Index

A

accumulation_steps() (in module torchcell.trainers.int_hetero_cell) adapter_drift_against() (in module torchcell.knowledge_graphs.kg_manifest) adapter_file_relpaths() (in module torchcell.knowledge_graphs.kg_manifest) adapter_node_sites() (in module torchcell.datamodels.ontology_checks) adapter_optional_traversals() (in module torchcell.datamodels.ontology_checks) adapter_property_mismatches() (in module torchcell.datamodels.ontology_checks) AdapterContribution (class in torchcell.knowledge_graphs.build_time_projection) AdapterDrift (class in torchcell.knowledge_graphs.kg_manifest) AdapterNodeSite (class in torchcell.datamodels.ontology_checks) AdapterRate (class in torchcell.knowledge_graphs.build_time_projection) AdapterTiming (class in torchcell.knowledge_graphs.build_time_projection) AdaptiveWeighting (class in torchcell.losses.mle_dist_supcr) (class in torchcell.losses.mle_wasserstein) add() (SharedRecordRules method) (VerificationReport method) add_all() (SharedRecordRules method) add_gene_protein_overview() (SCerevisiaeGraph static method) add_genetic_edges() (SCerevisiaeGraph static method) add_json_data_to_graph() (SCerevisiaeGraph static method) add_loci_information() (SCerevisiaeGraph static method) add_pathway_annotation() (SCerevisiaeGraph static method) add_physical_edges() (SCerevisiaeGraph static method) add_regulatory_edges() (SCerevisiaeGraph static method) AdmissionReport (class in torchcell.knowledge_graphs.kg_manifest) aggregate_check() (Aggregator method) (DeletionKeyedGenotypeAggregator method) (GenotypeAggregator method) aggregate_key_raw() (Aggregator method) (DeletionKeyedGenotypeAggregator method) (GenotypeAggregator method) AggregationNormNotImplementedError (class in torchcell.models.hetero_cell_bipartite_dango_gi)

Aggregator (class in torchcell.data) all_dataloader() (CellDataModule method) all_genes (RecordFilter attribute) all_go_terms (SCerevisiaeGraph property) AlleleEdit (class in torchcell.datamodels.schema) AllelePerturbation (class in torchcell.datamodels.schema) alleles_at() (StrainBackground method) AlleleSpec (class in torchcell.datamodels.strain_background) AminoAcidCooper2010Adapter (class in torchcell.adapters) AminoAcidCooper2010Dataset (class in torchcell.datasets.scerevisiae.cooper2010) AminoAcidMulleder2016Adapter (class in torchcell.adapters) AminoAcidMulleder2016Dataset (class in torchcell.datasets.scerevisiae.mulleder2016) analyze_reactions_without_genes() (in module torchcell.metabolism.yeast_GEM) analyze_references() (in module torchcell.knowledge_graphs.incremental_import) any_genes (RecordFilter attribute) apply() (MediaBounds method) apply_paper_style() (in module torchcell.utils) apply_pathway() (in module torchcell.metabolism.pathway) AssayType (class in torchcell.datamodels.schema) assemble() (in module torchcell.datamodels.compound_identity_curate) asset_images_dir() (in module torchcell.utils) AttentionalGraphAggregation (class in torchcell.models.hetero_cell_bipartite_dango) (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) (class in torchcell.models.hetero_cell_nsa_retry) AttentionConvWrapper (class in torchcell.models.hetero_cell_bipartite_dango) (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) audit_sourced_value() (in module torchcell.verification) AutoBinStrategy (class in torchcell.transforms.coo_regression_to_classification) (class in torchcell.transforms.regression_to_classification)

B

