6870e-05,-5.7043e-05,-5.6875e-05,-2.8688e-05,2.8688e-05,-2.8692e-05,2.8692e-05,-2.8695e-05,2.8695e-05,-2.8690e-05,2.8690e-05}
grad*pCur = -3.282874583433699E-13
parameters = {5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,2.8332e-05,-2.8331e-05,2.8332e-05,-2.8332e-05,2.8332e-05,-2.8332e-05,2.8332e-05,-2.8332e-05}
|grad|/|x| = 4.495712456207589E-7
>>>> Exception caugth. Parameters reverted.
> Parameter: {5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,2.8332e-05,-2.8331e-05,2.8332e-05,-2.8332e-05,2.8332e-05,-2.8332e-05,2.8332e-05,-2.8332e-05}
> Gradient: {1.1264e-10,-1.2947e-07,1.1264e-10,-1.2972e-07,1.1264e-10,-1.2991e-07,1.1264e-10,-1.2956e-07,1.2964e-07,-1.2964e-07,1.2989e-07,-1.2989e-07,1.3008e-07,-1.3008e-07,1.2973e-07,-1.2973e-07}
>>>> Re-trying (1/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,5.6319e-05,5.6145e-05,2.8332e-05,-2.8331e-05,2.8332e-05,-2.8332e-05,2.8332e-05,-2.8332e-05,2.8332e-05,-2.8332e-05}
> Gradient: {1.1264e-10,-1.2947e-07,1.1264e-10,-1.2972e-07,1.1264e-10,-1.2991e-07,1.1264e-10,-1.2956e-07,1.2964e-07,-1.2964e-07,1.2989e-07,-1.2989e-07,1.3008e-07,-1.3008e-07,1.2973e-07,-1.2973e-07}
>>>> Re-trying (2/3).
Starting Function Value: 2.772684722239776
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 5 2.772684722239765 0.000000011471635 0.025516835223425 0.000000440967504
2 6 2.772684722239744 0.000000011471635 1.000000000000000 0.000000000356182
Convergence criteria met.
After: gradient norm = 3.5618244822987005E-10
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0000,-0.0000}
Count Table 1:
---------------
h: {0.0000,-0.0000}
Count Table 2:
---------------
h: {0.0000,-0.0000}
Count Table 3:
---------------
h: {0.0000,-0.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000}
Dinucleotide(d=1): 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Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Suggested variations:
key=0;0;0, description = Initial model.
> Optimizing variation "Initial model." (component0-2-variation0).
>> Starting new optimization: component0-2-variation0. (2021-05-21 21:19:16.093).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[8,9]},{"h":[10,11]},{"h":[12,13]},{"h":[14,15]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.7726847222397444
gradient = {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 3.561824478632604E-10
Already at minimum!
After: gradient norm = 3.561824478632604E-10
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0000,-0.0000}
Count Table 1:
---------------
h: {0.0000,-0.0000}
Count Table 2:
---------------
h: {0.0000,-0.0000}
Count Table 3:
---------------
h: {0.0000,-0.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000}
Dinucleotide(d=1): 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Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component0-2-variation0.
> No varitions possible for Binding mode 0.
> Optimizing the full model (component0-4-all).
>> Starting new optimization: component0-4-all. (2021-05-21 21:19:16.197).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[8,9]},{"h":[10,11]},{"h":[12,13]},{"h":[14,15]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.7726847222397444
gradient = {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 3.5618244863819044E-10
Already at minimum!
After: gradient norm = 3.5618244863819044E-10
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0000,-0.0000}
Count Table 1:
---------------
h: {0.0000,-0.0000}
Count Table 2:
---------------
h: {0.0000,-0.0000}
Count Table 3:
---------------
h: {0.0000,-0.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000}
Dinucleotide(d=1): 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Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
==================================
== Starts fiting Binding mode 1 ==
==================================
> Optimizing h (component1-0-h).
>> Starting new optimization: component1-0-h. (2021-05-21 21:19:17.493).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 6.644522997697911
gradient = {-0.4790,0.4790,-0.4580,0.4580,-0.4435,0.4435,-0.4369,0.4369}
gradient norm = 1.2858938938463065
Starting Function Value: 6.644522997697911
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 5.409531814438447 1.000000000000000 0.777669141120848 1.173982314300481
2 4 2.932514597842342 3.378104252409563 0.280648720214209 0.297831388909606
3 5 2.850883163370067 0.943922337839465 1.000000000000000 0.128956303227025
4 6 2.832704503036311 0.285185384380070 1.000000000000000 0.002088869948669
5 7 2.832699994262679 0.005049160025242 1.000000000000000 0.000447259333674
6 8 2.832699790145977 0.001167403837976 1.000000000000000 0.000108969435447
7 9 2.832699777265116 0.000241743453303 1.000000000000000 0.000004365306018
8 10 2.832699777244520 0.000241743453303 1.000000000000000 0.000000207784008
Convergence criteria met.
After: gradient norm = 2.0778400750437186E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.9820,-1.9820}
Count Table 1:
---------------
h: {1.6872,-1.6872}
Count Table 2:
---------------
h: {1.4866,-1.4866}
Count Table 3:
---------------
h: {1.4242,-1.4242}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000}
Dinucleotide(d=1): 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Activity(exp=0): {6.0786,6.0786}
Activity(exp=1): {6.0786,6.0786}
Activity(exp=2): {6.0786,6.0786}
Activity(exp=3): {6.0786,6.0786}
> Initial optimization (component1-1-f1).
>> Starting new optimization: component1-1-f1. (2021-05-21 21:19:22.071).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.8326997772445357
gradient = {0.0282,-0.0136,-0.0069,-0.0030,-0.0049,-0.0060,-0.0025,-0.0061,0.0118,0.0305,0.0357,-0.0350,-0.0081,-0.0038,-0.0041,-0.0049,-0.0033,-0.0063,0.0271,0.0304,0.0276,-0.0057,-0.0102,-0.0055,-0.0062,-0.0041,-0.0041,-0.0134,0.0152,0.0337,0.0237,-0.0038,-0.0110,-0.0054,-0.0055,-0.0062,-0.0044,-0.0108,0.0357,0.0150,0.0212,-0.0407,-0.0124,-0.0054,-0.0092,-0.0055,-0.0021,-0.0132,-0.0082,0.1029,0.0948,-0.0091,-0.0136,-0.0039,-0.0432,-0.0092,-0.0045,-0.0125,-0.0029,0.0317,0.0000,0.0008,0.0000,0.0028,0.0000,0.0035,0.0000,0.0067,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 0.19296503378373964
Starting Function Value: 2.8326997772445357
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.822170463517949 0.105169683624661 0.545019382851128 0.248824762142205
2 4 2.809231024388729 0.092089042848549 1.000000000000000 0.229292286432901
3 5 2.735429538586571 1.191885498737644 1.000000000000000 0.248257664837406
4 6 2.725379999715964 0.129115947039556 1.000000000000000 0.070338868425748
5 7 2.720398658233052 0.119693952559609 1.000000000000000 0.095794065902478
6 8 2.713127195480425 0.249741733963439 1.000000000000000 0.138429698019125
7 9 2.701446271274253 0.372910893804246 1.000000000000000 0.131484980002827
8 10 2.693498927668481 0.533003382781785 1.000000000000000 0.116136682872148
9 11 2.688037951768787 0.135586826203399 1.000000000000000 0.038153880660405
10 12 2.686478671993983 0.092380072764192 1.000000000000000 0.028097632209213
11 13 2.684102738519536 0.177377229538759 1.000000000000000 0.051706669218847
12 14 2.682074267294574 0.233813361734655 1.000000000000000 0.057888382822764
13 15 2.679162639822209 0.323235738167507 1.000000000000000 0.033230455022142
14 16 2.677084401482982 0.353677607882803 1.000000000000000 0.018999445425202
15 17 2.676106289358133 0.150239366056900 1.000000000000000 0.022839919565109
16 18 2.674719086595299 0.204414562081460 1.000000000000000 0.028025361608847
17 19 2.672401699461645 0.388652929875292 1.000000000000000 0.022429991805670
18 20 2.670786322624565 0.300017044931844 1.000000000000000 0.019652338392613
19 21 2.669850195137686 0.155246225130207 1.000000000000000 0.017317908946946
20 22 2.669432582741651 0.111724911536255 1.000000000000000 0.007991263481917
21 23 2.669243374987359 0.057727341443519 1.000000000000000 0.007190460527387
22 24 2.668807755026196 0.190115958958514 1.000000000000000 0.006727261527026
23 25 2.668133279744240 0.267529963603705 1.000000000000000 0.008775233789384
24 26 2.667189700123002 0.622800544617111 1.000000000000000 0.033109697314146
25 27 2.666454855073478 0.288926225673563 1.000000000000000 0.025267635239160
26 28 2.665404080684432 0.352297913074428 1.000000000000000 0.027020939808950
27 30 2.663686493896524 0.581096477836280 0.492570778228667 0.050720287123853
28 31 2.661512766881710 0.863729379762748 1.000000000000000 0.045629715227032
29 32 2.658948555393587 0.227763752357986 1.000000000000000 0.050806587426243
30 34 2.658126971630143 0.185468236967852 0.374219044689913 0.023114219013960
31 35 2.656740205064866 0.478650984180818 1.000000000000000 0.078166236791679
32 36 2.655918189014535 0.084987994908938 1.000000000000000 0.049717911356620
33 37 2.654534646154074 0.258508298530829 1.000000000000000 0.031589205148683
34 38 2.652081710031569 0.514206456846110 1.000000000000000 0.045925272278967
35 39 2.649987952971548 0.824776345211354 1.000000000000000 0.095731858927011
36 40 2.644492263538044 0.384544015084288 1.000000000000000 0.033739705015721
37 41 2.640744179191978 0.334265100824167 1.000000000000000 0.023574556153404
38 42 2.638729471521285 0.915162176435179 1.000000000000000 0.074302695081934
39 43 2.635571169679251 0.283705027685509 1.000000000000000 0.028222096216263
40 44 2.634193504093291 0.190339949926251 1.000000000000000 0.021488872355413
41 45 2.631375771174051 0.723991648532891 1.000000000000000 0.032771561733064
42 46 2.629272088967129 0.430043411357233 1.000000000000000 0.026403393371284
43 47 2.626275673054673 0.774277540302441 1.000000000000000 0.016854598392549
44 48 2.624834209824322 0.536677140576799 1.000000000000000 0.010952282500157
45 49 2.623914143870795 0.667575675137410 1.000000000000000 0.016577175540493
46 50 2.623011563293689 0.454897185130310 1.000000000000000 0.011246750885232
47 51 2.622192607718762 0.513110096134934 1.000000000000000 0.008962045463686
