pymob.inference package#

Submodules#

pymob.inference.numpyro_backend module#

class pymob.inference.numpyro_backend.ErrorModelFunction(*args, **kwargs)#: Bases: Protocol

class pymob.inference.numpyro_backend.NumpyroBackend(simulation: SimulationBase)#

Bases: InferenceBackend

property adapt_state_size#

calculate_log_likelihood(model, posterior_samples)#

static cast_to_precision(value, precision='64')#

property chains#

int([x]) -> integer int(x, base=10) -> integer

Convert a number or string to an integer, or return 0 if no arguments are given. If x is a number, return x.__int__(). For floating point numbers, this truncates towards zero.

If x is not a number or if base is given, then x must be a string, bytes, or bytearray instance representing an integer literal in the given base. The literal can be preceded by ‘+’ or ‘-’ and be surrounded by whitespace. The base defaults to 10. Valid bases are 0 and 2-36. Base 0 means to interpret the base from the string as an integer literal. >>> int(‘0b100’, base=0) 4

check_gradients(theta: ~typing.Dict[str, float | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] | None = None, vectorize=False)#

check_log_likelihood(theta: ~typing.Dict[str, float | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] | None = None, vectorize=False)#

check_tolerance_and_jax_mode()#

combine_chains(chain_location='chains', drop_extra_vars=[], cluster_deviation='std')#

Combine chains if chains were computed in a fully parallelized manner (on different machines, jobs, etc.).

In addition, the method drops all data variables and ‘…_norm’ priors (i.e. helper priors with a normal base). This is done, in order to create slim data objects for storage.

Parameters:

chain_location (str, optional) – location of the chains, relative to the simulation.output_path, this parameter is simulteneously the string appended to the saved posterior. By default “chains”
drop_extra_vars (List, optional) – any additional variables to drop from the posterior

create_log_likelihood(seed=1, return_type: Literal['joint-log-likelihood', 'full', 'summed-by-site', 'summed-by-prior-data', 'custom'] = 'joint-log-likelihood', check=True, custom_return_fn: Callable | None = None, scaled=True, vectorize=False, gradients=False) → Tuple[Errorfunction, ErrorModelFunction]#

Log density relies heavily on the substitute utility

The log density is the scaled log-likelihood. In case the the scale handler is used, log_density reflects this. Usually, the scaled log-density should be returned, because it is loss used for the optimizer/sampler

The general method is actually quite simple. Values of all SAMPLE sites are replaced according to the key: value pairs in theta.

Then the model is calculated and the trace is obtained. Everything else is then just post-processing of the sites. Here the log_prob function of the sites in the trace are used and the values of the sites are inserted.

Note that the log-density can randomly fluctuate, if not all sites are replaced.

Note that the data-loglik can be used to calculate a maximum-likelihood estimate. Because it is independent of the prior

The method is equivalent using the log_likelihood method, but returns only the likelihood of the data given the model parameters.

Parameters:

return_type (str) –

The information which should be returned. With increasing level of computation:

joint-log-likelihood: returns a single value, the entire log: likelihood of the model, given the values in theta
full: joint-log, loglik-prior of each site and value,: loglik-data of each site and value
summed-by-site: joint-loglik, loglik-prior of sites,: loglik-data of sites
summed-by-prior-data:: joint-loglik, prior-loglik, data-loglik
custom:: uses the full log

property draws#

int([x]) -> integer int(x, base=10) -> integer

Convert a number or string to an integer, or return 0 if no arguments are given. If x is a number, return x.__int__(). For floating point numbers, this truncates towards zero.

drop_vars_from_posterior(posterior, drop_extra_vars)#: drops extra variables if they are included in the posterior

property gaussian_base_distribution#

static generate_transform(expression: Expression)#

static get_dict(group: Dataset)#

property init_strategy#

property kernel#

load_results(file='numpyro_posterior.nc', cluster: int | None = None)#

model()#

nuts_posterior(mcmc, model, key, obs)#

observation_parser() → Tuple[Dict, Dict]#

Transform a xarray.Dataset into a dictionary of jnp.Arrays. Creates boolean arrays of masks for nan values (missing values are tagged False)

Returns:: Dictionaries of observations (data) and masks (missing values)
Return type:: Tuple[Dict,Dict]

parse_deterministic_model() → Callable#

Parses an evaluation function from the Simulation object, which takes a single argument theta and defaults to passing no seed to the deterministic evaluator.

Returns:: The evaluation function
Return type:: callable

parse_probabilistic_model()#

property posterior#

posterior_draws_from_svi(guide, svi_result, n, key)#

posterior_predictions(n: int | None = None, seed=1)#

predict_observations(model, posterior_samples, key, n=100)#: there is a very small remark in the numpyro API that explains that if data input for observed variables is None, the data are sampled from the distributions instead of returning the input data https://num.pyro.ai/en/stable/getting_started.html#a-simple-example-8-schools