backfill_key() (in module torchcell.literature) backfill_mirror() (in module torchcell.literature) BackfillReport (class in torchcell.literature) BackgroundAllele (class in torchcell.datamodels.schema) backward() (FastSoftSort static method) BarcodedKanMxDeletionPerturbation (class in torchcell.datamodels.schema) BaseBinningStrategy (class in torchcell.transforms.coo_regression_to_classification) (class in torchcell.transforms.regression_to_classification) batch_report_from_members() (in module torchcell.knowledge_graphs.kg_manifest) BatchAdmissionReport (class in torchcell.knowledge_graphs.kg_manifest) behind_main() (in module torchcell.knowledge_graphs.releases) betaxanthin_demand_ids() (in module torchcell.metabolism.betaxanthin) BetaxanthinCachera2023Adapter (class in torchcell.adapters) BetaxanthinCachera2023Dataset (class in torchcell.datasets.scerevisiae.cachera2023) BiologicAgentClass (class in torchcell.datamodels.schema) BiologicPerturbation (class in torchcell.datamodels.schema) bipartite_graph (YeastGEM property) blank_literals() (in module torchcell.knowledge_graphs.supported_queries.cypher_deps) Bloom2019Adapter (class in torchcell.adapters) Bloom2019Dataset (class in torchcell.datasets.scerevisiae.bloom2019) bootstrap_manifest() (in module torchcell.knowledge_graphs.kg_manifest) bootstrap_package_version() (in module torchcell.knowledge_graphs.release_snapshot) bound_for() (UptakePolicy method)

box_plot() (in module torchcell.viz.fitness) (in module torchcell.viz.genetic_interaction_score) BufferedWeightedDistLoss (class in torchcell.losses.mle_dist_supcr) BufferedWeightedSupCRCell (class in torchcell.losses.mle_dist_supcr) (class in torchcell.losses.mle_wasserstein) BufferedWeightedWassersteinLoss (class in torchcell.losses.mle_wasserstein) build() (NodeEmbeddingBuilder class method) (ParameterTable class method) build_betaxanthin_pathway() (in module torchcell.metabolism.betaxanthin) build_cache() (IncidenceSubgraphRepresentation method) (LazySubgraphRepresentation method) build_dataset() (in module torchcell.database.build_dataset_lmdb) build_exchange_index() (in module torchcell.metabolism.media) build_gem_tensors() (in module torchcell.metabolism.constraints) build_gene_multigraph() (in module torchcell.graph) build_impact_report() (in module torchcell.provenance) build_layout() (in module torchcell.paper.ontology_svg) build_manifest() (in module torchcell.literature) build_mirror_record() (in module torchcell.knowledge_graphs.head_ontology) build_ontology_graph() (in module torchcell.paper.ontology_graph) BuildCommand (class in torchcell.database.build_command) BuildManifest (class in torchcell.provenance) BuildTimeProjection (class in torchcell.knowledge_graphs.build_time_projection) ByGenotype (class in torchcell.datamodels.strain_background)

C

calculate_rolling_correlation() (in module torchcell.models.hetero_cell_bipartite_dango_gi) (in module torchcell.models.hetero_cell_bipartite_dango_gi_lazy) calculate_weight_l2_norm() (in module torchcell.models.cell_graph_transformer) (in module torchcell.models.equivariant_cell_graph_transformer) (in module torchcell.models.hetero_cell_bipartite_dango_gi) (in module torchcell.models.hetero_cell_bipartite_dango_gi_lazy) calculate_window_bounds() (in module torchcell.sequence) calculate_window_bounds_symmetric() (in module torchcell.sequence) calibrate() (in module torchcell.knowledge_graphs.build_time_projection) CalibrationTimings (class in torchcell.knowledge_graphs.build_time_projection) CalmDataset (class in torchcell.datasets) CalMorphExperiment (class in torchcell.datamodels.schema) CalMorphExperimentReference (class in torchcell.datamodels.schema) CalMorphPhenotype (class in torchcell.datamodels.schema) canonical() (ContractSpec method) cap_for() (SubsetConfig method) Caption (class in torchcell.database.browser_style) capture_by_doi() (in module torchcell.literature) Card (class in torchcell.paper.ontology_svg) CarotenoidOzaydin2013Adapter (class in torchcell.adapters) CarotenoidOzaydin2013Dataset (class in torchcell.datasets.scerevisiae.ozaydin2013) CarrierGapCensus (class in torchcell.verification) CatalyticUnits (class in torchcell.metabolism.constraints) CategoricalEntropyRegLoss (class in torchcell.losses.multi_dim_nan_tolerant) CaudalPanTranscriptome2024Adapter (class in torchcell.adapters) CaudalPanTranscriptome2024Dataset (class in torchcell.datasets.scerevisiae.caudal2024) Cell (class in