Python Active-subspaces Utility Library
Python Active-subspaces Utility Library - Published in JOSS (2016)
Science Score: 95.0%
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Published in Journal of Open Source Software
Scientific Fields
Repository
Python Active-subspaces Utility Library
Basic Info
Statistics
- Stars: 74
- Watchers: 21
- Forks: 51
- Open Issues: 6
- Releases: 1
Metadata Files
README.md
Description
Active subspaces are part of an emerging set of tools for discovering low-dimensional structure in a given function of several variables. Interesting applications arise in deterministic computer simulations of complex physical systems, where the function is the map from the physical model's input parameters to its output quantity of interest. The active subspace is the span of particular directions in the input parameter space; perturbing the inputs along these active directions changes the output more, on average, than perturbing the inputs orthogonally to the active directions. By focusing on the model's response along active directions and ignoring the relatively inactive directions, we reduce the dimension for parameter studies---such as optimization and integration---that are essential to engineering tasks such as design and uncertainty quantification.
This library contains Python tools for discovering and exploiting a given model's active subspace. The user may provide a function handle to a complex model or its gradient with respect to the input parameters. Alternatively, the user may provide a set of input/output pairs from a previously executed set of runs (e.g., a Monte Carlo or Latin hypercube study). Essential classes and methods are documented; see documentation below. We also provide a set of Jupyter notebooks that demonstrate how to apply the code to a given model.
To see active subspace in action on real science and engineering applications, see the Active Subspaces Data Sets repository, which contains several Jupyter notebooks applying the methods to study input/output relationships in complex models.
Testing
We are using Travis CI for continuous integration testing. You can check out the current status here.
To run tests locally:
```bash
python test.py ```
Requirements and Dependencies
- numpy
- scipy, >= 0.15.0
- matplotlib
- Gurobi is an optional dependency. The same functionality is accomplished with SciPy's optimize package, albeit less accurately (particularly in the quadratic programs).
If you wish to use Gurobi, you will need to install it separately by following the instructions contained in their quick-start guides for Windows, Linux, or Mac. To test your installation of Gurobi, start a python interpreter and execute the command import gurobipy. If there is no import exception, the active subspaces library will be able to use Gurobi.
We had some initial trouble getting the Gurobi Python interface working with Enthought Python; Gurobi formally supports as subset of Python distributions, and Enthought is not one of them. However, we were able to get the interface working by following instructions in this thread.
Installation
To install the active subspaces package, open the terminal/command line and clone the repository with the command
bash
git clone https://github.com/paulcon/active_subspaces.git
Navigate into the active_subspaces folder (where the setup.py file is located) and run the command
bash
python setup.py install
You should now be able to import the active subspaces library in Python scripts and interpreters with the command import active_subspaces.
This method was tested on Windows 7 Professional, and Ubuntu 14.04 LTS, and Mac OSX El Capitan with the Enthought Python distribution (Python 2.7.11, NumPy 1.10.4, SciPy 0.17.0, and matplotlib 1.5.1).
Usage
For detailed examples of usage and results, see the Jupyter notebooks contained in the tutorials directory, the active subspaces website, and the Active Subspaces Data Sets repo.
The core class is the Subspaces class contained in the subspaces.py file. An instance of this class can compute the active subspace with a variety of methods that take either an array of gradients or input/output pairs. It contains the estimated eigenvalues (and bootstrap ranges), subspace errors (and bootstrap ranges), eigenvalues, and an array of the eigenvectors defining the active subspace. The utils/plotters.py file contains functions to plot these quantities and produce summary plots that show model output against the first 1 or 2 active variables. The utils/response_surfaces.py file contains classes for polynomial and radial-basis approximations that can be trained with input/output pairs. Both classes can predict the value and gradient at input points and have a coefficient of determination (R-squared) value that measures goodness-of-fit. The integrals.py and optimizers.py files contain functions for integrating and optimizing functions of the active variables; these rely on classes from the domains.py file.
Documentation
Documentation can be found on ReadTheDocs.
Community Guidelines
To contribute to this project, please follow these steps. Thanks to Marco Tezzele for providing this helpful template.
Submitting a patch
- Open a new issue describing the bug to fix or feature to add. Even if you think it's relatively minor, it's helpful to know what people are working on.
- Follow the normal process of forking the project, and set up a new branch to work in. It's important that each group of changes be done in separate branches to ensure that a pull request only includes the commits related to that bug or feature.
- Significant changes should be accompanied by tests. The project already has good test coverage, so look at some of the existing tests if you're unsure how to go about it.
- Push the commits to your fork and submit a pull request. Please, remember to rebase properly in order to maintain a clean, linear git history.
If you have questions or feedback, contact Paul Constantine.
Acknowledgments
This material is based upon work supported by the U.S. Department of Energy Office of Science, Office of Advanced Scientific Computing Research, Applied Mathematics program under Award Number DE-SC-0011077.
Owner
- Name: Paul Constantine
- Login: paulcon
- Kind: user
- Location: San Francisco
- Company: University of Colorado
- Website: http://paulconstantine.net/
- Repositories: 12
- Profile: https://github.com/paulcon
JOSS Publication
Python Active-subspaces Utility Library
Authors
Colorado School of Mines, Golden, CO
Colorado School of Mines, Golden, CO
Colorado School of Mines, Golden, CO
Colorado School of Mines, Golden, CO
University of Colorado Boulder, Boulder, CO
None
Editor
Kyle Niemeyer
Tags
python active subspaces dimension reduction uncertainty quantification sensitivity analysis surrogate modelingGitHub Events
Total
- Watch event: 6
- Fork event: 4
Last Year
- Watch event: 6
- Fork event: 4
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Paul Constantine | p****e@g****m | 190 |
| ryan-kelley-howard | r****d@m****u | 56 |
| Les Fletcher | l****r@g****m | 39 |
| zgrey | z****y@m****u | 7 |
| Paul M Diaz | p****z@m****u | 6 |
| Paul | p****z@m****u | 5 |
| Andrew Glaws | a****s@m****u | 4 |
| Marco Tezzele | m****z@g****m | 3 |
| Chris Maes | c****s@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 6
- Total pull requests: 47
- Average time to close issues: about 1 month
- Average time to close pull requests: 8 days
- Total issue authors: 5
- Total pull request authors: 13
- Average comments per issue: 0.5
- Average comments per pull request: 0.34
- Merged pull requests: 32
- 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
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- hmcfletch (1)
- HARVELIN (1)
- milesabarr (1)
- mathematicalmichael (1)
Pull Request Authors
- ryan-kelley-howard (19)
- jeffrey-hokanson (4)
- PaulMDiaz (4)
- hmcfletch (4)
- ConnectedSystems (3)
- mtezzele (3)
- aglaws (2)
- paulcon (2)
- zgrey (2)
- jiweiqi (1)
- aerialhedgehog (1)
- mathematicalmichael (1)
- cmaes (1)
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Packages
- Total packages: 1
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Total downloads:
- pypi 11 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: active-subspaces
Tools to apply active subspaces to analyze their models and data.
- Homepage: https://github.com/paulcon/active_subspaces
- Documentation: https://active-subspaces.readthedocs.io/
- License: MIT
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Latest release: 0.1.1
published over 2 years ago
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Maintainers (1)
Dependencies
- matplotlib *
- numpy *
- scipy >=0.15.0
- matplotlib *
- numpy *
- scipy *