Status
±
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", "pseudocount": 1000, "nThreads": 20, "lambdaL2": 1e-06}, {"function": "addTable", "leftFlank": "GAGTTCTACAGTCCGACCTGG", "nColumns": 3, "modeledColumns": [0, 1, 2], "countTableFile": "jobs/75f3dbb09f94/countTable.0.tsv.gz", "rightFlank": "CCAGGACTCGGACCTGGA", "inputFileType": "tsv.gz", "variableRegionLength": 10}, {"function": "addTable", "leftFlank": "GAGTTCTACAGTCCGACCTGG", "nColumns": 3, "modeledColumns": [0, 1, 2], "countTableFile": "jobs/75f3dbb09f94/countTable.1.tsv.gz", "rightFlank": "CCAGGACTCGGACCTGGA", "inputFileType": "tsv.gz", "variableRegionLength": 10}, {"function": "addTable", "leftFlank": "GAGTTCTACAGTCCGACCTGG", "nColumns": 3, "modeledColumns": [0, 1, 2], "countTableFile": "jobs/75f3dbb09f94/countTable.2.tsv.gz", "rightFlank": "CCAGGACTCGGACCTGGA", "inputFileType": "tsv.gz", "variableRegionLength": 10}, {"function": "addTable", "leftFlank": "GAGTTCTACAGTCCGACCTGG", "nColumns": 3, "modeledColumns": [0, 1, 2], "countTableFile": "jobs/75f3dbb09f94/countTable.3.tsv.gz", "rightFlank": "CCAGGACTCGGACCTGGA", "inputFileType": "tsv.gz", "variableRegionLength": 10}, {"function": "addSELEX", "concentration": 3300, "cumulativeEnrichment": false, "modelType": "RhoGamma"}, {"function": "addSELEX", "concentration": 1000, "cumulativeEnrichment": false, "modelType": "RhoGamma"}, {"function": "addSELEX", "concentration": 330, "cumulativeEnrichment": false, "modelType": "RhoGamma"}, {"function": "addSELEX", "concentration": 100, "cumulativeEnrichment": false, "modelType": "RhoGamma"}, {"function": "addNS"}, {"function": "addBindingMode", "flankLength": 6, "dinucleotideDistance": 10, "size": 10}, {"function": "bindingModeConstraints", "index": 0, "roundSpecificActivity": false, "experimentSpecificActivity": false}, {"function": "bindingModeConstraints", "index": 1, "roundSpecificActivity": false, "experimentSpecificActivity": false}, {"function": "enrichmentModelSeed", "gamma": [0, -1, -1], "rho": [0, 1, 0]}, {"function": "bindingModeSeed", "index": 1, "mononucleotideString": "..TAATTG.."}, {"function": "output", "outputPath": "jobs/75f3dbb09f94", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]Configuration File
±
ProBound configuration file:
{
"modelSeeding": {
"enrichmentModel": [
{
"rho": [
0,
1,
0
],
"gamma": [
0,
-1,
-1
]
},
{
"rho": [
0,
1,
0
],
"gamma": [
0,
-1,
-1
]
},
{
"rho": [
0,
1,
0
],
"gamma": [
0,
-1,
-1
]
},
{
"rho": [
0,
1,
0
],
"gamma": [
0,
-1,
-1
]
}
],
"bindingModes": [
{"seedScale": 1},
{
"seedScale": 1,
"mononucleotideString": "..TAATTG.."
}
]
},
"optimizerSetting": {
"nThreads": 20,
"likelihoodThreshold": 0,
"lambdaL2": 1.0E-6,
"pseudocount": 1000,
"patternSearchSettings": {},
"minimizerType": "lbfgs",
"nRetries": 3,
"hkSettings": {},
"output": {
"storeHessian": false,
"outputPath": "jobs/75f3dbb09f94",
"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,
"cumulativeEnrichment": false,
"concentration": 3300,
"modelType": "RhoGamma",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"cumulativeEnrichment": false,
"concentration": 1000,
"modelType": "RhoGamma",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"cumulativeEnrichment": false,
"concentration": 330,
"modelType": "RhoGamma",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"cumulativeEnrichment": false,
"concentration": 100,
"modelType": "RhoGamma",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [-1],
"modifications": []
}
],
"countTable": [
{
"leftFlank": "GAGTTCTACAGTCCGACCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 10,
"modeledColumns": [
0,
1,
2
],
"inputFileType": "tsv.gz",
"nColumns": 3,
"rightFlank": "CCAGGACTCGGACCTGGA",
"countTableFile": "jobs/75f3dbb09f94/countTable.0.tsv.gz"
},
{
"leftFlank": "GAGTTCTACAGTCCGACCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 10,
"modeledColumns": [
0,
1,
2
],
"inputFileType": "tsv.gz",
"nColumns": 3,
"rightFlank": "CCAGGACTCGGACCTGGA",
"countTableFile": "jobs/75f3dbb09f94/countTable.1.tsv.gz"
},
{
"leftFlank": "GAGTTCTACAGTCCGACCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 10,
"modeledColumns": [
0,
1,
2
],
"inputFileType": "tsv.gz",
"nColumns": 3,
"rightFlank": "CCAGGACTCGGACCTGGA",
"countTableFile": "jobs/75f3dbb09f94/countTable.2.tsv.gz"
},
{
"leftFlank": "GAGTTCTACAGTCCGACCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 10,
"modeledColumns": [
0,
1,
2
],
"inputFileType": "tsv.gz",
"nColumns": 3,
"rightFlank": "CCAGGACTCGGACCTGGA",
"countTableFile": "jobs/75f3dbb09f94/countTable.3.tsv.gz"
}
],
"bindingModeInteractions": [],
"bindingModes": [
{
"size": 0,
"fitLogActivity": true,
"flankLength": 0,
"dinucleotideDistance": 0,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 10,
"fitLogActivity": true,
"flankLength": 6,
"dinucleotideDistance": 10,
"positionBias": false,
"singleStrand": false,
"modifications": []
}
],
"letterComplement": "C-G,A-T"
},
"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": false,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": false,
"optimizeSize": false
},
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": false,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": false,
"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":false,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":false,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":false,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":false,"optimizeSize":false}]}
Entry=bindingModes, aEntry=[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":false,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":false,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":false,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":false,"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
Letter Order: ACGT
Optimizer settings:
===================
lambdaL2 = 1.0E-6
pseudocount = 1000.0
expBound = 40.0
fixedLibrarySize = false
>> Determining fitting order.
Summary of experiments
======================
Experiment 0:
-------------
Count table: Count table 0
Enrichment model: Rho-gamma enrichment model 0
Concentration: 3300.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 1:
-------------
Count table: Count table 1
Enrichment model: Rho-gamma enrichment model 1
Concentration: 1000.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 2:
-------------
Count table: Count table 2
Enrichment model: Rho-gamma enrichment model 2
Concentration: 330.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 3:
-------------
Count table: Count table 3
Enrichment model: Rho-gamma enrichment model 3
Concentration: 100.0
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 22:25:20.553).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[0,1,2]},{"h":[3,4,5]},{"h":[6,7,8]},{"h":[9,10,11]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 10.896249372117179
gradient = {0.1667,-0.3322,0.1655,0.1667,-0.3322,0.1655,0.1667,-0.3322,0.1655,0.1667,-0.3322,0.1655}
gradient norm = 0.8137209614205642
Starting Function Value: 10.896249372117179
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 6.905125475237026 5.000000000000000 6.144612510990479 0.758492080627081
2 5 5.071518666733314 6.854803295387769 0.098673842310091 0.683218972351404
3 6 4.658084017373439 3.266431685119595 1.000000000000000 0.370879488684239
4 7 4.402886558936966 1.136240337559923 1.000000000000000 0.064892984441601
5 8 4.396953664433909 0.248041585992052 1.000000000000000 0.018187807601965
6 9 4.396456874838060 0.056007103227113 1.000000000000000 0.001033411136063
7 10 4.396455328601387 0.003640705250089 1.000000000000000 0.000193604328937
8 11 4.396455272386062 0.000582856274082 1.000000000000000 0.000001838368381
9 12 4.396455272380620 0.000582856274082 1.000000000000000 0.000000041000997
Convergence criteria met.
After: gradient norm = 4.1000997224911216E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.0304,4.0586,-2.0282}
Count Table 1:
---------------
h: {-2.0304,4.0586,-2.0282}
Count Table 2:
---------------
h: {-2.0304,4.0586,-2.0282}
Count Table 3:
---------------
h: {-2.0304,4.0586,-2.0282}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-14.1885,-14.1885,-14.1885}
Activity(exp=1): {-12.9945,-12.9945,-12.9945}
Activity(exp=2): {-11.8859,-11.8859,-11.8859}
Activity(exp=3): {-10.6919,-10.6919,-10.6919}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
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}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000,0.0000}
> Initial optimization (component0-1-f0).
>> Starting new optimization: component0-1-f0. (2021-05-21 22:25:25.179).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[1,2,3]},{"h":[4,5,6]},{"h":[7,8,9]},{"h":[10,11,12]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0],[0,0,0],[0,0,0],[0,0,0]]},{}]}
Value and gradient before optimization:
=======================================
value = 4.396455272380808
gradient = {-0.0003,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000}
gradient norm = 3.3104514593660576E-4
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.0692e+01,-2.0304e+00,4.0586e+00,-2.0282e+00,-2.0304e+00,4.0586e+00,-2.0282e+00,-2.0304e+00,4.0586e+00,-2.0282e+00,-2.0304e+00,4.0586e+00,-2.0282e+00}
> Gradient: {1.3669e+00,-3.0276e-01,6.0758e-01,-3.0482e-01,-2.4845e-01,4.9859e-01,-2.5014e-01,-1.4386e-01,2.8870e-01,-1.4484e-01,1.6039e-08,-1.2167e-08,-3.8712e-09}
>>>> Re-trying (1/3).