torchcell.paper.tables) cell_adapter_source() (in module torchcell.datamodels.ontology_checks) cell_adapter_surface() (in module torchcell.knowledge_graphs.kg_manifest) CellAdapter (class in torchcell.adapters) CellDataModule (class in torchcell.datamodules) CellGraphTransformer (class in torchcell.models.cell_graph_transformer) (class in torchcell.models.equivariant_cell_graph_transformer) CellGraphTransformerMetabolism (class in torchcell.models.cell_graph_transformer_metabolism) CellposeSegConfig (class in torchcell.sga) census() (SharedRecordRules method) ChangeKind (class in torchcell.provenance) chebi_by_cids() (PubChemClient method) check_admission() (in module torchcell.knowledge_graphs.kg_manifest) check_all() (in module torchcell.provenance) check_batch_admission() (in module torchcell.knowledge_graphs.kg_manifest) check_learnable_embedding() (NodeEmbeddingBuilder class method) check_manifest() (in module torchcell.provenance) check_manifest_pin() (in module torchcell.data) check_positive() (DnaSelectionResult class method) check_pub_info() (Publication method) check_repo() (in module torchcell.knowledge_graphs.supported_queries.check) check_seq_len() (DnaSelectionResult class method) check_sorted_and_unique_indices() (DataModuleIndex class method) check_sorted_indices() (IndexSplit class method) check_strand() (DnaSelectionResult class method) check_temperature() (Temperature method) check_window() (DnaWindowResult class method) checkout_commit() (in module torchcell.knowledge_graphs.supported_queries.check) checkout_package_version() (in module torchcell.knowledge_graphs.kg_manifest) CheckReport (class in torchcell.knowledge_graphs.supported_queries.check) children_of() (OntologyGraph method) cid_property_url() (in module torchcell.datamodels.compound_identity_curate) clamp_values() (BaseBinningStrategy method), [1] classify_change() (in module torchcell.provenance) cleanup_lock_files() (FileLockHelper class method) close() (CpuExperimentLoaderMultiprocessing method) close_lmdb() (Aggregator method) (Converter method) (Deduplicator method) (ExperimentDataset method) (Neo4jCellDataset method) closure_at_ref() (in module torchcell.knowledge_graphs.kg_manifest) closure_compatibility() (in module torchcell.knowledge_graphs.releases) closure_in_worktree() (in module torchcell.knowledge_graphs.kg_manifest) CodonFrequencyDataset (class in torchcell.datasets) collate_fn() (DensePaddingCollater method) collect_pointers() (in module torchcell.datamodels.interned_constant) collection_key() (ZoteroLibrary method) collection_tree() (ZoteroLibrary method) Column (class in torchcell.paper.tables) combine() (ExperimentReferenceIndex method) combine_with_super_node() (SCerevisiaeGraph static method) CombinedCELoss (class in torchcell.losses.multi_dim_nan_tolerant) CombinedOrdinalCELoss (class in torchcell.losses.multi_dim_nan_tolerant) CombinedRegressionLoss (class in torchcell.losses.multi_dim_nan_tolerant) commit_date() (in module torchcell.knowledge_graphs.releases) commit_index() (in module torchcell.knowledge_graphs.releases) compare_reaction_delta_g() (in module torchcell.metabolism.constraints) CompartmentParameters (class in torchcell.metabolism.flux_layer) compatibility() (in module torchcell.knowledge_graphs.releases) compatibility_with_surface() (in module torchcell.knowledge_graphs.releases) ComponentDefinition (class in torchcell.datamodels.schema) ComponentResolution (class in torchcell.metabolism.media) composite_sha256() (in module torchcell.knowledge_graphs.release_snapshot) CompositeFitnessConverter (class in torchcell.datamodels.fitness_composite_conversion) composition_targets() (in module torchcell.datamodels.ontology_checks) CompositionEdge (class in torchcell.paper.ontology_graph) Compound (class in torchcell.datamodels.schema) compound_has_identity() (in module torchcell.datamodels.ontology_checks) compound_has_identity_gap() (in module torchcell.datamodels.ontology_checks) compound_identity_key() (in