Package: DatabionicSwarm 2.0.0

Michael Thrun

DatabionicSwarm: Swarm Intelligence for Self-Organized Clustering

Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called Databionic swarm (DBS) is introduced which was published in Thrun, M.C., Ultsch A.: "Swarm Intelligence for Self-Organized Clustering" (2020), Artificial Intelligence, <doi:10.1016/j.artint.2020.103237>. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matrix (GeneratePswarmVisualization()). The third module is the clustering method itself with non-critical parameters (DBSclustering()). Clustering can be verified by the visualization and vice versa. The term DBS refers to the method as a whole. It enables even a non-professional in the field of data mining to apply its algorithms for visualization and/or clustering to data sets with completely different structures drawn from diverse research fields. The comparison to common projection methods can be found in the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <doi:10.1007/978-3-658-20540-9>.

Authors:Michael Thrun [aut, cre, cph], Quirin Stier [aut, rev]

DatabionicSwarm_2.0.0.tar.gz
DatabionicSwarm_2.0.0.tar.gz(r-4.5-noble)DatabionicSwarm_2.0.0.tar.gz(r-4.4-noble)
DatabionicSwarm_2.0.0.tgz(r-4.4-emscripten)DatabionicSwarm_2.0.0.tgz(r-4.3-emscripten)
DatabionicSwarm.pdf |DatabionicSwarm.html
DatabionicSwarm/json (API)
NEWS

# Install 'DatabionicSwarm' in R:
install.packages('DatabionicSwarm', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mthrun/databionicswarm/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • DefaultColorSequence - Default color sequence for plots
  • Hepta - Hepta is part of the Fundamental Clustering Problem Suit (FCPS) [Thrun/Ultsch, 2020].
  • Lsun3D - Lsun3D is part of the Fundamental Clustering Problem Suit (FCPS) [Thrun/Ultsch, 2020].

openblascpp

3.39 score 1 packages 27 scripts 381 downloads 3 mentions 13 exports 35 dependencies

Last updated 6 months agofrom:d80080cd8b. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 30 2024
R-4.5-linux-x86_64OKDec 30 2024

Exports:DBSclusteringDelaunay4PointsDijkstraSSSPGeneratePswarmVisualizationProjectedPoints2GridPswarmRelativeDifferenceRobustNorm_BackTrafoRobustNormalizationsESOM4BMUssetGridSizeShortestGraphPathsCUniquePoints

Dependencies:ABCanalysisclicolorspacedeldirfansifarverGeneralizedUmatrixggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplotrixR6RColorBrewerRcppRcppArmadilloRcppParallelrlangscalestibbleutf8vctrsviridisLitewithr

Short Intro to the Databionic Swarm (DBS)

Rendered fromDatabionicSwarm.Rmdusingknitr::rmarkdownon Dec 30 2024.

Last update: 2024-06-21
Started: 2018-07-03

Readme and manuals

Help Manual

Help pageTopics
Swarm Intelligence for Self-Organized ClusteringDatabionicSwarm-package DatabionicSwarm
Databonic swarm clustering (DBS)DBSclustering
Default color sequence for plotsDefaultColorSequence
Adjacency matrix of the delaunay graph for BestMatches of PointsDelaunay4Points
intern function, do not use yourselfDelta3DWeightsC
Internal function: Dijkstra SSSPDijkstraSSSP
Intern function, do not use yourselffindPossiblePositionsCsingle
Generates the Umatrix for Pswarm algorithmGeneratePswarmVisualization
Intern function: Transformation of Databot indizes to coordinatesgetCartesianCoordinates
depricated! see GeneralizedUmatrix() Generalisierte U-Matrix fuer ProjektionsverfahrengetUmatrix4Projection
Hepta is part of the Fundamental Clustering Problem Suit (FCPS) [Thrun/Ultsch, 2020].Hepta
Lsun3D is part of the Fundamental Clustering Problem Suit (FCPS) [Thrun/Ultsch, 2020].Lsun3D
Intern function for plotting during the Pswarm annealing processplotSwarm
Transforms ProjectedPoints to a gridProjectedPoints2Grid
A Swarm of Databots based on polar coordinates (Polar Swarm).Pswarm
Intern function, do not use yourselfPswarmEpochsParallel
Intern function, do not use yourselfPswarmEpochsSequential
Intern function, do not use yourselfPswarmRadiusParallel
intern function, do not use yourselfPswarmRadiusSequential
Intern function for 'Pswarm'rDistanceToroidCsingle
Relative DifferenceRelativeDifference
Transforms the Robust Normalization backRobustNorm_BackTrafo
RobustNormalizationRobustNormalization
Intern function: Simplified Emergent Self-Organizing MapsESOM4BMUs
setdiffMatrix shortens Matrix2Curt by those rows that are in both matrices.setdiffMatrix
Sets the grid size for the Pswarm algorithmsetGridSize
Intern function: Sets the polar gridsetPolarGrid
Intern function: Estimates the minimal radius for the Databot scentsetRmin
Shortest GraphPaths = geodesic distancesShortestGraphPathsC
internal function for s-esomtrainstepC
internal function for s-esomtrainstepC2
Unique PointsUniquePoints