# aind-dynamic-foraging-models
[](LICENSE)
[](https://github.com/semantic-release/semantic-release)
AIND library for generative (RL) and descriptive (logistic regression) models of dynamic foraging tasks.
User documentation available on [readthedocs](https://aind-dynamic-foraging-models.readthedocs.io/).
## Reinforcement Learning (RL) models with Maximum Likelihood Estimation (MLE) fitting
### Overview
RL agents that can perform any dynamic foraging task in [aind-behavior-gym](https://github.com/AllenNeuralDynamics/aind-behavior-gym) and can fit behavior using MLE.
### Code structure
- To add more generative models, please subclass [`DynamicForagingAgentMLEBase`](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/11c858f93f67a0699ed23892364f3f51b08eab37/src/aind_dynamic_foraging_models/generative_model/base.py#L25C7-L25C34).
### Implemented foragers
- [`ForagerQLearning`](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/f9ab39bbdc2cbea350e5a8f11d3f935d6674e08b/src/aind_dynamic_foraging_models/generative_model/forager_q_learning.py): Simple Q-learning agents that incrementally update Q-values.
- Available `agent_kwargs`:
```python
number_of_learning_rate: Literal[1, 2] = 2,
number_of_forget_rate: Literal[0, 1] = 1,
choice_kernel: Literal["none", "one_step", "full"] = "none",
action_selection: Literal["softmax", "epsilon-greedy"] = "softmax",
```
- [`ForagerLossCounting`](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/f9ab39bbdc2cbea350e5a8f11d3f935d6674e08b/src/aind_dynamic_foraging_models/generative_model/forager_loss_counting.py): Loss counting agents with probabilistic `loss_count_threshold`.
- Available `agent_kwargs`:
```python
win_stay_lose_switch: Literal[False, True] = False,
choice_kernel: Literal["none", "one_step", "full"] = "none",
```
[Here is the full list](https://foraging-behavior-browser.allenneuraldynamics-test.org/RL_model_playground#all-available-foragers) of available foragers:
### Usage
- [Jupyter notebook](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/main/notebook/demo_RL_agents.ipynb)
- See also [these unittest functions](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/tree/main/tests).
### RL model playground
Play with the generative models [here](https://foraging-behavior-browser.allenneuraldynamics-test.org/RL_model_playground).
## Logistic regression
See [this demo notebook.](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/main/notebook/demo_logistic_regression.ipynb)
### Choosing logistic regression models
#### Su 2022
$$
logit(p(c_r)) \sim RewardedChoice+UnrewardedChoice
$$
#### Bari 2019
$$
logit(p(c_r)) \sim RewardedChoice+Choice
$$
#### Hattori 2019
$$
logit(p(c_r)) \sim RewardedChoice+UnrewardedChoice+Choice
$$
#### Miller 2021
$$
logit(p(c_r)) \sim Choice + Reward+ Choice*Reward
$$
#### Encodings
- Ignored trials are removed
| choice | reward | Choice | Reward | RewardedChoice | UnrewardedChoice | Choice * Reward |
| --- | --- | --- | --- | --- | --- | --- |
| L | yes | -1 | 1 | -1 | 0 | -1 |
| L | no | -1 | -1 | 0 | -1 | 1 |
| R | yes | 1 | 1 | 1 | 0 | 1 |
| L | yes | -1 | 1 | -1 | 0 | -1 |
| R | no | 1 | -1 | 0 | 1 | -1 |
| R | yes | 1 | 1 | 1 | 0 | 1 |
| L | no | -1 | -1 | 0 | -1 | 1 |
Some observations:
1. $RewardedChoice$ and $UnrewardedChoice$ are orthogonal
2. $Choice = RewardedChoice + UnrewardedChoice$
3. $Choice * Reward = RewardedChoice - UnrewardedChoice$
#### Comparison
| | Su 2022 | Bari 2019 | Hattori 2019 | Miller 2021 |
| --- | --- | --- | --- | --- |
| Equivalent to | RewC + UnrC | RewC + (RewC + UnrC) | RewC + UnrC + (RewC + UnrC) | (RewC + UnrC) + (RewC - UnrC) + Rew |
| Severity of multicollinearity | Not at all | Medium | Severe | Slight |
| Interpretation | Like a RL model with different learning rates on reward and unrewarded trials. | Like a RL model that only updates on rewarded trials, plus a choice kernel (tendency to repeat previous choices). | Like a RL model that has different learning rates on reward and unrewarded trials, plus a choice kernel (the full RL model from the same paper). | Like a RL model that has symmetric learning rates for rewarded and unrewarded trials, plus a choice kernel. However, the $Reward $ term seems to be a strawman assumption, as it means “if I get reward on any side, I’ll choose the right side more”, which doesn’t make much sense. |
| Conclusion | Probably the best | Okay | Not good due to the severe multicollinearity | Good |
### Regularization and optimization
The choice of optimizer depends on the penality term, as listed [here](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html#sklearn.linear_model.LogisticRegression).