module torchcell.datamodels.identity) CompoundIdentityIssue (class in torchcell.datamodels.ontology_checks) CompoundIdentityRecord (class in torchcell.datamodels.compound_identity) CompoundIdentityResolution (class in torchcell.datamodels.compound_identity) CompoundResolutionStatus (class in torchcell.datamodels.compound_identity) compute() (ListMLEMetric method) compute_bins() (AutoBinStrategy method), [1] (EqualFrequencyStrategy method), [1] (EqualWidthStrategy method), [1] compute_centers() (CategoricalEntropyRegLoss method) compute_codon_frequency() (in module torchcell.sequence) compute_dataset_name_index() (Neo4jCellDataset method) compute_diffusion_loss() (GeneInteractionDiff method) compute_dimension_loss() (SupCR method) compute_experiment_reference_index_parallel() (in module torchcell.data) compute_experiment_reference_index_sequential() (in module torchcell.data) compute_gene_set() (Bloom2019Dataset method) (ExperimentDataset method) (Genome method) compute_gene_set_parallel() (ExperimentDataset method) compute_gene_set_sequential() (ExperimentDataset method) compute_graph_regularization_loss() (CellGraphTransformer method), [1] compute_interaction_loss() (DangoLoss method) compute_is_any_deletion_gene_index() (Neo4jCellDataset method) compute_is_any_perturbed_gene_index() (Neo4jCellDataset method) compute_manifest() (in module torchcell.provenance) compute_onehot_labels() (BaseBinningStrategy method), [1] compute_ordinal_labels() (BaseBinningStrategy method), [1] compute_pairwise_distances() (CategoricalEntropyRegLoss method) compute_perturbation_count_index() (Neo4jCellDataset method) compute_phenotype_info() (Neo4jCellDataset method) compute_phenotype_label_index() (Neo4jCellDataset method) compute_phenotype_reference_std() (SmfCostanzo2016Dataset static method) compute_prediction_stats() (RegressionTask method) compute_reconstruction_loss() (DangoLoss method) compute_sha256_hash() (in module torchcell.data) compute_similarity() (SupCR method) compute_smoothness() (in module torchcell.models.cell_graph_transformer) (in module torchcell.models.equivariant_cell_graph_transformer) (VisGraphDegen static method)

compute_soft_labels() (BaseBinningStrategy method), [1] compute_target_distances() (CategoricalEntropyRegLoss method) compute_weighted_mse_loss() (DangoLoss method) Concentration (class in torchcell.datamodels.schema) concentration_prior() (in module torchcell.metabolism.parameters) ConcentrationUnit (class in torchcell.datamodels.schema) ConditionalAlleleClass (class in torchcell.datamodels.schema) ConditionalAllelePerturbation (class in torchcell.datamodels.schema) configure_optimizers() (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method), [1], [2], [3], [4] (SimpleLinearRegressionTask method) configured_head_ontology() (in module torchcell.knowledge_graphs.head_ontology) constant_id() (in module torchcell.datamodels.interned_constant) constraint_loss() (FluxLayer method) constraints_cypher() (in module torchcell.knowledge_graphs.incremental_import) ConstructedOrf (class in torchcell.datamodels.schema) content_hashes_from_csv() (in module torchcell.knowledge_graphs.releases) content_hashes_from_store() (in module torchcell.knowledge_graphs.releases) content_sha256() (in module torchcell.knowledge_graphs.releases) contract_spec() (in module torchcell.provenance) ContractSpec (class in torchcell.provenance) control_spec() (Bloom2019Dataset method) CONVENTION (EvidenceTier attribute) conversion_map (CompositeFitnessConverter property) (Converter property) (GeneEssentialityToFitnessConverter property) (SyntheticLethalityToFitnessConverter property) ConversionEntry (class in torchcell.datamodels.conversion) ConversionMap (class in torchcell.datamodels.conversion) convert() (CompositeFitnessConverter method) (Converter method) convert_and_validate_count() (RNASeqExpressionPhenotype class method) convert_and_validate_expression() (MicroarrayExpressionPhenotype