cubical persistent homology | handwritten digits data | preparation | a fixed-parameter walkthrough | pre-processing recipe | classification forest | fitting and evaluation | tuning hyperparameters | tunable pre-processing recipe | tunable classification forest | hyperparameter tuning
Package: tdarec 0.2.1
Jason Cory Brunson
tdarec: A 'recipes' Extension for Persistent Homology and Its Vectorizations
Topological data analytic methods in machine learning rely on vectorizations of the persistence diagrams that encode persistent homology, as surveyed by Ali &al (2000) <doi:10.48550/arXiv.2212.09703>. Persistent homology can be computed using 'TDA' and 'ripserr' and vectorized using 'TDAvec'. The Tidymodels package collection modularizes machine learning in R for straightforward extensibility; see Kuhn & Silge (2022, ISBN:978-1-4920-9644-3). These 'recipe' steps and 'dials' tuners make efficient algorithms for computing and vectorizing persistence diagrams available for Tidymodels workflows.
Authors:
tdarec_0.2.1.tar.gz
tdarec_0.2.1.zip(r-4.7)tdarec_0.2.1.zip(r-4.6)tdarec_0.2.1.zip(r-4.5)
tdarec_0.2.1.tgz(r-4.6-any)tdarec_0.2.1.tgz(r-4.5-any)
tdarec_0.2.1.tar.gz(r-4.7-any)tdarec_0.2.1.tar.gz(r-4.6-any)
tdarec_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tdarec/json (API)
| # Install 'tdarec' in R: |
| install.packages('tdarec', repos = c('https://tdaverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tdaverse/tdarec/issues
Datasets:
- mnist_test - MNIST handwritten digits
- mnist_train - MNIST handwritten digits
machine-learningpersistent-homologyrecipestidymodelstopological-data-analysisvectorization
Last updated from:bc97060770. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 249 | ||
| source / vignettes | OK | 250 | ||
| linux-release-x86_64 | OK | 245 | ||
| macos-release-arm64 | OK | 124 | ||
| macos-oldrel-arm64 | OK | 128 | ||
| windows-devel | OK | 178 | ||
| windows-release | OK | 188 | ||
| windows-oldrel | OK | 209 | ||
| wasm-release | OK | 162 |
Exports:bandwidthbirth_rangeblurblur_sigmasget_blur_rangeget_hom_rangeget_pairs_maxget_pers_max_fracget_pers_min_multhom_degreeimg_sigmalife_supportmax_hom_degreenum_barsnum_binsnum_coefnum_levelspairs_maxpairs_minpers_maxpers_minpers_rangeph_dimpoly_typestep_blurstep_pd_degreestep_pd_point_cloudstep_pd_rasterstep_vpd_algebraic_functionsstep_vpd_betti_curvestep_vpd_complex_polynomialstep_vpd_descriptive_statisticsstep_vpd_euler_characteristic_curvestep_vpd_normalized_life_curvestep_vpd_persistence_blockstep_vpd_persistence_imagestep_vpd_persistence_landscapestep_vpd_persistence_silhouettestep_vpd_persistent_entropy_summarystep_vpd_tent_template_functionsstep_vpd_tropical_coordinatestent_shiftweight_func_plweight_power
Dependencies:classcliclockcodetoolscpp11data.tablediagramdialsDiceDesigndigestdplyrfarverfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobandKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixnnetnumDerivparallellypillarpkgconfigprodlimprogressrpurrrR6RColorBrewerRcpprecipesrlangrpartS7scalessfdshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gaussian blur of an array | blur |
| Standard deviation of Gaussian blur | blur_sigmas |
| (Maximum) topological dimension or homological degree | get_blur_range get_hom_range hom_degree max_hom_degree |
| MNIST handwritten digits | mnist mnist_test mnist_train |
| Blur raster data | step_blur tidy.step_blur |
| Separate persistent pairs by homological degree | step_pd_degree tidy.step_pd_degree |
| Persistent homology of point clouds | step_pd_point_cloud tidy.step_pd_point_cloud |
| Persistent homology of raster data (images) | step_pd_raster tidy.step_pd_raster |
| Algebraic Functions Vectorization of Persistent Homology | step_vpd_algebraic_functions tidy.step_vpd_algebraic_functions |
| Betti Curve Vectorization of Persistent Homology | step_vpd_betti_curve tidy.step_vpd_betti_curve |
| Complex Polynomial Vectorization of Persistent Homology | step_vpd_complex_polynomial tidy.step_vpd_complex_polynomial |
| Descriptive Statistics Vectorization of Persistent Homology | step_vpd_descriptive_statistics tidy.step_vpd_descriptive_statistics |
| Euler Characteristic Curve Vectorization of Persistent Homology | step_vpd_euler_characteristic_curve tidy.step_vpd_euler_characteristic_curve |
| Normalized Life Curve Vectorization of Persistent Homology | step_vpd_normalized_life_curve tidy.step_vpd_normalized_life_curve |
| Persistence Block Vectorization of Persistent Homology | step_vpd_persistence_block tidy.step_vpd_persistence_block |
| Persistence Image Vectorization of Persistent Homology | step_vpd_persistence_image tidy.step_vpd_persistence_image |
| Persistence Landscape Vectorization of Persistent Homology | step_vpd_persistence_landscape tidy.step_vpd_persistence_landscape |
| Persistence Silhouette Vectorization of Persistent Homology | step_vpd_persistence_silhouette tidy.step_vpd_persistence_silhouette |
| Persistent Entropy Summary Vectorization of Persistent Homology | step_vpd_persistent_entropy_summary tidy.step_vpd_persistent_entropy_summary |
| Tent Template Functions Vectorization of Persistent Homology | step_vpd_tent_template_functions tidy.step_vpd_tent_template_functions |
| Tropical Coordinates Vectorization of Persistent Homology | step_vpd_tropical_coordinates tidy.step_vpd_tropical_coordinates |
| Tune Vectorizations of Persistent Homology | bandwidth img_sigma num_bars num_bins num_coef num_levels poly_type tent_shift vpd-dials weight_func_pl weight_power |
| Finalizers for persistent homology vectorizations | get_pairs_max get_pers_max_frac get_pers_min_mult vpd-finalizers |
| Summarize topological data | birth_range birth_range.data.frame birth_range.default birth_range.diagram birth_range.matrix birth_range.persistence birth_range.PHom life_support life_support.data.frame life_support.default life_support.diagram life_support.matrix life_support.persistence life_support.PHom pairs_max pairs_max.data.frame pairs_max.default pairs_max.diagram pairs_max.matrix pairs_max.persistence pairs_max.PHom pairs_min pairs_min.data.frame pairs_min.default pairs_min.diagram pairs_min.matrix pairs_min.persistence pairs_min.PHom pers_max pers_max.data.frame pers_max.default pers_max.diagram pers_max.matrix pers_max.persistence pers_max.PHom pers_min pers_min.data.frame pers_min.default pers_min.diagram pers_min.matrix pers_min.persistence pers_min.PHom pers_range pers_range.data.frame pers_range.default pers_range.diagram pers_range.matrix pers_range.persistence pers_range.PHom ph_dim ph_dim.array ph_dim.data.frame ph_dim.default ph_dim.dist ph_dim.matrix ph_dim.ts vpd-summarizers |
