Name | annubes JSON |
Version |
0.1.1
JSON |
| download |
home_page | None |
Summary | ANNUBeS: training Artificial Neural Networks to Uncover Behavioral Strategies in neuroscience |
upload_time | 2024-05-02 09:20:06 |
maintainer | None |
docs_url | None |
author | None |
requires_python | >=3.11 |
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keywords |
neuroscience
neural networks
|
VCS |
|
bugtrack_url |
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requirements |
No requirements were recorded.
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Travis-CI |
No Travis.
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coveralls test coverage |
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# ANNUBeS
| Badges | |
| :------------: | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| **fairness** | [![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8861/badge)](https://www.bestpractices.dev/projects/8861) [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) |
| **package** | [![PyPI version](https://badge.fury.io/py/annubes.svg)](https://badge.fury.io/py/annubes) |
| **docs** | [![Documentation](https://img.shields.io/badge/docs-mkdocs-259482)](https://annubs.github.io/annubes/latest/) [![RSD](https://img.shields.io/badge/rsd-annubes-00a3e3.svg)](https://research-software-directory.org/projects/annubes) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11098460.svg)](https://doi.org/10.5281/zenodo.11098460) |
| **tests** | [![build](https://github.com/ANNUBS/annubes/actions/workflows/build.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/build.yml) [![sonarcloud](https://github.com/ANNUBS/annubes/actions/workflows/sonarcloud.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/sonarcloud.yml) [![markdown-links](https://github.com/ANNUBS/annubes/actions/workflows/markdown-links.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/markdown-links.yml) [![cffconvert](https://github.com/ANNUBS/annubes/actions/workflows/cffconvert.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/cffconvert.yml) [![linting](https://github.com/ANNUBS/annubes/actions/workflows/linting.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/linting.yml) [![static-typing](https://github.com/ANNUBS/annubes/actions/workflows/static-typing.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/static-typing.yml) [![workflow scq badge](https://sonarcloud.io/api/project_badges/measure?project=ANNUBS_annubes&metric=alert_status)](https://sonarcloud.io/dashboard?id=ANNUBS_annubes) [![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=ANNUBS_annubes&metric=coverage)](https://sonarcloud.io/dashboard?id=ANNUBS_annubes) |
| **running on** | [![ubuntu](https://img.shields.io/badge/ubuntu-latest-8A2BE2?style=plastic)](https://github.com/actions/runner-images?tab=readme-ov-file#available-images) [![mac](https://img.shields.io/badge/macos-latest-8A2BE2?style=plastic)](https://github.com/actions/runner-images?tab=readme-ov-file#available-images) [![win](https://img.shields.io/badge/windows-latest-8A2BE2?style=plastic)](https://github.com/actions/runner-images?tab=readme-ov-file#available-images) [![Python](https://img.shields.io/badge/python-3.11-blue.svg)](https://www.python.org/downloads/release/python-3110/) [![Python](https://img.shields.io/badge/python-3.12-blue.svg)](https://www.python.org/downloads/release/python-3120/) |
| **license** | [![github license badge](https://img.shields.io/github/license/ANNUBS/annubes)](https://github.com/ANNUBS/annubes?tab=Apache-2.0-1-ov-file) |
## Overview
The use of animals in neuroscience research is a fundamental tool to understand the inner workings of the brain during perception and cognition in health and disease. Neuroscientists train animals, often rodents, in behavioral tasks over several months, however training protocols are sometimes not well defined and this leads to delays in research, additional costs, or the need of more animals. Finding strategies to optimize animal training in safe and ethical ways is therefore of crucial importance in neuroscience.
ANNUBeS, which stays for _Artificial Neural Networks to Uncover Behavioral Strategies_, is a deep learning framework meant to generate synthetic data and train on them neural networks aimed at developing and evaluating animals' training protocols in neuroscience. The package gives the users the possibility to generate behavioral data in a very flexible way, that can be used to train neural networks in the same way that animals are trained, and study whether the developed models can predict the behavior of the animals. The ultimate goal of the framework is to lead researchers to more efficient training protocols, thus improving neuroscience practices.
📚 [Documentation](https://annubs.github.io/annubes/latest/)
🐛 Bugs reports and ⭐ features requests [here](https://github.com/ANNUBS/annubes/issues)
🔧 [Pull Requests](https://github.com/ANNUBS/annubes/pulls)
For more details about how to contribute, see the [contribution guidelines](CONTRIBUTING.md).
❗❗ DISCLAIMER ❗❗
Please note that this software is currently in its early stages of development. As such, some features may not work exactly as intended or envisioned yet. We appreciate your patience and understanding. If you encounter any issues or have suggestions for improvement, we encourage you to open an issue on our repository. Thank you for your support!