48 52 2.621238806462942 0.629645294957318 1.000000000000000 0.011973875120546
49 53 2.620565982493645 0.534307201789922 1.000000000000000 0.008017484945529
50 54 2.620172764952091 0.352439463235590 1.000000000000000 0.005370391625780
51 55 2.619820461360298 0.380893973213412 1.000000000000000 0.006521683261394
52 56 2.619440402404600 0.372625361151608 1.000000000000000 0.006532881614567
53 57 2.619017411541816 0.475740535135362 1.000000000000000 0.005108984068213
54 58 2.618790926754144 0.480347446819900 1.000000000000000 0.003286273407461
55 59 2.618663203519279 0.470306875910397 1.000000000000000 0.002727475551902
56 60 2.618532854205674 0.424620470755549 1.000000000000000 0.002846556727424
57 61 2.618346718573904 0.596658795386294 1.000000000000000 0.002586117598938
58 62 2.618208824700391 0.406759745782272 1.000000000000000 0.002454281318704
59 63 2.618118074850504 0.229356468336372 1.000000000000000 0.001755222457796
60 64 2.618053775891369 0.205586974007373 1.000000000000000 0.001481364194552
61 65 2.618004527172970 0.233663034033881 1.000000000000000 0.001366025253396
62 66 2.617957952746422 0.134701535614384 1.000000000000000 0.001342840814948
63 67 2.617893413461006 0.203785505085546 1.000000000000000 0.001019093481187
64 68 2.617836503249618 0.286033730173573 1.000000000000000 0.001134711074774
65 69 2.617776409786283 0.389538832781190 1.000000000000000 0.001045120607314
66 70 2.617726623650858 0.346374271369702 1.000000000000000 0.000981846880971
67 71 2.617677238107400 0.286118646299197 1.000000000000000 0.000995808211227
68 72 2.617639216877453 0.247598581029562 1.000000000000000 0.000775161774108
69 73 2.617624105692349 0.116811400256912 1.000000000000000 0.000475912332592
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320 330 2.617079873869423 0.006637395080566 0.199985135358798 0.000009961750100
321 331 2.617079870193246 0.005924598206167 1.000000000000000 0.000005525568059
322 332 2.617079866320045 0.008515631401260 1.000000000000000 0.000006805242300
323 333 2.617079863927025 0.006141424704105 1.000000000000000 0.000014278881642
324 334 2.617079861111735 0.003931646218748 1.000000000000000 0.000010586157017
325 335 2.617079855839613 0.007756778914663 1.000000000000000 0.000005212666280
326 336 2.617079853123247 0.004261768806325 1.000000000000000 0.000005302208095
327 337 2.617079848733893 0.006867794153162 1.000000000000000 0.000006608711613
328 338 2.617079841774434 0.014511467687893 1.000000000000000 0.000008468943688
329 340 2.617079835910330 0.013911250300387 0.461438065902058 0.000012743694886
330 341 2.617079827702133 0.020092952742635 1.000000000000000 0.000020980278013
331 343 2.617079820035112 0.031466629706594 0.465806429474328 0.000011879135964
332 344 2.617079811851380 0.006061026242461 1.000000000000000 0.000008747719591
333 345 2.617079801055980 0.014621372398860 1.000000000000000 0.000014477105526
334 346 2.617079793601709 0.013342134332664 1.000000000000000 0.000017198312537
335 347 2.617079781735586 0.031702090177570 1.000000000000000 0.000026482233756
336 349 2.617079778421829 0.007896435160713 0.387587196958065 0.000022462565717
337 350 2.617079773930001 0.008393456409840 1.000000000000000 0.000010890296629
338 351 2.617079772435679 0.003059003761135 1.000000000000000 0.000005279645231
339 352 2.617079771893466 0.001344361316740 1.000000000000000 0.000004839575113
340 353 2.617079770549721 0.004378954940143 1.000000000000000 0.000006132392709
341 354 2.617079769687088 0.003946111694567 1.000000000000000 0.000005916313581
342 355 2.617079769003259 0.004074377380781 1.000000000000000 0.000002936646116
343 356 2.617079768724385 0.002434551420348 1.000000000000000 0.000003135764621
344 357 2.617079768623840 0.000863262654902 1.000000000000000 0.000004580811214
345 358 2.617079768476158 0.000858157295266 1.000000000000000 0.000003846379947
346 359 2.617079768358694 0.000636184991515 1.000000000000000 0.000003227382551
347 360 2.617079767828217 0.003196058236779 1.000000000000000 0.000002181135547
348 361 2.617079767393931 0.003273945179116 1.000000000000000 0.000003850030651
349 362 2.617079766552612 0.005608201793535 1.000000000000000 0.000004983618649
350 363 2.617079766135439 0.013032889054727 1.000000000000000 0.000011439294752
351 364 2.617079765177198 0.002359332951500 1.000000000000000 0.000007214231339
352 365 2.617079764531954 0.004501573778363 1.000000000000000 0.000004793043525
353 366 2.617079763946869 0.002417506414203 1.000000000000000 0.000006139759329
354 367 2.617079763090241 0.003954845536834 1.000000000000000 0.000008884435557
355 368 2.617079761941926 0.004440701506582 1.000000000000000 0.000009900138225
356 369 2.617079759534702 0.007139254203577 1.000000000000000 0.000011380657339
357 370 2.617079756227521 0.014769750382801 1.000000000000000 0.000010967879501
358 371 2.617079752956193 0.007268623224739 1.000000000000000 0.000009653730219
359 372 2.617079749321592 0.011582073205478 1.000000000000000 0.000009015075800
360 373 2.617079747548633 0.008090211853178 1.000000000000000 0.000006307673676
361 374 2.617079746268351 0.010292222883531 1.000000000000000 0.000013102447866
362 376 2.617079745751726 0.003530538211089 0.302185150290077 0.000006590850980
363 377 2.617079745213020 0.001677628794866 1.000000000000000 0.000004490197501
364 378 2.617079744278135 0.004486103724864 1.000000000000000 0.000004631655971
365 379 2.617079743520161 0.003074363756997 1.000000000000000 0.000004694766165
366 380 2.617079743281071 0.009257704432479 1.000000000000000 0.000010978934335
367 381 2.617079741948073 0.004455285013606 1.000000000000000 0.000003437731080
368 382 2.617079741414838 0.001641939756032 1.000000000000000 0.000002665919182
369 383 2.617079740303615 0.004264615878525 1.000000000000000 0.000003789428321
370 385 2.617079739956149 0.004717589669657 0.453970553398616 0.000003545907724
371 386 2.617079739717286 0.003035608630145 1.000000000000000 0.000004000791558
372 387 2.617079739519789 0.001836767527461 1.000000000000000 0.000002266238328
373 388 2.617079739313368 0.002006650299382 1.000000000000000 0.000001882808406
374 389 2.617079739198876 0.001028485174245 1.000000000000000 0.000001827941377
375 390 2.617079739097288 0.001796526787464 1.000000000000000 0.000002565115235
376 391 2.617079739023292 0.001796526787464 1.000000000000000 0.000001026592339
Convergence criteria met.
After: gradient norm = 1.0265923393424481E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0972,-0.0972}
Count Table 1:
---------------
h: {0.1894,-0.1894}
Count Table 2:
---------------
h: {0.0197,-0.0197}
Count Table 3:
---------------
h: {0.0363,-0.0363}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.1315,-1.6374,-1.0445,-0.6560,-1.0579,-2.4041,-1.3558,-0.5957,-0.8788,-1.0433,0.4471,-1.1071,-0.4321,-1.9905,-0.9226,-2.6364,-0.5063,-1.6621,-2.1162,-0.8788,-2.3398,-2.3664,-3.3951,2.3400,-1.8925,-1.7367,-2.1379,1.9911,-0.3294,-2.1162,-2.1857,-2.9427,0.4122,2.0793,-2.2474,-2.3269,-2.4599,0.0136,-1.9958,-0.3294,0.2521,-3.7271,0.1935,-0.4618,-0.1437,-2.2401,-1.0889,0.3495,-3.1206,-1.9958,-1.7656,0.1527,-1.7724,-1.3986,-1.6216,-0.6778,-1.5778,-0.4635,0.2623,-3.1206,-1.3986,-1.7724,0.1527,-1.7656,-0.4635,-1.5778,-0.6778,-1.6216,-3.1206,0.2623,-0.4618,0.1935,-3.7271,0.2521,0.3495,-1.0889,-2.2401,-0.1437,-1.9958,-3.1206,2.0793,0.4122,-2.9427,-2.1857,0.0136,-2.4599,-2.3269,-2.2474,-0.3294,-1.9958,2.3400,-3.3951,-2.3664,-2.3398,1.9911,-2.1379,-1.7367,-1.8925,-2.1162,-0.3294,-1.9905,-0.4321,-1.1071,0.4471,-1.6621,-0.5063,-2.6364,-0.9226,-0.8788,-2.1162,-0.6560,-1.0445,-1.6374,-1.1315,-0.5957,-1.3558,-2.4041,-1.0579,-1.0433,-0.8788}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0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Activity(exp=0): {0.0547,-2.8520}
Activity(exp=1): {0.0547,-2.5968}
Activity(exp=2): {0.0547,-4.0521}
Activity(exp=3): {0.0547,-2.6110}
Suggested variations:
key=12;3;0, description = Initial model.
> Optimizing variation "Initial model." (component1-2-variation0).
>> Starting new optimization: component1-2-variation0. (2021-05-21 21:23:43.417).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.617079739023292
gradient = {0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 1.0265923393427926E-6
Already at minimum!
After: gradient norm = 1.0265923393427926E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0972,-0.0972}
Count Table 1:
---------------
h: {0.1894,-0.1894}
Count Table 2:
---------------
h: {0.0197,-0.0197}
Count Table 3:
---------------
h: {0.0363,-0.0363}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.1315,-1.6374,-1.0445,-0.6560,-1.0579,-2.4041,-1.3558,-0.5957,-0.8788,-1.0433,0.4471,-1.1071,-0.4321,-1.9905,-0.9226,-2.6364,-0.5063,-1.6621,-2.1162,-0.8788,-2.3398,-2.3664,-3.3951,2.3400,-1.8925,-1.7367,-2.1379,1.9911,-0.3294,-2.1162,-2.1857,-2.9427,0.4122,2.0793,-2.2474,-2.3269,-2.4599,0.0136,-1.9958,-0.3294,0.2521,-3.7271,0.1935,-0.4618,-0.1437,-2.2401,-1.0889,0.3495,-3.1206,-1.9958,-1.7656,0.1527,-1.7724,-1.3986,-1.6216,-0.6778,-1.5778,-0.4635,0.2623,-3.1206,-1.3986,-1.7724,0.1527,-1.7656,-0.4635,-1.5778,-0.6778,-1.6216,-3.1206,0.2623,-0.4618,0.1935,-3.7271,0.2521,0.3495,-1.0889,-2.2401,-0.1437,-1.9958,-3.1206,2.0793,0.4122,-2.9427,-2.1857,0.0136,-2.4599,-2.3269,-2.2474,-0.3294,-1.9958,2.3400,-3.3951,-2.3664,-2.3398,1.9911,-2.1379,-1.7367,-1.8925,-2.1162,-0.3294,-1.9905,-0.4321,-1.1071,0.4471,-1.6621,-0.5063,-2.6364,-0.9226,-0.8788,-2.1162,-0.6560,-1.0445,-1.6374,-1.1315,-0.5957,-1.3558,-2.4041,-1.0579,-1.0433,-0.8788}
Dinucleotide(d=1): 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Activity(exp=0): {0.0547,-2.8520}
Activity(exp=1): {0.0547,-2.5968}
Activity(exp=2): {0.0547,-4.0521}
Activity(exp=3): {0.0547,-2.6110}
The Likelihood DID NOT improve. Discarding fit component1-2-variation0.
Suggested variations:
key=12;4;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation1).