class method) convert_and_validate_log2_ratio() (MicroarrayExpressionPhenotype class method) (PseudobulkExpressionPhenotype class method) convert_and_validate_log2_se() (MicroarrayExpressionPhenotype class method) convert_and_validate_n_replicates() (MicroarrayExpressionPhenotype class method) convert_and_validate_tpm() (RNASeqExpressionPhenotype class method) convert_and_validate_variance() (MicroarrayExpressionPhenotype class method) Converter (class in torchcell.datamodels.conversion) COOInverseCompose (class in torchcell.transforms.coo_regression_to_classification) COOLabelBinningTransform (class in torchcell.transforms.coo_regression_to_classification) COOLabelNormalizationTransform (class in torchcell.transforms.coo_regression_to_classification) copy_verified() (in module torchcell.data) CopyNumberVariantPerturbation (class in torchcell.datamodels.schema) CosineAnnealingWarmupRestarts (class in torchcell.scheduler.cosine_annealing_warmup) coverage() (in module torchcell.losses.distributional) coverage_report() (FluxLayer method) CpuExperimentLoaderMultiprocessing (class in torchcell.loader.cpu_experiment_loader) cql_file() (SupportedQuery method) create_aggregate_entry() (Aggregator method) create_app() (in module torchcell.literature) create_app_from_env() (in module torchcell.literature) create_calmorph_experiment() (ScmdOhnuki2018Dataset static method) (ScmdOhya2005Dataset static method) create_conv_layer() (in module torchcell.models.hetero_cell_bipartite_dango_gi) (in module torchcell.models.hetero_cell_bipartite_dango_gi_lazy) create_deduplicate_entry() (Deduplicator method) (MeanExperimentDeduplicator method) create_double_mutant_expression_experiment() (DmMicroarraySameith2015Dataset static method) create_experiment() (AminoAcidCooper2010Dataset method) (AminoAcidMulleder2016Dataset method) (BetaxanthinCachera2023Dataset method) (Bloom2019Dataset method) (CarotenoidOzaydin2013Dataset method) (CaudalPanTranscriptome2024Dataset method) (CrispriChemgenSmith2016Dataset method) (CrispriMormino2022Dataset method) (CrisprMagicLian2019Dataset method) (DmfCostanzo2016Dataset static method) (DmfKuzmin2018Dataset static method) (DmfKuzmin2020Dataset static method) (DmiCostanzo2016Dataset static method) (DmiKuzmin2018Dataset static method) (DmiKuzmin2020Dataset static method) (DmMicroarraySameith2015Dataset method) (EnvChemgenAuesukaree2009Dataset method) (EnvChemgenCostanzo2021Dataset method) (EnvChemgenHoepfner2014Dataset method) (EnvChemgenMota2024Dataset method) (EnvChemgenVanacloig2022Dataset method) (EnvChemgenWildenhain2015Dataset method) (ExperimentDataset method) (FattyAcidSmith2006Dataset method) (FattyAcidXue2025Dataset method) (GeneEssentialitySgdDataset static method) (MetaboliteDaSilveira2014Dataset method) (MetaboliteZelezniak2018Dataset method) (MicroarrayKemmeren2014Dataset method) (NadalRibellesPerturbSeq2025Dataset method) (OrganicAcidYoshida2012Dataset method) (ProteomeMessner2023Dataset method) (ProteomeZelezniak2018Dataset method) (ScmdOhnuki2018Dataset method) (ScmdOhnuki2022Dataset method) (ScmdOhya2005Dataset method) (SmfBaryshnikova2010Dataset method) (SmfCostanzo2016Dataset static method) (SmfKuzmin2018Dataset static method) (SmfKuzmin2020Dataset static method) (SmfODuibhir2014Dataset method) (SmMicroarraySameith2015Dataset method) (SynthLethalityYeastSynthLethDbDataset static method) (SynthRescueYeastSynthLethDbDataset static method) (TmfKuzmin2018Dataset static method) (TmfKuzmin2020Dataset static method) (TmiKuzmin2018Dataset static method) (TmiKuzmin2020Dataset static method) (YeastPhenomeDataset method) create_expression_experiment() (MicroarrayKemmeren2014Dataset static method) create_G_go() (SCerevisiaeGraph method) create_G_tflink() (SCerevisiaeGraph method) create_go_subgraph() (SCerevisiaeGraph method) create_single_mutant_expression_experiment() (SmMicroarraySameith2015Dataset static method) create_string_graphs() (SCerevisiaeGraph