Combined names for the hyperparameters for the kernel, noise kernel and (if present) mean function.
187684
def param_names(self):
        
        pn = CombinedBounds(self.k.param_names, self.noise_k.param_names)
        if self.mu is not None:
            pn = CombinedBounds(pn, self.mu.param_names)
        return pn
1296631
def hyper_parameter_search(
            self,
            param_distributions,
            n_iter=10,
            scoring=None,
            fit_params={},
            n_jobs=1,
            iid=True,
            refit=True,
            cv=None,
            verbose=0,
            pre_dispatch='2*njobs',
            random_state=None,
            error_score='raise',
            return_train_score=True,
            test=True,
            score=True,
            save=True,
            custom_data=None
    ):
        
        params = locals()
        params.pop('self')

        self.fitting = lore.metadata.Fitting.create(
            model=self.name,
            custom_data=custom_data,
            snapshot=lore.metadata.Snapshot(pipeline=self.pipeline.name,
                                            head=str(self.pipeline.training_data.head(2)),
                                            tail=str(self.pipeline.training_data.tail(2))
                                            )
        )

        result = RandomizedSearchCV(
            self.estimator,
            param_distributions,
            n_iter=n_iter,
            scoring=scoring,
            n_jobs=n_jobs,
            iid=iid,
            refit=refit,
            cv=cv,
            verbose=verbose,
            pre_dispatch=pre_dispatch,
            random_state=random_state,
            error_score=error_score,
            return_train_score=return_train_score
        ).fit(
            self.pipeline.encoded_training_data.x,
            y=self.pipeline.encoded_training_data.y,
            validation_x=self.pipeline.encoded_validation_data.x,
            validation_y=self.pipeline.encoded_validation_data.y,
            **fit_params
        )
        self.estimator = result.best_estimator_
        self.stats = {}
        self.estimator_kwargs = self.estimator.__getstate__()

        if test:
            self.stats['test'] = self.evaluate(self.pipeline.test_data)

        if score:
            self.stats['score'] = self.score(self.pipeline.test_data)

        self.complete_fitting()

        if save:
            self.save()
        return result
103356
def _create_model(self, X, Y):
        

        # --- define kernel
        self.input_dim = X.shape[1]
        if self.kernel is None:
            kern = GPy.kern.Matern52(self.input_dim, variance=1., ARD=self.ARD) #+ GPy.kern.Bias(self.input_dim)
        else:
            kern = self.kernel
            self.kernel = None

        # --- define model
        noise_var = Y.var()*0.01 if self.noise_var is None else self.noise_var

        if not self.sparse:
            self.model = GPy.models.GPRegression(X, Y, kernel=kern, noise_var=noise_var)
        else:
            self.model = GPy.models.SparseGPRegression(X, Y, kernel=kern, num_inducing=self.num_inducing)

        # --- restrict variance if exact evaluations of the objective
        if self.exact_feval:
            self.model.Gaussian_noise.constrain_fixed(1e-6, warning=False)
        else:
            # --- We make sure we do not get ridiculously small residual noise variance
            self.model.Gaussian_noise.constrain_bounded(1e-9, 1e6, warning=False)
383666
def inference(self, kern, X, likelihood, Y, mean_function=None, Y_metadata=None):
        
        assert mean_function is None, "inference with a mean function not implemented"

        # Compute K
        K = kern.K(X)

        #Find mode
        if self.bad_fhat or self.first_run:
            Ki_f_init = np.zeros_like(Y)
            self.first_run = False
        else:
            Ki_f_init = self._previous_Ki_fhat

        Ki_f_init = np.zeros_like(Y)# FIXME: take this out

        f_hat, Ki_fhat = self.rasm_mode(K, Y, likelihood, Ki_f_init, Y_metadata=Y_metadata)

        #Compute hessian and other variables at mode
        log_marginal, woodbury_inv, dL_dK, dL_dthetaL = self.mode_computations(f_hat, Ki_fhat, K, Y, likelihood, kern, Y_metadata)

        self._previous_Ki_fhat = Ki_fhat.copy()
        return Posterior(woodbury_vector=Ki_fhat, woodbury_inv=woodbury_inv, K=K), log_marginal, {'dL_dK':dL_dK, 'dL_dthetaL':dL_dthetaL}
1290059
def _evaluate(x, y, weights):
    '''
    