>> Starting new optimization: component1-2-variation1. (2021-05-21 21:23:44.102).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.617075907553616
gradient = {-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 3.453105684235613E-5
Starting Function Value: 2.617075907553616
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.617075905995637 0.000088684680674 2.568258512283306 0.000014114579764
2 4 2.617075905610133 0.000035281097894 1.000000000000000 0.000010240257153
3 5 2.617075904845144 0.000121004419594 1.000000000000000 0.000009971938545
4 6 2.617075904085845 0.000164178120311 1.000000000000000 0.000016097724215
5 7 2.617075902425587 0.000378411936646 1.000000000000000 0.000022174318241
6 8 2.617075899263589 0.000951312122537 1.000000000000000 0.000031599090858
7 10 2.617075897720104 0.000587813259059 0.439556556081219 0.000026637216836
8 11 2.617075896238230 0.000299421421320 1.000000000000000 0.000012314120718
9 12 2.617075895374649 0.000178001188045 1.000000000000000 0.000011002388471
10 13 2.617075894621447 0.000182736442700 1.000000000000000 0.000015330756139
11 14 2.617075892312447 0.000770493419300 1.000000000000000 0.000027457400612
12 15 2.617075890587471 0.001228334420307 1.000000000000000 0.000041581059365
13 16 2.617075888369032 0.000337229031128 1.000000000000000 0.000020246507729
14 17 2.617075887245527 0.000362536851002 1.000000000000000 0.000008402597438
15 18 2.617075886946375 0.000139350086787 1.000000000000000 0.000008313799648
16 19 2.617075886027604 0.000424792215523 1.000000000000000 0.000014335777216
17 20 2.617075884393491 0.000771723451167 1.000000000000000 0.000023184372806
18 21 2.617075881528285 0.001409369185166 1.000000000000000 0.000028543035369
19 22 2.617075877463947 0.001856850166948 1.000000000000000 0.000023490874295
20 23 2.617075871754253 0.002772854123308 1.000000000000000 0.000011776886046
21 24 2.617075867558131 0.002348821483984 1.000000000000000 0.000010604949011
22 25 2.617075865137342 0.001293570979361 1.000000000000000 0.000016345476760
23 26 2.617075862554251 0.001280278048668 1.000000000000000 0.000015383812176
24 27 2.617075857610618 0.002901909040747 1.000000000000000 0.000012756017883
25 29 2.617075856489520 0.001084125082084 0.458684654152241 0.000022264428584
26 30 2.617075855370522 0.000828856865274 1.000000000000000 0.000005686979953
27 31 2.617075855216419 0.000133537164180 1.000000000000000 0.000003614941066
28 32 2.617075854990996 0.000161104084120 1.000000000000000 0.000004013261438
29 33 2.617075854616113 0.000266710167600 1.000000000000000 0.000006471742054
30 34 2.617075854066590 0.000524249233465 1.000000000000000 0.000007956092530
31 35 2.617075853199226 0.000893016859032 1.000000000000000 0.000006534399422
32 36 2.617075852451168 0.001170287447792 1.000000000000000 0.000004072452072
33 37 2.617075852053539 0.000484336681378 1.000000000000000 0.000001745544945
34 38 2.617075851872025 0.000244575896855 1.000000000000000 0.000002844359087
35 39 2.617075851656006 0.000322204925222 1.000000000000000 0.000003349177630
36 40 2.617075851149538 0.000819637501941 1.000000000000000 0.000003606762906
37 41 2.617075850351285 0.001843279036150 1.000000000000000 0.000003810601952
38 42 2.617075849961577 0.002689582796367 1.000000000000000 0.000005138484703
39 43 2.617075849275652 0.000580145616455 1.000000000000000 0.000002310096639
40 44 2.617075848902483 0.000465998237890 1.000000000000000 0.000001999482743
41 45 2.617075848326229 0.001271175061538 1.000000000000000 0.000002082177753
42 46 2.617075847471366 0.002220254318098 1.000000000000000 0.000002137162520
43 47 2.617075847124724 0.005639040039004 1.000000000000000 0.000006469070212
44 48 2.617075845765880 0.000601887066674 1.000000000000000 0.000002550208271
45 49 2.617075845133000 0.000895328296051 1.000000000000000 0.000001892775578
46 50 2.617075844411035 0.002115953537643 1.000000000000000 0.000001944951136
47 51 2.617075843594392 0.002667102699467 1.000000000000000 0.000001665708526
48 52 2.617075842419852 0.004236234695106 1.000000000000000 0.000001890470912
49 53 2.617075842322306 0.005776402548755 1.000000000000000 0.000005357827603
50 54 2.617075841158927 0.000782684390374 1.000000000000000 0.000001757541365
51 55 2.617075840738516 0.000782684390374 1.000000000000000 0.000001381147085
Convergence criteria met.
After: gradient norm = 1.3811470849755388E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0973,-0.0973}
Count Table 1:
---------------
h: {0.1895,-0.1895}
Count Table 2:
---------------
h: {0.0197,-0.0197}
Count Table 3:
---------------
h: {0.0364,-0.0364}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.1331,-1.6380,-1.0464,-0.6580,-1.0592,-2.4045,-1.3582,-0.5982,-0.8810,-1.0447,0.4441,-1.1092,-0.4349,-1.9893,-0.9242,-2.6408,-0.5099,-1.6615,-2.1145,-0.8810,-2.3332,-2.3623,-3.3717,2.3418,-1.8936,-1.7371,-2.1411,1.9761,-0.3279,-2.1145,-2.1832,-2.9400,0.4121,2.0782,-2.2396,-2.3210,-2.4624,0.0149,-1.9947,-0.3279,0.2534,-3.7228,0.1944,-0.4600,-0.1417,-2.2385,-1.0875,0.3523,-3.1184,-1.9947,-1.7632,0.1531,-1.7704,-1.3964,-1.6158,-0.6768,-1.5769,-0.4611,0.2624,-3.1184,-1.3964,-1.7704,0.1531,-1.7632,-0.4611,-1.5769,-0.6768,-1.6158,-3.1184,0.2624,-0.4600,0.1944,-3.7228,0.2534,0.3523,-1.0875,-2.2385,-0.1417,-1.9947,-3.1184,2.0782,0.4121,-2.9400,-2.1832,0.0149,-2.4624,-2.3210,-2.2396,-0.3279,-1.9947,2.3418,-3.3717,-2.3623,-2.3332,1.9761,-2.1411,-1.7371,-1.8936,-2.1145,-0.3279,-1.9893,-0.4349,-1.1092,0.4441,-1.6615,-0.5099,-2.6408,-0.9242,-0.8810,-2.1145,-0.6580,-1.0464,-1.6380,-1.1331,-0.5982,-1.3582,-2.4045,-1.0592,-1.0447,-0.8810}
Dinucleotide(d=1): 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Activity(exp=0): {0.0491,-2.8504}
Activity(exp=1): {0.0491,-2.5950}
Activity(exp=2): {0.0491,-4.0490}
Activity(exp=3): {0.0491,-2.5941}
The Likelihood DID improve.
Suggested variations:
key=12;5;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation2).
>> Starting new optimization: component1-2-variation2. (2021-05-21 21:24:25.181).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.620859213533761
gradient = {0.0106,0.0017,0.0003,0.0000,0.0004,0.0003,0.0000,0.0002,0.0027,0.0026,0.0104,0.0043,0.0004,0.0000,0.0000,0.0004,0.0000,0.0000,0.0003,0.0031,0.0001,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0005,0.0181,0.0000,0.0001,0.0001,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0001,0.0075,0.0111,0.0001,0.0036,0.0004,0.0000,0.0000,0.0000,0.0000,0.0001,0.0015,0.0130,0.0104,0.0009,0.0001,0.0002,0.0036,0.0000,0.0000,0.0005,0.0021,0.0010,0.0000,0.0035,0.0000,0.0036,0.0000,0.0002,0.0000,0.0022,-0.0104,0.0104,-0.0108,0.0108,-0.0024,0.0024,-0.0079,0.0079}
gradient norm = 0.041292500541894914
Starting Function Value: 2.620859213533761
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.619024596692659 0.093709269506208 2.269401665591360 0.014666217119022
2 4 2.618684516176350 0.028054808715335 1.000000000000000 0.010873105783073
3 5 2.617818110961715 0.127900882977842 1.000000000000000 0.009696837375072
4 6 2.617270346140812 0.124855725375007 1.000000000000000 0.010497204852212
5 8 2.617008549795082 0.105756149998867 0.455252514381604 0.009229041680542
6 9 2.616874030920837 0.059993572837508 1.000000000000000 0.002013173085985
7 10 2.616863477830051 0.007066113774133 1.000000000000000 0.001572907143158
8 11 2.616843990041460 0.018322550757782 1.000000000000000 0.002537508688630
9 12 2.616812303211681 0.038030237595521 1.000000000000000 0.003624953216123
10 13 2.616773864765309 0.058401075673017 1.000000000000000 0.003069312718924
11 15 2.616769087918886 0.011997671726384 0.164828810132610 0.003106620799838
12 16 2.616754323534321 0.030698111588204 1.000000000000000 0.001110794553855
13 17 2.616750471617019 0.007498501247250 1.000000000000000 0.000698116264612
14 18 2.616747279477948 0.008485058566819 1.000000000000000 0.001063607152458
15 19 2.616742481718938 0.015365339491659 1.000000000000000 0.001378790300979
16 20 2.616734863904062 0.029600410381656 1.000000000000000 0.001168468801765
17 21 2.616725795933005 0.040360204190665 1.000000000000000 0.000818467548019
18 22 2.616720281063445 0.062297391170811 1.000000000000000 0.001664424816894
19 23 2.616715548469185 0.011389869646390 1.000000000000000 0.000654958136251
20 24 2.616714218588987 0.006565120207153 1.000000000000000 0.000546042205101
21 25 2.616711787557899 0.014684233465488 1.000000000000000 0.000369111374451
22 26 2.616708263812789 0.028178449702640 1.000000000000000 0.000503577861896
23 27 2.616704303960026 0.038585924513767 1.000000000000000 0.000738673478666
24 28 2.616699725641658 0.045375606442042 1.000000000000000 0.000633137545378
25 29 2.616692765766474 0.067125963317592 1.000000000000000 0.000441182877199
26 30 2.616684760201903 0.090993490156690 1.000000000000000 0.000256629097793
27 31 2.616678973897813 0.079043807451244 1.000000000000000 0.000416398369008
28 32 2.616673315559980 0.082969999502389 1.000000000000000 0.000452864138671
29 33 2.616665947484049 0.136907702623076 1.000000000000000 0.000943375901809
30 34 2.616662990583274 0.054371954773943 1.000000000000000 0.000296314087676
31 35 2.616662405942821 0.009273682772546 1.000000000000000 0.000114257187525
32 36 2.616662210002370 0.006004317440966 1.000000000000000 0.000131854860199
33 37 2.616661678144367 0.009980438887741 1.000000000000000 0.000190907210952
34 38 2.616660479764903 0.022062792830675 1.000000000000000 0.000266932436363
35 39 2.616658737721172 0.044014216207692 1.000000000000000 0.000268791687641
36 40 2.616656579870706 0.081557292406207 1.000000000000000 0.000257959034407
37 41 2.616655954289253 0.080569585293263 1.000000000000000 0.000135954117092
38 42 2.616655233253797 0.026540131004950 1.000000000000000 0.000044335290386
39 43 2.616655059763168 0.006058961318712 1.000000000000000 0.000032328710943
40 44 2.616654856662992 0.013423335385742 1.000000000000000 0.000084583351668
41 45 2.616654728652937 0.013178845959299 1.000000000000000 0.000050490376180
42 46 2.616654635298102 0.011180745917854 1.000000000000000 0.000038428788980
43 47 2.616654537860510 0.010528398631543 1.000000000000000 0.000070257664627
44 48 2.616654486225794 0.004910088737711 1.000000000000000 0.000053300334427
45 49 2.616654432290882 0.006131396177213 1.000000000000000 0.000032695293539
46 50 2.616654378138111 0.008681303926118 1.000000000000000 0.000023926363536
47 51 2.616654344264965 0.006610057342363 1.000000000000000 0.000036340659132
48 52 2.616654307317243 0.006773903878192 1.000000000000000 0.000038748945936
49 53 2.616654239213254 0.011102796830331 1.000000000000000 0.000028014664149
50 54 2.616654161793257 0.015862462846861 1.000000000000000 0.000015384220326
51 55 2.616654126248552 0.008656840466962 1.000000000000000 0.000028059793006
52 56 2.616654107198892 0.004975457355465 1.000000000000000 0.000027256217102
53 57 2.616654074207616 0.007340817651525 1.000000000000000 0.000013386973763
54 58 2.616654027173984 0.013707091498640 1.000000000000000 0.000024574145003
55 59 2.616653991944036 0.011214729265257 1.000000000000000 0.000026977917281
56 60 2.616653923656868 0.021899811887218 1.000000000000000 0.000036815902297
57 61 2.616653862120623 0.025149560668039 1.000000000000000 0.000020038243660
58 62 2.616653833783022 0.009111690988462 1.000000000000000 0.000021717838029
59 63 2.616653803281585 0.008858290261925 1.000000000000000 0.000026138047063
60 64 2.616653759267983 0.014473335204327 1.000000000000000 0.000018297529238
61 65 2.616653708038133 0.021991929029769 1.000000000000000 0.000018603146216
62 66 2.616653676524460 0.019280643215141 1.000000000000000 0.000034575726957
63 67 2.616653658322850 0.002400708807246 1.000000000000000 0.000019647887972
64 68 2.616653643456328 0.003607451477668 1.000000000000000 0.000011373106277
65 69 2.616653629134719 0.004883805214568 1.000000000000000 0.000011532407502
66 70 2.616653596860476 0.014997213636594 1.000000000000000 0.000020774564839
67 71 2.616653574952466 0.012566989999922 1.000000000000000 0.000019666639795
68 72 2.616653544557656 0.014703206784364 1.000000000000000 0.000007437694306
69 73 2.616653527091217 0.011182483869342 1.000000000000000 0.000013242316250
70 74 2.616653520523044 0.003784880424959 1.000000000000000 0.000014287421816
71 75 2.616653509163339 0.006727209823155 1.000000000000000 0.000006522409509
72 76 2.616653502290079 0.005460528771013 1.000000000000000 0.000013072171418
73 77 2.616653497931904 0.003338677221345 1.000000000000000 0.000014993285012
74 78 2.616653489877375 0.006363403153333 1.000000000000000 0.000013522033394
75 79 2.616653482435918 0.006282552440431 1.000000000000000 0.000006194384973
76 80 2.616653478326477 0.004196913455373 1.000000000000000 0.000010300465265
77 81 2.616653476031604 0.001859906211769 1.000000000000000 0.000010274990188
78 82 2.616653471548986 0.003735371505698 1.000000000000000 0.000009849365197
79 83 2.616653465681640 0.006075168987596 1.000000000000000 0.000007017646058
80 84 2.616653461342808 0.005877496045806 1.000000000000000 0.000004286647797
81 85 2.616653458615752 0.003441468890585 1.000000000000000 0.000005352788865
82 86 2.616653455887513 0.003632146139999 1.000000000000000 0.000005924695169
83 87 2.616653453126046 0.003250615299223 1.000000000000000 0.000006853548987
84 88 2.616653447362487 0.007674572564916 1.000000000000000 0.000006515301422
85 89 2.616653443844464 0.005723469683878 1.000000000000000 0.000003805178510
86 90 2.616653442249417 0.002694356709340 1.000000000000000 0.000003624685336
87 91 2.616653441623946 0.000825478073243 1.000000000000000 0.000002756591382
88 92 2.616653441031357 0.000741142348493 1.000000000000000 0.000003286761617
89 93 2.616653439889345 0.001698044370581 1.000000000000000 0.000003899455976
90 94 2.616653438515763 0.002785633998740 1.000000000000000 0.000003216439240
91 95 2.616653437168421 0.003324111540919 1.000000000000000 0.000001981238416
92 96 2.616653436416760 0.002424258741801 1.000000000000000 0.000001833378482
93 97 2.616653436186656 0.002424258741801 1.000000000000000 0.000001063197670
Convergence criteria met.