- `lbfgs` - [`l2`, None]
- `liblinear` - [`l1`, `l2`]
- `newton-cg` - [`l2`, None]
- `newton-cholesky` - [`l2`, None]
- `sag` - [`l2`, None]
- `saga` - [`elasticnet`, `l1`, `l2`, None]
## See also
- Foraging model simulation, model recovery, etc.: https://github.com/hanhou/Dynamic-Foraging
## Installation
To install the software, run
```bash
pip install aind-dynamic-foraging-models
```
To develop the code, clone the repo to your local machine, and run
```bash
pip install -e .[dev]
```
## Contributing
### Linters and testing
There are several libraries used to run linters, check documentation, and run tests.
- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
```bash
coverage run -m unittest discover && coverage report
```
- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
```bash
interrogate .
```
- Use **flake8** to check that code is up to standards (no unused imports, etc.):
```bash
flake8 .
```
- Use **black** to automatically format the code into PEP standards:
```bash
black .
```
- Use **isort** to automatically sort import statements:
```bash
isort .
```
### Pull requests
For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
```text
<type>(<scope>): <short summary>
```
where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
- **docs**: Documentation only changes
- **feat**: A new feature
- **fix**: A bugfix
- **perf**: A code change that improves performance
- **refactor**: A code change that neither fixes a bug nor adds a feature
- **test**: Adding missing tests or correcting existing tests
### Semantic Release
The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
| Commit message | Release type |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
### Documentation
To generate the rst files source files for documentation, run
```bash
sphinx-apidoc -o doc_template/source/ src
```
Then to create the documentation HTML files, run
```bash
sphinx-build -b html doc_template/source/ doc_template/build/html
```
More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
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"description": "# aind-dynamic-foraging-models\n\n[](LICENSE)\n\n[](https://github.com/semantic-release/semantic-release)\n\n\n\n\nAIND library for generative (RL) and descriptive (logistic regression) models of dynamic foraging tasks.\n\nUser documentation available on [readthedocs](https://aind-dynamic-foraging-models.readthedocs.io/).\n\n## Reinforcement Learning (RL) models with Maximum Likelihood Estimation (MLE) fitting\n\n### Overview\nRL agents that can perform any dynamic foraging task in [aind-behavior-gym](https://github.com/AllenNeuralDynamics/aind-behavior-gym) and can fit behavior using MLE.\n\n\n\n### Code structure\n\n- To add more generative models, please subclass [`DynamicForagingAgentMLEBase`](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/11c858f93f67a0699ed23892364f3f51b08eab37/src/aind_dynamic_foraging_models/generative_model/base.py#L25C7-L25C34).\n\n### Implemented foragers\n- [`ForagerQLearning`](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/f9ab39bbdc2cbea350e5a8f11d3f935d6674e08b/src/aind_dynamic_foraging_models/generative_model/forager_q_learning.py): Simple Q-learning agents that incrementally update Q-values.\n - Available `agent_kwargs`:\n ```python\n number_of_learning_rate: Literal[1, 2] = 2,\n number_of_forget_rate: Literal[0, 1] = 1,\n choice_kernel: Literal[\"none\", \"one_step\", \"full\"] = \"none\",\n action_selection: Literal[\"softmax\", \"epsilon-greedy\"] = \"softmax\",\n ```\n- [`ForagerLossCounting`](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/f9ab39bbdc2cbea350e5a8f11d3f935d6674e08b/src/aind_dynamic_foraging_models/generative_model/forager_loss_counting.py): Loss counting agents with probabilistic `loss_count_threshold`.\n - Available `agent_kwargs`:\n ```python\n win_stay_lose_switch: Literal[False, True] = False,\n choice_kernel: Literal[\"none\", \"one_step\", \"full\"] = \"none\",\n ```\n[Here is the full list](https://foraging-behavior-browser.allenneuraldynamics-test.org/RL_model_playground#all-available-foragers) of available foragers:\n\n\n\n\n\n\n### Usage\n- [Jupyter notebook](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/main/notebook/demo_RL_agents.ipynb)\n- See also [these unittest functions](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/tree/main/tests).\n\n### RL model playground\n\nPlay with the generative models [here](https://foraging-behavior-browser.allenneuraldynamics-test.org/RL_model_playground).