Beam search

beam_search

logger = ColorLog(console, __name__).logger module-attribute

BeamSearchDecoder(model: Decodable, suppressed_residues: list[str] | None = None, mass_scale: int = MASS_SCALE, disable_terminal_residues_anywhere: bool = True, keep_invalid_mass_sequences: bool = True, float_dtype: torch.dtype = torch.float64)

Bases: Decoder

A class for decoding from de novo sequence models using beam search.

This class conforms to the Decoder interface and decodes from models that conform to the Decodable interface.

mass_scale = mass_scale instance-attribute

disable_terminal_residues_anywhere = disable_terminal_residues_anywhere instance-attribute

keep_invalid_mass_sequences = keep_invalid_mass_sequences instance-attribute

float_dtype = float_dtype instance-attribute

residue_masses = torch.zeros((len(self.model.residue_set),), dtype=(self.float_dtype)) instance-attribute

terminal_residue_indices = torch.tensor(terminal_residues_idx, dtype=(torch.long)) instance-attribute

suppressed_residue_indices = torch.tensor(suppressed_residues_idx, dtype=(torch.long)) instance-attribute

residue_target_offsets = torch.tensor(residue_target_offsets, dtype=(self.float_dtype)) instance-attribute

vocab_size = len(self.model.residue_set) instance-attribute

decode(spectra: Float[Spectrum, ' batch'], precursors: Float[PrecursorFeatures, ' batch'], beam_size: int, max_length: int, mass_tolerance: float = 5e-05, max_isotope: int = 1, min_log_prob: float = -float('inf'), return_encoder_output: bool = False, encoder_output_reduction: Literal['mean', 'max', 'sum', 'full'] = 'mean', return_beam: bool = False, **kwargs) -> dict[str, Any]

Decode predicted residue sequence for a batch of spectra using beam search.

PARAMETER	DESCRIPTION
spectra	The spectra to be sequenced. TYPE: FloatTensor
precursors	The precursor mass, charge and mass-to-charge ratio. TYPE: torch.FloatTensor[batch size, 3]
beam_size	The maximum size of the beam. Ignored in beam search. TYPE: int
max_length	The maximum length of a residue sequence. TYPE: int
mass_tolerance	The maximum relative error for which a predicted sequence is still considered to have matched the precursor mass. TYPE: float DEFAULT: 5e-05
max_isotope	The maximum number of additional neutrons for isotopes whose mass a predicted sequence's mass is considered when comparing to the precursor mass. All additional nucleon numbers from 1 to max_isotope inclusive are considered. TYPE: int DEFAULT: 1
min_log_prob	Minimum log probability to stop decoding early. If a sequence probability is less than this value it is marked as complete. Defaults to -inf. TYPE: float DEFAULT: -float('inf')
return_beam	Optionally return beam-search results. Ignored in greedy search. TYPE: bool DEFAULT: False

RETURNS	DESCRIPTION
dict[str, Any]	list[list[str]]: The predicted sequence as a list of residue tokens. This method will return an empty list for each spectrum in the batch where decoding fails i.e. no sequence that fits the precursor mass to within a tolerance is found.