After: gradient norm = 1.0631976695989666E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1066,-0.1066}
Count Table 1:
---------------
h: {0.2020,-0.2020}
Count Table 2:
---------------
h: {0.0222,-0.0222}
Count Table 3:
---------------
h: {0.0413,-0.0413}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.0891,-1.9499,-0.9562,-0.5815,-0.9952,-2.3340,-1.3516,-0.6048,-0.8989,-1.0665,0.4997,-1.3576,-0.3824,-1.8710,-0.9129,-2.6659,-0.5108,-1.5710,-2.1568,-0.8989,-2.4391,-2.5060,-3.4011,2.1845,-1.7664,-1.7980,-2.2845,2.6306,-0.3789,-2.1568,-2.1445,-2.9542,0.2412,2.1324,-1.9910,-2.3242,-2.4575,-0.0420,-1.9970,-0.3789,0.2785,-3.6778,0.1472,-0.3909,-0.1648,-2.2651,-1.1048,0.3718,-3.1128,-1.9970,-1.7065,0.1077,-1.7068,-1.3654,-1.5012,-0.7544,-1.6527,-0.4350,0.2114,-3.1128,-1.3654,-1.7068,0.1077,-1.7065,-0.4350,-1.6527,-0.7544,-1.5012,-3.1128,0.2114,-0.3909,0.1472,-3.6778,0.2785,0.3718,-1.1048,-2.2651,-0.1648,-1.9970,-3.1128,2.1324,0.2412,-2.9542,-2.1445,-0.0420,-2.4575,-2.3242,-1.9910,-0.3789,-1.9970,2.1845,-3.4011,-2.5060,-2.4391,2.6306,-2.2845,-1.7980,-1.7664,-2.1568,-0.3789,-1.8710,-0.3824,-1.3576,0.4997,-1.5710,-0.5108,-2.6659,-0.9129,-0.8989,-2.1568,-0.5815,-0.9562,-1.9499,-1.0891,-0.6048,-1.3516,-2.3340,-0.9952,-1.0665,-0.8989}
Dinucleotide(d=1): 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Activity(exp=0): {0.0390,-2.6750}
Activity(exp=1): {0.0390,-2.4040}
Activity(exp=2): {0.0390,-3.9192}
Activity(exp=3): {0.0390,-3.0376}
The Likelihood DID improve.
Suggested variations:
key=12;6;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation3).
>> Starting new optimization: component1-2-variation3. (2021-05-21 21:25:45.674).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.6165934695734743
gradient = {-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0001,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0001,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0002,0.0002,-0.0002,0.0002,-0.0001,0.0001,-0.0001,0.0001}
gradient norm = 4.5514545732755783E-4
Starting Function Value: 2.6165934695734743
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.616593198000110 0.001171923399330 2.574832683623285 0.000204643989638
2 4 2.616593121113386 0.000506241337107 1.000000000000000 0.000139956780761
3 5 2.616592997599438 0.001388789464923 1.000000000000000 0.000123811541394
4 6 2.616592867799837 0.001943327236292 1.000000000000000 0.000185868088622
5 7 2.616592577422411 0.006079024032257 1.000000000000000 0.000308042809732
6 8 2.616592339431166 0.007878225942075 1.000000000000000 0.000383596755078
7 9 2.616592123527829 0.001825520826764 1.000000000000000 0.000176290889874
8 10 2.616592010773358 0.001895951248147 1.000000000000000 0.000110184468933
9 11 2.616591956139253 0.001155413177375 1.000000000000000 0.000133552706700
10 12 2.616591636681048 0.008268356531818 1.000000000000000 0.000263436041208
11 13 2.616591422699500 0.011670432682028 1.000000000000000 0.000455904764905
12 14 2.616591125735668 0.006445809962662 1.000000000000000 0.000232650148024
13 15 2.616590987721384 0.002647088803956 1.000000000000000 0.000108596772740
14 16 2.616590934022632 0.001494299530012 1.000000000000000 0.000098921504373
15 17 2.616590866116963 0.002147609437501 1.000000000000000 0.000143663716624
16 18 2.616590702436946 0.005760092055443 1.000000000000000 0.000237218994784
17 19 2.616590414131827 0.011629970964640 1.000000000000000 0.000316391678341
18 20 2.616590129076162 0.016621342445244 1.000000000000000 0.000320672139811
19 21 2.616589916447715 0.005774408149541 1.000000000000000 0.000131005195985
20 22 2.616589820683067 0.001587749167229 1.000000000000000 0.000105382149044
21 23 2.616589757202941 0.001451542544743 1.000000000000000 0.000138854847193
22 24 2.616589621495549 0.004928194335589 1.000000000000000 0.000169220728286
23 25 2.616589475860229 0.007850899266660 1.000000000000000 0.000107487114299
24 26 2.616589377674205 0.006491219087118 1.000000000000000 0.000049842007247
25 27 2.616589307420739 0.005261521582013 1.000000000000000 0.000093347063241
26 28 2.616589238537832 0.004823596421213 1.000000000000000 0.000131830410794
27 29 2.616589147629719 0.006117473762811 1.000000000000000 0.000114255133139
28 30 2.616589032441771 0.007520413648387 1.000000000000000 0.000059878487912
29 31 2.616588944934102 0.007566286981033 1.000000000000000 0.000041038424601
30 32 2.616588912839376 0.003095044689005 1.000000000000000 0.000056809048027
31 33 2.616588865176099 0.004587769790915 1.000000000000000 0.000050437771414
32 34 2.616588797572904 0.008171950978185 1.000000000000000 0.000034394888024
33 35 2.616588768840369 0.006927358506913 1.000000000000000 0.000027446312801
34 36 2.616588749167258 0.001375880398516 1.000000000000000 0.000017558422624
35 37 2.616588732421371 0.002241160879928 1.000000000000000 0.000020005388871
36 38 2.616588710936113 0.003894935251607 1.000000000000000 0.000020942222432
37 39 2.616588669868626 0.008664282758094 1.000000000000000 0.000020316949731
38 40 2.616588616454070 0.014362325813140 1.000000000000000 0.000019056446216
39 42 2.616588594533647 0.008592651812296 0.410088694550959 0.000019550987457
40 43 2.616588570500250 0.006511826517297 1.000000000000000 0.000010528213077
41 44 2.616588562259929 0.002256429035426 1.000000000000000 0.000006833888292
42 45 2.616588556771156 0.001861745548075 1.000000000000000 0.000007421755380
43 46 2.616588548399188 0.004201430693558 1.000000000000000 0.000008754560073
44 47 2.616588540844048 0.004899110426681 1.000000000000000 0.000015411471888
45 48 2.616588537324084 0.001365818587555 1.000000000000000 0.000006276088354
46 49 2.616588535842039 0.001259414413979 1.000000000000000 0.000004190454542
47 50 2.616588535044326 0.000561661146332 1.000000000000000 0.000004832843764
48 51 2.616588531959783 0.002308852722579 1.000000000000000 0.000006390972752
49 52 2.616588528739276 0.002481367237551 1.000000000000000 0.000006537144066
50 53 2.616588523290314 0.005584909819131 1.000000000000000 0.000006478844353
51 54 2.616588520392305 0.002778549799488 1.000000000000000 0.000004039178678
52 55 2.616588518474344 0.001998645346387 1.000000000000000 0.000003870790844
53 56 2.616588516877711 0.001824589559999 1.000000000000000 0.000003340058894
54 57 2.616588514870788 0.002577718454578 1.000000000000000 0.000003794418007
55 58 2.616588511828004 0.004103694557255 1.000000000000000 0.000004489566464
56 59 2.616588509044661 0.004913307113159 1.000000000000000 0.000005460349311
57 60 2.616588507671536 0.001987537428268 1.000000000000000 0.000002712191783
58 61 2.616588506565105 0.001431476416549 1.000000000000000 0.000003592683201
59 62 2.616588504478687 0.002662524837480 1.000000000000000 0.000004891873963
60 63 2.616588500046229 0.007238709001548 1.000000000000000 0.000004341987510
61 64 2.616588495667682 0.009334507342021 1.000000000000000 0.000014785437923
62 65 2.616588493445937 0.004048829066421 1.000000000000000 0.000006928197608
63 66 2.616588492589201 0.001420897259099 1.000000000000000 0.000003099531829
64 67 2.616588492264130 0.000372093098683 1.000000000000000 0.000003040191374
65 68 2.616588491579738 0.000987177372195 1.000000000000000 0.000003413286042
66 69 2.616588490846622 0.001421164232317 1.000000000000000 0.000003229286366
67 70 2.616588489738729 0.002709734259745 1.000000000000000 0.000002934681893
68 71 2.616588489040860 0.003260057944659 1.000000000000000 0.000005315202952
69 72 2.616588488588128 0.000400011428011 1.000000000000000 0.000003909350355
70 73 2.616588487698912 0.001552458476430 1.000000000000000 0.000002776870852
71 74 2.616588487105561 0.001623103312154 1.000000000000000 0.000002280703979
72 75 2.616588486505361 0.001623103312154 1.000000000000000 0.000001385712503
Convergence criteria met.