    '''
    i = _validI(x, y, weights)
    xx = x[i]
    y = y[i]

    try:
        fitParams = _fit(xx, y)
        # bound noise fn to min defined y value:
        minY = function(xx[0], *fitParams)
        fitParams = np.insert(fitParams, 0, minY)
        fn = lambda x, minY=minY: boundedFunction(x, *fitParams)
    except RuntimeError:
        print(
            "couldn't fit noise function with filtered indices, use polynomial fit instead")
        fitParams = None
        fn = smooth(xx, y, weights[i])
    return fitParams, fn, i
1053406
def super_lm_base():
  """"""
  hparams = common_hparams.basic_params1()
  hparams.hidden_size = 512
  hparams.moe_hidden_sizes = "512"
  hparams.batch_size = 16384
  hparams.max_length = 0
  # All hyperparameters ending in "dropout" are automatically set to 0.0
  # when not in training mode.
  hparams.layer_prepostprocess_dropout = 0.0
  hparams.symbol_dropout = 0.1
  hparams.add_hparam("attention_dropout", 0.0)
  hparams.label_smoothing = 0.0
  hparams.clip_grad_norm = 0.  # i.e. no gradient clipping
  hparams.optimizer = "Adafactor"
  hparams.learning_rate_decay_scheme = "noam"
  hparams.learning_rate = 0.1
  hparams.learning_rate_warmup_steps = 8000
  hparams.initializer_gain = 1.0
  hparams.initializer = "uniform_unit_scaling"
  hparams.weight_decay = 0.0
  hparams.shared_embedding_and_softmax_weights = False
  hparams.layer_preprocess_sequence = "n"
  hparams.layer_postprocess_sequence = "da"
  # we only want one data shard.
  hparams.no_data_parallelism = True
  # bypass the symbol modality so that we can use model parallelism.
  hparams.bottom = {
      "inputs": modalities.identity_bottom,
      "targets": modalities.identity_bottom,
  }
  hparams.top = {
      "targets": modalities.identity_top,
  }
  hparams.add_hparam("filter_size", 512)
  hparams.add_hparam("mix_fraction", 0.5)
  # attention-related flags
  hparams.add_hparam("multihead_attention_num_heads", 4)
  hparams.add_hparam("multihead_attention_key_channels", 0)
  hparams.add_hparam("multihead_attention_value_channels", 0)
  hparams.add_hparam("pos", "timing")  # timing, none
  hparams.add_hparam(
      "layers", ("n,att,m,d,a," "n,ffn,m,d,a,") * 4 + "n,ffn,d")
  # Number of model shards - each one has separate parameters.
  # Changing this number invalidates checkpoints.
  hparams.add_hparam("num_model_shards", 8)
  hparams.add_hparam("diet_experts", False)
  return hparams
627645
def addRandomEffect(self,K=None,covar_type='freeform',is_noise=False,normalize=True,Ks=None,offset=1e-4,rank=1,covar_K0=None):
        
        if self.P==1:	self.addSingleTraitTerm(K=K,is_noise=is_noise,normalize=normalize,Ks=Ks)
        else:			self.addMultiTraitTerm(K=K,covar_type=covar_type,is_noise=is_noise,normalize=normalize,Ks=Ks,offset=offset,rank=rank,covar_K0=covar_K0)
547836
def _safe_split(estimator, X, y, indices, train_indices=None):
    """"""
    if hasattr(estimator, 'kernel') and isinstance(estimator.kernel, collections.Callable):
        # cannot compute the kernel values with custom function
        raise ValueError("Cannot use a custom kernel function. "
                         "Precompute the kernel matrix instead.")