## Table of contents
- [ANNUBeS](#annubes)
- [Overview](#overview)
- [Table of contents](#table-of-contents)
- [Installation](#installation)
- [Repository installation](#repository-installation)
- [Pip installation](#pip-installation)
- [Get started](#get-started)
- [Generate synthetic data](#generate-synthetic-data)
- [Train neural networks](#train-neural-networks)
- [Contributing](#contributing)
- [Credits](#credits)
- [Package development](#package-development)
## Installation
### Repository installation
We advise to install the package inside a virtual environment (using [conda](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [venv](https://docs.python.org/3/library/venv.html)).
After having created and activated your environment, to install ANNUBeS from GitHub repository, do:
```console
git clone git@github.com:ANNUBS/annubes.git
cd annubes
pip install .
```
### Pip installation
Under development.
## Get started
### Generate synthetic data
The `Task` data class can be used for defining a behavioral task, and many parameters can be set. The configuration of the trials that can appear during a session is given by a dictionary representing the ratio of the different trials within the task (`session`). Trials with a single modality (e.g., a visual trial) must be represented by single characters, while trials with multiple modalities (e.g., an audiovisual trial) are represented by the character combination of those trials. The probability of catch trials (denoted by X) in the session can be set using the `catch_prob` parameter.
```python
from annubes.task import Task
task = Task(name='example_task',
session={"v":0.5, "a":0.5},
stim_intensities=[0.7, 0.9],
stim_time=2000,
catch_prob=0.3)
```
For more details about the `Task` class parameters, see the [API Documentation](https://annubs.github.io/annubes/latest/api/task/#annubes.task.Task).
Then, trials can be generated:
```python
NTRIALS = 10
trials = task.generate_trials(NTRIALS)
```
And plotted:
```python
task.plot_trials(NTRIALS)
```
<p align="center">
<img src="https://github.com/ANNUBS/annubes/blob/ead1437b7ee6ad6998ce2b3653fd0b3b3d875e25/docs/example_trials_plot.png?raw=true" width="700">
</p>
### Train neural networks
This functionality is still under development.
## Contributing
If you want to contribute to the development of annubes,
have a look at the [contribution guidelines](CONTRIBUTING.md).
## Credits
This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [NLeSC/python-template](https://github.com/NLeSC/python-template).
## Package development
If you're looking for developer documentation, go [here](https://github.com/ANNUBS/annubes/blob/main/README.dev.md).
Raw data
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"keywords": "neuroscience, neural networks",
"author": null,
"author_email": "Giulia Crocioni <g.crocioni@esciencecenter.nl>, Dani Bodor <d.bodor@esciencecenter.nl>",
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"description": "# ANNUBeS\n\n| Badges | |\n| :------------: | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |\n| **fairness** | [![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8861/badge)](https://www.bestpractices.dev/projects/8861) [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) |\n| **package** | [![PyPI version](https://badge.fury.io/py/annubes.svg)](https://badge.fury.io/py/annubes) |\n| **docs** | [![Documentation](https://img.shields.io/badge/docs-mkdocs-259482)](https://annubs.github.io/annubes/latest/) [![RSD](https://img.shields.io/badge/rsd-annubes-00a3e3.svg)](https://research-software-directory.org/projects/annubes) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11098460.svg)](https://doi.org/10.5281/zenodo.11098460) |\n| **tests** | [![build](https://github.com/ANNUBS/annubes/actions/workflows/build.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/build.yml) [![sonarcloud](https://github.com/ANNUBS/annubes/actions/workflows/sonarcloud.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/sonarcloud.yml) [![markdown-links](https://github.com/ANNUBS/annubes/actions/workflows/markdown-links.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/markdown-links.yml) [![cffconvert](https://github.com/ANNUBS/annubes/actions/workflows/cffconvert.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/cffconvert.yml) [![linting](https://github.com/ANNUBS/annubes/actions/workflows/linting.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/linting.yml) [![static-typing](https://github.com/ANNUBS/annubes/actions/workflows/static-typing.yml/badge.svg)](https://github.com/ANNUBS/annubes/actions/workflows/static-typing.yml) [![workflow scq badge](https://sonarcloud.io/api/project_badges/measure?project=ANNUBS_annubes&metric=alert_status)](https://sonarcloud.io/dashboard?id=ANNUBS_annubes) [![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=ANNUBS_annubes&metric=coverage)](https://sonarcloud.io/dashboard?id=ANNUBS_annubes) |\n| **running on** | [![ubuntu](https://img.shields.io/badge/ubuntu-latest-8A2BE2?style=plastic)](https://github.com/actions/runner-images?tab=readme-ov-file#available-images) [![mac](https://img.shields.io/badge/macos-latest-8A2BE2?style=plastic)](https://github.com/actions/runner-images?tab=readme-ov-file#available-images) [![win](https://img.shields.io/badge/windows-latest-8A2BE2?style=plastic)](https://github.com/actions/runner-images?tab=readme-ov-file#available-images) [![Python](https://img.shields.io/badge/python-3.11-blue.svg)](https://www.python.org/downloads/release/python-3110/) [![Python](https://img.shields.io/badge/python-3.12-blue.svg)](https://www.python.org/downloads/release/python-3120/) |\n| **license** | [![github license badge](https://img.shields.io/github/license/ANNUBS/annubes)](https://github.com/ANNUBS/annubes?tab=Apache-2.0-1-ov-file) |\n\n## Overview\n\nThe use of animals in neuroscience research is a fundamental tool to understand the inner workings of the brain during perception and cognition in health and disease. Neuroscientists train animals, often rodents, in behavioral tasks over several months, however training protocols are sometimes not well defined and this leads to delays in research, additional costs, or the need of more animals. Finding strategies to optimize animal training in safe and ethical ways is therefore of crucial importance in neuroscience.