After: gradient norm = 1.3857125034214606E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1078,-0.1078}
Count Table 1:
---------------
h: {0.2035,-0.2035}
Count Table 2:
---------------
h: {0.0227,-0.0227}
Count Table 3:
---------------
h: {0.0421,-0.0421}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.0800,-1.9336,-0.9486,-0.5753,-0.9849,-2.3238,-1.3503,-0.5945,-0.8945,-1.0620,0.4987,-1.3403,-0.3797,-1.8499,-0.9000,-2.6626,-0.5165,-1.5462,-2.1565,-0.8945,-2.4214,-2.3895,-3.3840,2.1628,-1.7331,-1.7982,-2.2939,2.5860,-0.3844,-2.1565,-2.1226,-2.9290,0.2374,2.1228,-1.9427,-2.3236,-2.4614,-0.0286,-1.9801,-0.3844,0.2809,-3.6467,0.1504,-0.3800,-0.1579,-2.2560,-1.1118,0.3835,-3.0945,-1.9801,-1.6897,0.1048,-1.6820,-1.3503,-1.4712,-0.7544,-1.6577,-0.4286,0.2114,-3.0945,-1.3503,-1.6820,0.1048,-1.6897,-0.4286,-1.6577,-0.7544,-1.4712,-3.0945,0.2114,-0.3800,0.1504,-3.6467,0.2809,0.3835,-1.1118,-2.2560,-0.1579,-1.9801,-3.0945,2.1228,0.2374,-2.9290,-2.1226,-0.0286,-2.4614,-2.3236,-1.9427,-0.3844,-1.9801,2.1628,-3.3840,-2.3895,-2.4214,2.5860,-2.2939,-1.7982,-1.7331,-2.1565,-0.3844,-1.8499,-0.3797,-1.3403,0.4987,-1.5462,-0.5165,-2.6626,-0.9000,-0.8945,-2.1565,-0.5753,-0.9486,-1.9336,-1.0800,-0.5945,-1.3503,-2.3238,-0.9849,-1.0620,-0.8945}
Dinucleotide(d=1): 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Activity(exp=0): {0.0336,-2.6643}
Activity(exp=1): {0.0336,-2.3955}
Activity(exp=2): {0.0336,-3.8913}
Activity(exp=3): {0.0336,-3.0107}
The Likelihood DID improve.
Suggested variations:
key=12;7;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation4).
>> Starting new optimization: component1-2-variation4. (2021-05-21 21:26:53.733).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.6165869152407075
gradient = {0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 1.5204543231684456E-5
Starting Function Value: 2.6165869152407075
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.616586914940553 0.000038845547101 2.554864457878136 0.000007090340245
2 4 2.616586914845485 0.000017197181348 1.000000000000000 0.000005502228592
3 5 2.616586914568724 0.000078830954052 1.000000000000000 0.000005962397398
4 6 2.616586914252712 0.000120689294272 1.000000000000000 0.000009529226216
5 7 2.616586913677667 0.000302987586453 1.000000000000000 0.000012816621408
6 8 2.616586913255014 0.000321648198840 1.000000000000000 0.000013924779801
7 9 2.616586912974261 0.000060078083878 1.000000000000000 0.000006123128835
8 10 2.616586912872054 0.000030150547158 1.000000000000000 0.000003921765775
9 11 2.616586912803474 0.000030302349718 1.000000000000000 0.000004872586737
10 12 2.616586912469975 0.000189005077746 1.000000000000000 0.000009422191028
11 13 2.616586911973644 0.000365083340111 1.000000000000000 0.000013333423382
12 14 2.616586911939486 0.000825363595077 1.000000000000000 0.000028225327990
13 15 2.616586911056642 0.000056165001965 1.000000000000000 0.000010031294603
14 16 2.616586910805278 0.000085798611404 1.000000000000000 0.000005969214771
15 17 2.616586910589202 0.000183517664637 1.000000000000000 0.000006665674248
16 18 2.616586910304759 0.000257174732456 1.000000000000000 0.000009543485837
17 19 2.616586909567062 0.000686941990829 1.000000000000000 0.000014792740178
18 20 2.616586908556227 0.000971405063871 1.000000000000000 0.000015646142279
19 21 2.616586907019574 0.001297914745846 1.000000000000000 0.000010059357358
20 22 2.616586906202696 0.000904176310101 1.000000000000000 0.000003707313920
21 23 2.616586905973186 0.000222683393256 1.000000000000000 0.000004985343112
22 24 2.616586905796805 0.000178280808009 1.000000000000000 0.000005675076179
23 25 2.616586905575125 0.000271928781511 1.000000000000000 0.000007215909130
24 26 2.616586905371141 0.000291075087942 1.000000000000000 0.000002958475582
25 27 2.616586905258854 0.000213639803326 1.000000000000000 0.000003224073341
26 28 2.616586905167312 0.000158808992187 1.000000000000000 0.000004259454458
27 29 2.616586904994018 0.000263601561815 1.000000000000000 0.000004615735937
28 30 2.616586904700244 0.000445404141111 1.000000000000000 0.000003772135437
29 31 2.616586904361820 0.000581633816185 1.000000000000000 0.000002094010210
30 32 2.616586904125957 0.000482374619185 1.000000000000000 0.000002138662929
31 33 2.616586903967203 0.000366571645076 1.000000000000000 0.000002782630892
32 34 2.616586903780610 0.000539798286814 1.000000000000000 0.000002174426602
33 35 2.616586903585660 0.000638774560671 1.000000000000000 0.000001998733292
34 36 2.616586903401658 0.000638774560671 1.000000000000000 0.000001043405048
Convergence criteria met.
After: gradient norm = 1.0434050476148634E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1079,-0.1079}
Count Table 1:
---------------
h: {0.2036,-0.2036}
Count Table 2:
---------------
h: {0.0227,-0.0227}
Count Table 3:
---------------
h: {0.0422,-0.0422}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.0797,-1.9332,-0.9485,-0.5751,-0.9849,-2.3243,-1.3501,-0.5942,-0.8943,-1.0620,0.4987,-1.3396,-0.3796,-1.8492,-0.8999,-2.6628,-0.5175,-1.5455,-2.1566,-0.8943,-2.4210,-2.3854,-3.3837,2.1625,-1.7326,-1.7982,-2.2941,2.5844,-0.3847,-2.1566,-2.1225,-2.9225,0.2366,2.1217,-1.9421,-2.3238,-2.4618,-0.0287,-1.9815,-0.3847,0.2811,-3.6451,0.1505,-0.3792,-0.1576,-2.2564,-1.1106,0.3845,-3.0950,-1.9815,-1.6891,0.1049,-1.6810,-1.3498,-1.4705,-0.7545,-1.6580,-0.4278,0.2115,-3.0950,-1.3498,-1.6810,0.1049,-1.6891,-0.4278,-1.6580,-0.7545,-1.4705,-3.0950,0.2115,-0.3792,0.1505,-3.6451,0.2811,0.3845,-1.1106,-2.2564,-0.1576,-1.9815,-3.0950,2.1217,0.2366,-2.9225,-2.1225,-0.0287,-2.4618,-2.3238,-1.9421,-0.3847,-1.9815,2.1625,-3.3837,-2.3854,-2.4210,2.5844,-2.2941,-1.7982,-1.7326,-2.1566,-0.3847,-1.8492,-0.3796,-1.3396,0.4987,-1.5455,-0.5175,-2.6628,-0.8999,-0.8943,-2.1566,-0.5751,-0.9485,-1.9332,-1.0797,-0.5942,-1.3501,-2.3243,-0.9849,-1.0620,-0.8943}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0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Activity(exp=0): {0.0331,-2.6639}
Activity(exp=1): {0.0331,-2.3950}
Activity(exp=2): {0.0331,-3.8901}
Activity(exp=3): {0.0331,-3.0094}
The Likelihood DID improve.
Suggested variations:
key=12;8;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation5).
>> Starting new optimization: component1-2-variation5. (2021-05-21 21:27:28.908).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.616586894934355
gradient = {-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000}
gradient norm = 1.124691451332946E-6
Already at minimum!
After: gradient norm = 1.124691451332946E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1079,-0.1079}
Count Table 1:
---------------
h: {0.2036,-0.2036}
Count Table 2:
---------------
h: {0.0227,-0.0227}
Count Table 3:
---------------
h: {0.0422,-0.0422}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.0797,-1.9332,-0.9485,-0.5751,-0.9849,-2.3243,-1.3501,-0.5942,-0.8943,-1.0620,0.4987,-1.3396,-0.3796,-1.8492,-0.8999,-2.6628,-0.5175,-1.5455,-2.1566,-0.8943,-2.4210,-2.3854,-3.3837,2.1625,-1.7326,-1.7982,-2.2941,2.5844,-0.3847,-2.1566,-2.1225,-2.9225,0.2366,2.1217,-1.9421,-2.3238,-2.4618,-0.0287,-1.9815,-0.3847,0.2811,-3.6451,0.1505,-0.3792,-0.1576,-2.2564,-1.1106,0.3845,-3.0950,-1.9815,-1.6891,0.1049,-1.6810,-1.3498,-1.4705,-0.7545,-1.6580,-0.4278,0.2115,-3.0950,-1.3498,-1.6810,0.1049,-1.6891,-0.4278,-1.6580,-0.7545,-1.4705,-3.0950,0.2115,-0.3792,0.1505,-3.6451,0.2811,0.3845,-1.1106,-2.2564,-0.1576,-1.9815,-3.0950,2.1217,0.2366,-2.9225,-2.1225,-0.0287,-2.4618,-2.3238,-1.9421,-0.3847,-1.9815,2.1625,-3.3837,-2.3854,-2.4210,2.5844,-2.2941,-1.7982,-1.7326,-2.1566,-0.3847,-1.8492,-0.3796,-1.3396,0.4987,-1.5455,-0.5175,-2.6628,-0.8999,-0.8943,-2.1566,-0.5751,-0.9485,-1.9332,-1.0797,-0.5942,-1.3501,-2.3243,-0.9849,-1.0620,-0.8943}
Dinucleotide(d=1): 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Activity(exp=0): {0.0331,-2.6639}
Activity(exp=1): {0.0331,-2.3950}
Activity(exp=2): {0.0331,-3.8901}
Activity(exp=3): {0.0331,-3.0094}
The Likelihood DID improve.
Suggested variations:
key=12;9;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation6).
>> Starting new optimization: component1-2-variation6. (2021-05-21 21:27:29.949).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.6165868868424202
gradient = {-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 1.180675879843308E-6
Already at minimum!
After: gradient norm = 1.180675879843308E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1079,-0.1079}
Count Table 1:
---------------
h: {0.2036,-0.2036}
Count Table 2:
---------------
h: {0.0227,-0.0227}
Count Table 3:
---------------
h: {0.0422,-0.0422}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.0797,-1.9332,-0.9485,-0.5751,-0.9849,-2.3243,-1.3501,-0.5942,-0.8943,-1.0620,0.4987,-1.3396,-0.3796,-1.8492,-0.8999,-2.6628,-0.5175,-1.5455,-2.1566,-0.8943,-2.4210,-2.3854,-3.3837,2.1625,-1.7326,-1.7982,-2.2941,2.5844,-0.3847,-2.1566,-2.1225,-2.9225,0.2366,2.1217,-1.9421,-2.3238,-2.4618,-0.0287,-1.9815,-0.3847,0.2811,-3.6451,0.1505,-0.3792,-0.1576,-2.2564,-1.1106,0.3845,-3.0950,-1.9815,-1.6891,0.1049,-1.6810,-1.3498,-1.4705,-0.7545,-1.6580,-0.4278,0.2115,-3.0950,-1.3498,-1.6810,0.1049,-1.6891,-0.4278,-1.6580,-0.7545,-1.4705,-3.0950,0.2115,-0.3792,0.1505,-3.6451,0.2811,0.3845,-1.1106,-2.2564,-0.1576,-1.9815,-3.0950,2.1217,0.2366,-2.9225,-2.1225,-0.0287,-2.4618,-2.3238,-1.9421,-0.3847,-1.9815,2.1625,-3.3837,-2.3854,-2.4210,2.5844,-2.2941,-1.7982,-1.7326,-2.1566,-0.3847,-1.8492,-0.3796,-1.3396,0.4987,-1.5455,-0.5175,-2.6628,-0.8999,-0.8943,-2.1566,-0.5751,-0.9485,-1.9332,-1.0797,-0.5942,-1.3501,-2.3243,-0.9849,-1.0620,-0.8943}
Dinucleotide(d=1): 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Activity(exp=0): {0.0331,-2.6639}
Activity(exp=1): {0.0331,-2.3950}
Activity(exp=2): {0.0331,-3.8901}
Activity(exp=3): {0.0331,-3.0094}
The Likelihood DID improve.
Suggested variations:
key=12;10;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation7).
>> Starting new optimization: component1-2-variation7. (2021-05-21 21:27:31.054).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[68,69]},{"h":[70,71]},{"h":[72,73]},{"h":[74,75]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[60,61],[62,63],[64,65],[66,67]]}]}
Value and gradient before optimization:
=======================================
value = 2.616586953260057
gradient = {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 3.0559142903424785E-6
Starting Function Value: 2.616586953260057
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.616586953249541 0.000006588552735 2.156000498884284 0.000001013929531
2 4 2.616586953247321 0.000006588552735 1.000000000000000 0.000001026981592
Convergence criteria met.