    if not hasattr(X, "shape"):
        if getattr(estimator, "_pairwise", False):
            raise ValueError("Precomputed kernels or affinity matrices have "
                             "to be passed as arrays or sparse matrices.")
        X_subset = [X[idx] for idx in indices]
    else:
        if getattr(estimator, "_pairwise", False):
            # X is a precomputed square kernel matrix
            if X.shape[0] != X.shape[1]:
                raise ValueError("X should be a square kernel matrix")
            if train_indices is None:
                X_subset = X[np.ix_(indices, indices)]
            else:
                X_subset = X[np.ix_(indices, train_indices)]
        else:
            X_subset = safe_indexing(X, indices)

    if y is not None:
        y_subset = safe_indexing(y, indices)
    else:
        y_subset = None

    return X_subset, y_subset
194038
def basic_params1():
  """"""
  return hparam.HParams(
      # If the problem consists of variable-length sequences
      # (see problem.batch_size_means_tokens()), then this is the number
      # of tokens per batch per GPU or per TPU core.  Otherwise, this is
      # the number of examples per GPU or per TPU core.
      batch_size=4096,
      batch_shuffle_size=512,
      # If True, then if the features are of variable length, the batch_size is
      # used as the actual batch size (and not tokens per batch).
      use_fixed_batch_size=False,
      num_hidden_layers=4,
      kernel_height=3,
      kernel_width=1,
      hidden_size=64,
      compress_steps=0,
      # All hyperparameters ending in "dropout" are automatically set to 0.0
      # when not in training mode.
      dropout=0.2,
      clip_grad_norm=2.0,
      grad_noise_scale=0.0,
      summarize_grads=False,
      # Flag for whether mlperf mode is on
      mlperf_mode=False,
      # Whether to log the name and size of every variable
      summarize_vars=False,
      initializer="orthogonal",
      initializer_gain=1.5,
      label_smoothing=0.1,
      optimizer="adam",
      optimizer_adam_epsilon=1e-6,
      optimizer_adam_beta1=0.85,
      optimizer_adam_beta2=0.997,
      optimizer_momentum_momentum=0.9,
      optimizer_momentum_nesterov=False,
      optimizer_adafactor_beta1=0.0,
      optimizer_adafactor_beta2=0.999,
      optimizer_adafactor_factored=True,
      optimizer_adafactor_decay_type="pow",
      optimizer_adafactor_memory_exponent=0.8,
      optimizer_adafactor_clipping_threshold=1.0,
      optimizer_adafactor_multiply_by_parameter_scale=True,
      # Number of accumulating steps for multi step optimizers.
      optimizer_multistep_accumulate_steps=0,
      # Loss scaling used.
      # Generally only necessary with mixed precision training.
      # Mixed precision training only supports exponential scaling currently
      # To disable the scaler, see to 0/False
      mixed_precision_optimizer_loss_scaler="exponential",
      # Determines the initial loss scaling value for mixed precision
      mixed_precision_optimizer_init_loss_scale=2**15,
      # Whether to zero gradients that were not computed, so that the
      # appropriate slots are created. Useful for sharing checkpoints between
      # models with different sets of heads.
      optimizer_zero_grads=False,
      weight_decay=1e-6,
      weight_noise=0.0,
      # Defines the learning rate as a product of named functions.
      # Available functions are listed in learning_rate._LEARNING_RATE_FUNCTIONS
      # e.g. "constant*linear_warmup*rsqrt_decay*rsqrt_hidden_size"
      learning_rate_schedule="legacy",
      learning_rate_constant=1.0,
      # If learning_rate_schedule=="legacy",
      # then we specify decay scheme here.  Warmup is always exponential,
      # except with "noam" learning rate decay scheme.
      # see optimize.legacy_learning_rate_schedule()
      # TODO(noam): migrate everyone away from this.
      learning_rate_decay_scheme="none",
      # decay_steps and decay_staircase for learning_rate_decay_scheme=="exp"
      learning_rate_decay_steps=5000,
      learning_rate_decay_staircase=False,