Starting Function Value: 6.4499538932470815
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 5.140011553453499 1.000000000000000 0.585211562827723 0.919706726641803
2 3 4.588016856832925 1.436848799534762 1.000000000000000 0.491102131909426
3 4 4.474009412565136 0.300696143096574 1.000000000000000 0.270847288867302
4 5 4.401923108180475 0.617881404256980 1.000000000000000 0.114410142598397
5 6 4.396528137774874 0.084889276757531 1.000000000000000 0.016204197764833
6 7 4.396289481147461 0.033111939142316 1.000000000000000 0.002385815285449
7 8 4.396282333051777 0.004416307187505 1.000000000000000 0.000940395087533
8 9 4.396280938673619 0.002878857663170 1.000000000000000 0.000166289745900
9 10 4.396280851964820 0.000543732622171 1.000000000000000 0.000170442901207
10 11 4.396277017193407 0.031425951282731 1.000000000000000 0.000964881528042
11 12 4.396270438497644 0.064023204598947 1.000000000000000 0.001896222348645
12 13 4.396249713040135 0.219466009840647 1.000000000000000 0.003715593147244
13 14 4.396197722879421 0.574487301443581 1.000000000000000 0.006405390979486
14 15 4.396079353129150 1.770881884107577 1.000000000000000 0.012554689986182
15 16 4.395935352665972 0.551408290688600 1.000000000000000 0.010716574348580
16 18 4.395790509185408 0.158713895740500 0.451229544812521 0.004285595744744
17 20 4.395670844189797 0.812329852104425 0.220112699153154 0.003255357125849
18 21 4.395656559490694 0.360955629508569 1.000000000000000 0.006071882061195
19 22 4.395627502791355 0.024792769246878 1.000000000000000 0.004428957937451
20 23 4.395596207627726 0.200283125629727 1.000000000000000 0.003767707620865
21 25 4.395544371212243 0.456223333685053 0.248699198309281 0.004518653681186
22 27 4.395503226862730 0.338866656219853 0.481829307674284 0.004512559306365
23 28 4.395464121013603 0.229573851995220 1.000000000000000 0.003279532440391
24 30 4.395437234753276 0.305493770950290 0.460689631160571 0.004127405452122
25 31 4.395408616563626 0.322682557595063 1.000000000000000 0.005127540407782
26 32 4.395383596326122 0.019899171732296 1.000000000000000 0.003160125557965
27 33 4.395354398601417 0.235103314514285 1.000000000000000 0.002828692145656
28 35 4.395333141021126 0.276628187622667 0.500367616883256 0.003822956098986
29 36 4.395307889861185 0.143852600495907 1.000000000000000 0.002810950078228
30 37 4.395283966826125 0.316480978059350 1.000000000000000 0.003910453419842
31 38 4.395231668396697 0.347787003147312 1.000000000000000 0.002558704087764
32 39 4.395202877583790 0.220096859354863 1.000000000000000 0.001606778672669
33 41 4.395192422908427 0.171250660921408 0.162371532601347 0.002807718398019
34 43 4.395172218920893 0.215762114426761 0.419830375135291 0.003054830701194
35 44 4.395137963451438 0.275475246987184 1.000000000000000 0.002169261656291
36 45 4.395122562047118 0.344004733992063 1.000000000000000 0.004135317093730
37 46 4.395080170908405 0.252424619493564 1.000000000000000 0.002269998227387
38 48 4.395064514763343 0.204890575271213 0.385997817038511 0.002750735206594
39 49 4.395047081035356 0.297143652391044 1.000000000000000 0.003778650273795
40 50 4.395040740410249 0.082749409589910 1.000000000000000 0.002266448783848
41 51 4.395020970215840 0.149098403449918 1.000000000000000 0.000960684044666
42 53 4.395011221755478 0.186869370221043 0.520498419912038 0.002360751285974
43 54 4.394999774362058 0.144960616785196 1.000000000000000 0.002534441085149
44 55 4.394972840001314 0.251891297124872 1.000000000000000 0.001725129899758
45 57 4.394961518788957 0.209607684132026 0.482740389957202 0.002689969288044
46 58 4.394929304946327 0.360460318296486 1.000000000000000 0.002311859178009
47 60 4.394917717415447 0.141759155391792 0.490806682462006 0.002264005176266
48 61 4.394916778226438 0.087094820362152 1.000000000000000 0.003065380059109
49 63 4.394879139916013 0.328232692234829 0.489186316286008 0.000863734493120
50 65 4.394875277585078 0.103198292266094 0.109511191963019 0.001781036412400
51 66 4.394870507743629 0.067851938627994 1.000000000000000 0.001815191288498
52 67 4.394858660669302 0.184737939704410 1.000000000000000 0.002194035342009
53 68 4.394843232595654 0.209722507144730 1.000000000000000 0.002167552559438
54 69 4.394826500640572 0.362651745341004 1.000000000000000 0.003166991931392
55 70 4.394782811325854 0.548438021172921 1.000000000000000 0.001964848385617
56 72 4.394779049022042 0.114271124547024 0.469468123544973 0.002313974345152
57 73 4.394763509334401 0.469626261378782 1.000000000000000 0.004150503630962
58 74 4.394762272581870 0.138998082263467 1.000000000000000 0.002670554722855
59 75 4.394744864808924 0.134519889248260 1.000000000000000 0.000498410977246
60 76 4.394740392601811 0.231972053661471 1.000000000000000 0.002453727217857
61 77 4.394733789598504 0.008757266353996 1.000000000000000 0.001266474158927
62 78 4.394719285387639 0.258782054705625 1.000000000000000 0.000912141191456
63 80 4.394711244778608 0.246595539424783 0.500068860315781 0.001942456591647
64 81 4.394697680970018 0.286321841065961 1.000000000000000 0.001953965150194
65 83 4.394691991719872 0.093098406710373 0.365830071305441 0.001597805154276
66 84 4.394677520474130 0.351747717144049 1.000000000000000 0.001795135514666
67 85 4.394671932544608 0.215205667228650 1.000000000000000 0.002284758111249
68 87 4.394667037918427 0.162386206479150 0.471082384140336 0.002591938990994
69 88 4.394657641758181 0.087794882308956 1.000000000000000 0.001445345498405
70 89 4.394651242868762 0.186593372782599 1.000000000000000 0.001620128785975
71 90 4.394641826174068 0.287477834902903 1.000000000000000 0.001762141704373
72 91 4.394634529097123 0.158291096970176 1.000000000000000 0.001169617149413
73 93 4.394629559744073 0.224194791624840 0.215106712433940 0.001735281892291
74 94 4.394618969471194 0.411504410947377 1.000000000000000 0.001972069445595
75 95 4.394610861082878 0.170579230175704 1.000000000000000 0.000928914185645
76 96 4.394603847406773 0.611916341674514 1.000000000000000 0.002517256034009
77 97 4.394598764075965 0.130507711350669 1.000000000000000 0.000387017813676
78 98 4.394593760195739 0.268410836033080 1.000000000000000 0.000643070764032
79 100 4.394589366438035 0.383595864781824 0.472062573306460 0.001499620811063
80 101 4.394584626813912 0.287932208580463 1.000000000000000 0.001324584251223
81 102 4.394578513745581 0.339989665821341 1.000000000000000 0.000126028026476
82 104 4.394575920549573 0.362566404524771 0.416258573747336 0.000742564948793
83 105 4.394574222027378 0.314521852662416 1.000000000000000 0.000875811401293
84 106 4.394572372442909 0.245563546189926 1.000000000000000 0.000121575923612
85 107 4.394571951729226 0.263024597518022 1.000000000000000 0.000267720862437
86 108 4.394571835341317 0.059548891607515 1.000000000000000 0.000025532758924
87 109 4.394571829192715 0.036716627476393 1.000000000000000 0.000010567210034
88 110 4.394571829151460 0.000312700657402 1.000000000000000 0.000006681869349
89 111 4.394571829090983 0.000312700657402 1.000000000000000 0.000000410919980
Convergence criteria met.
After: gradient norm = 4.109199804990866E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.3171,-2.3162,4.6333}
Count Table 1:
---------------
h: {-1.9206,-1.9175,3.8381}
Count Table 2:
---------------
h: {-1.5553,-1.5458,3.1011}
Count Table 3:
---------------
h: {-1.1718,-1.1406,2.3124}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-1.1522,-1.1522,-1.1522}
Activity(exp=1): {-1.1522,-1.1522,-1.1522}
Activity(exp=2): {-1.1522,-1.1522,-1.1522}
Activity(exp=3): {-1.1522,-1.1522,-1.1522}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
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}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000,0.0000}
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 22:26:08.631).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[1,2,3]},{"h":[4,5,6]},{"h":[7,8,9]},{"h":[10,11,12]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0],[0,0,0],[0,0,0],[0,0,0]]},{}]}
Value and gradient before optimization:
=======================================
value = 4.394571829090983
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}
gradient norm = 4.1091998049881237E-7
Already at minimum!