After: gradient norm = 1.0269815922213113E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1079,-0.1079}
Count Table 1:
---------------
h: {0.2036,-0.2036}
Count Table 2:
---------------
h: {0.0227,-0.0227}
Count Table 3:
---------------
h: {0.0422,-0.0422}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-1.0797,-1.9332,-0.9485,-0.5751,-0.9849,-2.3243,-1.3501,-0.5942,-0.8943,-1.0620,0.4987,-1.3396,-0.3796,-1.8492,-0.8999,-2.6628,-0.5175,-1.5455,-2.1566,-0.8943,-2.4210,-2.3854,-3.3837,2.1625,-1.7326,-1.7982,-2.2941,2.5844,-0.3847,-2.1566,-2.1225,-2.9225,0.2366,2.1217,-1.9421,-2.3238,-2.4618,-0.0287,-1.9815,-0.3847,0.2811,-3.6451,0.1505,-0.3792,-0.1576,-2.2564,-1.1106,0.3845,-3.0950,-1.9815,-1.6891,0.1049,-1.6810,-1.3498,-1.4705,-0.7545,-1.6580,-0.4278,0.2115,-3.0950,-1.3498,-1.6810,0.1049,-1.6891,-0.4278,-1.6580,-0.7545,-1.4705,-3.0950,0.2115,-0.3792,0.1505,-3.6451,0.2811,0.3845,-1.1106,-2.2564,-0.1576,-1.9815,-3.0950,2.1217,0.2366,-2.9225,-2.1225,-0.0287,-2.4618,-2.3238,-1.9421,-0.3847,-1.9815,2.1625,-3.3837,-2.3854,-2.4210,2.5844,-2.2941,-1.7982,-1.7326,-2.1566,-0.3847,-1.8492,-0.3796,-1.3396,0.4987,-1.5455,-0.5175,-2.6628,-0.8999,-0.8943,-2.1566,-0.5751,-0.9485,-1.9332,-1.0797,-0.5942,-1.3501,-2.3243,-0.9849,-1.0620,-0.8943}
Dinucleotide(d=1): 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Activity(exp=0): {0.0331,-2.6639}
Activity(exp=1): {0.0331,-2.3950}
Activity(exp=2): {0.0331,-3.8901}
Activity(exp=3): {0.0331,-3.0094}
The Likelihood DID NOT improve. Discarding fit component1-2-variation7.
> No varitions possible for Binding mode 1.
> Unfreezing component (component1-3-f0).
>> Starting new optimization: component1-3-f0. (2021-05-21 21:27:35.967).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[623,624]},{"h":[625,626]},{"h":[627,628]},{"h":[629,630]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,9,8,2,3,6,7,4,5,11,10,19,18,12,13,16,17,14,15,21,20,29,28,22,23,26,27,24,25,31,30,39,38,32,33,36,37,34,35,41,40,49,48,42,43,46,47,44,45,51,50,59,58,52,53,56,57,54,55,58,59,50,51,57,56,53,52,55,54,48,49,40,41,47,46,43,42,45,44,38,39,30,31,37,36,33,32,35,34,28,29,20,21,27,26,23,22,25,24,18,19,10,11,17,16,13,12,15,14,8,9,0,1,7,6,3,2,5,4],"activity":[[615,616],[617,618],[619,620],[621,622]],"dinucleotide":[[71,70,79,78,72,73,76,77,74,75,61,60,69,68,62,63,66,67,64,65,151,150,159,158,152,153,156,157,154,155,141,140,149,148,142,143,146,147,144,145,81,80,89,88,82,83,86,87,84,85,91,90,99,98,92,93,96,97,94,95,121,120,129,128,122,123,126,127,124,125,131,130,139,138,132,133,136,137,134,135,101,100,109,108,102,103,106,107,104,105,111,110,119,118,112,113,116,117,114,115,171,170,179,178,172,173,176,177,174,175,161,160,169,168,162,163,166,167,164,165,251,250,259,258,252,253,256,257,254,255,241,240,249,248,242,243,246,247,244,245,181,180,189,188,182,183,186,187,184,185,191,190,199,198,192,193,196,197,194,195,221,220,229,228,222,223,226,227,224,225,231,230,239,238,232,233,236,237,234,235,201,200,209,208,202,203,206,207,204,205,211,210,219,218,212,213,216,217,214,215,271,270,279,278,272,273,276,277,274,275,261,260,269,268,262,263,266,267,264,265,351,350,359,358,352,353,356,357,354,355,341,340,349,348,342,343,346,347,344,345,281,280,289,288,282,283,286,287,284,285,291,290,299,298,292,293,296,297,294,295,321,320,329,328,322,323,326,327,324,325,331,330,339,338,332,333,336,337,334,335,301,300,309,308,302,303,306,307,304,305,311,310,319,318,312,313,316,317,314,315,371,370,379,378,372,373,376,377,374,375,361,360,369,368,362,363,366,367,364,365,451,450,459,458,452,453,456,457,454,455,441,440,449,448,442,443,446,447,444,445,381,380,389,388,382,383,386,387,384,385,391,390,399,398,392,393,396,397,394,395,421,420,429,428,422,423,426,427,424,425,431,430,439,438,432,433,436,437,434,435,401,400,409,408,402,403,406,407,404,405,411,410,419,418,412,413,416,417,414,415,471,470,479,478,472,473,476,477,474,475,461,460,469,468,462,463,466,467,464,465,551,550,559,558,552,553,556,557,554,555,541,540,549,548,542,543,546,547,544,545,481,480,489,488,482,483,486,487,484,485,491,490,499,498,492,493,496,497,494,495,521,520,529,528,522,523,526,527,524,525,531,530,539,538,532,533,536,537,534,535,501,500,509,508,502,503,506,507,504,505,511,510,519,518,512,513,516,517,514,515,571,570,568,578,572,573,576,577,574,575,561,560,569,568,562,563,566,567,564,565,612,614,560,570,609,605,587,579,600,594,613,612,561,571,610,606,588,580,601,595,580,579,567,577,581,582,585,586,583,584,588,587,566,576,589,590,593,585,591,592,606,605,563,573,607,608,590,582,603,597,610,609,562,572,611,607,589,581,602,596,595,594,565,575,596,597,592,584,598,599,601,600,564,574,602,603,591,583,604,598,548,558,468,478,538,528,498,488,518,508,549,559,469,479,539,529,499,489,519,509,540,550,460,470,530,520,490,480,510,500,541,551,461,471,531,521,491,481,511,501,547,557,467,477,537,527,497,487,517,507,546,556,466,476,536,526,496,486,516,506,543,553,463,473,533,523,493,483,513,503,542,552,462,472,532,522,492,482,512,502,545,555,465,475,535,525,495,485,515,505,544,554,464,474,534,524,494,484,514,504,448,458,368,378,438,428,398,388,418,408,449,459,369,379,439,429,399,389,419,409,440,450,360,370,430,420,390,380,410,400,441,451,361,371,431,421,391,381,411,401,447,457,367,377,437,427,397,387,417,407,446,456,366,376,436,426,396,386,416,406,443,453,363,373,433,423,393,383,413,403,442,452,362,372,432,422,392,382,412,402,445,455,365,375,435,425,395,385,415,405,444,454,364,374,434,424,394,384,414,404,348,358,268,278,338,328,298,288,318,308,349,359,269,279,339,329,299,289,319,309,340,350,260,270,330,320,290,280,310,300,341,351,261,271,331,321,291,281,311,301,347,357,267,277,337,327,297,287,317,307,346,356,266,276,336,326,296,286,316,306,343,353,263,273,333,323,293,283,313,303,342,352,262,272,332,322,292,282,312,302,345,355,265,275,335,325,295,285,315,305,344,354,264,274,334,324,294,284,314,304,248,258,168,178,238,228,198,188,218,208,249,259,169,179,239,229,199,189,219,209,240,250,160,170,230,220,190,180,210,200,241,251,161,171,231,221,191,181,211,201,247,257,167,177,237,227,197,187,217,207,246,256,166,176,236,226,196,186,216,206,243,253,163,173,233,223,193,183,213,203,242,252,162,172,232,222,192,182,212,202,245,255,165,175,235,225,195,185,215,205,244,254,164,174,234,224,194,184,214,204,148,158,68,78,138,128,98,88,118,108,149,159,69,79,139,129,99,89,119,109,140,150,60,70,130,120,90,80,110,100,141,151,61,71,131,121,91,81,111,101,147,157,67,77,137,127,97,87,117,107,146,156,66,76,136,126,96,86,116,106,143,153,63,73,133,123,93,83,113,103,142,152,62,72,132,122,92,82,112,102,145,155,65,75,135,125,95,85,115,105,144,154,64,74,134,124,94,84,114,104]]}]}
Value and gradient before optimization:
=======================================
value = 2.616586886842424
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gradient norm = 0.008042798150519946
Starting Function Value: 2.616586886842424
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
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2 4 2.612627187859788 0.131112653445670 0.182679140942008 0.011143645030431
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6 8 2.611273323121492 0.275480131556452 1.000000000000000 0.015630571144452
7 9 2.610961152598186 0.135250301031454 1.000000000000000 0.005660764252908
8 10 2.610881278965419 0.030506351444963 1.000000000000000 0.003702179509906
9 11 2.610780376343067 0.052336808916935 1.000000000000000 0.004572369529834
10 12 2.610617970050095 0.112489796954673 1.000000000000000 0.006881546450172
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416 441 2.603013358198812 0.012835375166532 1.000000000000000 0.000028302881136
417 443 2.603013339170186 0.009121792324434 0.414589542652824 0.000074557235536
418 444 2.603013310810466 0.011221258615187 1.000000000000000 0.000045502538740
419 445 2.603013285002677 0.007915484301574 1.000000000000000 0.000027035352716
420 446 2.603013256448707 0.010662046189890 1.000000000000000 0.000031988838764
421 447 2.603013227336152 0.011913095559404 1.000000000000000 0.000040321578504
422 449 2.603013215684333 0.008727615948840 0.269080155079080 0.000076214622614
423 450 2.603013183654826 0.012675386872635 1.000000000000000 0.000045196059615
424 451 2.603013156063439 0.008713212529133 1.000000000000000 0.000028191221069
425 452 2.603013129497800 0.009956139633545 1.000000000000000 0.000032200582362
426 453 2.603013105152130 0.007828398574280 1.000000000000000 0.000034879456518
427 454 2.603013062435675 0.012362230757748 1.000000000000000 0.000039444785028
428 456 2.603013052938270 0.004347667415964 0.196918771065144 0.000053610808088
429 457 2.603013014907428 0.016901762007116 1.000000000000000 0.000033085013728
430 458 2.603012987151087 0.013436302608732 1.000000000000000 0.000029441478929
431 459 2.603012955705310 0.018443570365583 1.000000000000000 0.000036517664378
432 461 2.603012949862953 0.003313430748808 0.140318055238644 0.000049237696806
433 462 2.603012937142053 0.004155423554073 1.000000000000000 0.000037312354584
434 463 2.603012914014635 0.008303817420915 1.000000000000000 0.000024766020741
435 464 2.603012899398160 0.007301426146342 1.000000000000000 0.000029508851729
436 465 2.603012896674009 0.025311887822823 1.000000000000000 0.000117510080600
437 466 2.603012855105880 0.009999343530898 1.000000000000000 0.000039063470377
438 467 2.603012837453946 0.004809827877042 1.000000000000000 0.000021452414010
439 468 2.603012819713976 0.009092457400505 1.000000000000000 0.000034900054703
440 469 2.603012798535188 0.011469169305725 1.000000000000000 0.000039232497289
441 470 2.603012764330154 0.030608983555467 1.000000000000000 0.000088035630928
442 471 2.603012724635913 0.024848357643877 1.000000000000000 0.000037747079086
443 472 2.603012705457696 0.006294929797254 1.000000000000000 0.000023267444904
444 473 2.603012680936083 0.006340286292925 1.000000000000000 0.000024901426345
445 474 2.603012657879807 0.007031006401369 1.000000000000000 0.000030474350858
446 476 2.603012639019172 0.015532421509517 0.381207574765096 0.000051858377556
447 477 2.603012603694079 0.013885766208816 1.000000000000000 0.000031100208881
448 478 2.603012571923042 0.016399025230836 1.000000000000000 0.000021900455823
449 479 2.603012546078199 0.016151984024389 1.000000000000000 0.000054901213471
450 480 2.603012535418754 0.022749994667227 1.000000000000000 0.000069810349258
