Source code for bnpy.allocmodel.AllocModel

from __future__ import division

[docs]class AllocModel(object): def __init__(self, inferType): self.inferType = inferType def set_prior(self, **kwargs): pass def get_keys_for_memoized_local_params(self): ''' Return LP field names required for warm starts of local step ''' return list() def getCompDims(self): ''' Get the dimensions of the latent clusters for this object. Returns ------- dimTuple : tuple with dimensions of latent clusters. ''' return ('K',)
[docs] def calc_local_params(self, Data, LP): ''' Compute local parameters for each data item and component. This is the E-step of EM algorithm. Returned LP contains optimal values of local parameters specific to the provided dataset. Updated values computed using current global parameter attributes. Possible keyword arguments control model-specific computations. Args ---- Data : :class:`.DataObj` Dataset to compute local parameters for. LP : dict Must contain cond. likelihoods in field 'E_log_soft_ev', a 2D array that is N x K provided by the observation model. Returns ------- LP : dict Contains updated fields for all K clusters in current model. * 'resp' : N x K 2D array, soft assignments for each data atom. ''' pass
[docs] def get_global_suff_stats(self, Data, SS, LP, **kwargs): ''' Compute low-dim summaries for provided local params. Returned sufficient statistics are deterministic given Data, LP. Possible keyword arguments control model-specific computations. Args ---- Data : :class:`.DataObj` Dataset to be summarized. SS : :class:`.SuffStatBag` If present, all summaries will be added to this bag. If None, new bag will be created and returned. LP : dict Holds valid local params for K' clusters and all atoms in Data. Returns ------- SS : :class:`.SuffStatBag` Updated fields for each of K' clusters represented in LP ''' pass
def update_global_params(self, SS, rho=None, **kwargs): ''' Update global parameter attributes for this model. This is the M-step of EM algorithm. Args ---- SS : :class:`.SuffStatBag` Sufficient statistics needed for update. Returns ------- None Post Condition -------------- Attribute K reset to the number of active clusters in SS. Global parameter attributes updated in-place or reallocated. ''' self.K = SS.K if self.inferType == 'EM': self.update_global_params_EM(SS) elif self.inferType == 'VB' or self.inferType.count('moVB'): self.update_global_params_VB(SS, **kwargs) elif self.inferType == 'GS': self.update_global_params_VB(SS, **kwargs) elif self.inferType == 'soVB': if rho is None or rho == 1: self.update_global_params_VB(SS, **kwargs) else: self.update_global_params_soVB(SS, rho, **kwargs) else: raise ValueError( 'Unrecognized Inference Type! %s' % (self.inferType))
[docs] def calc_evidence(self, Data, SS, LP, todict=0, **kwargs): """ Calculate ELBO objective function value for provided state. Args ---- Data : optional, If not provided, relies exclusively on summaries in SS SS : :class:`.SuffStatBag` Contains valid summaries for desired dataset. LP : optional, dict If not provided, relies exclusively on summaries in SS If provided, used in place of summaries in SS when possible. Keyword Args ------------ todict : boolean If True, return a dict with different ELBO terms under named keys like 'Ldata' and 'Lentropy' If False [default], return scalar value equal to sum of terms. Returns ------- L : float Represents sum of all terms in optimization objective. Will be a dict if todict option is True. """ pass
def calcELBOFromLP(self, Data, LP): """ Calculate ELBO value for provided data & local parameters TODO implement this """ pass def calcELBOFromSS(self, SS): """ Calculate ELBO value for provided sufficient stats. TODO implement this """ pass def get_info_string(self): ''' Returns one-line human-readable terse description of this object ''' pass def sample_local_params(self, obsModel, Data, SS, LP): ''' Sample local assignments for each data item. ''' pass def to_dict_essential(self): PDict = dict(name=self.__class__.__name__, inferType=self.inferType) if hasattr(self, 'K'): PDict['K'] = self.K return PDict def to_dict(self): pass def from_dict(self): pass def get_prior_dict(self): pass def make_hard_asgn_local_params(self, LP): ''' Convert soft to hard assignments for provided local params Parameters -------- LP : dict Local parameters as key/value string/array pairs * resp : 2D array, size N x K ''' LP['Z'] = np.argmax(LP['resp'], axis=1) K = LP['resp'].shape[1] LP['resp'].fill(0) for k in xrange(K): LP['resp'][LP['Z'] == k, k] = 1 return LP def getHandleCalcLocalParams(self): return self.calc_local_params def getHandleCalcSummaryStats(self): return self.get_global_suff_stats