After: gradient norm = 4.1091998049881237E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.3171,-2.3162,4.6333}
Count Table 1:
---------------
h: {-1.9206,-1.9175,3.8381}
Count Table 2:
---------------
h: {-1.5553,-1.5458,3.1011}
Count Table 3:
---------------
h: {-1.1718,-1.1406,2.3124}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-1.1522,-1.1522,-1.1522}
Activity(exp=1): {-1.1522,-1.1522,-1.1522}
Activity(exp=2): {-1.1522,-1.1522,-1.1522}
Activity(exp=3): {-1.1522,-1.1522,-1.1522}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
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}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000,0.0000}
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 22:26:09.011).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[1,2,3]},{"h":[4,5,6]},{"h":[7,8,9]},{"h":[10,11,12]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0],[0,0,0],[0,0,0],[0,0,0]]},{}]}
Value and gradient before optimization:
=======================================
value = 4.394571829090983
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}
gradient norm = 4.109199804990696E-7
Already at minimum!
After: gradient norm = 4.109199804990696E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.3171,-2.3162,4.6333}
Count Table 1:
---------------
h: {-1.9206,-1.9175,3.8381}
Count Table 2:
---------------
h: {-1.5553,-1.5458,3.1011}
Count Table 3:
---------------
h: {-1.1718,-1.1406,2.3124}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-1.1522,-1.1522,-1.1522}
Activity(exp=1): {-1.1522,-1.1522,-1.1522}
Activity(exp=2): {-1.1522,-1.1522,-1.1522}
Activity(exp=3): {-1.1522,-1.1522,-1.1522}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
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}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000,0.0000}
==================================
== Starts fiting Binding mode 1 ==
==================================
> Optimizing h (component1-0-h).
>> Starting new optimization: component1-0-h. (2021-05-21 22:26:10.184).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[0,1,2]},{"h":[3,4,5]},{"h":[6,7,8]},{"h":[9,10,11]}],"bindingModeInteractions":[],"bindingModes":[{},{}]}
Value and gradient before optimization:
=======================================
value = 4.489270698532296
gradient = {0.0634,0.0636,-0.1270,0.0655,0.0661,-0.1316,0.0668,0.0687,-0.1354,0.0655,0.0720,-0.1375}
gradient norm = 0.32572587565374705
Starting Function Value: 4.489270698532296
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 4.297197995247033 1.000000000000000 3.070066195978300 0.044704150110049
2 3 4.294195524099670 0.159270972880645 1.000000000000000 0.007302869529756
3 4 4.294115064237118 0.022372984794266 1.000000000000000 0.000105316208159
4 5 4.294115047445954 0.022372984794266 1.000000000000000 0.000000239715403
Convergence criteria met.
After: gradient norm = 2.397154025680151E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.5362,-2.5357,5.0719}
Count Table 1:
---------------
h: {-2.1488,-2.1473,4.2961}
Count Table 2:
---------------
h: {-1.7902,-1.7855,3.5758}
Count Table 3:
---------------
h: {-1.4057,-1.3906,2.7963}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-1.1522,-1.1522,-1.1522}
Activity(exp=1): {-1.1522,-1.1522,-1.1522}
Activity(exp=2): {-1.1522,-1.1522,-1.1522}
Activity(exp=3): {-1.1522,-1.1522,-1.1522}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
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}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-0.4592,-0.4592,-0.4592}
Activity(exp=1): {-0.4592,-0.4592,-0.4592}
Activity(exp=2): {-0.4592,-0.4592,-0.4592}
Activity(exp=3): {-0.4592,-0.4592,-0.4592}
> Initial optimization (component1-1-f1).
>> Starting new optimization: component1-1-f1. (2021-05-21 22:26:18.489).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[41,42,43]},{"h":[44,45,46]},{"h":[47,48,49]},{"h":[50,51,52]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],"activity":[[40,40,40],[40,40,40],[40,40,40],[40,40,40]]}]}
Value and gradient before optimization:
=======================================
value = 4.313457964416957
gradient = {-0.0178,0.0066,-0.0207,-0.0069,-0.0176,0.0051,-0.0049,-0.0214,-0.0059,0.0032,0.0114,-0.0475,-0.0471,0.0059,0.0091,-0.0067,-0.0596,0.0114,0.0121,-0.0027,-0.0070,0.0080,0.0079,-0.0477,-0.0057,-0.0001,0.0036,-0.0366,-0.0287,0.0020,-0.0021,-0.0100,-0.0165,-0.0126,0.0010,-0.0106,-0.0065,-0.0222,0.0021,-0.0121,-0.0388,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000}
gradient norm = 0.13342451730978777
Starting Function Value: 4.313457964416957
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 4.295294335306454 0.217222977983904 1.628058938220111 0.139748262108249
2 4 4.274289446243304 0.253446043630575 1.000000000000000 0.184753041892495
3 5 4.233099618557147 1.548707281165699 1.000000000000000 0.488047042354439
4 6 4.178909790172391 0.322634817483375 1.000000000000000 0.139128368710201
5 7 4.164410567155331 0.338325600842131 1.000000000000000 0.048131961826483
6 8 4.159424828039989 0.276017453353531 1.000000000000000 0.040890553768023
7 9 4.151873051396740 0.280223319123287 1.000000000000000 0.037116088226629
8 10 4.138955795307774 1.042051299817916 1.000000000000000 0.064873982229089
9 11 4.133124786156896 0.258569482538860 1.000000000000000 0.023797569832815
10 12 4.130960054344215 0.187240112846751 1.000000000000000 0.019325770709384
11 13 4.127084929627543 0.403645403640749 1.000000000000000 0.016115670424067
12 14 4.122354248774047 0.716181170753749 1.000000000000000 0.038278766213320
13 15 4.120115558575086 0.336348701753646 1.000000000000000 0.029465699511446
14 16 4.118050547123867 0.462192524709233 1.000000000000000 0.025010735673573
15 17 4.116450650016484 0.590256446669718 1.000000000000000 0.018054976235137
16 18 4.115602454539491 0.320215172721557 1.000000000000000 0.007637778165856
17 19 4.115377137971096 0.076833514908209 1.000000000000000 0.004935130367191
18 20 4.115092141175364 0.191802851911369 1.000000000000000 0.005821916327116
19 21 4.114765293933695 0.165439743415734 1.000000000000000 0.008837098570790
20 22 4.114454073616851 0.300830297943395 1.000000000000000 0.003457025291092
21 23 4.114338993671022 0.081413330764549 1.000000000000000 0.003820852029497
22 24 4.114261097827757 0.087715291840783 1.000000000000000 0.004033081892998
23 25 4.114190710465437 0.043740903015642 1.000000000000000 0.002333931358149
24 26 4.114136516061105 0.051443803652556 1.000000000000000 0.002390850235383
25 27 4.114098375277210 0.065117870474854 1.000000000000000 0.002618373308675
26 28 4.114080242322007 0.066845179594065 1.000000000000000 0.002543078891557
27 29 4.114066849347115 0.016369725055895 1.000000000000000 0.000937560136316
28 30 4.114060963242570 0.013932930522921 1.000000000000000 0.000774453313587
29 31 4.114053685266069 0.021864898679243 1.000000000000000 0.000957550195374
30 32 4.114041105675055 0.043423726218317 1.000000000000000 0.001137991828195
31 33 4.114040634537102 0.053725615190871 1.000000000000000 0.002963520895724
32 34 4.114028041470545 0.011821720647004 1.000000000000000 0.001083178829955
33 35 4.114025134606301 0.010775215146065 1.000000000000000 0.000840374562311
34 36 4.114020564076535 0.026321258860696 1.000000000000000 0.000660529527163
35 37 4.114015684493876 0.029530328093918 1.000000000000000 0.000681798609472
36 38 4.114007376546154 0.054938639727831 1.000000000000000 0.001029504028281
37 39 4.113999313835542 0.053602837134647 1.000000000000000 0.001259116148432
38 40 4.113990725249320 0.076741024094277 1.000000000000000 0.001751328856474
39 41 4.113983578871587 0.075901177108801 1.000000000000000 0.001156047350020
40 42 4.113979400389031 0.022292873403898 1.000000000000000 0.000508466546439
41 43 4.113977303062050 0.012500207316970 1.000000000000000 0.000342861719092
42 44 4.113976101089320 0.010764375128617 1.000000000000000 0.000353378677451
43 45 4.113973485399171 0.027753494852185 1.000000000000000 0.000313982240356
44 46 4.113970866610296 0.033797440160550 1.000000000000000 0.000408421919829
45 48 4.113970177155584 0.012707034815637 0.228357362021584 0.000353978797818
46 49 4.113969378050064 0.011827120863571 1.000000000000000 0.000169224002894
47 50 4.113969019810947 0.005105152381839 1.000000000000000 0.000160553751369
48 51 4.113968561730772 0.007611597068608 1.000000000000000 0.000157614023809
49 52 4.113968068213981 0.011267213186264 1.000000000000000 0.000102516866446
50 53 4.113967791694451 0.009876658495433 1.000000000000000 0.000082635813576
51 54 4.113967611923814 0.007092110152065 1.000000000000000 0.000081253446762
52 55 4.113967440903512 0.007329980491830 1.000000000000000 0.000104639534796
53 56 4.113967161763999 0.013660523161903 1.000000000000000 0.000117999898338
54 57 4.113966989579778 0.026981788961517 1.000000000000000 0.000169917162738
55 58 4.113966707834472 0.006643519988785 1.000000000000000 0.000068811093613
56 59 4.113966568280093 0.004328558215617 1.000000000000000 0.000056330131064
57 60 4.113966423249977 0.008168022547224 1.000000000000000 0.000081126234705
58 61 4.113966187041114 0.014518186600786 1.000000000000000 0.000105644476184
59 62 4.113965671198441 0.036335616676847 1.000000000000000 0.000125761442195
60 63 4.113965100667452 0.048930682046709 1.000000000000000 0.000176610420060
61 64 4.113964593844256 0.038450553723171 1.000000000000000 0.000093422477784
62 65 4.113964103589687 0.034717955867243 1.000000000000000 0.000119779465140
63 66 4.113963591383127 0.032747815479098 1.000000000000000 0.000129158887127
64 67 4.113962561042604 0.073622200888529 1.000000000000000 0.000133708828483
65 68 4.113961274565828 0.117455824746473 1.000000000000000 0.000166162335597
66 69 4.113959465045293 0.130002676547521 1.000000000000000 0.000193045350542
67 70 4.113955246386763 0.324218773685123 1.000000000000000 0.000296036277597
68 71 4.113951227309165 0.436190271190340 1.000000000000000 0.000405628912571
69 72 4.113948680080150 0.294582763778115 1.000000000000000 0.000251795931305
70 73 4.113947680079723 0.075837822620238 1.000000000000000 0.000081388785465
71 74 4.113947555596818 0.028821680509334 1.000000000000000 0.000024758465721
72 75 4.113947539952821 0.002491934546249 1.000000000000000 0.000021096428207
73 76 4.113947475344287 0.013635601890446 1.000000000000000 0.000062744258047
74 77 4.113947416767829 0.010695305420062 1.000000000000000 0.000080514802920
75 78 4.113947321052928 0.016157242486203 1.000000000000000 0.000067873440626
76 80 4.113947300643979 0.004501903504997 0.453536252788224 0.000041143475016
77 81 4.113947282906224 0.002840942715704 1.000000000000000 0.000015561433575
78 82 4.113947279773329 0.002968999642681 1.000000000000000 0.000004569780217
79 83 4.113947279240278 0.000754624572503 1.000000000000000 0.000005350637502
80 84 4.113947276958224 0.002117451784873 1.000000000000000 0.000010556336820
81 85 4.113947272116114 0.002957196102945 1.000000000000000 0.000018302922404
82 86 4.113947258695288 0.006524936404578 1.000000000000000 0.000031828827566
83 87 4.113947225168297 0.015322648014157 1.000000000000000 0.000052275053482
84 88 4.113947138961182 0.039765896894219 1.000000000000000 0.000083829659500
85 89 4.113946925615990 0.101088745970597 1.000000000000000 0.000129681345256
86 90 4.113946430518919 0.242783337314833 1.000000000000000 0.000188826868023
87 91 4.113945469113402 0.496465622363628 1.000000000000000 0.000239372986174
88 92 4.113944209310513 0.704501715155358 1.000000000000000 0.000222454843919
89 94 4.113944083971595 0.099080972096315 0.165597360266640 0.000173553249104
90 95 4.113943363506714 0.373563391818819 1.000000000000000 0.000094559924571
91 96 4.113943189385553 0.037461519442629 1.000000000000000 0.000037744774645
92 97 4.113943165578826 0.056750388966103 1.000000000000000 0.000013745067676
93 98 4.113943164681561 0.018974125235605 1.000000000000000 0.000002094887266
94 99 4.113943164647600 0.018974125235605 1.000000000000000 0.000000591767320
Convergence criteria met.