451 481 2.603012514258725 0.007454311459822 1.000000000000000 0.000026032793239
452 482 2.603012499183415 0.003808182097563 1.000000000000000 0.000023414172181
453 483 2.603012482958190 0.004303308702913 1.000000000000000 0.000029366316837
454 484 2.603012449932840 0.010166816647474 1.000000000000000 0.000032352931542
455 485 2.603012416637315 0.035920479929181 1.000000000000000 0.000076315841382
456 486 2.603012364544687 0.016216763043396 1.000000000000000 0.000025247706187
457 487 2.603012341170808 0.006771502854745 1.000000000000000 0.000021761278105
458 488 2.603012307786623 0.017745553022946 1.000000000000000 0.000027868928678
459 490 2.603012291572691 0.015008332051983 0.417933126106629 0.000037281904808
460 491 2.603012256963214 0.019262116914519 1.000000000000000 0.000027036902555
461 492 2.603012209326454 0.021906347249979 1.000000000000000 0.000022729022800
462 493 2.603012151800678 0.040993781183637 1.000000000000000 0.000032033003102
463 494 2.603012118944611 0.030952230751780 1.000000000000000 0.000061362124465
464 495 2.603012084680181 0.020530161456392 1.000000000000000 0.000063468711544
465 496 2.603012044170689 0.008243679224266 1.000000000000000 0.000029095854040
466 497 2.603012009421088 0.009858450415550 1.000000000000000 0.000018369822789
467 498 2.603011974450360 0.017777867600690 1.000000000000000 0.000023096170307
468 499 2.603011924291020 0.025772939793006 1.000000000000000 0.000024841754036
469 501 2.603011911231357 0.015028893527944 0.282667252294779 0.000036326743940
470 502 2.603011884163168 0.017314940089561 1.000000000000000 0.000020789695030
471 503 2.603011859531313 0.016131526442054 1.000000000000000 0.000016372190356
472 504 2.603011817284546 0.027224309784504 1.000000000000000 0.000020247875003
473 505 2.603011774015253 0.025586275089646 1.000000000000000 0.000022260299671
474 507 2.603011756370239 0.017850275939185 0.271573987780948 0.000035454897086
475 508 2.603011716491480 0.019348055300578 1.000000000000000 0.000023533222487
476 509 2.603011706505613 0.020262127898218 1.000000000000000 0.000044812858160
477 510 2.603011683611848 0.010710195285504 1.000000000000000 0.000019062994966
478 511 2.603011669131593 0.005952415912459 1.000000000000000 0.000017096371869
479 512 2.603011649124149 0.011936139900713 1.000000000000000 0.000020108492539
480 513 2.603011610473150 0.023078815796258 1.000000000000000 0.000022518330493
481 514 2.603011606596761 0.037571154064147 1.000000000000000 0.000068517318568
482 515 2.603011551456483 0.012595220411454 1.000000000000000 0.000019962949896
483 516 2.603011538325297 0.003258951062600 1.000000000000000 0.000014137645407
484 517 2.603011520010045 0.008982537060916 1.000000000000000 0.000015874772637
485 518 2.603011502301061 0.016471814647884 1.000000000000000 0.000036012167646
486 519 2.603011477176744 0.018704529329328 1.000000000000000 0.000022150045510
487 520 2.603011456341703 0.014630672377215 1.000000000000000 0.000015142321506
488 521 2.603011441957387 0.014789478380950 1.000000000000000 0.000037431799426
489 522 2.603011426202785 0.010653307592572 1.000000000000000 0.000017179284617
490 523 2.603011413137449 0.004388051537392 1.000000000000000 0.000017500179823
491 524 2.603011390337583 0.013339181483594 1.000000000000000 0.000020394925192
492 525 2.603011370367188 0.010861536301672 1.000000000000000 0.000018733694526
493 527 2.603011356554292 0.013569564265273 0.288489025409811 0.000045410706468
494 528 2.603011330429177 0.017616823991333 1.000000000000000 0.000017027926842
495 529 2.603011322468033 0.002952808573412 1.000000000000000 0.000014510473813
496 530 2.603011306497491 0.007153577977131 1.000000000000000 0.000021020420734
497 531 2.603011294082231 0.007177136483497 1.000000000000000 0.000017586996584
498 532 2.603011275411182 0.013809329094702 1.000000000000000 0.000018060447881
499 533 2.603011256800480 0.019849504216167 1.000000000000000 0.000029899666284
500 534 2.603011239730857 0.007472991307391 1.000000000000000 0.000019137899212
>>> Maximum iteration count reached.
After: gradient norm = 1.9137899211905857E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1939,-0.1939}
Count Table 1:
---------------
h: {0.3457,-0.3457}
Count Table 2:
---------------
h: {0.1184,-0.1184}
Count Table 3:
---------------
h: {0.2318,-0.2318}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0001,0.0001}
Activity(exp=1): {0.0001,0.0001}
Activity(exp=2): {0.0001,0.0001}
Activity(exp=3): {0.0001,0.0001}
Binding mode 1:
---------------
Mononucleotide: {-0.3496,-0.7476,-0.4637,-0.2676,-0.2640,-1.2697,-0.9291,-0.0882,-0.4752,-0.5743,-0.1131,-0.7307,-0.3074,-0.5961,-0.0701,-1.3699,-0.5495,-0.2322,-0.9847,-0.4752,-0.7133,-1.0713,-0.8827,0.2649,0.1601,-0.9307,-1.0050,0.2239,-0.4888,-0.9847,-0.5288,-0.7535,-0.5605,-0.3873,0.1771,-0.4374,-1.6418,0.0274,-0.8338,-0.4888,0.0132,-1.2209,-1.0003,-0.0724,0.4251,-0.9623,-0.7205,-0.0437,-1.0118,-0.8338,-0.6400,-0.1244,-1.0904,-0.4696,-0.0793,-0.6795,-1.2017,-0.1994,0.0685,-1.0118,-0.4696,-1.0904,-0.1244,-0.6400,-0.1994,-1.2017,-0.6795,-0.0793,-1.0118,0.0685,-0.0724,-1.0003,-1.2209,0.0132,-0.0437,-0.7205,-0.9623,0.4251,-0.8338,-1.0118,-0.3873,-0.5605,-0.7535,-0.5288,0.0274,-1.6418,-0.4374,0.1771,-0.4888,-0.8338,0.2649,-0.8827,-1.0713,-0.7133,0.2239,-1.0050,-0.9307,0.1601,-0.9847,-0.4888,-0.5961,-0.3074,-0.7307,-0.1131,-0.2322,-0.5495,-1.3699,-0.0701,-0.4752,-0.9847,-0.2676,-0.4637,-0.7476,-0.3496,-0.0882,-0.9291,-1.2697,-0.2640,-0.5743,-0.4752}
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Activity(exp=0): {0.0042,-1.7429}
Activity(exp=1): {0.0042,-1.4046}
Activity(exp=2): {0.0042,-1.7653}
Activity(exp=3): {0.0042,-1.1623}
> Optimizing the full model (component1-4-all).
>> Starting new optimization: component1-4-all. (2021-05-21 21:49:20.554).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[631,632]},{"h":[633,634]},{"h":[635,636]},{"h":[637,638]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7]]},{"mononucleotide":[9,8,17,16,10,11,14,15,12,13,19,18,27,26,20,21,24,25,22,23,29,28,37,36,30,31,34,35,32,33,39,38,47,46,40,41,44,45,42,43,49,48,57,56,50,51,54,55,52,53,59,58,67,66,60,61,64,65,62,63,66,67,58,59,65,64,61,60,63,62,56,57,48,49,55,54,51,50,53,52,46,47,38,39,45,44,41,40,43,42,36,37,28,29,35,34,31,30,33,32,26,27,18,19,25,24,21,20,23,22,16,17,8,9,15,14,11,10,13,12],"activity":[[623,624],[625,626],[627,628],[629,630]],"dinucleotide":[[79,78,87,86,80,81,84,85,82,83,69,68,77,76,70,71,74,75,72,73,159,158,167,166,160,161,164,165,162,163,149,148,157,156,150,151,154,155,152,153,89,88,97,96,90,91,94,95,92,93,99,98,107,106,100,101,104,105,102,103,129,128,137,136,130,131,134,135,132,133,139,138,147,146,140,141,144,145,142,143,109,108,117,116,110,111,114,115,112,113,119,118,127,126,120,121,124,125,122,123,179,178,187,186,180,181,184,185,182,183,169,168,177,176,170,171,174,175,172,173,259,258,267,266,260,261,264,265,262,263,249,248,257,256,250,251,254,255,252,253,189,188,197,196,190,191,194,195,192,193,199,198,207,206,200,201,204,205,202,203,229,228,237,236,230,231,234,235,232,233,239,238,247,246,240,241,244,245,242,243,209,208,217,216,210,211,214,215,212,213,219,218,227,226,220,221,224,225,222,223,279,278,287,286,280,281,284,285,282,283,269,268,277,276,270,271,274,275,272,273,359,358,367,366,360,361,364,365,362,363,349,348,357,356,350,351,354,355,352,353,289,288,297,296,290,291,294,295,292,293,299,298,307,306,300,301,304,305,302,303,329,328,337,336,330,331,334,335,332,333,339,338,347,346,340,341,344,345,342,343,309,308,317,316,310,311,314,315,312,313,319,318,327,326,320,321,324,325,322,323,379,378,387,386,380,381,384,385,382,383,369,368,377,376,370,371,374,375,372,373,459,458,467,466,460,461,464,465,462,463,449,448,457,456,450,451,454,455,452,453,389,388,397,396,390,391,394,395,392,393,399,398,407,406,400,401,404,405,402,403,429,428,437,436,430,431,434,435,432,433,439,438,447,446,440,441,444,445,442,443,409,408,417,416,410,411,414,415,412,413,419,418,427,426,420,421,424,425,422,423,479,478,487,486,480,481,484,485,482,483,469,468,477,476,470,471,474,475,472,473,559,558,567,566,560,561,564,565,562,563,549,548,557,556,550,551,554,555,552,553,489,488,497,496,490,491,494,495,492,493,499,498,507,506,500,501,504,505,502,503,529,528,537,536,530,531,534,535,532,533,539,538,547,546,540,541,544,545,542,543,509,508,517,516,510,511,514,515,512,513,519,518,527,526,520,521,524,525,522,523,579,578,576,586,580,581,584,585,582,583,569,568,577,576,570,571,574,575,572,573,620,622,568,578,617,613,595,587,608,602,621,620,569,579,618,614,596,588,609,603,588,587,575,585,589,590,593,594,591,592,596,595,574,584,597,598,601,593,599,600,614,613,571,581,615,616,598,590,611,605,618,617,570,580,619,615,597,589,610,604,603,602,573,583,604,605,600,592,606,607,609,608,572,582,610,611,599,591,612,606,556,566,476,486,546,536,506,496,526,516,557,567,477,487,547,537,507,497,527,517,548,558,468,478,538,528,498,488,518,508,549,559,469,479,539,529,499,489,519,509,555,565,475,485,545,535,505,495,525,515,554,564,474,484,544,534,504,494,524,514,551,561,471,481,541,531,501,491,521,511,550,560,470,480,540,530,500,490,520,510,553,563,473,483,543,533,503,493,523,513,552,562,472,482,542,532,502,492,522,512,456,466,376,386,446,436,406,396,426,416,457,467,377,387,447,437,407,397,427,417,448,458,368,378,438,428,398,388,418,408,449,459,369,379,439,429,399,389,419,409,455,465,375,385,445,435,405,395,425,415,454,464,374,384,444,434,404,394,424,414,451,461,371,381,441,431,401,391,421,411,450,460,370,380,440,430,400,390,420,410,453,463,373,383,443,433,403,393,423,413,452,462,372,382,442,432,402,392,422,412,356,366,276,286,346,336,306,296,326,316,357,367,277,287,347,337,307,297,327,317,348,358,268,278,338,328,298,288,318,308,349,359,269,279,339,329,299,289,319,309,355,365,275,285,345,335,305,295,325,315,354,364,274,284,344,334,304,294,324,314,351,361,271,281,341,331,301,291,321,311,350,360,270,280,340,330,300,290,320,310,353,363,273,283,343,333,303,293,323,313,352,362,272,282,342,332,302,292,322,312,256,266,176,186,246,236,206,196,226,216,257,267,177,187,247,237,207,197,227,217,248,258,168,178,238,228,198,188,218,208,249,259,169,179,239,229,199,189,219,209,255,265,175,185,245,235,205,195,225,215,254,264,174,184,244,234,204,194,224,214,251,261,171,181,241,231,201,191,221,211,250,260,170,180,240,230,200,190,220,210,253,263,173,183,243,233,203,193,223,213,252,262,172,182,242,232,202,192,222,212,156,166,76,86,146,136,106,96,126,116,157,167,77,87,147,137,107,97,127,117,148,158,68,78,138,128,98,88,118,108,149,159,69,79,139,129,99,89,119,109,155,165,75,85,145,135,105,95,125,115,154,164,74,84,144,134,104,94,124,114,151,161,71,81,141,131,101,91,121,111,150,160,70,80,140,130,100,90,120,110,153,163,73,83,143,133,103,93,123,113,152,162,72,82,142,132,102,92,122,112]]}]}
