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matrix-profile-foundation/tsmp: R Functions implementing UCR Matrix Profile Algorithm

Francisco Bischoff

• 18 Aug 2022

This version is being maintained to keep up with CRAN standards. As soon as possible a new version (with possible breaking changes) with less dependencies will be released later in 2022 or beginning of 2023.

R Functions implementing UCR Matrix Profile Algorithm (http://www.cs.ucr.edu/~eamonn/MatrixProfile.html).

This package allows you to use the Matrix Profile concept as a toolkit.

This package provides:

• Algorithms to build a Matrix Profile: STAMP, STOMP, SCRIMP++, SIMPLE, MSTOMP and VALMOD.
• Algorithms for MOTIF search for Unidimensional and Multidimensional Matrix Profiles.
• Algorithm for Chains search for Unidimensional Matrix Profile.
• Algorithms for Semantic Segmentation (FLUSS) and Weakly Labeled data (SDTS).
• Algorithm for Salient Subsections detection allowing MDS plotting.
• Basic plotting for all outputs generated here.
• Sequencial workflow, see below.

# Basic workflow:
matrix <- tsmp(data, window_size = 30) %>%
  find_motif(n_motifs = 3) %T>%
  plot()

# SDTS still have a unique way to work:
model <- sdts_train(data, labels, windows)
result <- sdts_predict(model, data, round(mean(windows)))

Please refer to the User Manual for more details.

Please be welcome to suggest improvements.

set.seed(2018)
data <- cumsum(sample(c(-1, 1), 40000, TRUE))

WIP in this version

# Install the released version from CRAN
install.packages("tsmp")

# Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("matrix-profile-foundation/tsmp")

• STAMP (single and multi-thread versions)
• STOMP (single and multi-thread versions)
• STOMPi (On-line version)
• SCRIMP (single-thread, not for AB-joins yet)
• Time Series Chains
• Multivariate STOMP (mSTOMP)
• Multivariate MOTIF Search (from mSTOMP)
• Salient Subsequences search for Multidimensional Space
• Scalable Dictionary learning for Time Series (SDTS) prediction
• FLUSS (Fast Low-cost Unipotent Semantic Segmentation)
• FLOSS (Fast Low-cost On-line Unipotent Semantic Segmentation)
• SiMPle-Fast (Fast Similarity Matrix Profile for Music Analysis and Exploration)
• Annotation vectors (e.g., Stop-word MOTIF bias, Actionability bias)
• FLUSS Arc Plot and SiMPle Arc Plot
• Exact Detection of Variable Length Motifs (VALMOD)
• MPdist: Matrix Profile Distance
• Time Series Snippets
• Subsetting Matrix Profiles (head(), tail(), [, etc.)
• Misc:
  • MASS v2.0
  • MASS v3.0
  • MASS extensions: ADP (Approximate Distance Profile, with PAA)
  • MASS extensions: WQ (Weighted Query)
  • MASS extensions: QwG (Query with Gap)
  • Fast moving average
  • Fast moving SD

• Profile-Based Shapelet Discovery
• GPU-STOMP

• Python: https://github.com/target/matrixprofile-ts
• Python: https://github.com/ZiyaoWei/pyMatrixProfile
• Python: https://github.com/juanbeleno/owlpy
• Python: https://github.com/javidlakha/matrix-profile
• Python: https://github.com/shapelets/khiva-python
• R: https://github.com/shapelets/khiva-r
• Matlab: https://github.com/shapelets/khiva-matlab
• Java: https://github.com/shapelets/khiva-java
• Java: https://github.com/ensozos/Matrix-Profile
• Kotlin: https://github.com/shapelets/khiva-kotlin
• C++ (CUDA and OPENCL): https://github.com/shapelets/khiva
• CUDA: https://github.com/zpzim/STOMPSelfJoin
• CUDA: https://github.com/zpzim/SCAMP

Our next step unifying the Matrix Profile implementation in several programming languages.

Visit: Matrix Profile Foundation

Please note that the ‘tsmp’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

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