\n\n\n\n\n## Logistic regression\nSee [this demo notebook.](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models/blob/main/notebook/demo_logistic_regression.ipynb)\n\n### Choosing logistic regression models\n\n#### Su 2022\n\n\n\n$$\nlogit(p(c_r)) \\sim RewardedChoice+UnrewardedChoice\n$$\n\n#### Bari 2019\n\n\n\n\n\n$$\nlogit(p(c_r)) \\sim RewardedChoice+Choice\n$$\n\n#### Hattori 2019\n\n\n\n$$\nlogit(p(c_r)) \\sim RewardedChoice+UnrewardedChoice+Choice\n$$\n\n#### Miller 2021\n\n\n\n$$\nlogit(p(c_r)) \\sim Choice + Reward+ Choice*Reward\n$$\n\n#### Encodings\n\n- Ignored trials are removed\n\n| choice | reward | Choice | Reward | RewardedChoice | UnrewardedChoice | Choice * Reward |\n| --- | --- | --- | --- | --- | --- | --- |\n| L | yes | -1 | 1 | -1 | 0 | -1 |\n| L | no | -1 | -1 | 0 | -1 | 1 |\n| R | yes | 1 | 1 | 1 | 0 | 1 |\n| L | yes | -1 | 1 | -1 | 0 | -1 |\n| R | no | 1 | -1 | 0 | 1 | -1 |\n| R | yes | 1 | 1 | 1 | 0 | 1 |\n| L | no | -1 | -1 | 0 | -1 | 1 |\n\nSome observations:\n\n1. $RewardedChoice$ and $UnrewardedChoice$ are orthogonal\n2. $Choice = RewardedChoice + UnrewardedChoice$\n3. $Choice * Reward = RewardedChoice - UnrewardedChoice$\n\n#### Comparison\n\n| | Su 2022 | Bari 2019 | Hattori 2019 | Miller 2021 |\n| --- | --- | --- | --- | --- |\n| Equivalent to | RewC + UnrC | RewC + (RewC + UnrC) | RewC + UnrC + (RewC + UnrC) | (RewC + UnrC) + (RewC - UnrC) + Rew |\n| Severity of multicollinearity | Not at all | Medium | Severe | Slight |\n| Interpretation | Like a RL model with different learning rates on reward and unrewarded trials. | Like a RL model that only updates on rewarded trials, plus a choice kernel (tendency to repeat previous choices). | Like a RL model that has different learning rates on reward and unrewarded trials, plus a choice kernel (the full RL model from the same paper). | Like a RL model that has symmetric learning rates for rewarded and unrewarded trials, plus a choice kernel. However, the $Reward $ term seems to be a strawman assumption, as it means \u201cif I get reward on any side, I\u2019ll choose the right side more\u201d, which doesn\u2019t make much sense. |\n| Conclusion | Probably the best | Okay | Not good due to the severe multicollinearity | Good |\n\n\n### Regularization and optimization\nThe choice of optimizer depends on the penality term, as listed [here](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html#sklearn.linear_model.LogisticRegression).\n\n- `lbfgs` - [`l2`, None]\n- `liblinear` - [`l1`, `l2`]\n- `newton-cg` - [`l2`, None]\n- `newton-cholesky` - [`l2`, None]\n- `sag` - [`l2`, None]\n- `saga` - [`elasticnet`, `l1`, `l2`, None]\n\n## See also\n- Foraging model simulation, model recovery, etc.: https://github.com/hanhou/Dynamic-Foraging\n\n## Installation\nTo install the software, run\n```bash\npip install aind-dynamic-foraging-models\n```\n\nTo develop the code, clone the repo to your local machine, and run\n```bash\npip install -e .[dev]\n```\n\n## Contributing\n\n### Linters and testing\n\nThere are several libraries used to run linters, check documentation, and run tests.\n\n- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:\n\n```bash\ncoverage run -m unittest discover && coverage report\n```\n\n- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:\n\n```bash\ninterrogate .\n```\n\n- Use **flake8** to check that code is up to standards (no unused imports, etc.):\n```bash\nflake8 .\n```\n\n- Use **black** to automatically format the code into PEP standards:\n```bash\nblack .\n```\n\n- Use **isort** to automatically sort import statements:\n```bash\nisort .\n```\n\n### Pull requests\n\nFor internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:\n```text\n<type>(<scope>): <short summary>\n```\n\nwhere scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:\n\n- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)\n- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)\n- **docs**: Documentation only changes\n- **feat**: A new feature\n- **fix**: A bugfix\n- **perf**: A code change that improves performance\n- **refactor**: A code change that neither fixes a bug nor adds a feature\n- **test**: Adding missing tests or correcting existing tests\n\n### Semantic Release\n\nThe table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):\n\n| Commit message | Release type |\n| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |\n| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |\n| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |\n| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |\n\n### Documentation\nTo generate the rst files source files for documentation, run\n```bash\nsphinx-apidoc -o doc_template/source/ src \n```\nThen to create the documentation HTML files, run\n```bash\nsphinx-build -b html doc_template/source/ doc_template/build/html\n```\nMore info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).\n",
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