method) CrisprActivationPerturbation (class in torchcell.datamodels.schema) CrisprConstruct (class in torchcell.datamodels.schema) CrisprDeletionPerturbation (class in torchcell.datamodels.schema) CrispriChemgenSmith2016Dataset (class in torchcell.datasets.scerevisiae.smith2016) CrispriMormino2022Dataset (class in torchcell.datasets.scerevisiae.mormino2022) CrisprInterferencePerturbation (class in torchcell.datamodels.schema) CrisprMagicLian2019Dataset (class in torchcell.datasets.scerevisiae.lian2019) CrossAttention (class in torchcell.models.diffusion_decoder) CrossAttnHead (class in torchcell.models.equivariant_cell_graph_transformer) CrossGeneMixing (class in torchcell.models.equivariant_cell_graph_transformer) CsvGroup (class in torchcell.knowledge_graphs.incremental_import) CultureEnvironment (class in torchcell.datamodels.schema) CultureFormat (class in torchcell.datamodels.schema) curate() (in module torchcell.datamodels.compound_identity_curate) curated (CompoundIdentityResolution property) CuratedRow (class in torchcell.datamodels.compound_identity_curate) CurationDirective (class in torchcell.datamodels.compound_identity_curate) cx (Card property) cy (Card property)

D

DampPerturbation (class in torchcell.datamodels.schema) Dango (class in torchcell.models.dango) DangoLikeHyperSAGNN (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) DangoLoss (class in torchcell.losses.dango) DangoLossSched (class in torchcell.losses.dango) DangoPreTrain (class in torchcell.models.dango) data (MonotonicParameter property) data_chunker() (CellAdapter method) DataModuleIndex (class in torchcell.datamodules) DataModuleIndexDetails (class in torchcell.datamodules) dataset_adapter_files() (in module torchcell.knowledge_graphs.kg_manifest) dataset_conf_methods() (in module torchcell.knowledge_graphs.kg_manifest) dataset_default_root() (in module torchcell.database.build_dataset_lmdb) dataset_name_index (Neo4jCellDataset property) dataset_registry (in module torchcell.datasets.dataset_registry) dataset_sizes() (in module torchcell.knowledge_graphs.build_time_projection) DatasetCheck (class in torchcell.provenance) DatasetDrift (class in torchcell.knowledge_graphs.releases) datasets() (in module torchcell.knowledge_graphs.releases) DatasetSignalRecord (class in torchcell.paper.tables) DatasetSize (class in torchcell.knowledge_graphs.build_time_projection) DatasetSplit (class in torchcell.datamodules) db (Genome property) DCell (class in torchcell.models.dcell) DCellGraphProcessor (class in torchcell.data) DCellLoss (class in torchcell.losses.dcell) DCellOpt (class in torchcell.models.dcell_opt) DCellRegressionSlimTask (class in torchcell.trainers.dcell_regression_slim) DCellRegressionTask (class in torchcell.trainers.dcell_regression) DCellSubsystem (class in torchcell.models.dcell) (class in torchcell.models.dcell_opt) Deduplicator (class in torchcell.data) DeepSet (class in torchcell.models.deep_set) default_phenotype_bytes() (in module torchcell.paper.tables) default_retry_delay (FileLockHelper attribute) default_timeout (FileLockHelper attribute) DeletionKeyedGenotypeAggregator (class in torchcell.data) DeletionPerturbation (class in torchcell.datamodels.schema) denoise() (DiffusionDecoder method) DenoisingBlock (class in torchcell.models.diffusion_decoder) denormalize() (COOLabelNormalizationTransform method) (LabelNormalizationTransform method) dense_padded_collate() (in module torchcell.loader.dense_padding_data_loader) dense_padded_from_data_list() (in module torchcell.loader.dense_padding_data_loader) DensePaddingCollater (class in torchcell.loader.dense_padding_data_loader) DensePaddingDataLoader (class in torchcell.loader.dense_padding_data_loader) DerivationMethod (class in torchcell.verification) derive_se() (in module torchcell.datamodels.schema) DERIVED (EvidenceTier attribute) descendants_of() (OntologyGraph method) describe() (AdapterDrift