static preprocessing(**kwargs)#

prior: Dict[str, DistributionMeta]#

prior_predictions(n=None, seed=1)#

run(print_debug=True, render_model=True)#

run_mcmc(model, keys, kernel)#

static run_svi(model, keys, learning_rate, iterations, kernel)#

static select_cluster(idata: InferenceData, cluster: int)#

store_results(output=None)#

property svi_iterations#

property svi_learning_rate#

svi_posterior(svi_result, model, guide, key, n=1000)#

property thinning#

to_arviz_idata(prior: ~typing.Dict[str, ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] = {}, posterior: ~typing.Dict[str, ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] = {}, log_likelihood: ~typing.Dict[str, ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] = {}, prior_predictive: ~typing.Dict[str, ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] = {}, posterior_predictive: ~typing.Dict[str, ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] = {}, observed_data: ~typing.Dict[str, ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.float16'>, <class 'numpy.float32'>, <class 'numpy.float64'>, <class 'numpy.float32'>, <class 'numpy.float64'>)] | ~numpydantic.vendor.nptyping.base_meta_classes.NDArray[~typing.Any, (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.int16'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>, <class 'numpy.uint16'>)]] = {}, n_draws: int | None = None, n_chains: int | None = None, **kwargs)#: Create an Arviz idata object from samples. TODO: Outsource to base.InferenceBackend

property user_defined_error_model#

property user_defined_preprocessing#

property user_defined_probability_model#

property warmup#

class pymob.inference.numpyro_backend.NumpyroDistribution(name: str, random_variable: RandomVariable, dims: Tuple[str, ...], shape: Tuple[int, ...])#

Bases: Distribution

property dist_name#

distribution_map: Dict[str, Tuple[DistributionMeta, Dict[str, str]]] = {'bernoulli': (<function Bernoulli>, {'p': 'probs'}), 'beta': (<class 'numpyro.distributions.continuous.Beta'>, {'a': 'concentration1', 'b': 'concentration0'}), 'binom': (<function Binomial>, {'n': 'total_count', 'p': 'probs'}), 'binomial': (<function Binomial>, {'n': 'total_count', 'p': 'probs'}), 'categorical': (<function Categorical>, {'p': 'probs'}), 'cauchy': (<class 'numpyro.distributions.continuous.Cauchy'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 'scale': 'scale'}), 'chi2': (<class 'numpyro.distributions.continuous.Chi2'>, {'df': 'df', 'high': 'high', 'low': 'low'}), 'deterministic': (<function deterministic>, {'value': 'value'}), 'dirichlet': (<class 'numpyro.distributions.continuous.Dirichlet'>, {'alpha': 'concentration'}), 'expon': (<class 'numpyro.distributions.continuous.Exponential'>, {'high': 'high', 'scale': 'rate'}), 'exponential': (<class 'numpyro.distributions.continuous.Exponential'>, {'high': 'high', 'scale': 'rate'}), 'gamma': (<class 'numpyro.distributions.continuous.Gamma'>, {'a': 'concentration', 'high': 'high', 'low': 'low', 'scale': 'rate'}), 'geom': (<function Geometric>, {'p': 'probs'}), 'gumbel_l': (<function <lambda>>, {}), 'gumbel_r': (<class 'numpyro.distributions.continuous.Gumbel'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 'scale': 'scale'}), 'halfnorm': (<class 'numpyro.distributions.continuous.HalfNormal'>, {'high': 'high', 'scale': 'scale'}), 'halfnormal': (<class 'numpyro.distributions.continuous.HalfNormal'>, {'high': 'high', 'scale': 'scale'}), 'laplace': (<class 'numpyro.distributions.continuous.Laplace'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 'scale': 'scale'}), 'logistic': (<class 'numpyro.distributions.continuous.Logistic'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 'scale': 'scale'}), 'lognorm': (<class 'numpyro.distributions.continuous.LogNormal'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 's': 'scale', 'scale': 'loc'}), 'lognormal': (<class 'numpyro.distributions.continuous.LogNormal'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 's': 'scale', 'scale': 'loc'}), 'multinomial': (<function Multinomial>, {'n': 'total_count', 'p': 'probs'}), 'multivariate_normal': (<class 'numpyro.distributions.continuous.MultivariateNormal'>, {'cov': 'covariance_matrix', 'mean': 'loc'}), 'nbinom': (<class 'numpyro.distributions.conjugate.NegativeBinomialProbs'>, {'n': 'total_count', 'p': 'probs'}), 'norm': (<class 'numpyro.distributions.continuous.Normal'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 'scale': 'scale'}), 'normal': (<class 'numpyro.distributions.continuous.Normal'>, {'high': 'high', 'loc': 'loc', 'low': 'low', 'scale': 'scale'}), 'pareto': (<class 'numpyro.distributions.continuous.Pareto'>, {'b': 'scale', 'high': 'high', 'low': 'low', 'scale': 'alpha'}), 'poisson': (<class 'numpyro.distributions.discrete.Poisson'>, {'mu': 'rate'}), 't': (<class 'numpyro.distributions.continuous.StudentT'>, {'df': 'df', 'high': 'high', 'loc': 'loc', 'low': 'low', 'scale': 'scale'}), 'uniform': (<class 'numpyro.distributions.continuous.Uniform'>, {'loc': 'low', 'scale': 'high'})}#

static parameter_converter(x)#

pymob.inference.numpyro_backend.catch_patterns(expression_str)#

pymob.inference.pyabc_backend module#

class pymob.inference.pyabc_backend.Posterior(samples)#

Bases: object

draw(i)#

mean()#

to_dict()#

class pymob.inference.pyabc_backend.PyabcBackend(simulation: SimulationBase)#