Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary
Keywords
Repository
ugtm: a Python package for Generative Topographic Mapping
Basic Info
- Host: GitHub
- Owner: hagax8
- License: mit
- Language: HTML
- Default Branch: master
- Homepage: https://ugtm.readthedocs.io/en/latest/overview.html
- Size: 12.2 MB
Statistics
- Stars: 51
- Watchers: 4
- Forks: 9
- Open Issues: 4
- Releases: 0
Topics
Metadata Files
README.md
ugtm: Generative Topographic Mapping with Python.
Link to the package documentation: http://ugtm.readthedocs.io/en/latest/
GTM (Generative Topographic Mapping) is a dimensionality reduction algorithm (as t-SNE, LLE, etc) created by Bishop et al. (https://www.microsoft.com/en-us/research/wp-content/uploads/1998/01/bishop-gtm-ncomp-98.pdf) and a probabilistic counterpart of Kohonen maps.
ugtm is a python package implementing GTM and GTM prediction algorithms. ugtm contains the core functions and runGTM.py (in bin directory) is an easy-to-use program. The kernel version of the algorithm (kGTM) is also implemented. You can also generate regression or classification maps, or evaluate the predictive accuracy (classification) or RMSE/R2 (regression) in repeated cross-validation experiments.
Install ugtm
Simple installation: - pip install ugtm
If you get error messages, try upgrading packages: - pip install --upgrade pip numpy scikit-learn matplotlib scipy mpld3 jinja2 - sudo pip install --upgrade pip numpy scikit-learn matplotlib scipy mpld3 jinja2
If you have problems with anaconda packages, try to create a virtual env called "p2" for python 2.7.14: - conda create -n p2 python=2.7.14 numpy=1.14.5 scikit-learn=0.20 matplotlib=2.2.2 scipy=0.19.1 mpld3=0.3 jinja2=2.10 - source activate p2 - pip install ugtm
Or p3 for python 3.6.6: - conda create -n p3 python=3.6.6 numpy=1.14.5 scikit-learn=0.20 matplotlib=2.2.2 scipy=0.19.1 mpld3=0.3 jinja2=2.10 - source activate p3 - pip install ugtm
Documentation
Prerequisites
Python 2.7 or + (tested on Python 3.4.6 and Python 2.7.14)
and following packages: - scikit-learn>=0.20 - numpy>=1.14.5 - matplotlib>=2.2.2 - scipy>=0.19.1 - mpld3>=0.3 - jinja2>=2.10
Citing ugtm
Cite ugtm version and the following paper:
@ARTICLE{Gaspar2018-qt,
title = "ugtm: A Python Package for Data Modeling and Visualization Using
Generative Topographic Mapping",
author = "Gaspar, H{\'e}l{\'e}na Alexandra",
journal = "Journal of Open Research Software",
volume = 6,
pages = "215",
month = dec,
year = 2018
}
Principal author / admin
Héléna A. Gaspar, hagax8@gmail.com, https://github.com/hagax8
Owner
- Name: Héléna A. Gaspar
- Login: hagax8
- Kind: user
- Location: London
- Website: lovingscience.com
- Repositories: 10
- Profile: https://github.com/hagax8
Cheminformatician + musician. PhD in Cheminformatics from the Université de Strasbourg.
GitHub Events
Total
- Watch event: 5
Last Year
- Watch event: 5
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Héléna A. Gaspar | h****8@g****m | 77 |
| git | g****t@g****m | 36 |
| EngineerCoding | E****g@h****l | 4 |
| Héléna Gaspar | h****r@b****i | 4 |
| hagax8 | k****6@l****e | 3 |
| sshojiro | s****a@g****m | 2 |
| EngineerCoding | E****g@h****l | 1 |
| Héléna Gaspar | h****8@M****l | 1 |
| Philippe Rivière | f****l@r****t | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 7
- Total pull requests: 7
- Average time to close issues: 13 days
- Average time to close pull requests: 19 days
- Total issue authors: 5
- Total pull request authors: 4
- Average comments per issue: 1.0
- Average comments per pull request: 1.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- hagax8 (3)
- UnixJunkie (1)
- kirtov (1)
- EngineerCoding (1)
- stsouko (1)
Pull Request Authors
- EngineerCoding (3)
- hagax8 (2)
- sshojiro (1)
- Fil (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 121 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 7
- Total maintainers: 1
pypi.org: ugtm
Generative Topographic Mapping (GTM) for python, GTM classification and GTM regression
- Homepage: http://github.com/hagax8/ugtm
- Documentation: https://ugtm.readthedocs.io/
- License: MIT
-
Latest release: 2.0.0
published over 7 years ago
Rankings
Maintainers (1)
Dependencies
- altair >=2.2.2
- contextlib2 *
- docutils *
- jinja2 >=2.10
- matplotlib >=2.2.2
- mpld3 >=0.3
- numpy >=1.14.5
- scikit-learn >=0.20
- scipy >=0.19.1
- jinja2 >=2.10.0
- matplotlib >=2.2.2
- mpld3 >=0.3
- numpy >=1.14.5
- scikit-learn >=0.20.0
- scipy >=0.19.1
- altair >=2.2.2
- contextlib2 *
- jinja2 >=2.10.0
- matplotlib >=2.2.2
- mpld3 >=0.3
- numpy >=1.14.5
- scikit-learn >=0.20.0
- scipy >=0.19.1