method) description (DampPerturbation attribute) dev_experiment_ids() (in module torchcell.knowledge_graphs.kg_manifest) df (ExperimentDataset property) df_summary() (DataModuleIndexDetails method) diff() (in module torchcell.knowledge_graphs.releases) diff_bounds() (in module torchcell.metabolism.media) diff_surfaces() (in module torchcell.provenance) DiffusionDecoder (class in torchcell.models.diffusion_decoder) DiffusionLoss (class in torchcell.losses.diffusion_loss) DiffusionRegressionTask (class in torchcell.trainers.int_hetero_cell) discover_csv_groups() (in module torchcell.knowledge_graphs.incremental_import) display_label() (in module torchcell.utils) dist_param_dim() (in module torchcell.losses.distributional) DistHead (class in torchcell.losses.distributional) DmfCostanzo2016Adapter (class in torchcell.adapters) DmfCostanzo2016Dataset (class in torchcell.datasets.scerevisiae.costanzo2016) DmfKuzmin2018Adapter (class in torchcell.adapters) DmfKuzmin2018Dataset (class in torchcell.datasets.scerevisiae.kuzmin2018) DmfKuzmin2020Adapter (class in torchcell.adapters) DmfKuzmin2020Dataset (class in torchcell.datasets.scerevisiae.kuzmin2020)

DmiCostanzo2016Adapter (class in torchcell.adapters) DmiCostanzo2016Dataset (class in torchcell.datasets.scerevisiae.costanzo2016) DmiKuzmin2018Adapter (class in torchcell.adapters) DmiKuzmin2018Dataset (class in torchcell.datasets.scerevisiae.kuzmin2018) DmiKuzmin2020Adapter (class in torchcell.adapters) DmiKuzmin2020Dataset (class in torchcell.datasets.scerevisiae.kuzmin2020) DmMicroarraySameith2015Adapter (class in torchcell.adapters) DmMicroarraySameith2015Dataset (class in torchcell.datasets.scerevisiae.sameith2015) DnaSelectionResult (class in torchcell.sequence) DnaWindowResult (class in torchcell.sequence) doi_in_library() (ZoteroLibrary method) DoseBasis (class in torchcell.datamodels.schema) download() (AminoAcidCooper2010Dataset method) (AminoAcidMulleder2016Dataset method) (BetaxanthinCachera2023Dataset method) (Bloom2019Dataset method) (CarotenoidOzaydin2013Dataset method) (CaudalPanTranscriptome2024Dataset method) (CrispriChemgenSmith2016Dataset method) (CrispriMormino2022Dataset method) (CrisprMagicLian2019Dataset method) (DmfCostanzo2016Dataset method) (DmfKuzmin2018Dataset method) (DmfKuzmin2020Dataset method) (DmiCostanzo2016Dataset method) (DmiKuzmin2018Dataset method) (DmiKuzmin2020Dataset method) (DmMicroarraySameith2015Dataset method) (EnvChemgenAuesukaree2009Dataset method) (EnvChemgenCostanzo2021Dataset method) (EnvChemgenHoepfner2014Dataset method) (EnvChemgenMota2024Dataset method) (EnvChemgenVanacloig2022Dataset method) (EnvChemgenWildenhain2015Dataset method) (ExperimentDataset method) (FattyAcidSmith2006Dataset method) (FattyAcidXue2025Dataset method) (GeneEssentialitySgdDataset method) (MetaboliteDaSilveira2014Dataset method) (MetaboliteZelezniak2018Dataset method) (MicroarrayKemmeren2014Dataset method) (NadalRibellesPerturbSeq2025Dataset method) (OrganicAcidYoshida2012Dataset method) (ProteomeMessner2023Dataset method) (ProteomeZelezniak2018Dataset method) (ScmdOhnuki2018Dataset method) (ScmdOhnuki2022Dataset method) (ScmdOhya2005Dataset method) (SmfBaryshnikova2010Dataset method) (SmfCostanzo2016Dataset method) (SmfKuzmin2018Dataset method) (SmfKuzmin2020Dataset method) (SmfODuibhir2014Dataset method) (SmMicroarraySameith2015Dataset method) (SynthLethalityYeastSynthLethDbDataset method) (SynthRescueYeastSynthLethDbDataset method) (TmfKuzmin2018Dataset method) (TmfKuzmin2020Dataset method) (TmiKuzmin2018Dataset method) (TmiKuzmin2020Dataset method) (YeastPhenomeDataset method) download_artifact() (ZoteroLibrary method) download_string_data() (SCerevisiaeGraph method) download_tflink_data() (SCerevisiaeGraph method) dropout() (in module torchcell.datamodels.media) dryad_files() (in module torchcell.literature) dumps() (QueryRegistry method) duplicate_check() (Deduplicator method) (MeanExperimentDeduplicator method) duplicate_key() (Deduplicator method) (MeanExperimentDeduplicator method) dynamic_box() (FluxLayer method)