      learning_rate_minimum=None,
      learning_rate_decay_rate=1.0,
      learning_rate_warmup_steps=100,
      learning_rate_cosine_cycle_steps=250000,
      learning_rate=0.1,
      sampling_method="argmax",  # "argmax" or "random"
      sampling_temp=1.0,  # temperature for sampling
      sampling_keep_top_k=-1,  # If >0, ignore all but the top k logits
      # expand the logits a piece at a time - saves memory.
      factored_logits=False,
      multiply_embedding_mode="sqrt_depth",
      # Parameters related to mixtures of experts.
      moe_hidden_sizes="2048",  # hidden layer sizes (comma-separated)
      moe_num_experts=64,  # number of experts per layer
      moe_k=2,  # how many experts to use for each batch element
      moe_loss_coef=1e-2,
      # Sequences of operations to perform on layer input and layer output.
      # Used by common_layers.layer_preprocess, common_layers.layer_postprocess
      # Each character represents an operation:
      # none: no preprocessing
      #    d: apply dropout
      #    n: apply normalization (see norm_type and norm_epsilon)
      #    a: add layer input (residual connection - only during postprocess)
      # The special string "none" is used instead of the empty string
      # to indicate no pre/postprocessing, since the empty string causes
      # trouble for hyperparameter tuning.
      # TODO(noam): The current settings ("", "dan") are the published version
      # of the transformer.  ("n", "da") seems better for harder-to-learn
      # models, so it should probably be the default.
      layer_preprocess_sequence="none",
      layer_postprocess_sequence="dan",
      # dropout rate to use during layer_preprocess and layer_postprocess
      layer_prepostprocess_dropout=0.1,
      # broadcast dimensions for layer_prepostprocess_dropout
      # a comma-separated list of integers.
      # see common_layers.dropout_with_broadcast_dims()
      # Change this to "1" to save memory.
      layer_prepostprocess_dropout_broadcast_dims="",
      # dropout some symbols (set them to 0) before embedding.
      symbol_dropout=0.0,
      # What type of normalization to use
      norm_type="layer",  # "batch", layer", "noam", "none".
      # epsilon parameter to normalization function
      norm_epsilon=1e-6,
      # pad vocabularies so that this value divides the vocabulary size.
      vocab_divisor=1,
      # During training, we drop sequences whose inputs and targets are shorter
      # than min_length
      min_length=0,
      # During training, we drop sequences whose inputs or targets are longer
      # than max_length.
      # If max_length==0, we use hparams.batch_size instead.
      max_length=0,
      # Pack examples on the fly.
      pack_dataset=False,
      # Use custom ops not included in standard tensorflow.
      use_custom_ops=True,
      # Split targets on the first axis into chunks of this length.
      split_targets_chunk_length=0,
      split_targets_max_chunks=100,
      split_targets_strided_training=False,
      # Maximum length in the smallest length bucket.  Setting this
      # flag too high will result in wasteful padding of short
      # sequences.  Due to some (hopefully) temporary hacks in the
      # data reading and batching code, setting this flag too low
      # results in a very long batch-shuffling queue.
      # TODO(noam): change this once the Datasets API changes.
      min_length_bucket=8,
      # This flag controls the number of length buckets in the data
      # reader.  The buckets have maximum lengths from
      # min_bucket_length to (max_length or batch_size), increasing
      # (approximately) by factors of length_bucket_step.
      length_bucket_step=1.1,
      # If set to True, drop sequences longer than max_length during eval.
      # This affects the validity of the evaluation metrics.
      eval_drop_long_sequences=False,
      # If True, run the model autoregressively instead of teacher-forcing
      # during eval
      eval_run_autoregressive=False,
      # (For features with symbol modality) If True, share all of the
      # input embeddings, target embeddings, and softmax weights.
      shared_embedding_and_softmax_weights=False,
      # (For features with symbol modality) If True, share the input embeddings
      # and target embeddings.
      shared_embedding=False,
      # (For features with symbol modality) Number to shard embeddings by.
      symbol_modality_num_shards=1,
      # Feature transformations are optional dictionaries comprising key-value
      # pairs of a feature name (str) and its transformation (function). If not
      # specified, T2TModel applies a default transformation according to the
      # feature's modality. Bottom is applicable to all features; loss, top, and
      # weights_fn are only applicable to target features.
      # TODO(trandustin): `name` is an optional hparam for legacy reasons,
      # defining variable scope names. Remove this hparam in the future.
      bottom={},
      loss={},
      name={},
      top={},
      weights_fn={},
      # The maximum length of "input" sequence.
      # Sequences longer than this value will be truncated. 0 or negative values
      # mean there is no maximum or truncation.
      # You can change this behavior by overriding preprocess_example() method
      # in your problem class.
      max_input_seq_length=0,
      # The maximum length of "target" sequence.
      # Sequences longer than this value will be truncated. 0 or negative values
      # mean there is no maximum or truncation.
      # You can change this behavior by overriding preprocess_example() method
      # in your problem class.
      max_target_seq_length=0,
      # if nonzero, we split the target sequences on example read.
      # This is for use with language modeling problems with fixed length
      # examples.  e.g.  The examples may be written with length 65536, but we
      # want to split each example into 64 examples of length 1024.
      split_to_length=0,
      # Video settings: how many frames to batch on input and targets.
      video_num_input_frames=1,
      video_num_target_frames=1,
      # This flag allows us to optionally treat a seq-to-seq problem
      # as a language model.  Legal values are:
      #
      # "none" - Do not prepend the inputs to the targets.
      # "prepend_inputs_masked_attention"
      #     replace "targets" in preprocessing with
      #     tf.concat([inputs, [0], targets], axis=1)
      #     i.e. we prepend the inputs to the targets with a single
      #     padding token in between.  Use masked self-attention on the
      #     entire resulting sequence.  During training, we compute losses on
      #     the combined sequence.  During eval, we compute the metrics
      #     on only the targets portion.
      # "prepend_inputs_full_attention"
      #     similar to the previous option except that each
      #     position in the inputs portion can see the
      #     entire inputs portion.  This removes the challenge of
      #     autoregressively predicting the inputs portion.
      prepend_mode="none",
      # Scheduled sampling is interesting for auto-regressive models.
      # It runs an additional step using the generated output as autoregressive
      # targets, which can improve the models inference results later. The
      # parameter scheduled_sampling_prob determines with what probability
      # will such additional step be run. It's turned off (0.0) by default.
      # This probability will exponentially warm up for the number of
      # steps determined by scheduled_sampling_warmup_steps.
      # The tensor used for the n-th pass will consist of outputs from
      # the (n-1)-th pass mixed with gold truth, with the proportion of gold
      # determined by scheduled_sampling_gold_mixin_prob. Control the number
      # of passes with scheduled_sampling_num_passes.
      scheduled_sampling_prob=0.0,
      scheduled_sampling_warmup_steps=50000,
      scheduled_sampling_gold_mixin_prob=0.5,
      # TODO(duckworthd): Uncomment when we can ascertain why adding an
      # extra field to HParam causes test failures.
      # scheduled_sampling_num_passes=1,

