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uplinger
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Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

Original announcement: https://www.worldcommunitygrid.org/forums/wcg/viewthread_thread,42074

Please post your issues or observations in this thread.

Thanks,
-Uplinger
[Jan 8, 2020 4:28:10 PM]   Link   Report threatening or abusive post: please login first  Go to top 
Former Member
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

Lucked into 5 of them, received 21:59, last returned 1:13AM. Barely 3 hours a piece.
[Jan 10, 2020 8:52:45 AM]   Link   Report threatening or abusive post: please login first  Go to top 
Former Member
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

Got 4 on the 8th, all finished on the 9th.
All ran about 7hrs 15 mins.
They are now awaiting validation along with all the wingmen.
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[Edit 1 times, last edit by Former Member at Jan 10, 2020 1:22:10 PM]
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

These are still awaiting validation.

BETA_ MCM1_ 9800013_ 0084_ 0-- iMac.local Pending Validation 1/8/20 16:38:39 1/9/20 21:20:52 7.22 / 7.26 346.2 / 0.0
BETA_ MCM1_ 9800013_ 0020_ 1-- iMac.local Pending Validation 1/8/20 16:38:39 1/9/20 21:20:52 7.26 / 7.30 348.0 / 0.0
BETA_ MCM1_ 9800013_ 0083_ 1-- iMac.local Pending Validation 1/8/20 16:38:39 1/9/20 21:20:52 7.28 / 7.32 349.2 / 0.0
BETA_ MCM1_ 9800013_ 0021_ 0-- iMac.local Pending Validation 1/8/20 16:38:39 1/9/20 21:20:52 7.28 / 7.32 349.0 / 0.0
This is what the first on looks like.

BETA_ MCM1_ 9800013_ 0084_ 0-- Darwin 16.7.0 744 Pending Validation 1/8/20 16:38:39 1/9/20 21:20:52 7.22 346.2 / 0.0
BETA_ MCM1_ 9800013_ 0084_ 1-- Darwin 17.7.0 744 Pending Validation 1/8/20 16:29:23 1/9/20 07:38:35 6.91 210.4 / 0.0

Result Log
Result Name: BETA_ MCM1_ 9800013_ 0084_ 0--
<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
Commandline = wcgrid_beta17_map_7.44_x86_64-apple-darwin -SettingsFile MCM1_9800013_0084.txt -DatabaseFile dataset-sarc-draft1.txt
Settings File
DateOfDesign = 20191101
Designer = Krembil/cubes
WorkOrderID = MCM1_9800013_0084
DatasetID = sarc-draft1
RSeed = 3565
PositiveClasses = 5 6
NumberOfGenesInStartingSignature = 20
NumberOfGenesInSignatureMin = 20
NumberOfGenesInSignatureMax = 20
StartingGeneSignatureAlgorithm = randomFixedLengthSearch
SearchAlgorithmNumberToCreate = 14754
//SearchAlgorithmSequentialStartPosition = 304
RunPermutationAlgorithm = 0
//PermutationGroups = C
//PermutationGroupsForReplacement = F
//PermutationAlgorithm = insertEnumerateFromGroup
//PermutationsNumIterations = 5
//OptimizationAlgorithmFrequency = 0 0 1

// Do we need these?
FBeta = 1.5
SimAnnealIMax = 20000
SimAnnealAlpha = 0.9996
//Pseudocounts = 0.2

FitnessFn = 0
MinFitness = 0.65

NReps = 100
VMethod = CV
TrainFrac = 0.7
// Alternatively
////NReps = 10
////TrainFrac = 0.7
////NFolds = 10
//VMethod = LOO

// Apparently the default
//ModelType = SVM
SvmArgs = "-v 0 -t 1 -c 0.01 -d 2 -r 2 -s 1"
SvmLearnLimit = 250000

[07:04:13] Initializing
[07:04:34] Running
[07:04:34] EvaluateFitnessOfStartingGeneSignatures 14754
[14:19:38] Writing final output
[14:19:38] Closing Output Stream
[14:19:38] Cleaning up
Result.out = 94015.000000
Run complete, CPU time: 25990.438176
14:19:38 (46601): called boinc_finish(0)

</stderr_txt>
Result Log

Result Name: BETA_ MCM1_ 9800013_ 0084_ 0--
<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
Commandline = wcgrid_beta17_map_7.44_x86_64-apple-darwin -SettingsFile MCM1_9800013_0084.txt -DatabaseFile dataset-sarc-draft1.txt
Settings File
DateOfDesign = 20191101
Designer = Krembil/cubes
WorkOrderID = MCM1_9800013_0084
DatasetID = sarc-draft1
RSeed = 3565
PositiveClasses = 5 6
NumberOfGenesInStartingSignature = 20
NumberOfGenesInSignatureMin = 20
NumberOfGenesInSignatureMax = 20
StartingGeneSignatureAlgorithm = randomFixedLengthSearch
SearchAlgorithmNumberToCreate = 14754
//SearchAlgorithmSequentialStartPosition = 304
RunPermutationAlgorithm = 0
//PermutationGroups = C
//PermutationGroupsForReplacement = F
//PermutationAlgorithm = insertEnumerateFromGroup
//PermutationsNumIterations = 5
//OptimizationAlgorithmFrequency = 0 0 1

// Do we need these?
FBeta = 1.5
SimAnnealIMax = 20000
SimAnnealAlpha = 0.9996
//Pseudocounts = 0.2

FitnessFn = 0
MinFitness = 0.65

NReps = 100
VMethod = CV
TrainFrac = 0.7
// Alternatively
////NReps = 10
////TrainFrac = 0.7
////NFolds = 10
//VMethod = LOO

// Apparently the default
//ModelType = SVM
SvmArgs = "-v 0 -t 1 -c 0.01 -d 2 -r 2 -s 1"
SvmLearnLimit = 250000

[07:04:13] Initializing
[07:04:34] Running
[07:04:34] EvaluateFitnessOfStartingGeneSignatures 14754
[14:19:38] Writing final output
[14:19:38] Closing Output Stream
[14:19:38] Cleaning up
Result.out = 94015.000000
Run complete, CPU time: 25990.438176
14:19:38 (46601): called boinc_finish(0)

</stderr_txt>
----------------------------------------
[Edit 1 times, last edit by Former Member at Jan 14, 2020 1:20:02 PM]
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

All 700+ of them. A normal production 7 day deadline would have been fine too.
[Jan 14, 2020 1:15:05 PM]   Link   Report threatening or abusive post: please login first  Go to top 
uplinger
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

Validator was just enabled for the project. It looks like most validated properly. There was a handful from a couple of hosts that did not. Because they have a common denominator, I'm considering this a success. When the resends get sent out, we will send the results to the researchers for them to confirm the success.

Thanks,
-Uplinger
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

we appreciate the update.
[Jan 15, 2020 12:38:01 AM]   Link   Report threatening or abusive post: please login first  Go to top 
3A4scLiRhJVcdT2K9q9kQNxzxYJ9
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

** sorry ** wrong thread. (Cannot delete due to reply to my post)
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[Edit 1 times, last edit by SHOPXXL-COM at Jan 24, 2020 2:07:14 PM]
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Re: Mapping Cancer Markers Beta Test January 8, 2020 [ Issues Thread ]

You're commenting to the January 8 test for none-android, which moved to production. wink
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[Edit 1 times, last edit by Former Member at Jan 24, 2020 1:51:55 PM]
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