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cl-mds

Cluster-based multidimensional scaling embedding tool for data visualization

https://github.com/mcaroba/cl-mds

Science Score: 67.0%

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    Links to: iop.org
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Repository

Cluster-based multidimensional scaling embedding tool for data visualization

Basic Info
  • Host: GitHub
  • Owner: mcaroba
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 750 KB
Statistics
  • Stars: 3
  • Watchers: 5
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created about 6 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

cl-MDS

Cluster-based multidimensional scaling (cl-MDS) embedding tool for data visualization

cl-MDS is copyright (c) 2018-2022 by Patricia Hernández-León and Miguel A. Caro. It is distributed under the GNU General Public License version 3. cl-MDS is shipped with other codes it relies on for some of its functionalities, but which are not copyright of the cl-MDS authors. They are shipped for the user's convenience in accordance with their own licenses/terms of usage. See the LICENSE.md file for detailed information on this software's license.

-- this documentation file is a work in progress --

Installation

Prerrequisites

  • Numpy
  • Sklearn
  • Scipy
  • A Fortran compiler (successfully tested with gfortran)

Optional python modules (necessary for atomic databases): - ASE - Ovito

Building the libraries

Clone the cl-MDS repository recursively:

git clone --recursive http://github.com/mcaroba/cl-MDS.git

Execute the build script:

cd cl-MDS/
./build_libraries.sh

Add the root directory to your Python path:

echo "export PYTHONPATH=$(pwd):\$PYTHONPATH" >> ~/.bashrc
source ~/.bashrc

Basic Example

Check examples/ folder (we will add more here and there soon). For atomic databases, check examples/tutorial_atoms_file/ folder.

Advanced features

Customized sparse set

Using an existing clustering

Hierarchical clustering

Adding data to an existing cl-MDS map

Attribution

If you use cl-MDS, please provide a link to this GitHub repository and cite:

Patricia Hernández-León, Miguel A. Caro. Cluster-based multidimensional scaling embedding tool for data visualization. Phys. Scr. 99 066004 (2024).

Owner

  • Name: Miguel A. Caro
  • Login: mcaroba
  • Kind: user
  • Location: Espoo, Finland
  • Company: Aalto University

I am a physicist by training, with a PhD in condensed matter. I currently work as Academy of Finland Research Fellow on computational simulation of materials.

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: cl-MDS
message: "If you use this software, please cite it as below."
authors:
  - given-names: Miguel A.
    family-names: Caro
    orcid: 'https://orcid.org/0000-0001-9304-4261'
  - given-names: Patricia
    family-names: Hernández-León
    orcid: 'https://orcid.org/0000-0002-3402-2553'
identifiers:
  - type: url
    value: 'https://github.com/mcaroba/cl-MDS'
repository-code: 'https://github.com/mcaroba/cl-MDS'

GitHub Events

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Last Year
  • Watch event: 2
  • Member event: 1
  • Push event: 11
  • Fork event: 1
  • Create event: 1