S3M — Statistically Significant Shapelet Mining

This is the implementation of the method described in the ISMB 2018 paper “Association mapping in biomedical time series via statistically significant shapelet mining”.

Installation

For Mac OS X, we recommend installing S3M using the Homebrew package manager:

$ brew install BorgwardtLab/mlcb/s3m

For Debian and Ubuntu, please use the .deb file of the latest release and install it using:

$ sudo apt install s3m-latest.deb

For Arch Linux, please install S3M from AUR using pacaur or trizen, for example:

$ pacaur -S s3m
$ trizen -S s3m

Please refer to the advanced build instructions for more advanced build processes, including source builds and Docker installations.

Example

We provide a synthetic data set that illustrates the utility of S3M. After installation, the command

$ s3m -i data/example/synthetic.csv -m 15 -o results/example.json

runs S3M on it and stores its results in the results folder. The below figure shows how the method identifies the case-characteristic two spikes as the most significant shapelet (p-value: 5.42e-20).

Help

If you have questions concerning S3M or you encounter problems when trying to build the tool under your own system, please open an issue in the issue tracker. Try to describe the issue in sufficient detail in order to make it possible for us to help you.

Contributors

S3M is developed and maintained by members of the Machine Learning and Computational Biology Lab of Prof. Dr. Karsten Borgwardt:

Christian Bock (GitHub)
Thomas Gumbsch (GitHub)
Max Horn (GitHub)
Michael Moor (GitHub)
Bastian Rieck (GitHub)

Citation

Please use the following BibTeX citation when using our method or comparing against it:

@article{Bock18,
  author  = {Bock, Christian and Gumbsch, Thomas and Moor, Michael and Rieck, Bastian and Roqueiro, Damian and Borgwardt, Karsten},
  title   = {Association mapping in biomedical time series via statistically significant shapelet mining},
  journal = {Bioinformatics},
  volume  = {34},
  number  = {13},
  pages   = {i438--i446},
  year    = {2018},
  doi     = {10.1093/bioinformatics/bty246},
}

Failed to install S3M

When we run the following command:

$ sudo apt install s3m-latest.deb

It gave me the error:

Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
E: Unable to locate package s3m-latest.deb
E: Couldn't find any package by glob 's3m-latest.deb'

So, we installed the s3m-latest.deb externally and install it.
Now we run the the following command:

s3m -i data/example/synthetic.csv -m 15 -o results/example.json

But, it gave me the error

s3m: error while loading shared libraries: libboost_log.so.1.58.0: cannot open shared object file: No such file or directory

So, we go to the advanced build instructions to solve the above error. we follow the Building S3M from source instructions. We installed cmake, libboost-all-dev, build-essential. After that we create the build directory and run the following command inside the build directory

cmake ../code/cpp/

And the command run successfully. After that, we run the make command but it gave the error

$ make
Consolidate compiler generated dependencies of target s3m
[  4%] Building CXX object CMakeFiles/s3m.dir/source/TimeSeries.cc.o
In file included from /home/mohsin-siddiqui/Desktop/S3M/code/cpp/source/TimeSeries.cc:2:
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh: In function ‘T convert(const S&, bool&)’:
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:109:21: error: ‘numeric_limits’ is not a member of ‘std’
  109 |       result = std::numeric_limits<T>::infinity();
      |                     ^~~~~~~~~~~~~~
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:109:37: error: expected primary-expression before ‘>’ token
  109 |       result = std::numeric_limits<T>::infinity();
      |                                     ^
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:109:40: error: ‘::infinity’ has not been declared
  109 |       result = std::numeric_limits<T>::infinity();
      |                                        ^~~~~~~~
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:111:22: error: ‘numeric_limits’ is not a member of ‘std’
  111 |       result = -std::numeric_limits<T>::infinity();
      |                      ^~~~~~~~~~~~~~
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:111:38: error: expected primary-expression before ‘>’ token
  111 |       result = -std::numeric_limits<T>::infinity();
      |                                      ^
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:111:41: error: ‘::infinity’ has not been declared
  111 |       result = -std::numeric_limits<T>::infinity();
      |                                         ^~~~~~~~
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:113:21: error: ‘numeric_limits’ is not a member of ‘std’
  113 |       result = std::numeric_limits<T>::quiet_NaN();
      |                     ^~~~~~~~~~~~~~
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:113:37: error: expected primary-expression before ‘>’ token
  113 |       result = std::numeric_limits<T>::quiet_NaN();
      |                                     ^
/home/mohsin-siddiqui/Desktop/S3M/code/cpp/include/Utilities.hh:113:40: error: ‘::quiet_NaN’ has not been declared
  113 |       result = std::numeric_limits<T>::quiet_NaN();
      |                                        ^~~~~~~~~
make[2]: *** [CMakeFiles/s3m.dir/build.make:188: CMakeFiles/s3m.dir/source/TimeSeries.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:102: CMakeFiles/s3m.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

So, we have tried another way that is Building with Docker. we build the docker image by the following command,

docker build -t s3m_container -f code/cpp/packages/DOCKER/Dockerfile .

But it gives the pip version error.

borgwardtlab / s3m Goto Github PK

s3m's Introduction

S3M — Statistically Significant Shapelet Mining

Installation

Example

Help

Contributors

Citation

s3m's People

Contributors

Stargazers

Watchers

Forkers

s3m's Issues

Can this package be conducted in R

Provide bootstrap script for Linux and Mac OS X

Failed to install S3M

PKGBUILD for AUR "make -jN"

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent