Monday, February 25, 2013

MDS New Runs Tracking

Input

Separated Fasta from 446k New Run after Region Refinement


Description

Distance: PID, Normalized Score (divided by average)
Core Algorithm: All varied DA-SMACOF, Fixed sample MDS.

Comparison

Selected Region: 4 (as most different from old run), 5 (as most similar to old run)
Methods:  1) Twister-DASMACOF vs Manxcat-DASMACOF; 2) PID vs Normalized Score; 3) New Region vs Old Region

Tracking Table:




Posted by at No comments:

Fungi New Run vs Old Run


Input

Total: 446k Fungi Fasta File
Sample Data: first 100k sequences,.
OutSample Data: rest 346k sequences
Input Cluster Information: 7 Regions after Region Refinement from Old Run

Description

Aligner: SmithWaterman
OpenGapPentalty: -16
GapExtensionPenalty: -4
WithReverseCompliment: No
ScoringMatrix: EDNAFULL

Region Refinement Configuration

Lowest level: 0
Maximum Points: 200
Minimum Points: 0
Region 7 starting Point: 85147
Extend Region 7 by 0.01 to Region 1
Extend Region 7 by 0.025 to Region 3
From Plot, Region 7 is created from old Region 3

Summary

Before Region Refinement
In Old and New In Old NOT New In New NOT Old Old Total New Total
0 109035 2194 14780 111229 123815
1 42711 7524 7054 50235 49765
2 112379 2244 12231 114623 124610
3 41662 512 7541 42174 49203
4 34304 39581 361 73885 34665
5 36386 2057 5135 38443 41521
6 12940 2512 9522 15452 22462
7 0 0 0 0 0
After Region Refinement
In Old and New In Old NOT New In New NOT Old Old Total New Total
0 109158 2071 16640 111229 125798
1 40634 9601 6405 50235 47039
2 112163 2460 12046 114623 124209
3 34480 7694 4732 42174 39212
4 34315 39570 446 73885 34761
5 36399 2044 5471 38443 41870
6 12967 2485 9745 15452 22712
7 0 0 10440 0 10440
Posted by at No comments:

Tuesday, March 27, 2012

Fungi 100K+197 PercentIdentity with Sammon Last 100K Fixed and Random Init

Description

DataSet: Haixu 100K+197 Size: 100197 Unique: Yes
Aligner: SmithWaterman ScoringMatrix: EDNAFULL GapOpen: -16 GapExt: -4
DistanceType: (1-PercentIdentity) Transformation: None
Mapping: Sammon DistanceCut: None
Initialization: Random
Fixed: [197-100196] to DA-SMACOF points
Varied: [0-196]<br>DensitySat: 0.85

Links


Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\millions\haixu_100K+197\100k+197_swg_c#.bin


ManxcatCore
 AddonforQcomputation:          2
 CalcFixedCrossFixed:           True
 CGResidualLimit:               1E-05
 ChisqChangePerPoint:           0.001
 Chisqnorm:                     2
 ChisqPrintConstant:            1000
 ConversionInformation:         
 ConversionOption:              
 DataPoints:                    100197
 Derivtest:                     False
 DiskDistanceOption:            2
 DistanceCut:                   -1
 DistanceFormula:               1
 DistanceProcessingOption:      0
 DistanceWeigthsCuts:           
 Eigenvaluechange:              0.001
 Eigenvectorchange:             0.001
 ExtraOption1:                  0
 Extraprecision:                0.05
 FixedPointCriterion:           originalpoint
 FletcherRho:                   0.25
 FletcherSigma:                 0.75
 FullSecondDerivativeOption:    0
 FunctionErrorCalcMultiplier:   10
 HistogramBinCount              100
 InitializationLoops:           2
 InitializationOption:          0
 InitialSteepestDescents:       0
 LinkCut:                       5
 LocalVectorDimension:          3
 Maxit:                         120
 MinimumDistance:               -0.001
 MPIIOStrategy:                 0
 Nbadgo:                        6
 Omega:                         1.25
 OmegaOption:                   0
 PowerIterationLimit:           200
 ProcessingOption:              0
 QgoodReductionFactor:          0.5
 QHighInitialFactor:            0.01
 QLimiscalecalculationInterval: 1
 RotationOption:                0
 Selectedfixedpoints:           197-100196
 Selectedvariedpoints:          
 StoredDistanceOption:          2
 TimeCutmillisec:               -1
 TransformMethod:               0
 TransformParameter:            0.125
 UndefindDistanceValue:         -1
 VariedPointCriterion:          rest
 WeightingOption:               0
 Write2Das3D:                   True


Density
 Alpha:                         2
 Pcutf:                         0.85
 SelectedClusters:              
 XmaxBound:                     1
 Xres:                          50
 YmaxBound:                     1
 Yres:                          50
Posted by at No comments:
Labels: , , , , ,

Fungi 100K+197 Normalized Score with Sammon Last 100K Fixed and Random Init

Description

DataSet: Haixu 100K+197 Size: 100197 Unique: Yes
Aligner: SmithWaterman ScoringMatrix: EDNAFULL GapOpen: -16 GapExt: -4
DistanceType: Normalized SWG Score (2AB/AA+BB) Transformation: None
Mapping: Sammon DistanceCut: None
Initialization: Random
Fixed: [197-100196] to DA-SMACOF points
Varied: [0-196]
DensitySat: 0.85

Links


Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\millions\haixu_100K+197\100k+197_swg_distance_normscore_c#.bin


ManxcatCore
 AddonforQcomputation:          2
 CalcFixedCrossFixed:           True
 CGResidualLimit:               1E-05
 ChisqChangePerPoint:           0.001
 Chisqnorm:                     2
 ChisqPrintConstant:            1000
 ConversionInformation:         
 ConversionOption:              
 DataPoints:                    100197
 Derivtest:                     False
 DiskDistanceOption:            2
 DistanceCut:                   -1
 DistanceFormula:               1
 DistanceProcessingOption:      0
 DistanceWeigthsCuts:           
 Eigenvaluechange:              0.001
 Eigenvectorchange:             0.001
 ExtraOption1:                  0
 Extraprecision:                0.05
 FixedPointCriterion:           originalpoint
 FletcherRho:                   0.25
 FletcherSigma:                 0.75
 FullSecondDerivativeOption:    0
 FunctionErrorCalcMultiplier:   10
 HistogramBinCount              100
 InitializationLoops:           2
 InitializationOption:          0
 InitialSteepestDescents:       0
 LinkCut:                       5
 LocalVectorDimension:          3
 Maxit:                         120
 MinimumDistance:               -0.001
 MPIIOStrategy:                 0
 Nbadgo:                        6
 Omega:                         1.25
 OmegaOption:                   0
 PowerIterationLimit:           200
 ProcessingOption:              0
 QgoodReductionFactor:          0.5
 QHighInitialFactor:            0.01
 QLimiscalecalculationInterval: 1
 RotationOption:                0
 Selectedfixedpoints:           197-100196
 Selectedvariedpoints:          
 StoredDistanceOption:          2
 TimeCutmillisec:               -1
 TransformMethod:               0
 TransformParameter:            0.125
 UndefindDistanceValue:         -1
 VariedPointCriterion:          rest
 WeightingOption:               0
 Write2Das3D:                   True


Density
 Alpha:                         2
 Pcutf:                         0.85
 SelectedClusters:              
 XmaxBound:                     1
 Xres:                          50
 YmaxBound:                     1
 Yres:                          50
Posted by at No comments:
Labels: , , , , ,
Subscribe to: Posts (Atom)