After: gradient norm = 5.917673204841328E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.5320,-2.5315,5.0634}
Count Table 1:
---------------
h: {-2.1840,-2.1826,4.3665}
Count Table 2:
---------------
h: {-1.8612,-1.8574,3.7186}
Count Table 3:
---------------
h: {-1.5006,-1.4893,2.9900}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-1.1522,-1.1522,-1.1522}
Activity(exp=1): {-1.1522,-1.1522,-1.1522}
Activity(exp=2): {-1.1522,-1.1522,-1.1522}
Activity(exp=3): {-1.1522,-1.1522,-1.1522}
Binding mode 1:
---------------
Mononucleotide: {-1.0111,-0.9314,-0.7237,-0.7661,-0.7344,-1.0458,-1.2120,-0.4401,-0.8016,-1.6296,-2.1134,1.1122,1.8371,-2.7822,-0.2756,-2.2119,2.6236,-2.2340,-2.0003,-1.8218,-1.4555,-1.4985,-1.5164,1.0379,-1.2133,-1.1662,-1.1106,0.0575,-0.0068,-1.9663,0.1160,-1.5753,-1.1990,-0.6005,-0.7446,-0.8883,-1.0941,-0.6162,-1.2537,-0.4683}
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}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-0.2861,-0.2861,-0.2861}
Activity(exp=1): {-0.2861,-0.2861,-0.2861}
Activity(exp=2): {-0.2861,-0.2861,-0.2861}
Activity(exp=3): {-0.2861,-0.2861,-0.2861}
Suggested variations:
key=10;6;0, description = Initial model.
> Optimizing variation "Initial model." (component1-2-variation0).
>> Starting new optimization: component1-2-variation0. (2021-05-21 22:30:05.743).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[41,42,43]},{"h":[44,45,46]},{"h":[47,48,49]},{"h":[50,51,52]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],"activity":[[40,40,40],[40,40,40],[40,40,40],[40,40,40]]}]}
Value and gradient before optimization:
=======================================
value = 4.1139431646475995
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}
gradient norm = 5.917673204844377E-7
Already at minimum!
After: gradient norm = 5.917673204844377E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.5320,-2.5315,5.0634}
Count Table 1:
---------------
h: {-2.1840,-2.1826,4.3665}
Count Table 2:
---------------
h: {-1.8612,-1.8574,3.7186}
Count Table 3:
---------------
h: {-1.5006,-1.4893,2.9900}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-1.1522,-1.1522,-1.1522}
Activity(exp=1): {-1.1522,-1.1522,-1.1522}
Activity(exp=2): {-1.1522,-1.1522,-1.1522}
Activity(exp=3): {-1.1522,-1.1522,-1.1522}
Binding mode 1:
---------------
Mononucleotide: {-1.0111,-0.9314,-0.7237,-0.7661,-0.7344,-1.0458,-1.2120,-0.4401,-0.8016,-1.6296,-2.1134,1.1122,1.8371,-2.7822,-0.2756,-2.2119,2.6236,-2.2340,-2.0003,-1.8218,-1.4555,-1.4985,-1.5164,1.0379,-1.2133,-1.1662,-1.1106,0.0575,-0.0068,-1.9663,0.1160,-1.5753,-1.1990,-0.6005,-0.7446,-0.8883,-1.0941,-0.6162,-1.2537,-0.4683}
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}
Dinucleotide(d=2): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=3): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=4): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=5): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=6): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=7): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=8): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Dinucleotide(d=9): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {-0.2861,-0.2861,-0.2861}
Activity(exp=1): {-0.2861,-0.2861,-0.2861}
Activity(exp=2): {-0.2861,-0.2861,-0.2861}
Activity(exp=3): {-0.2861,-0.2861,-0.2861}
The Likelihood DID NOT improve. Discarding fit component1-2-variation0.
> No varitions possible for Binding mode 1.
> Unfreezing component (component1-3-f0).
>> Starting new optimization: component1-3-f0. (2021-05-21 22:30:07.971).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[761,762,763]},{"h":[764,765,766]},{"h":[767,768,769]},{"h":[770,771,772]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],"activity":[[760,760,760],[760,760,760],[760,760,760],[760,760,760]],"dinucleotide":[[40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183],[184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311],[312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423],[424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519],[520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599],[600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663],[664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711],[712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743],[744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759]]}]}
Value and gradient before optimization:
=======================================
value = 4.779364457985152
gradient = 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gradient norm = 0.020477598323599876
Starting Function Value: 4.779364457985152
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 4.775309361599797 0.380966179273606 18.604045906816744 0.102111317598649
2 4 4.769876038667174 0.388595602519228 1.000000000000000 0.050289147770284
3 5 4.767089205101490 0.364375460714493 1.000000000000000 0.026661201642220
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253 269 4.750531535441677 0.018528629388711 1.000000000000000 0.000038643197106
254 270 4.750531511510629 0.014356321596773 1.000000000000000 0.000044100354167
255 271 4.750531481165730 0.026459046657005 1.000000000000000 0.000079867764669
256 272 4.750531451707778 0.031026543946987 1.000000000000000 0.000069815300083
257 273 4.750531427969047 0.004516289438045 1.000000000000000 0.000040016914481
258 274 4.750531401168231 0.007817349916145 1.000000000000000 0.000035614782018
259 275 4.750531384615807 0.004130997846173 1.000000000000000 0.000038285392209
260 276 4.750531372290474 0.018479460296387 1.000000000000000 0.000096992100307
261 277 4.750531340708814 0.002069670408614 1.000000000000000 0.000029534173683
262 278 4.750531332395145 0.004869609794124 1.000000000000000 0.000027892972107
263 279 4.750531312450233 0.013994827975542 1.000000000000000 0.000028455267387
264 280 4.750531298179551 0.015159274531766 1.000000000000000 0.000051477918714
265 281 4.750531281094391 0.007397671241503 1.000000000000000 0.000025162489901
266 282 4.750531272025842 0.003837091274238 1.000000000000000 0.000022263942202
267 283 4.750531265730041 0.012560302799940 1.000000000000000 0.000037128007067
268 284 4.750531259198201 0.002645500326771 1.000000000000000 0.000019234824689
269 285 4.750531252630321 0.001819036051792 1.000000000000000 0.000023383995115
270 286 4.750531246151502 0.002057691500980 1.000000000000000 0.000024784594608
271 287 4.750531238943871 0.004585747387697 1.000000000000000 0.000028742172577
272 288 4.750531234358121 0.006173581598598 1.000000000000000 0.000026339485250
273 289 4.750531230328379 0.001819182831345 1.000000000000000 0.000014674481843
274 290 4.750531228460658 0.000717202635217 1.000000000000000 0.000012220580081
275 291 4.750531225829719 0.000753160766167 1.000000000000000 0.000012528440910
