Source code for selene_sdk.predict.predict_handlers.diff_score_handler

Handles computing and outputting the difference scores
from .handler import PredictionsHandler

[docs]class DiffScoreHandler(PredictionsHandler): """ The "diff score" is the difference between `alt` and `ref` predictions (`alt - ref`). Parameters ---------- features : list(str) List of sequence-level features, in the same order that the model will return its predictions. columns_for_ids : list(str) Columns in the file that help to identify the input sequence or variant to which the model prediction scores correspond. output_path_prefix : str Path to the file to which Selene will write the difference scores. The path may contain a filename prefix. Selene will append `diffs` to the end of the prefix if specified (otherwise the file will be named `diffs.tsv`/`.h5`). output_format : {'tsv', 'hdf5'} Specify the desired output format. TSV can be specified if you would like the final file to be easily perused (e.g. viewed in a text editor/Excel). However, saving to a TSV file is much slower than saving to an HDF5 file. output_size : int, optional The total number of rows in the output. Must be specified when the output_format is hdf5. write_mem_limit : int, optional Default is 1500. Specify the amount of memory you can allocate to storing model predictions/scores for this particular handler, in MB. Handler will write to file whenever this memory limit is reached. write_labels : bool, optional Default is True. If you initialize multiple write handlers for the same set of inputs with output format `hdf5`, set `write_label` to False on all handlers except 1 so that only 1 handler writes the row labels to an output file. Attributes ---------- needs_base_pred : bool Whether the handler needs the base (reference) prediction as input to compute the final output """ def __init__(self, features, columns_for_ids, output_path_prefix, output_format, output_size=None, write_mem_limit=1500, write_labels=True): """ Constructs a new `DiffScoreHandler` object. """ super(DiffScoreHandler, self).__init__( features, columns_for_ids, output_path_prefix, output_format, output_size=output_size, write_mem_limit=write_mem_limit, write_labels=write_labels) self.needs_base_pred = True self._results = [] self._samples = [] self._features = features self._columns_for_ids = columns_for_ids self._output_path_prefix = output_path_prefix self._output_format = output_format self._write_mem_limit = write_mem_limit self._write_labels = write_labels self._create_write_handler("diffs")
[docs] def handle_batch_predictions(self, batch_predictions, batch_ids, baseline_predictions): """ Handles the model predictions for a batch of sequences. Computes the difference between the predictions for 1 or a batch of reference sequences and a batch of alternate sequences (i.e. sequences slightly changed/mutated from the reference). Parameters ---------- batch_predictions : arraylike The predictions for a batch of sequences. This should have dimensions of :math:`B \\times N` (where :math:`B` is the size of the mini-batch and :math:`N` is the number of features). batch_ids : list(arraylike) Batch of sequence identifiers. Each element is `arraylike` because it may contain more than one column (written to file) that together make up a unique identifier for a sequence. base_predictions : arraylike The baseline prediction(s) used to compute the diff scores. Must either be a vector of dimension :math:`N` values or a matrix of dimensions :math:`B \\times N` (where :math:`B` is the size of the mini-batch, and :math:`N` is the number of features). """ diffs = batch_predictions - baseline_predictions self._results.append(diffs) self._samples.append(batch_ids) if self._reached_mem_limit(): self.write_to_file()
[docs] def write_to_file(self): """ Writes stored scores to a file. """ super().write_to_file()