Value and gradient before optimization:
=======================================
value = 2.603011239730858
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gradient norm = 1.9599454170853483E-5
Starting Function Value: 2.603011239730858
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
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214 222 2.603006285606786 0.000826911389680 0.184194666727589 0.000014457703135
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217 225 2.603006283493212 0.002333862427582 1.000000000000000 0.000006158571313
218 226 2.603006282643617 0.001914400113783 1.000000000000000 0.000006739764483
219 227 2.603006281914136 0.004487787844758 1.000000000000000 0.000013744171397
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222 230 2.603006280250298 0.001510561435297 1.000000000000000 0.000009339783302
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230 239 2.603006276711241 0.001991935780032 1.000000000000000 0.000004345652430
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232 242 2.603006276011103 0.001323722477666 1.000000000000000 0.000004829133430
233 243 2.603006275475780 0.001756410524637 1.000000000000000 0.000004008837084
234 244 2.603006274654603 0.002432583208486 1.000000000000000 0.000004277323677
235 245 2.603006273689718 0.002860899364743 1.000000000000000 0.000006942431610
236 246 2.603006273542478 0.006258411591164 1.000000000000000 0.000011740215117
237 247 2.603006272419755 0.003200586925923 1.000000000000000 0.000003475657255
238 248 2.603006272061186 0.001168225089576 1.000000000000000 0.000003177591013
239 249 2.603006271368652 0.001655884162742 1.000000000000000 0.000003708577695
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241 252 2.603006270094230 0.001763702933185 0.278277978994278 0.000005809855357
242 253 2.603006269331715 0.002669087055255 1.000000000000000 0.000003627865034
243 254 2.603006268543676 0.002354071324816 1.000000000000000 0.000003644073245
244 255 2.603006268429130 0.004831511664118 1.000000000000000 0.000013775972843
245 256 2.603006267367424 0.001491654847963 1.000000000000000 0.000004041899129
246 257 2.603006267090537 0.001271486410088 1.000000000000000 0.000002944305803
247 258 2.603006266744816 0.002115595292972 1.000000000000000 0.000002879257893
248 259 2.603006266266538 0.001785735478235 1.000000000000000 0.000003092705779
249 260 2.603006265949436 0.005477843678414 1.000000000000000 0.000008615723898
250 261 2.603006265093256 0.001572811465641 1.000000000000000 0.000002840652174
251 262 2.603006264866087 0.001399955538628 1.000000000000000 0.000002187349913
252 263 2.603006264497554 0.001713823905007 1.000000000000000 0.000002069126778
253 264 2.603006264019206 0.002162399044955 1.000000000000000 0.000002937131448
254 266 2.603006263725741 0.001239208489087 0.333773399067612 0.000004649833000
255 267 2.603006263295065 0.001839087746736 1.000000000000000 0.000002749222369
256 268 2.603006262923591 0.001887476544171 1.000000000000000 0.000002038445114
257 269 2.603006262568671 0.001909773074635 1.000000000000000 0.000002196925700
258 270 2.603006262056212 0.002238700900320 1.000000000000000 0.000003234622524
259 272 2.603006261710025 0.003471965308623 0.458777637764734 0.000004519002691
260 273 2.603006261294895 0.001143370466406 1.000000000000000 0.000002592136579
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267 280 2.603006258241252 0.001440519588641 1.000000000000000 0.000002361548052
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269 282 2.603006256922438 0.003956299222810 1.000000000000000 0.000003488805337
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286 300 2.603006250756079 0.002173910949087 1.000000000000000 0.000005936478717
287 301 2.603006250299818 0.001678573497857 1.000000000000000 0.000002226234861
288 302 2.603006250079575 0.000842076991425 1.000000000000000 0.000001719128302
289 303 2.603006249831935 0.001652792077577 1.000000000000000 0.000001853581679
290 304 2.603006249469049 0.002254225440070 1.000000000000000 0.000001938462964
291 305 2.603006248942933 0.003335064946106 1.000000000000000 0.000002991572536
292 306 2.603006248789061 0.003312081310325 1.000000000000000 0.000005699736441
293 307 2.603006248320535 0.000919050031096 1.000000000000000 0.000001772285073
294 308 2.603006248163438 0.000757170353579 1.000000000000000 0.000001540466322
295 309 2.603006247902109 0.001113484199314 1.000000000000000 0.000001595828696
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302 316 2.603006246156285 0.002214854819062 1.000000000000000 0.000002341189590
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305 319 2.603006245542991 0.000597845524421 1.000000000000000 0.000006418349286
306 320 2.603006245497780 0.001206339809808 1.000000000000000 0.000008066337521
307 321 2.603006245414876 0.000234404043081 1.000000000000000 0.000002432907059
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309 323 2.603006245250931 0.000961888413224 1.000000000000000 0.000003761875494
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311 326 2.603006245041290 0.000663387006966 0.217719840096461 0.000008187812272
312 327 2.603006244847896 0.001834134788265 1.000000000000000 0.000004764344203
313 328 2.603006244698261 0.001164850403250 1.000000000000000 0.000002222320767
314 329 2.603006244613350 0.000491899316672 1.000000000000000 0.000001631147262
315 330 2.603006244518251 0.000493920810924 1.000000000000000 0.000001956841315
316 331 2.603006244407004 0.001053510023391 1.000000000000000 0.000007156426288
317 332 2.603006244312135 0.001144444247421 1.000000000000000 0.000005378494297
318 333 2.603006244233815 0.000228392076596 1.000000000000000 0.000002071122994
319 334 2.603006244171912 0.000350433834940 1.000000000000000 0.000001771998631
320 335 2.603006244114223 0.000453720606772 1.000000000000000 0.000002362928355
321 336 2.603006243984042 0.001097254312700 1.000000000000000 0.000003150510560
322 338 2.603006243927911 0.000871805769589 0.429307467509720 0.000003069722929
323 339 2.603006243813893 0.001411190761770 1.000000000000000 0.000001737801913
324 340 2.603006243699608 0.000863220231101 1.000000000000000 0.000001757983593
325 342 2.603006243655742 0.000715978455666 0.246851817394390 0.000004665050911
326 343 2.603006243548447 0.000585389602156 1.000000000000000 0.000002439155426
327 344 2.603006243491447 0.000414932115580 1.000000000000000 0.000001647995235
328 345 2.603006243433883 0.000522590798698 1.000000000000000 0.000001421607679
329 346 2.603006243363135 0.000671517777015 1.000000000000000 0.000001891932599
330 347 2.603006243246821 0.000915438724178 1.000000000000000 0.000002296635823
331 349 2.603006243183387 0.001656221563413 0.406117615058506 0.000003785741417
332 350 2.603006243072900 0.000755911294766 1.000000000000000 0.000002465967754
333 351 2.603006243003470 0.000979337838980 1.000000000000000 0.000002656168806
334 352 2.603006242949268 0.000574558148033 1.000000000000000 0.000002198528880
335 353 2.603006242915266 0.000157276984748 1.000000000000000 0.000002232290588
336 354 2.603006242801676 0.000615267821199 1.000000000000000 0.000002603302112
337 355 2.603006242690356 0.000945648904994 1.000000000000000 0.000002660316004
338 356 2.603006242548366 0.001508852871965 1.000000000000000 0.000002359138085
339 358 2.603006242492357 0.000877478613693 0.343543000831436 0.000002911440231
340 359 2.603006242404187 0.000900609300473 1.000000000000000 0.000001398600154
341 360 2.603006242342015 0.000693353529675 1.000000000000000 0.000001916268244
342 361 2.603006242270868 0.000906599855883 1.000000000000000 0.000002612666829
343 362 2.603006242169117 0.001188239326639 1.000000000000000 0.000002615661480
344 363 2.603006241996001 0.001781059863417 1.000000000000000 0.000003209649677
345 365 2.603006241938596 0.000775508213836 0.397386685279379 0.000002374129067
346 366 2.603006241865238 0.000775508213836 1.000000000000000 0.000001142154086
Convergence criteria met.
After: gradient norm = 1.1421540862462752E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.6011,-0.6011}
Count Table 1:
---------------
h: {0.6558,-0.6558}
Count Table 2:
---------------
h: {0.5448,-0.5448}
Count Table 3:
---------------
h: {0.5167,-0.5167}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {0.0000,0.8140}
Activity(exp=1): {0.0000,0.6190}
Activity(exp=2): {0.0000,0.8518}
Activity(exp=3): {0.0000,0.5699}
Binding mode 1:
---------------
Mononucleotide: {-0.3175,-0.7118,-0.4308,-0.2299,-0.2348,-1.2682,-0.9090,-0.0601,-0.4580,-0.5457,-0.0679,-0.6913,-0.2745,-0.5384,-0.0403,-1.4116,-0.5033,-0.2029,-0.9777,-0.4580,-0.6885,-1.0390,-0.8264,0.3186,0.1814,-0.9931,-0.9697,0.2973,-0.4688,-0.9777,-0.5159,-0.7452,-0.5237,-0.3238,0.1842,-0.3778,-1.6058,0.0455,-0.8346,-0.4688,0.0644,-1.1786,-0.9618,-0.0291,0.4539,-0.9575,-0.7123,-0.0093,-1.0010,-0.8346,-0.6053,-0.0882,-1.0712,-0.4164,-0.0600,-0.6614,-1.1892,-0.1736,0.1005,-1.0010,-0.4164,-1.0712,-0.0882,-0.6053,-0.1736,-1.1892,-0.6614,-0.0600,-1.0010,0.1005,-0.0291,-0.9618,-1.1786,0.0644,-0.0093,-0.7123,-0.9575,0.4539,-0.8346,-1.0010,-0.3238,-0.5237,-0.7452,-0.5159,0.0455,-1.6058,-0.3778,0.1842,-0.4688,-0.8346,0.3186,-0.8264,-1.0390,-0.6885,0.2973,-0.9697,-0.9931,0.1814,-0.9777,-0.4688,-0.5384,-0.2745,-0.6913,-0.0679,-0.2029,-0.5033,-1.4116,-0.0403,-0.4580,-0.9777,-0.2299,-0.4308,-0.7118,-0.3175,-0.0601,-0.9090,-1.2682,-0.2348,-0.5457,-0.4580}
Dinucleotide(d=1): 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Activity(exp=0): {0.0000,-1.4278}
Activity(exp=1): {0.0000,-1.2836}
Activity(exp=2): {0.0000,-1.4101}
Activity(exp=3): {0.0000,-1.0943}
> Optimization done.
Probound Model
±
Optimized model:
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Viewer
±
Binding Mode 0
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Binding Mode 1
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Mononucleotide (12bp)
Dinucleotide (12bp)