276 292 4.750531221331926 0.002697072659654 1.000000000000000 0.000027040392476
277 293 4.750531217488254 0.005786455118435 1.000000000000000 0.000016610150937
278 294 4.750531215073051 0.001247613057793 1.000000000000000 0.000011919342837
279 295 4.750531213124975 0.001801055504337 1.000000000000000 0.000010159711266
280 296 4.750531210833325 0.003663658245331 1.000000000000000 0.000008814292881
281 297 4.750531208817399 0.001341454219591 1.000000000000000 0.000009992120104
282 298 4.750531207320667 0.003300453868622 1.000000000000000 0.000007349281216
283 299 4.750531205792815 0.003873137867572 1.000000000000000 0.000007440797057
284 300 4.750531204640729 0.002901077974371 1.000000000000000 0.000010377555602
285 301 4.750531204165017 0.002534619409812 1.000000000000000 0.000017196482416
286 302 4.750531203356310 0.002201527616068 1.000000000000000 0.000005637293338
287 303 4.750531203022090 0.000992698673238 1.000000000000000 0.000005473955524
288 304 4.750531202408897 0.001718220288060 1.000000000000000 0.000007154287614
289 305 4.750531201779650 0.002505258464385 1.000000000000000 0.000008233485321
290 306 4.750531201214076 0.001356442912432 1.000000000000000 0.000004325997394
291 307 4.750531200824114 0.000497938955439 1.000000000000000 0.000003874075311
292 308 4.750531200437120 0.000544107609864 1.000000000000000 0.000005008045383
293 309 4.750531200303048 0.000612006440235 1.000000000000000 0.000012008353059
294 310 4.750531199905975 0.000220022508614 1.000000000000000 0.000004481141852
295 311 4.750531199719194 0.000175550441515 1.000000000000000 0.000002764684435
296 312 4.750531199580146 0.000245942821125 1.000000000000000 0.000004129511493
297 313 4.750531199405393 0.000497228144945 1.000000000000000 0.000004425703358
298 314 4.750531199064591 0.000737907869930 1.000000000000000 0.000004370690938
299 316 4.750531198917570 0.001566442327776 0.456574357065929 0.000004028361613
300 317 4.750531198760328 0.000344478017815 1.000000000000000 0.000002270062164
301 318 4.750531198676148 0.000243731140712 1.000000000000000 0.000002346408180
302 319 4.750531198589111 0.000435728968407 1.000000000000000 0.000004573060060
303 320 4.750531198498892 0.000171367909991 1.000000000000000 0.000002354194063
304 321 4.750531198424783 0.000244855397136 1.000000000000000 0.000001781540475
305 322 4.750531198389777 0.000169670151245 1.000000000000000 0.000002478266674
306 324 4.750531198375388 0.000071937404897 0.378762057096504 0.000003691363738
307 325 4.750531198340225 0.000327423981272 1.000000000000000 0.000001788310233
308 326 4.750531198312110 0.000174832015889 1.000000000000000 0.000001633548204
309 327 4.750531198264519 0.000134651476371 1.000000000000000 0.000001652408699
310 328 4.750531198205007 0.000245953751442 1.000000000000000 0.000001469741811
311 329 4.750531198169355 0.000762404883987 1.000000000000000 0.000003703497035
312 330 4.750531198147591 0.000482923715308 1.000000000000000 0.000003099119795
313 331 4.750531198125826 0.000482923715308 1.000000000000000 0.000001134305701
Convergence criteria met.
After: gradient norm = 1.134305701049707E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-2.5416,-2.5411,5.0827}
Count Table 1:
---------------
h: {-2.1986,-2.1973,4.3959}
Count Table 2:
---------------
h: {-1.8794,-1.8758,3.7552}
Count Table 3:
---------------
h: {-1.5201,-1.5094,3.0295}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-1.1522,-1.1522,-1.1522}
Activity(exp=1): {-1.1522,-1.1522,-1.1522}
Activity(exp=2): {-1.1522,-1.1522,-1.1522}
Activity(exp=3): {-1.1522,-1.1522,-1.1522}
Binding mode 1:
---------------
Mononucleotide: {-0.3618,-0.3418,-0.3490,-0.3168,-0.3142,-0.4020,-0.3850,-0.2683,-0.2728,-0.5085,-0.5501,-0.0380,0.2012,-0.7352,-0.2329,-0.6026,0.3939,-0.6387,-0.5522,-0.5724,-0.4529,-0.4267,-0.5113,0.0213,-0.4004,-0.3717,-0.4596,-0.1377,-0.1716,-0.5834,-0.1545,-0.4600,-0.4186,-0.2987,-0.3140,-0.3381,-0.4067,-0.3101,-0.4243,-0.2284}
Dinucleotide(d=1): {-0.1861,0.0755,-0.1552,-0.0960,-0.1463,-0.1455,0.0529,-0.0956,0.0963,-0.1161,-0.1683,-0.1644,-0.0822,-0.2192,-0.1101,0.0908,-0.1870,0.0224,-0.3681,0.1720,0.1200,-0.2531,-0.1907,-0.0823,-0.1831,-0.1437,0.0684,-0.1091,-0.0384,-0.1251,-0.0755,0.0038,-0.1288,-0.1541,0.0848,-0.0060,-0.1607,-0.0782,-0.0781,-0.0950,-0.2829,-0.0813,-0.0115,-0.0891,0.6219,-0.3289,-0.2106,-0.3709,0.7404,-0.3247,-0.1915,-0.2780,-0.4793,-0.0507,-0.0556,-0.0499,0.1953,-0.1244,-0.1471,-0.1073,-0.3098,-0.0528,-0.0746,-0.0595,-0.0609,-0.0102,-0.1474,0.5758,-0.1216,-0.1305,-0.1023,-0.2601,-0.0957,-0.1421,-0.0686,-0.2435,-0.1138,-0.0897,-0.1260,-0.2331,-0.5850,0.5866,-0.3831,-0.2060,0.4228,-0.4484,0.1636,-0.6336,-0.2888,-0.2269,-0.5141,0.5047,0.0762,-0.3485,0.3367,0.1744,-0.2734,0.2076,-0.1632,-0.0808,-0.3332,-0.5153,0.1188,0.3002,0.2733,0.0142,-0.5013,-0.2511,0.1756,-0.2679,0.3521,-0.4249,-0.7618,0.3779,-0.1698,0.1613,0.1034,-0.3737,-0.1124,-0.1280,-0.0080,-0.0542,0.0345,-0.0123,0.1386,-0.3107,0.0385,-0.2929,-0.3834,-0.0521,0.0065,-0.0149,0.0325,-0.1143,-0.2392,0.0188,-0.0789,-0.0997,-0.0197,-0.0978,-0.0077,-0.0284,-0.1725,-0.1186}
Dinucleotide(d=2): {-0.1594,-0.0694,-0.2750,0.1187,-0.0648,-0.0776,-0.0407,-0.1432,-0.0438,-0.1204,-0.1916,0.0132,-0.0127,-0.2406,-0.0464,-0.0157,-0.0568,-0.1627,0.0376,-0.1190,0.1324,-0.1384,-0.1930,-0.2179,0.0164,-0.1968,-0.0891,-0.1018,0.1436,-0.2082,-0.0437,-0.1724,0.0604,-0.0820,-0.0998,-0.0660,-0.1289,-0.0899,-0.0962,-0.0890,-0.2804,-0.1125,0.0079,-0.0753,0.6502,-0.3040,-0.3522,-0.3117,-0.0040,0.0769,-0.0700,0.2427,-0.1196,-0.1201,-0.1344,-0.3201,-0.2112,-0.2320,-0.1465,0.2556,-0.0965,-0.1476,-0.1229,-0.2200,0.0567,0.0799,-0.0197,0.3421,-0.1934,-0.0939,-0.1740,-0.1854,-0.1627,-0.1908,-0.1221,-0.1045,-0.0835,-0.1534,-0.1093,-0.2556,-0.2427,-0.0656,0.0058,-0.0920,0.3087,-0.0000,-0.5606,-0.3158,-0.2536,-0.3689,0.2129,-0.1188,-0.0081,-0.0880,0.1128,0.1043,-0.2027,0.0020,-0.0145,-0.1873,-0.0284,-0.1213,-0.3171,0.0702,-0.2118,-0.1635,-0.0067,-0.0704,0.0254,-0.0047,0.0106,-0.1495,-0.0790,0.0140,0.0402,-0.1486,-0.1653,-0.0810,-0.2763,-0.0517,-0.1439,-0.0634,-0.0651,0.1117,-0.0102,-0.1744,-0.1326,-0.1439}
Dinucleotide(d=3): {0.0336,-0.1332,-0.0433,-0.2145,0.0090,-0.1241,-0.1074,-0.1035,0.1291,-0.2794,-0.0906,-0.1296,0.0694,-0.1793,-0.0391,-0.1669,0.1298,-0.1332,-0.1205,-0.1865,0.1275,-0.1560,-0.2639,-0.1157,0.0045,-0.1450,-0.1019,-0.1139,0.2174,-0.2183,-0.1070,-0.1866,-0.1173,-0.0843,-0.0547,0.0237,-0.1347,-0.0314,-0.1057,-0.1856,-0.1524,0.0184,-0.0376,-0.3543,-0.0063,-0.3139,-0.2747,0.4416,-0.0379,0.1010,0.0465,0.1333,-0.1237,-0.1374,-0.2318,-0.2142,-0.1374,-0.1885,-0.0632,0.0933,-0.0830,-0.1535,-0.2115,-0.1613,0.3239,-0.2522,0.4008,-0.0913,-0.1625,-0.0802,-0.2893,-0.0942,-0.2175,-0.1073,-0.1047,-0.1219,-0.1519,-0.0736,-0.2578,-0.0897,-0.0876,-0.0322,-0.0426,-0.2914,-0.3335,0.0319,-0.2677,0.0932,-0.1993,-0.2302,0.0107,-0.0839,0.1707,-0.0494,-0.0019,-0.0563,-0.1363,-0.0721,-0.0144,-0.1682,-0.1234,-0.1086,-0.3624,0.1675,-0.1239,-0.0917,-0.0680,-0.1577,-0.0076,-0.0202,0.0016,-0.0841}
