README

Francisco Bischoff - 07 Jul 2019

Time Series with Matrix Profile

	Build	Dev
Linux x86_64
OSX
Windows
Coverage

Overview

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) %>%
  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.

Performance on an Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz using a random walk dataset

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

	Elapsed Time	Data size	Window size	Threads
stomp_par()	52.72s	40000	1000	8
scrimp()	92.44s	40000	1000	1
stomp()	136.01s	40000	1000	1
stamp_par()	140.25s	40000	1000	8
stamp()	262.03s	40000	1000	1

Installation

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

# Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("franzbischoff/tsmp")

Currently available Features

• 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

Roadmap

• Profile-Based Shapelet Discovery
• GPU-STOMP

Other projects with Matrix Profile

• Python: https://github.com/target/matrixprofile-ts
• Python: https://github.com/ZiyaoWei/pyMatrixProfile
• Python: https://github.com/jbeleno/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

Matrix Profile Foundation

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

Visit: Matrix Profile Foundation

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project, you agree to abide by its terms.