jaxili 0.1.3

This package provides tools to execute and implement Implicit Likelihood Inference tools in JAX.

JaxILI

This is a package to run Neural Density Estimation using Jax. The training is performed using optax (documentation available here) and the neural network are created using flax (see documentation).

The code is meant to provide tools to train Normalizing Flows easily to perform Implicit Likelihood Inference.

Installation

Install jaxili using PyPI:

$ pip install jaxili

First example: performing Neural Posterior Estimation

from jaxili.inference import NPE

First fetch the data you want to train on:

theta, x = ... #Theta corresponds to the parameter to be infered and x to the simulator output given theta.

Then create an inference object, add the simulations and train:

inference = NPE()
inference = inference.append_simulations(theta, x)

learning_rate = ... #Choose your learning rate
num_epochs = ... #Choose the number of epochs
batch_size = ... #Choose the batch size
checkpoint_path = ... #Choose the checkpoint path
checkpoint_path = os.path.abspath(checkpoint_path) #Beware, this should be an absolute path.

metrics, density_estimator = inference.train(
    training_batch_size=batch_size,
    learning_rate=learning_rate,
    checkpoint_path=checkpoint_path,
    num_epochs=num_epochs
)

You can then fetch the posterior to sample from it.

posterior = inference.build_posterior()

observation = ... #The observation should have the shape [1, data vector size].
samples = posterior.sample(x=observation, num_samples=..., key=...) #You have to give a PRNGKey and specify the number of samples.

Training a conditional MAF

If you want to control the architecture of the network you can use the following code to train e.g. a Masked Autoregressive Flow (MAF).

import jax
import jax.numpy

from jaxili.utils import create_data_loader  #To create data loaders
from jaxili.train import TrainerModule #To perform the training
from jaxili.model import ConditionalMAF #The model used to learn the target distribution
from jaxili.loss import loss_nll_npe #Losses to train NFs with different configurations are provided

Given a train, validation and test set, one can create associated data loaders to perform the training.

train_loader, val_loader, test_loader = create_data_loader(
    train_set, val_set, test_set,
    train = [True, False, False],
    batch_size=128
)

You can then specify hyperparameters for your training

CHECKPOINT_PATH = ... #Path to save the weights of your neural network

loss_fn = loss_nll_npe

model_hparams_maf = {
    'n_in': dim_theta,
    'n_cond': dim_obs,
    'n_layers': 5,
    'layers': [50, 50],
    'activation': jax.nn.relu,
    'use_reverse': True,
    'seed' : 42
}

optimizer_hparams = { #hyperparameters of the optimizer for training
    'lr': 5e-4,
    'optimizer_name': 'adam'
}

logger_params = {
    'base_log_dir': CHECKPOINT_PATH
}

check_val_every_epoch = 1

debug = False

nde_class= "NPE"

A TrainerModule object can then be created to train the Neural Network:

trainer_maf_npe = TrainerModule(
    model_class=ConditionalMAF,
    model_hparams=model_hparams_maf,
    optimizer_hparams=optimizer_hparams,
    loss_fn=loss_fn,
    exmp_input=next(iter(train_loader)),
    logger_params=logger_params,
    debug=debug,
    check_val_every_epoch=check_val_every_epoch,
    nde_class=nde_class    
)

#Train the Neural Density Estimator
metrics_maf_npe = trainer_maf_npe.train_model(
    train_loader, val_loader, test_loader=test_loader, num_epochs=500, patience=20
)

The trained model can then be used to sample from or compute the log-probability of the learned distribution:

model_maf_npe = trainer_maf_npe.bind_model()

key, jax.random.PRNGKey(0)
samples_maf_npe = model_maf_npe.sample(
    observation, num_samples=10000, key=key
)
log_prob = model_maf_npe.apply(params, samples_maf_npe, observation, method="log_prob")