      # This setting controls whether to copy variables around in a daisy chain
      # (if true) or leave their placement to TensorFlow. It only affects multi
      # device training and mostly should be turned on for performance. One
      # exception are recurrent models: with dynamic loops it must be off.
      daisy_chain_variables=True,
      # If True in PREDICT mode, then last-position-only optimizations are not
      # used.
      force_full_predict=False,
      # Set this for pure model parallelism.  There is only one data shard.
      no_data_parallelism=False,
      # dtype used for activations. - "float32" or "bfloat16"
      # activation_dtype="bfloat16" currently only works on TPU.
      #    It lowers activation-memory usage
      #    and does not appear to affect quality.
      #    You can train on TPU with activation_dtype="bfloat16" and evaluate
      #    on CPU/GPU with activation_dtype="float32"
      activation_dtype="float32",
      # dtype used for parameters: "float32" or "bfloat16"
      # bfloat16 currently only works with optimizer="adafactor".
      #   The savings in memory allow for training larger models.
      #   Weights are encoded as (w*128)^8, using pseudostochastic
      #   roundoff.  Initial experiments show that model quality is similar
      #   to baseline for about 3M training steps, but worse thereafter.
      weight_dtype="float32",
      # Directory containing a checkpoint for a pretrained model. This will only
      # be used if a new run is being started. Parameters not found in the
      # pretrained model will be randomly initialized. Superfluous parameters in
      # the pretrained model will be ignored.
      pretrained_model_dir="",
      # Threshold used for two cases: the primary task probability for the
      # constant mixing schedule, and the exponential schedule limit for when
      # mixing should stop (eg: 0.5 means stop at 50-50 mixing, 0.8 means stop
      # at 20-80 mixing for the primary-others mixing case.)
      multiproblem_schedule_threshold=0.5,
      # For more than 2 tasks, we may want to specify per-task thresholds here.
      # In that case, this needs to be a string with as many floating point
      # numbers as the number of tasks in the multi-problem. These numbers
      # are later normalized to add up to 1 and taken as probabilities for
      # each task. This enforces a constant mixing schedule and if this is
      # empty then the threshold from above is used for the first task and
      # the other tasks get the remaining probability split uniformly.
      multiproblem_per_task_threshold="",
      # The number of examples at which the proportion of the mixed in datasets
      # is multiproblem_schedule_threshold
      multiproblem_schedule_max_examples=1e7,
      # When training multiproblems, we can mix the data according to different
      # schedules. Example: a constant schedule mixing 20-80 between the primary
      # and other tasks.
      # A list of supported schedules can be found in
      # `data_generators.multi_problem.py`.
      multiproblem_mixing_schedule="constant",
      # A boolean that decides whether input sequence losses and target label
      # losses in classification problems should be reweighted.
      multiproblem_reweight_label_loss=False,
      # How much weight the targets in classification problems receive. Inputs
      # receive 1 minus this weight.
      multiproblem_label_weight=0.5,
      # Hyperparameters for relative attention.
      # The maximum relative positional distance to learn an embedding for.
      max_relative_position=0,
      # If heads share the same relative embedding.
      heads_share_relative_embedding=False,
      # If relative embedding terms are added to values too.
      add_relative_to_values=False,
      # If enable the host_call which is executed every training step.
      # There could be a performance drop if host_call function is slow and
      # cannot keep up with the TPU-side computation.
      tpu_enable_host_call=False,
      # Pad batch dim of inputs to nearest multiple of batch multiple.
      pad_batch=False,
      # When true, do not evaluate on the language model data when running the
      # multiproblem since it can take a while. If False, set eval_steps to
      # something large like 6000 or 10000.
      multiproblem_target_eval_only=False,
      # Max out the vocab size to a power of 2 for efficiency and to reserve
      # extra space in the vocabulary for new task ids and label classes.
      multiproblem_vocab_size=-1,
      # When using multiproblem with generation tasks, need to truncate the
      # inputs and targets manually before concatenating them.
      multiproblem_max_input_length=-1,
      multiproblem_max_target_length=-1,
      # If positive, makes training targets fixed-length in MultiProblem.
      multiproblem_fixed_train_length=-1,
      # Load weights from a second model. For instance, when using
      # pre-trained weights, you might want to initialize the encoder
      # and decoder by loading different models.
      warm_start_from_second="",
      # Area attention hyper parameters
      area_value_mode="none",
      area_key_mode="none",
      # Using area attention for the number of layers from the bottom
      num_area_layers=0,
      max_area_width=1,
      max_area_height=1,
      memory_height=1
  )
258587
@Override
  public FittingFunctionResult eval(double x, double[] params) {
    final int len = params.length;
    // We always need triples: (mean, stddev, scaling)
    assert (len % 3) == 0;

