Description
DataSet: COG Size: 50000 Unique: YesAligner: Blast ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4
DistanceType: Normalized BitScore (2*AB/AA+BB) Transformation: None
Mapping: Chisq1 DistanceCut: 0.96
Initialization: Random
Fixed: None
Varied: All
DensitySat: 0.85
Links
Images
Full Sample with Selected Clusters
Configuration
I/O CoordinateWriteFrequency: 0 DistanceMatrixFile: F:\Salsa\saliya\cog\100k\input\cog_95672_bitscore_refined_first50k_c#.bin ManxcatCore AddonforQcomputation: 2 CalcFixedCrossFixed: True CGResidualLimit: 1E-05 ChisqChangePerPoint: 0.001 Chisqnorm: 1 ChisqPrintConstant: 1 ConversionInformation: ConversionOption: DataPoints: 50000 Derivtest: False DiskDistanceOption: 2 DistanceCut: 0.96 DistanceFormula: 1 DistanceProcessingOption: 0 DistanceWeigthsCuts: Eigenvaluechange: 0.001 Eigenvectorchange: 0.001 ExtraOption1: 0 Extraprecision: 0.05 FixedPointCriterion: none FletcherRho: 0.25 FletcherSigma: 0.75 FullSecondDerivativeOption: 0 FunctionErrorCalcMultiplier: 10 HistogramBinCount 100 InitializationLoops: 1 InitializationOption: 1 InitialSteepestDescents: 0 LinkCut: 5 LocalVectorDimension: 3 Maxit: 80 MinimumDistance: -0.001 MPIIOStrategy: 0 Nbadgo: 6 Omega: 1.25 OmegaOption: 0 PowerIterationLimit: 200 ProcessingOption: 100 QgoodReductionFactor: 0.5 QHighInitialFactor: 0.01 QLimiscalecalculationInterval: 1 RotationOption: 0 Selectedfixedpoints: Selectedvariedpoints: StoredDistanceOption: 2 TimeCutmillisec: -1 TransformMethod: 0 TransformParameter: 0.125 UndefindDistanceValue: -1 VariedPointCriterion: all WeightingOption: 0 Write2Das3D: True Density Alpha: 2 Pcutf: 0.85 SelectedClusters: 63,82,145,265,362,684,708 XmaxBound: 1.8 Xres: 50 YmaxBound: 1.8 Yres: 50
There are two things one tries to do
ReplyDeletea) Transform input distance distribution so that one preserves order i.e. distance --> function(distance)such that f(d1) > f(d2) if d1 > d2. Transform Method 10 and 4D transformation aim at this
b) weight contributions to Chisq sum of (euclidean mapped distance - input distance)^2
Here SMACOF has weight 1
Sammon has weight 1/distance
Chisq1 refers to parameter Chisqnorm = 1 which is weight 1/distance^1.5
Sammon (chisqnorm 2) and Chisq1 enhance small distances compared to traditional SMACOF