ssm-simulators 0.7.2

SSMS is a package collecting simulators and training data generators for a bunch of generative models of interest in the cognitive science / neuroscience and approximate bayesian computation communities

SSMS (Sequential Sampling Model Simulators)

Python Package which collects simulators for Sequential Sampling Models.

Find the package documentation here.

Quick Start

The ssms package serves two purposes.

1. Easy access to fast simulators of sequential sampling models
2. Support infrastructure to construct training data for various approaches to likelihood / posterior amortization

We provide two minimal examples here to illustrate how to use each of the two capabilities.

Install

Let's start with installing the ssms package.

You can do so by typing,

pip install git+https://github.com/AlexanderFengler/ssm_simulators

in your terminal.

Below you find a basic tutorial on how to use the package.

Tutorial

# Import necessary packages
import numpy as np
import pandas as pd
import ssms

Using the Simulators

Let's start with using the basic simulators. You access the main simulators through the ssms.basic_simulators.simulator function.

To get an idea about the models included in ssms, use the config module. The central dictionary with metadata about included models sits in ssms.config.model_config.

# Check included models
list(ssms.config.model_config.keys())[:10]

['ddm',
 'ddm_legacy',
 'angle',
 'weibull',
 'levy',
 'levy_angle',
 'full_ddm',
 'ornstein',
 'ornstein_angle',
 'ddm_sdv']

# Take an example config for a given model
ssms.config.model_config['ddm']

{'name': 'ddm',
 'params': ['v', 'a', 'z', 't'],
 'param_bounds': [[-3.0, 0.3, 0.1, 0.0], [3.0, 2.5, 0.9, 2.0]],
 'boundary': <function ssms.basic_simulators.boundary_functions.constant(t=0)>,
 'n_params': 4,
 'default_params': [0.0, 1.0, 0.5, 0.001],
 'hddm_include': ['z'],
 'nchoices': 2}

Note: The usual structure of these models includes,

• Parameter names ('params')
• Bounds on the parameters ('param_bounds')
• A function that defines a boundary for the respective model ('boundary')
• The number of parameters ('n_params')
• Defaults for the parameters ('default_params')
• The number of choices the process can produce ('nchoices')

The 'hddm_include' key concerns information useful for integration with the hddm python package, which facilitates hierarchical bayesian inference for sequential sampling models. It is not important for the present tutorial.

from ssms.basic_simulators.simulator import simulator
sim_out = simulator(model = 'ddm', 
                    theta = {'v': 0, 
                             'a': 1,
                             'z': 0.5,
                             't': 0.5,
                    },
                    n_samples = 1000)

The output of the simulator is a dictionary with three elements.

1. rts (array)
2. choices (array)
3. metadata (dictionary)

The metadata includes the named parameters, simulator settings, and more.

Using the Training Data Generators

The training data generators sit on top of the simulator function to turn raw simulations into usable training data for training machine learning algorithms aimed at posterior or likelihood armortization.

We will use the data_generator class from ssms.dataset_generators. Initializing the data_generator boils down to supplying two configuration dictionaries.

1. The generator_config, concerns choices as to what kind of training data one wants to generate.
2. The model_config concerns choices with respect to the underlying generative sequential sampling model.

We will consider a basic example here, concerning data generation to prepare for training LANs.

Let's start by peeking at an example generator_config.

ssms.config.data_generator_config['lan']['mlp']

{'output_folder': 'data/lan_mlp/',
 'dgp_list': 'ddm',
 'nbins': 0,
 'n_samples': 100000,
 'n_parameter_sets': 10000,
 'n_parameter_sets_rejected': 100,
 'n_training_samples_by_parameter_set': 1000,
 'max_t': 20.0,
 'delta_t': 0.001,
 'pickleprotocol': 4,
 'n_cpus': 'all',
 'kde_data_mixture_probabilities': [0.8, 0.1, 0.1],
 'simulation_filters': {'mode': 20,
  'choice_cnt': 0,
  'mean_rt': 17,
  'std': 0,
  'mode_cnt_rel': 0.9},
 'negative_rt_cutoff': -66.77497,
 'n_subruns': 10,
 'bin_pointwise': False,
 'separate_response_channels': False}

You usually have to make just few changes to this basic configuration dictionary. An example below.

from copy import deepcopy
# Initialize the generator config (for MLP LANs)
generator_config = deepcopy(ssms.config.data_generator_config['lan']['mlp'])
# Specify generative model (one from the list of included models mentioned above)
generator_config['dgp_list'] = 'angle' 
# Specify number of parameter sets to simulate
generator_config['n_parameter_sets'] = 100 
# Specify how many samples a simulation run should entail
generator_config['n_samples'] = 1000

Now let's define our corresponding model_config.

model_config = ssms.config.model_config['angle']
print(model_config)

{'name': 'angle', 'params': ['v', 'a', 'z', 't', 'theta'], 
'param_bounds': [[-3.0, 0.3, 0.1, 0.001, -0.1], [3.0, 3.0, 0.9, 2.0, 1.3]], 
'boundary': <function angle at 0x11b2a7c10>, 
'n_params': 5, 
'default_params': [0.0, 1.0, 0.5, 0.001, 0.0], 
'hddm_include': ['z', 'theta'], 'nchoices': 2}

We are now ready to initialize a data_generator, after which we can generate training data using the generate_data_training_uniform function, which will use the hypercube defined by our parameter bounds from the model_config to uniformly generate parameter sets and corresponding simulated datasets.

my_dataset_generator = ssms.dataset_generators.data_generator(generator_config = generator_config,
                                                              model_config = model_config)

n_cpus used:  6
checking:  data/lan_mlp/

training_data = my_dataset_generator.generate_data_training_uniform(save = False)

simulation round: 1  of 10
simulation round: 2  of 10
simulation round: 3  of 10
simulation round: 4  of 10
simulation round: 5  of 10
simulation round: 6  of 10
simulation round: 7  of 10
simulation round: 8  of 10
simulation round: 9  of 10
simulation round: 10  of 10

training_data is a dictionary containing four keys:

1. data the features for LANs, containing vectors of model parameters, as well as rts and choices.
2. labels which contain approximate likelihood values
3. generator_config, as defined above
4. model_config, as defined above

You can now use this training data for your purposes. If you want to train LANs yourself, you might find the LANfactory package helpful.

You may also simply find the basic simulators provided with the ssms package useful, without any desire to use the outputs into training data for amortization purposes.

END