torchcell.data.Unperturbed

class Unperturbed[source]

Bases: GraphProcessor

Preserve the original graph, storing perturbation and phenotype data alongside.

Keeps the base graph structure intact for later perturbation in the pipeline.

This processor: 1. Keeps the original graph structure intact 2. Stores perturbation information separately 3. Records phenotype data without modifying the graph 4. Can be used as a base for applying perturbations later in the pipeline

Attributes remain unchanged:

  • Node features: X ∈ ℝ^(N×d) stays as X ∈ ℝ^(N×d)

  • Edge structure: E ∈ ℤ^(2×|E|) stays as E ∈ ℤ^(2×|E|)

process(cell_graph: HeteroData, phenotype_info: list[Phenotype | FitnessPhenotype | GeneInteractionPhenotype | GeneEssentialityPhenotype | GradedGeneEssentialityPhenotype | SyntheticLethalityPhenotype | SyntheticRescuePhenotype | CalMorphPhenotype | MicroarrayExpressionPhenotype | MicroarrayExpressionScorePhenotype | MicroarrayExpressionRatioPhenotype | InductionTimecourseExpressionPhenotype | RNASeqExpressionPhenotype | PseudobulkExpressionPhenotype | VisualScorePhenotype | MetabolitePhenotype | ProteinAbundancePhenotype | ProteinFoldChangePhenotype | EnvironmentResponsePhenotype | ProductTiterPhenotype | ProteinTurnoverPhenotype | ProteinSynthesisRatePhenotype | PhosphositeIntensityPhenotype | FluxPhenotype | PromoterActivityPhenotype | PooledSortSeqExpressionPhenotype | BiosensorFluorescencePhenotype | MorphologyPhenotype | MrnaNumberFractionPhenotype | FitnessContrastPhenotype | SingleCellExpressionPhenotype | LifeCyclePhenotype | GenomeArchitecturePhenotype], data: list[dict[str, Experiment | FitnessExperiment | GeneInteractionExperiment | GeneEssentialityExperiment | SyntheticLethalityExperiment | SyntheticRescueExperiment | CalMorphExperiment | MicroarrayExpressionExperiment | MicroarrayExpressionScoreExperiment | MicroarrayExpressionRatioExperiment | InductionTimecourseExpressionExperiment | RNASeqExpressionExperiment | PseudobulkExpressionExperiment | VisualScoreExperiment | MetaboliteExperiment | ProteinAbundanceExperiment | ProteinFoldChangeExperiment | EnvironmentResponseExperiment | StrainEnvironmentResponseExperiment | SegregantGrowthExperiment | SegregantPerturbationExperiment | ProductTiterExperiment | ProteinTurnoverExperiment | ProteinSynthesisRateExperiment | FluxExperiment | PromoterActivityExperiment | PooledSortSeqExpressionExperiment | BiosensorFluorescenceExperiment | GradedGeneEssentialityExperiment | PhosphositeIntensityExperiment | MorphologyExperiment | MrnaNumberFractionExperiment | FitnessContrastExperiment | SegregantExpressionExperiment | LifeCycleExperiment | PseudobulkUmiCountExperiment | GenomeArchitectureExperiment | ExperimentReference | FitnessExperimentReference | GeneInteractionExperimentReference | GeneEssentialityExperimentReference | SyntheticLethalityExperimentReference | SyntheticRescueExperimentReference | CalMorphExperimentReference | MicroarrayExpressionExperimentReference | MicroarrayExpressionScoreExperimentReference | MicroarrayExpressionRatioExperimentReference | InductionTimecourseExpressionExperimentReference | RNASeqExpressionExperimentReference | PseudobulkExpressionExperimentReference | VisualScoreExperimentReference | MetaboliteExperimentReference | ProteinAbundanceExperimentReference | ProteinFoldChangeExperimentReference | EnvironmentResponseExperimentReference | StrainEnvironmentResponseExperimentReference | SegregantGrowthExperimentReference | SegregantPerturbationExperimentReference | ProductTiterExperimentReference | ProteinTurnoverExperimentReference | ProteinSynthesisRateExperimentReference | FluxExperimentReference | PromoterActivityExperimentReference | PooledSortSeqExpressionExperimentReference | BiosensorFluorescenceExperimentReference | GradedGeneEssentialityExperimentReference | PhosphositeIntensityExperimentReference | MorphologyExperimentReference | MrnaNumberFractionExperimentReference | FitnessContrastExperimentReference | SegregantExpressionExperimentReference | LifeCycleExperimentReference | PseudobulkUmiCountExperimentReference | GenomeArchitectureExperimentReference]]) → HeteroData[source]

Return the original graph with perturbation and phenotype data attached.