    double y = 0.0;
    double[] gradients = new double[len];

    // Loosely based on the book:
    // Numerical Recipes in C: The Art of Scientific Computing
    // Due to their license, we cannot use their code, but we have to implement
    // the mathematics ourselves. We hope the loss in precision is not too big.
    for(int i = 2; i < params.length; i += 3) {
      // Standardized Gaussian parameter (centered, scaled by stddev)
      double stdpar = (x - params[i - 2]) / params[i - 1];
      double e = FastMath.exp(-.5 * stdpar * stdpar);
      double localy = params[i] / (params[i - 1] * MathUtil.SQRTTWOPI) * e;

      y += localy;
      // mean gradient
      gradients[i - 2] = localy * stdpar;
      // stddev gradient
      gradients[i - 1] = (stdpar * stdpar - 1.0) * localy;
      // amplitude gradient
      gradients[i] = e / (params[i - 1] * MathUtil.SQRTTWOPI);
    }

    return new FittingFunctionResult(y, gradients);
  }
391667
def get_mean_and_stddevs(self, sites, rup, dists, imt, stddev_types):
        
        mean, stds = self._get_mean_and_stddevs(sites, rup, dists, imt,
                                                stddev_types)
        stddevs = [np.ones(len(dists.repi))*get_sigma(imt)]
        return mean, stddevs
380648
def get_mean_and_stddevs(self, sites, rup, dists, imt, stddev_types):
        

        dists_mod = copy.deepcopy(dists)
        dists_mod.rrup[dists.rrup <= 5.] = 5.

        return super().get_mean_and_stddevs(
            sites, rup, dists_mod, imt, stddev_types)
786755
def fit_deriv(x, amplitude, mean, stddev):
        
        import operator
        return list(map(
            operator.neg, Gaussian1D.fit_deriv(x, amplitude, mean, stddev)))
482034
def set_kernel_parameter_and_add_padding(node, kp,
                                         pad_mode, pad_val,
                                         base_name, func_counter):
    
    dims = []
    strides = []
    pads = []
    kernel = []
    for attr in node.attribute:
        if attr.name == "strides":
            if attr.type != AttributeProto.INTS:
                raise ValueError("Only INTS are supported for strides in {}"
                                 .format(node.op_type))
            strides.extend(attr.ints)
            dims.append(len(strides))
        elif attr.name == "pads":
            if attr.type != AttributeProto.INTS:
                raise ValueError("Only INTS are supported for pads in {}"
                                 .format(node.op_type))
            pads.extend(attr.ints)
            dims.append(len(pads))
        elif attr.name == "kernel_shape":
            if attr.type != AttributeProto.INTS:
                raise ValueError("Only INTS are supported for kernel_shape in {}"
                                 .format(node.op_type))
            kernel.extend(attr.ints)
            dims.append(len(kernel))
        elif attr.name == "count_include_pad":
            if attr.type != AttributeProto.INT:
                raise ValueError("Only INT is supported for count_include_pad in {} op_type"
                                 .format(node.op_type))
            kp.including_pad = bool(attr.i)
        else:
            raise ValueError("Unsupported attribute {} was specified at {}"
                             .format(attr.name, node.op_type))
    # NNabla requires for the dimensions of strides, pads, kernels to match.
    # We align the dimensions for all three attributes to the shortest one.
    dim = min(dims)
    padf = None
    if strides:
        kp.stride.dim.extend(strides[:])
    if pads:
        padval = []
        asymmetry = check_padding(pads, dim, padval)
        if asymmetry:
            # Add a separate padding function for
            # asymmetry padding
            input = node.input[0]
            padded = input+"_pad"
            pad_width = rearrange_pads(pads)
            padf = generate_pad(node.name, input, padded,
                                pad_mode, pad_width, pad_val,
                                base_name, func_counter)
        kp.pad.dim.extend(padval)
    else:
        # In case we don't have padding set,
        # we set zero padding just in case NNabla does not set the
        # default padding values correctly (such as in AveragePooling).
        # This code should not be needed
        # if NNabla handles default values correctly.
        kp.pad.dim.extend([0]*dim)
    if kernel:
        kp.kernel.dim.extend(kernel[:])
    return padf
880520
def multi_conv_res(x, padding, name, layers, hparams, mask=None, source=None):
  """"""
  with tf.variable_scope(name):
    padding_bias = None
    if mask is not None:
      padding_bias = (1.0 - mask) * -1e9  # Bias to not attend to padding.
      if padding == "LEFT":  # Do not mask anything when left-padding.
        mask = None
    if (hparams.kernel_scheme in _KERNEL_SCHEMES and
        hparams.dilation_scheme in _DILATION_SCHEMES):
      kernels = _KERNEL_SCHEMES[hparams.kernel_scheme]
      dilations = _DILATION_SCHEMES[hparams.dilation_scheme]
      dilations_and_kernels = list(zip(dilations, kernels))
      dilations_and_kernels1 = dilations_and_kernels[:2]
      dilations_and_kernels2 = dilations_and_kernels[2:]
    else:
      k = (hparams.kernel_height, hparams.kernel_width)
      k2 = (hparams.large_kernel_size, 1)
      dilations_and_kernels1 = [((1, 1), k), ((1, 1), k)]
      dilations_and_kernels2 = [((1, 1), k2), ((4, 4), k2)]
    separabilities1 = [hparams.separability, hparams.separability]
    separabilities2 = [hparams.separability] * len(dilations_and_kernels2)
    if hparams.separability < 0:
      separabilities1 = [hparams.separability - 1, hparams.separability]
      separabilities2 = [
          hparams.separability - i
          for i in reversed(range(len(dilations_and_kernels2)))
      ]

