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20200430 Pikairos Is it possible to extend a distance matrix V4

20200428_Pikairos Is it possible to extend a distance matrix

I have an iterative workflow where a distance matrix is calculated using the Distance Matrix Calculate node. At each new iteration there are only few new data points, because most of them came from older iterations. Is there a way to avoid re-calculating all the distances of the old points at each iteration?

I can save the distance matrix but then I don’t know how to extend it with the new data points, calculating only the distances between the new data points and the old ones (and of course between the new data points themselves). I think to a sort of “distance matrix extension/concatenation”. Is this possible?

One step classical Solution : How to convert the "Column based Table Matrix Distances" into a "Matrix distance type" column Generate 1 columnwith 100Random NumbersHere only 1 columnbut it could be manyfor the example.It doesn't change anythingnor the metrics, etc.Work outEuclideanDistancesExtract pairsAs you can seethere are lessthan 100x100This is becauseit only returnsthe values ofthe half-matrixminus the diagonalTo do the sameas with theDistance MatrixPair Extractoryou need herea recursive loopDirect resultsusingthe Distance MatrixCalculate nodeIn this examplewe add one by onethe rows tothe distance matrixbut you could add hereas many as you want.This is just an example :)Start with first rowagainst itselfSend the lastdistance matrix resultsto the recursive startingloop node to addnew incoming distancesOld vs NewDo itssimilaritysearchKeep onlythe headerThis is only whatwe need at this stageto have the right table headerfor the recursive loopOld vs OldpreviouslycalculateddistancesFilter INNumbers &RowIDEliminateany possibleduplicated resultThis is just to geta cleaner result ifyou have duplicatedcoming rowsRegenatea clean RowIDto reinject to therecursive startingloop nodeNew vs OldFilter INNumbers &RowIDGeneratea unique Identifierfor all the rowsThis is important latersince Similarity Searchworks based ona Row IdentifierFilter OUTany duplicatedcomparisonSort by1st match-pair Identifierand then by2nd match-pair IdentifierFilter uselesscolumnsNew vs NewConcatenateall the calculateddistancesso farGroup by 1st IdentifierSort again by1st Identifierto get the equivalentof a full matrix distance(not exactly the same thoughsince this is the full matrix)That's all FolksWork out final #of iterations :here in thisexample 10because the tablehas 10 rows andwe add one rowto the matrixat each iterationThe Final # of Rowsis needed tostop the followingrecursive loopSet the RowIDwith the new identifierThis node savesdistance matrix inCSV formatThis node reads adistance matrix froma CSV file and stores itin "Distance Matrix" formatThe equivalent inCSV format"Distance Matrix" formatIts equivalenttable formatWrite distancematrixin a csv fileThis node reads adistance matrix froma CSV file and stores itin a "Distance Matrix" format"Distance Matrix"formatTableYou need to Pivot columnsTo put back distancesin matrix formatFilter uselesscolumnsSet uppertriangular matrixas EmptyCreateDiagonalMatrixCreateLowerTriangular"1" valuesmatrixConcatenateas tableDo the productcell by cellof both previouslyconcatenated tablesAdd extra columnwith current RowIDAdd extra columnwith current RowIDFilter uselesscolumns"Distance Matrix"formatTable Random NumbersGenerator Distance MatrixCalculate Distance MatrixPair Extractor RecursiveLoop Start InteractiveTable (local) Rule-basedRow Filter Row Filter Recursive Loop End Similarity Search Similarity Search Row Filter Column Splitter Column Filter DuplicateRow Filter RowID Similarity Search Column Filter Math Formula DuplicateRow Filter Sorter Column Filter Similarity Search Concatenate GroupBy Sorter InteractiveTable (local) Math Formula Table Rowto Variable RowID DistanceMatrix Writer DistanceMatrix Reader File Reader InteractiveTable (local) InteractiveTable (local) CSV Writer DistanceMatrix Reader InteractiveTable (local) Pivoting Column Filter Math Formula(Multi Column) Math Formula(Multi Column) Moving Aggregation Concatenate GroupBy RowID RowID Column Filter InteractiveTable (local) One step classical Solution : How to convert the "Column based Table Matrix Distances" into a "Matrix distance type" column Generate 1 columnwith 100Random NumbersHere only 1 columnbut it could be manyfor the example.It doesn't change anythingnor the metrics, etc.Work outEuclideanDistancesExtract pairsAs you can seethere are lessthan 100x100This is becauseit only returnsthe values ofthe half-matrixminus the diagonalTo do the sameas with theDistance MatrixPair Extractoryou need herea recursive loopDirect resultsusingthe Distance MatrixCalculate nodeIn this examplewe add one by onethe rows tothe distance matrixbut you could add hereas many as you want.This is just an example :)Start with first rowagainst itselfSend the lastdistance matrix resultsto the recursive startingloop node to addnew incoming distancesOld vs NewDo itssimilaritysearchKeep onlythe headerThis is only whatwe need at this stageto have the right table headerfor the recursive loopOld vs OldpreviouslycalculateddistancesFilter INNumbers &RowIDEliminateany possibleduplicated resultThis is just to geta cleaner result ifyou have duplicatedcoming rowsRegenatea clean RowIDto reinject to therecursive startingloop nodeNew vs OldFilter INNumbers &RowIDGeneratea unique Identifierfor all the rowsThis is important latersince Similarity Searchworks based ona Row IdentifierFilter OUTany duplicatedcomparisonSort by1st match-pair Identifierand then by2nd match-pair IdentifierFilter uselesscolumnsNew vs NewConcatenateall the calculateddistancesso farGroup by 1st IdentifierSort again by1st Identifierto get the equivalentof a full matrix distance(not exactly the same thoughsince this is the full matrix)That's all FolksWork out final #of iterations :here in thisexample 10because the tablehas 10 rows andwe add one rowto the matrixat each iterationThe Final # of Rowsis needed tostop the followingrecursive loopSet the RowIDwith the new identifierThis node savesdistance matrix inCSV formatThis node reads adistance matrix froma CSV file and stores itin "Distance Matrix" formatThe equivalent inCSV format"Distance Matrix" formatIts equivalenttable formatWrite distancematrixin a csv fileThis node reads adistance matrix froma CSV file and stores itin a "Distance Matrix" format"Distance Matrix"formatTableYou need to Pivot columnsTo put back distancesin matrix formatFilter uselesscolumnsSet uppertriangular matrixas EmptyCreateDiagonalMatrixCreateLowerTriangular"1" valuesmatrixConcatenateas tableDo the productcell by cellof both previouslyconcatenated tablesAdd extra columnwith current RowIDAdd extra columnwith current RowIDFilter uselesscolumns"Distance Matrix"formatTable Random NumbersGenerator Distance MatrixCalculate Distance MatrixPair Extractor RecursiveLoop Start InteractiveTable (local) Rule-basedRow Filter Row Filter Recursive Loop End Similarity Search Similarity Search Row Filter Column Splitter Column Filter DuplicateRow Filter RowID Similarity Search Column Filter Math Formula DuplicateRow Filter Sorter Column Filter Similarity Search Concatenate GroupBy Sorter InteractiveTable (local) Math Formula Table Rowto Variable RowID DistanceMatrix Writer DistanceMatrix Reader File Reader InteractiveTable (local) InteractiveTable (local) CSV Writer DistanceMatrix Reader InteractiveTable (local) Pivoting Column Filter Math Formula(Multi Column) Math Formula(Multi Column) Moving Aggregation Concatenate GroupBy RowID RowID Column Filter InteractiveTable (local)

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Created by: Molina
Created at: 2020-04-28
On NodePit since: 2022-02-06
Last update: 2024-12-21
Created with KNIME version: v4.1.2
Tags: Recursive matrix distance

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