Dinucleotide(d=4): {0.0573,-0.1073,-0.1454,-0.1489,0.1417,-0.1708,-0.1864,-0.1314,0.1840,-0.2017,-0.1611,-0.1923,0.0994,-0.1767,-0.0975,-0.1325,-0.1092,-0.1582,-0.0844,0.0353,-0.1761,-0.0808,-0.1620,0.0143,-0.1337,-0.0880,-0.1771,0.0122,-0.0466,-0.1122,-0.0927,-0.0104,-0.1158,-0.0222,-0.1087,-0.0375,-0.1097,-0.1501,-0.2203,-0.0340,-0.0802,-0.1698,-0.1090,-0.1850,-0.0889,-0.0332,-0.0210,0.1159,0.2166,-0.0381,0.1980,-0.1458,-0.2341,-0.1016,-0.2587,-0.0929,0.0786,-0.2530,0.1105,-0.2403,-0.2713,-0.1415,-0.2379,0.0421,-0.0137,0.2373,0.2250,0.0186,-0.1003,-0.2272,-0.2124,-0.1139,-0.1317,-0.1691,-0.1912,-0.0925,-0.1379,-0.1752,-0.1663,-0.1189,-0.1104,-0.1312,-0.1343,-0.0834,-0.2152,-0.0070,-0.1683,-0.0580,-0.1531,-0.1294,-0.1644,-0.0661,0.0611,-0.0394,0.0390,-0.0093}
Dinucleotide(d=5): {-0.0398,-0.1943,-0.1203,-0.0080,-0.1815,-0.0804,-0.1111,0.0294,-0.0988,-0.1283,-0.1451,0.0240,-0.1459,-0.0400,-0.1359,0.0067,-0.0864,-0.0783,-0.0770,-0.0704,-0.1390,-0.0951,-0.1338,-0.0343,-0.0882,-0.1129,-0.1265,-0.0563,-0.0905,-0.0896,-0.1221,0.0308,0.0626,-0.2287,0.0138,-0.1540,-0.1349,-0.1276,-0.0767,-0.1653,-0.1064,-0.1421,-0.0868,-0.2066,0.0016,-0.0695,0.0008,0.0503,0.0317,0.0512,0.1234,0.0354,-0.1504,-0.2015,-0.1912,-0.1671,-0.0955,-0.0866,-0.0351,-0.0634,-0.1972,-0.0574,-0.2305,-0.1353,0.0502,0.2492,-0.0101,0.1814,-0.1401,-0.2468,-0.1038,-0.1640,-0.1580,-0.1574,-0.1578,-0.1111,-0.1381,-0.2042,-0.1221,-0.1367}
Dinucleotide(d=6): {-0.0857,-0.1271,-0.1184,-0.0310,-0.1156,-0.0974,-0.1048,-0.0242,-0.1156,-0.0681,-0.1386,-0.0280,-0.0875,-0.0847,-0.0979,-0.0449,-0.0396,-0.1232,-0.0181,-0.1344,-0.0459,-0.2085,-0.0411,-0.1104,-0.0687,-0.1343,-0.0603,-0.1192,-0.0204,-0.1082,-0.0358,-0.1013,-0.0685,-0.1048,-0.0408,-0.0733,-0.1293,-0.1102,-0.1377,-0.1335,-0.1531,-0.0901,-0.1757,-0.1290,-0.0626,0.0082,0.0330,-0.0022,0.0023,0.1212,0.0289,0.0875,-0.1395,-0.2613,-0.1485,-0.1648,-0.1073,-0.0377,-0.1034,-0.0335,-0.1501,-0.1546,-0.1952,-0.1135}
Dinucleotide(d=7): {-0.0553,-0.1571,-0.0339,-0.1149,-0.0040,-0.1967,-0.0154,-0.1335,-0.0557,-0.1010,-0.0818,-0.1060,-0.0600,-0.1189,-0.0248,-0.1106,-0.0994,-0.0857,-0.0656,-0.0641,-0.1151,-0.1048,-0.0854,-0.0961,-0.0957,-0.0766,-0.1101,-0.1027,-0.1065,-0.0324,-0.0536,-0.0758,-0.1225,-0.0414,-0.1385,0.0103,-0.1364,-0.1312,-0.1211,-0.1202,-0.1720,-0.1185,-0.1801,-0.0772,0.0204,-0.0179,0.0128,-0.0360}
Dinucleotide(d=8): {-0.0784,-0.1232,-0.0868,-0.0730,-0.0939,-0.0577,-0.0860,-0.1038,-0.1488,-0.0484,-0.0766,-0.0769,-0.0967,-0.0704,-0.0643,-0.0846,-0.0890,-0.0462,-0.1029,-0.0761,-0.0894,-0.1389,-0.1308,-0.0438,-0.1391,-0.0978,-0.0974,-0.0513,-0.0894,-0.0314,-0.0921,-0.0540}
Dinucleotide(d=9): {-0.0902,-0.0802,-0.1582,-0.0350,-0.1030,-0.1033,-0.1055,-0.0302,-0.1054,-0.0557,-0.0716,-0.1155,-0.1075,-0.0722,-0.0895,-0.0464}
Activity(exp=0): {-0.1142,-0.1142,-0.1142}
Activity(exp=1): {-0.1142,-0.1142,-0.1142}
Activity(exp=2): {-0.1142,-0.1142,-0.1142}
Activity(exp=3): {-0.1142,-0.1142,-0.1142}
> Optimizing the full model (component1-4-all).
>> Starting new optimization: component1-4-all. (2021-05-21 23:11:29.301).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{}],"countTable":[{"h":[762,763,764]},{"h":[765,766,767]},{"h":[768,769,770]},{"h":[771,772,773]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,0,0],[0,0,0],[0,0,0],[0,0,0]]},{"mononucleotide":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40],"activity":[[761,761,761],[761,761,761],[761,761,761],[761,761,761]],"dinucleotide":[[41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184],[185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312],[313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424],[425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520],[521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600],[601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664],[665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712],[713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744],[745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760]]}]}
Value and gradient before optimization:
=======================================
value = 4.750531198125826
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gradient norm = 0.003330971392969222
Starting Function Value: 4.750531198125826
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
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152 163 4.273366391756705 0.025718089954045 1.000000000000000 0.000279272099904
153 164 4.273366173431296 0.017209743333614 1.000000000000000 0.000161951668182
154 165 4.273365881408854 0.033222251764502 1.000000000000000 0.000127129427617
155 166 4.273365693427981 0.021714167223596 1.000000000000000 0.000138460796193
156 167 4.273365431760576 0.040781508077570 1.000000000000000 0.000293595681051
157 168 4.273365135904435 0.030397471988864 1.000000000000000 0.000172181300055
158 169 4.273364953234403 0.004492330745608 1.000000000000000 0.000135906892519
159 170 4.273364780935268 0.008579073625569 1.000000000000000 0.000136774764888
160 171 4.273364582034282 0.022128413391745 1.000000000000000 0.000188219171692
161 172 4.273364249222099 0.040713955846707 1.000000000000000 0.000129476487375
162 173 4.273363986564867 0.038610899894140 1.000000000000000 0.000154720548691
163 174 4.273363912845698 0.049311527186148 1.000000000000000 0.000364144241004
164 175 4.273363675279755 0.016459944903879 1.000000000000000 0.000106944896228
165 176 4.273363596593299 0.007135411983566 1.000000000000000 0.000092061259731
166 177 4.273363467833171 0.004371619387968 1.000000000000000 0.000133109262935
167 178 4.273363324786396 0.015597312501144 1.000000000000000 0.000144913397310
168 179 4.273363237070467 0.035734435639643 1.000000000000000 0.000276566446003
169 180 4.273363143791896 0.007109196093205 1.000000000000000 0.000091484738796
170 181 4.273363097325877 0.007955535134089 1.000000000000000 0.000119014483513
171 182 4.273363044558287 0.007733025080602 1.000000000000000 0.000134467175746
172 183 4.273362922216075 0.013119750797478 1.000000000000000 0.000152575583082
173 185 4.273362861447065 0.005439764828393 0.339404297362248 0.000152257976037
174 186 4.273362765997095 0.009838557702146 1.000000000000000 0.000098581990797
175 187 4.273362700771385 0.005409312663830 1.000000000000000 0.000165367706858
176 188 4.273362628839679 0.005752647708696 1.000000000000000 0.000114533106157
177 189 4.273362543848882 0.006916285520940 1.000000000000000 0.000094879524648
178 190 4.273362451307653 0.012652744738793 1.000000000000000 0.000076246869014
179 191 4.273362386407492 0.018360571349755 1.000000000000000 0.000100417291358
180 192 4.273362322526592 0.008660674705337 1.000000000000000 0.000082172327674