\n\nANNUBeS, which stays for _Artificial Neural Networks to Uncover Behavioral Strategies_, is a deep learning framework meant to generate synthetic data and train on them neural networks aimed at developing and evaluating animals' training protocols in neuroscience. The package gives the users the possibility to generate behavioral data in a very flexible way, that can be used to train neural networks in the same way that animals are trained, and study whether the developed models can predict the behavior of the animals. The ultimate goal of the framework is to lead researchers to more efficient training protocols, thus improving neuroscience practices.\n\n\ud83d\udcda [Documentation](https://annubs.github.io/annubes/latest/)\n\n\ud83d\udc1b Bugs reports and \u2b50 features requests [here](https://github.com/ANNUBS/annubes/issues)\n\n\ud83d\udd27 [Pull Requests](https://github.com/ANNUBS/annubes/pulls)\n\nFor more details about how to contribute, see the [contribution guidelines](CONTRIBUTING.md).\n\n\u2757\u2757 DISCLAIMER \u2757\u2757\n\nPlease note that this software is currently in its early stages of development. As such, some features may not work exactly as intended or envisioned yet. We appreciate your patience and understanding. If you encounter any issues or have suggestions for improvement, we encourage you to open an issue on our repository. Thank you for your support!\n\n## Table of contents\n\n- [ANNUBeS](#annubes)\n - [Overview](#overview)\n - [Table of contents](#table-of-contents)\n - [Installation](#installation)\n - [Repository installation](#repository-installation)\n - [Pip installation](#pip-installation)\n - [Get started](#get-started)\n - [Generate synthetic data](#generate-synthetic-data)\n - [Train neural networks](#train-neural-networks)\n - [Contributing](#contributing)\n - [Credits](#credits)\n - [Package development](#package-development)\n\n## Installation\n\n### Repository installation\n\nWe advise to install the package inside a virtual environment (using [conda](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [venv](https://docs.python.org/3/library/venv.html)).\n\nAfter having created and activated your environment, to install ANNUBeS from GitHub repository, do:\n\n```console\ngit clone git@github.com:ANNUBS/annubes.git\ncd annubes\npip install .\n```\n\n### Pip installation\n\nUnder development.\n\n## Get started\n\n### Generate synthetic data\n\nThe `Task` data class can be used for defining a behavioral task, and many parameters can be set. The configuration of the trials that can appear during a session is given by a dictionary representing the ratio of the different trials within the task (`session`). Trials with a single modality (e.g., a visual trial) must be represented by single characters, while trials with multiple modalities (e.g., an audiovisual trial) are represented by the character combination of those trials. The probability of catch trials (denoted by X) in the session can be set using the `catch_prob` parameter.\n\n```python\nfrom annubes.task import Task\n\ntask = Task(name='example_task',\n session={\"v\":0.5, \"a\":0.5},\n stim_intensities=[0.7, 0.9],\n stim_time=2000,\n catch_prob=0.3)\n```\n\nFor more details about the `Task` class parameters, see the [API Documentation](https://annubs.github.io/annubes/latest/api/task/#annubes.task.Task).\n\nThen, trials can be generated:\n\n```python\n\nNTRIALS = 10\ntrials = task.generate_trials(NTRIALS)\n```\n\nAnd plotted:\n\n```python\ntask.plot_trials(NTRIALS)\n```\n\n<p align=\"center\">\n <img src=\"https://github.com/ANNUBS/annubes/blob/ead1437b7ee6ad6998ce2b3653fd0b3b3d875e25/docs/example_trials_plot.png?raw=true\" width=\"700\">\n</p>\n\n### Train neural networks\n\nThis functionality is still under development.\n\n## Contributing\n\nIf you want to contribute to the development of annubes,\nhave a look at the [contribution guidelines](CONTRIBUTING.md).\n\n## Credits\n\nThis package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [NLeSC/python-template](https://github.com/NLeSC/python-template).\n\n## Package development\n\nIf you're looking for developer documentation, go [here](https://github.com/ANNUBS/annubes/blob/main/README.dev.md).\n",
"bugtrack_url": null,
"license": " Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. \"License\" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. \"Licensor\" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. \"Legal Entity\" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, \"control\" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. \"You\" (or \"Your\") shall mean an individual or Legal Entity exercising permissions granted by this License. \"Source\" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. \"Object\" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. \"Work\" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). \"Derivative Works\" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. 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