    def norm_fn(x, name):
      with tf.variable_scope(name, default_name="norm"):
        return common_layers.apply_norm(
            x, hparams.norm_type, hparams.hidden_size, hparams.norm_epsilon)

    for layer in range(layers):
      with tf.variable_scope("layer_%d" % layer):
        y = common_layers.subseparable_conv_block(
            x,
            hparams.hidden_size,
            dilations_and_kernels1,
            normalizer_fn=norm_fn,
            padding=padding,
            mask=mask,
            separabilities=separabilities1,
            name="residual1")
        x += common_layers.subseparable_conv_block(
            x + y,
            hparams.hidden_size,
            dilations_and_kernels2,
            normalizer_fn=norm_fn,
            padding=padding,
            mask=mask,
            separabilities=separabilities2,
            name="residual2") + y
        if source is not None and hparams.attention_type != "none":
          x += attention(x, source, norm_fn, hparams, bias=padding_bias)
        if mask is not None:
          x *= mask
    return tf.nn.dropout(x, 1.0 - hparams.dropout)
1032053
def params(self):
        
        p = CombinedBounds(self.k.params, self.noise_k.params)
        if self.mu is not None:
            p = CombinedBounds(p, self.mu.params)
        return p
411558
def _fit(
    indexed_params,
    penalization,
    lam,
    lam_perturb,
    lam_scale_,
    estimator,
    penalty_name,
    subsample,
    bootstrap,
    prng,
    X=None,
):
    
    index = indexed_params

    if isinstance(X, np.ndarray):
        local_X = X
    else:
        local_X = X.value

    n_samples, n_features = local_X.shape

    prec_is_real = False
    while not prec_is_real:
        boot_lam = None
        if penalization == "subsampling":
            pass
        elif penalization == "random":
            boot_lam = _fix_weights(_random_weights, n_features, lam, lam_perturb, prng)
        elif penalization == "fully-random":
            boot_lam = _fix_weights(_fully_random_weights, n_features, lam_scale_, prng)
        else:
            raise NotImplementedError(
                (
                    "Only penalization = 'subsampling', "
                    "'random', and 'fully-random' have "
                    "been implemented. Found {}.".format(penalization)
                )
            )

        # new instance of estimator
        new_estimator = clone(estimator)
        if boot_lam is not None:
            new_estimator.set_params(**{penalty_name: boot_lam})

        # fit estimator
        num_subsamples = int(subsample * n_samples)
        rp = bootstrap(n_samples, num_subsamples, prng)
        new_estimator.fit(local_X[rp, :])

        # check that new_estimator.precision_ is real
        # if not, skip this boot_lam and try again
        if isinstance(new_estimator.precision_, list):
            prec_real_bools = []
            for prec in new_estimator.precision_:
                prec_real_bools.append(np.all(np.isreal(prec)))

            prec_is_real = np.all(np.array(prec_real_bools) is True)

        elif isinstance(new_estimator.precision_, np.ndarray):
            prec_is_real = np.all(np.isreal(new_estimator.precision_))

        else:
            raise ValueError("Estimator returned invalid precision_.")

    return index, (boot_lam, rp, new_estimator)