181 193 4.273362263669034 0.004477412265930 1.000000000000000 0.000078379775448
182 194 4.273362198727253 0.012465865705900 1.000000000000000 0.000133419437205
183 195 4.273362142484030 0.004066424815200 1.000000000000000 0.000089165968950
184 196 4.273362115645297 0.000851994095511 1.000000000000000 0.000057120629808
185 197 4.273362074943260 0.003778667245597 1.000000000000000 0.000052901038265
186 198 4.273362038019539 0.005289683063618 1.000000000000000 0.000064056823647
187 199 4.273362013042577 0.014647558814318 1.000000000000000 0.000163989513382
188 200 4.273361955676139 0.002729439208296 1.000000000000000 0.000051199364380
189 201 4.273361937986644 0.001188536017387 1.000000000000000 0.000038235991596
190 202 4.273361913430722 0.003128163746302 1.000000000000000 0.000046213524609
191 203 4.273361883761704 0.004486461949687 1.000000000000000 0.000046690961411
192 204 4.273361872401704 0.008284210299693 1.000000000000000 0.000127132803166
193 205 4.273361831850079 0.001644344584004 1.000000000000000 0.000036066534414
194 206 4.273361819067300 0.000693868821384 1.000000000000000 0.000034449563455
195 207 4.273361799780861 0.002366368687327 1.000000000000000 0.000044011231971
196 208 4.273361773254241 0.004886921000746 1.000000000000000 0.000061957239762
197 209 4.273361755707841 0.008434612922022 1.000000000000000 0.000066404003321
198 210 4.273361736335538 0.001206416367045 1.000000000000000 0.000026229499962
199 211 4.273361727765805 0.000838722637263 1.000000000000000 0.000027808031332
200 212 4.273361716903785 0.002004997589711 1.000000000000000 0.000038395224452
201 213 4.273361705097473 0.003183494507048 1.000000000000000 0.000040725109541
202 214 4.273361695764343 0.001808304073598 1.000000000000000 0.000021034389127
203 215 4.273361688009673 0.001771132974262 1.000000000000000 0.000023379527636
204 216 4.273361681782734 0.001676104522284 1.000000000000000 0.000027823167111
205 217 4.273361673798281 0.002965173121924 1.000000000000000 0.000034827115031
206 218 4.273361667502782 0.000951462114698 1.000000000000000 0.000018305299021
207 219 4.273361663954004 0.000512168358215 1.000000000000000 0.000019400068654
208 220 4.273361658308523 0.001227906073391 1.000000000000000 0.000020216018091
209 222 4.273361654958454 0.001241322724946 0.432512406565232 0.000027019942164
210 223 4.273361650893112 0.001525866950663 1.000000000000000 0.000014676350623
211 224 4.273361647781942 0.001307912790787 1.000000000000000 0.000014183855904
212 225 4.273361644883828 0.001372024541364 1.000000000000000 0.000019444332969
213 226 4.273361642125055 0.001201083053644 1.000000000000000 0.000018215798442
214 227 4.273361639847713 0.000463630479738 1.000000000000000 0.000011366778785
215 228 4.273361637586554 0.000691054120549 1.000000000000000 0.000012477022341
216 229 4.273361636115501 0.000555281718879 1.000000000000000 0.000014076417423
217 230 4.273361633866784 0.001074070836854 1.000000000000000 0.000010118199194
218 231 4.273361631547521 0.001312144071210 1.000000000000000 0.000010973377217
219 232 4.273361630778109 0.001426293071571 1.000000000000000 0.000022409235965
220 233 4.273361629327664 0.000391726674468 1.000000000000000 0.000008087130130
221 234 4.273361628853724 0.000242682991137 1.000000000000000 0.000006510534403
222 235 4.273361627981807 0.000368096303644 1.000000000000000 0.000007955869992
223 236 4.273361626958370 0.000671047779311 1.000000000000000 0.000012615511966
224 237 4.273361626094715 0.000789426904815 1.000000000000000 0.000009076456967
225 238 4.273361625518206 0.000562263558896 1.000000000000000 0.000006874601389
226 239 4.273361625110207 0.000346592753697 1.000000000000000 0.000005972419117
227 240 4.273361624603087 0.000270740866589 1.000000000000000 0.000006209817639
228 242 4.273361624468159 0.000170737143132 0.173464385358095 0.000018596959593
229 243 4.273361623985370 0.000357075083211 1.000000000000000 0.000009343037475
230 244 4.273361623736800 0.000284736975296 1.000000000000000 0.000006789200466
231 245 4.273361623551713 0.000219418306315 1.000000000000000 0.000007057527510
232 246 4.273361623104275 0.000405124767526 1.000000000000000 0.000008291856119
233 247 4.273361622677106 0.000607934158962 1.000000000000000 0.000012576548828
234 248 4.273361622464862 0.000360776606950 1.000000000000000 0.000010548582954
235 249 4.273361622330697 0.000086216744092 1.000000000000000 0.000005365779973
236 250 4.273361622187955 0.000125789667756 1.000000000000000 0.000005543752367
237 251 4.273361622047095 0.000138435343282 1.000000000000000 0.000006946684073
238 252 4.273361621747095 0.000345409244415 1.000000000000000 0.000006935663978
239 253 4.273361621359641 0.000494858124526 1.000000000000000 0.000006807058653
240 254 4.273361621187441 0.000729317949434 1.000000000000000 0.000011132245885
241 255 4.273361620891506 0.000256855170647 1.000000000000000 0.000003559448827
242 256 4.273361620808660 0.000085857853954 1.000000000000000 0.000003460043424
243 257 4.273361620622719 0.000230743664205 1.000000000000000 0.000006031869893
244 258 4.273361620561137 0.000728651829663 1.000000000000000 0.000010046797745
245 259 4.273361620370466 0.000380539254219 1.000000000000000 0.000003120310257
246 260 4.273361620301006 0.000165741125732 1.000000000000000 0.000003057587949
247 261 4.273361620209225 0.000177533206815 1.000000000000000 0.000003418407525
248 262 4.273361620050931 0.000357126499145 1.000000000000000 0.000004525320811
249 263 4.273361620029396 0.000700474322675 1.000000000000000 0.000008901263419
250 264 4.273361619872166 0.000243047421208 1.000000000000000 0.000002294871170
251 265 4.273361619839237 0.000048403093138 1.000000000000000 0.000002220962955
252 266 4.273361619794092 0.000111208291356 1.000000000000000 0.000003419262272
253 267 4.273361619747082 0.000140595120743 1.000000000000000 0.000003678508025
254 268 4.273361619705734 0.000099246004448 1.000000000000000 0.000002280332200
255 269 4.273361619648745 0.000217441557473 1.000000000000000 0.000002205243990
256 270 4.273361619614132 0.000095761263355 1.000000000000000 0.000002299780519
257 271 4.273361619585826 0.000299040425504 1.000000000000000 0.000006440875629
258 272 4.273361619509251 0.000214489268236 1.000000000000000 0.000001668967989
259 273 4.273361619491851 0.000214489268236 1.000000000000000 0.000001385811123
Convergence criteria met.
After: gradient norm = 1.3858111231343961E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.4918,0.5466,-0.0548}
Count Table 1:
---------------
h: {-0.5888,0.9306,-0.3418}
Count Table 2:
---------------
h: {-0.7211,1.3001,-0.5790}
Count Table 3:
---------------
h: {-0.9330,1.7987,-0.8657}
Enrichment model0:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model1:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model2:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Enrichment model3:
--------------------
rho: {0.0000,1.0000,0.0000}
gamma: {0.0000,-1.0000,-1.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-10.7926,-10.7926,-10.7926}
Activity(exp=1): {-10.7926,-10.7926,-10.7926}
Activity(exp=2): {-10.7926,-10.7926,-10.7926}
Activity(exp=3): {-10.7926,-10.7926,-10.7926}
Binding mode 1:
---------------
Mononucleotide: {-0.7463,-0.6946,-0.7175,-0.6888,-0.6800,-0.8033,-0.7282,-0.6358,-0.6413,-0.9198,-0.8897,-0.3965,-0.1080,-1.1760,-0.5849,-0.9784,0.0929,-1.0161,-0.9243,-0.9998,-0.8531,-0.7774,-0.9044,-0.3123,-0.7956,-0.7138,-0.8560,-0.4818,-0.5115,-0.9784,-0.5180,-0.8394,-0.8041,-0.6798,-0.6789,-0.6845,-0.7899,-0.6875,-0.7999,-0.5700}
Dinucleotide(d=1): {-0.2931,0.0123,-0.3034,-0.1619,-0.2430,-0.2714,0.0324,-0.2096,0.0398,-0.2002,-0.2830,-0.2766,-0.1852,-0.3460,-0.1790,0.0208,-0.3199,-0.0288,-0.5183,0.1191,0.0521,-0.4009,-0.2664,-0.1879,-0.2842,-0.2295,0.0289,-0.2215,-0.1023,-0.2453,-0.1643,-0.0779,-0.2146,-0.2398,0.0169,-0.0836,-0.2821,-0.1699,-0.1288,-0.1852,-0.4902,-0.1185,-0.0875,-0.0915,0.6461,-0.5102,-0.3390,-0.5693,0.7314,-0.4495,-0.2641,-0.4524,-0.6675,-0.1318,-0.1306,-0.1264,0.1128,-0.1983,-0.2646,-0.1622,-0.4016,-0.1296,-0.1560,-0.1567,-0.1575,-0.1125,-0.3532,0.6146,-0.1952,-0.1625,-0.1115,-0.5295,-0.1738,-0.2474,-0.1365,-0.3334,-0.2185,-0.1579,-0.2038,-0.3688,-0.8975,0.6474,-0.5263,-0.3180,0.4771,-0.6647,0.1430,-0.8690,-0.4281,-0.2953,-0.6566,0.5190,0.0278,-0.5045,0.3253,0.1731,-0.4043,0.1827,-0.2344,-0.1996,-0.4764,-0.7058,0.0395,0.3316,0.2361,-0.0287,-0.6874,-0.3706,0.1649,-0.3992,0.3316,-0.6273,-1.0611,0.3728,-0.3010,0.1405,0.0834,-0.5780,-0.1578,-0.2332,-0.0900,-0.1123,-0.0676,-0.0653,0.0852,-0.4541,0.0121,-0.4209,-0.5918,-0.1237,-0.0559,-0.0832,-0.0226,-0.2298,-0.3708,-0.0600,-0.1621,-0.1926,-0.0965,-0.1962,-0.0725,-0.1146,-0.2749,-0.2001}
Dinucleotide(d=2): {-0.2981,-0.1790,-0.3699,0.0703,-0.1482,-0.1660,-0.0993,-0.2612,-0.1484,-0.1863,-0.3030,-0.0674,-0.0564,-0.3804,-0.1251,-0.1291,-0.1896,-0.2696,-0.0347,-0.1610,0.0830,-0.2247,-0.2805,-0.4056,-0.0880,-0.2885,-0.2007,-0.1234,0.1191,-0.3383,-0.1292,-0.3154,-0.1048,-0.1158,-0.1435,-0.1007,-0.2263,-0.1717,-0.1787,-0.1493,-0.4908,-0.1737,0.0193,-0.1206,0.7261,-0.4483,-0.6061,-0.5625,-0.0955,-0.0220,-0.1507,0.2066,-0.2236,-0.1971,-0.2416,-0.4552,-0.3040,-0.3292,-0.2569,0.1872,-0.1984,-0.2181,-0.2087,-0.3401,-0.0587,0.0293,-0.0856,0.2858,-0.2713,-0.1754,-0.3379,-0.2425,-0.2694,-0.3184,-0.2045,-0.1666,-0.1627,-0.2372,-0.1894,-0.4427,-0.3724,-0.1595,-0.0512,-0.1843,0.2689,-0.0356,-0.7697,-0.4378,-0.3715,-0.5419,0.1852,-0.2073,-0.0584,-0.1691,0.0077,0.0495,-0.3716,-0.0744,-0.0614,-0.2943,-0.0857,-0.2451,-0.4661,0.0404,-0.3179,-0.2679,-0.0909,-0.1596,-0.0319,-0.0730,-0.0774,-0.2707,-0.2105,-0.0634,-0.0024,-0.2380,-0.2561,-0.2024,-0.3935,-0.1134,-0.2485,-0.1500,-0.1698,0.0427,-0.0645,-0.2623,-0.2510,-0.2641}
Dinucleotide(d=3): {-0.0311,-0.2393,-0.1096,-0.3699,-0.0770,-0.2235,-0.1641,-0.2078,0.0611,-0.4147,-0.2072,-0.1849,-0.0142,-0.2636,-0.1623,-0.2391,0.0701,-0.1901,-0.2080,-0.3502,0.0759,-0.3106,-0.3728,-0.2055,-0.1409,-0.1868,-0.1823,-0.1704,0.1783,-0.3491,-0.2062,-0.2987,-0.2423,-0.1759,-0.1273,-0.0377,-0.2235,-0.1090,-0.2248,-0.2832,-0.2080,-0.0416,-0.0855,-0.5444,-0.1123,-0.4264,-0.4194,0.4141,-0.1193,-0.0203,-0.0309,0.1070,-0.2098,-0.2380,-0.3472,-0.3361,-0.2159,-0.2961,-0.1407,-0.0053,-0.2265,-0.1566,-0.3406,-0.2710,0.2580,-0.4650,0.4090,-0.1646,-0.2502,-0.1115,-0.4722,-0.1719,-0.2961,-0.1680,-0.2303,-0.2115,-0.2333,-0.1560,-0.3860,-0.1977,-0.1747,-0.1507,-0.0765,-0.4554,-0.4787,-0.0504,-0.3770,0.0588,-0.3200,-0.3234,-0.0827,-0.1578,0.1245,-0.1217,-0.1190,-0.1425,-0.2417,-0.1821,-0.0732,-0.2841,-0.2217,-0.2055,-0.5099,0.1405,-0.2090,-0.1844,-0.1511,-0.2836,-0.0920,-0.0896,-0.0913,-0.1686}
Dinucleotide(d=4): {-0.0075,-0.2032,-0.2594,-0.2592,0.0436,-0.2377,-0.2587,-0.2356,0.1145,-0.2796,-0.2630,-0.3151,0.0437,-0.3211,-0.1902,-0.2188,-0.2274,-0.2606,-0.1631,-0.0335,-0.3056,-0.1696,-0.2737,-0.0595,-0.1930,-0.1802,-0.2835,-0.0722,-0.1409,-0.1835,-0.1890,-0.1119,-0.2206,-0.0914,-0.2047,-0.1319,-0.2364,-0.2468,-0.3484,-0.0890,-0.1456,-0.2524,-0.1446,-0.3494,-0.1823,-0.1237,-0.1528,0.0725,0.1929,-0.1131,0.1651,-0.3199,-0.3481,-0.1620,-0.4069,-0.1690,0.0365,-0.3432,0.0692,-0.4341,-0.4410,-0.2713,-0.3918,0.0893,-0.1306,0.2141,0.1877,-0.1071,-0.1649,-0.3568,-0.3104,-0.2007,-0.2251,-0.3095,-0.3267,-0.1066,-0.2294,-0.2883,-0.2721,-0.2208,-0.2100,-0.2285,-0.2233,-0.1963,-0.3202,-0.0983,-0.2741,-0.1154,-0.2423,-0.2502,-0.2590,-0.1540,-0.0282,-0.1097,-0.0474,-0.0904}
Dinucleotide(d=5): {-0.1338,-0.2892,-0.2246,-0.0974,-0.2786,-0.1534,-0.2044,-0.0587,-0.1905,-0.2392,-0.2461,-0.0432,-0.2636,-0.1184,-0.2291,-0.0770,-0.1743,-0.1643,-0.1662,-0.1720,-0.2574,-0.1795,-0.2688,-0.1006,-0.1823,-0.1924,-0.2158,-0.1364,-0.1861,-0.1834,-0.2047,-0.0630,0.0122,-0.3966,-0.0352,-0.2777,-0.2231,-0.2022,-0.2083,-0.2694,-0.2171,-0.2210,-0.1636,-0.2776,-0.0884,-0.1447,-0.1059,-0.0285,-0.0218,-0.0413,0.0610,-0.0564,-0.2429,-0.2926,-0.3182,-0.2757,-0.1718,-0.2270,-0.0872,-0.1577,-0.3657,-0.1081,-0.3648,-0.1770,-0.0071,0.2077,-0.0978,0.0769,-0.2518,-0.3626,-0.2006,-0.2233,-0.2488,-0.2712,-0.2579,-0.1866,-0.2620,-0.3355,-0.2058,-0.2208}
Dinucleotide(d=6): {-0.1919,-0.2244,-0.2131,-0.1170,-0.2080,-0.1619,-0.2074,-0.1170,-0.2133,-0.1570,-0.2402,-0.1091,-0.1865,-0.1788,-0.1943,-0.1273,-0.1212,-0.2262,-0.0938,-0.2421,-0.1307,-0.3231,-0.1441,-0.2089,-0.1531,-0.2114,-0.1567,-0.2035,-0.1082,-0.2066,-0.1266,-0.1912,-0.1688,-0.2144,-0.1288,-0.1461,-0.2430,-0.2136,-0.2272,-0.2328,-0.2390,-0.1970,-0.2492,-0.2065,-0.1478,-0.0574,-0.0773,-0.0985,-0.0831,0.0413,-0.0518,0.0282,-0.2528,-0.3464,-0.2450,-0.2924,-0.2030,-0.1507,-0.1884,-0.1051,-0.2365,-0.2524,-0.3088,-0.2006}
Dinucleotide(d=7): {-0.1526,-0.2677,-0.1123,-0.2144,-0.0790,-0.2746,-0.1214,-0.2258,-0.1366,-0.1981,-0.1756,-0.2027,-0.1465,-0.2249,-0.1125,-0.2027,-0.1964,-0.1850,-0.1485,-0.1508,-0.2059,-0.2060,-0.2103,-0.1785,-0.1754,-0.1775,-0.1941,-0.1813,-0.2234,-0.1131,-0.1276,-0.1736,-0.2101,-0.1507,-0.2451,-0.0582,-0.2437,-0.2439,-0.2203,-0.2068,-0.2612,-0.1991,-0.2523,-0.1786,-0.0779,-0.0948,-0.0836,-0.1208}
Dinucleotide(d=8): {-0.1775,-0.2265,-0.1757,-0.1662,-0.1798,-0.1524,-0.1796,-0.1819,-0.2464,-0.1375,-0.1704,-0.1653,-0.1988,-0.1653,-0.1530,-0.1710,-0.1888,-0.1352,-0.2011,-0.1547,-0.1864,-0.2521,-0.2481,-0.1183,-0.2189,-0.1876,-0.1829,-0.1390,-0.1949,-0.1191,-0.1677,-0.1524}
Dinucleotide(d=9): {-0.1691,-0.1857,-0.2345,-0.1556,-0.1851,-0.1986,-0.2154,-0.0969,-0.2055,-0.1349,-0.1670,-0.2093,-0.2301,-0.1707,-0.1827,-0.1063}
Activity(exp=0): {-0.2373,-0.2373,-0.2373}
Activity(exp=1): {-0.2373,-0.2373,-0.2373}
Activity(exp=2): {-0.2373,-0.2373,-0.2373}
Activity(exp=3): {-0.2373,-0.2373,-0.2373}
> Optimization done.
Probound Model
±
Optimized model:
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Dinucleotide (10bp)