E

edge_incidence_cache (IncidenceSubgraphRepresentation property) (LazySubgraphRepresentation property) effective_records() (SubsetConfig method) embed() (Esm2 method) (FungalUpDownTransformer method) (NucleotideModel method) (NucleotideTransformer method) (PeptideModel method) (ProtT5 method) enable_profiling() (DCellOpt method) end_leq_start() (DnaSelectionResult method) EndpointRule (class in torchcell.datamodels.schema) energy_score() (in module torchcell.losses.distributional) EngineeredCopyNumberPerturbation (class in torchcell.datamodels.schema) enriched (BackfillReport property) enum_value_collisions() (in module torchcell.datamodels.ontology_checks) EnvChemgenAuesukaree2009Adapter (class in torchcell.adapters) EnvChemgenAuesukaree2009Dataset (class in torchcell.datasets.scerevisiae.auesukaree2009) EnvChemgenCostanzo2021Adapter (class in torchcell.adapters) EnvChemgenCostanzo2021Dataset (class in torchcell.datasets.scerevisiae.costanzo2021) EnvChemgenHoepfner2014Adapter (class in torchcell.adapters) EnvChemgenHoepfner2014Dataset (class in torchcell.datasets.scerevisiae.hoepfner2014) EnvChemgenMota2024Adapter (class in torchcell.adapters) EnvChemgenMota2024Dataset (class in torchcell.datasets.scerevisiae.mota2024) EnvChemgenVanacloig2022Adapter (class in torchcell.adapters) EnvChemgenVanacloig2022Dataset (class in torchcell.datasets.scerevisiae.vanacloig2022) EnvChemgenWildenhain2015Adapter (class in torchcell.adapters) EnvChemgenWildenhain2015Dataset (class in torchcell.datasets.scerevisiae.wildenhain2015) Environment (class in torchcell.datamodels.schema) environment() (SmfBaryshnikova2010Dataset static method) environment_compound_collisions() (in module torchcell.datamodels.ontology_checks) environment_identity() (in module torchcell.datamodels.identity) environment_perturbation_identity() (in module torchcell.datamodels.identity) EnvironmentCompoundCollision (class in torchcell.datamodels.ontology_checks) EnvironmentPerturbation (class in torchcell.datamodels.schema) EnvironmentPhysicalPerturbation (class in torchcell.datamodels.schema) EnvironmentResponseExperiment (class in torchcell.datamodels.schema) EnvironmentResponseExperimentReference (class in torchcell.datamodels.schema) EnvironmentResponsePhenotype (class in torchcell.datamodels.schema) EqualFrequencyStrategy (class in torchcell.transforms.coo_regression_to_classification) (class in torchcell.transforms.regression_to_classification) EqualWidthStrategy (class in torchcell.transforms.coo_regression_to_classification) (class in torchcell.transforms.regression_to_classification) EquivariantPerturbationTransform (class in torchcell.models.equivariant_cell_graph_transformer) Esm2 (class in torchcell.models.esm2) Esm2Dataset (class in torchcell.datasets) evidence_census() (HeterologousPathway method) EvidenceTier (class in torchcell.metabolism.pathway) ExchangeBound (class in torchcell.metabolism.media) ExchangeIndex (class in torchcell.metabolism.media) excluded_names (MediaBounds property) ExistingEdgeFilter (class in torchcell.knowledge_graphs.incremental_import) Experiment (class in torchcell.datamodels.schema) experiment_class (AminoAcidCooper2010Dataset property) (AminoAcidMulleder2016Dataset property) (BetaxanthinCachera2023Dataset property) (Bloom2019Dataset property) (CarotenoidOzaydin2013Dataset property) (CaudalPanTranscriptome2024Dataset property) (CrispriChemgenSmith2016Dataset property) (CrispriMormino2022Dataset property) (CrisprMagicLian2019Dataset property) (DmfCostanzo2016Dataset property) (DmfKuzmin2018Dataset property) (DmfKuzmin2020Dataset property) (DmiCostanzo2016Dataset property) (DmiKuzmin2018Dataset property) (DmiKuzmin2020Dataset property) (DmMicroarraySameith2015Dataset property) (EnvChemgenAuesukaree2009Dataset property) (EnvChemgenCostanzo2021Dataset property) (EnvChemgenHoepfner2014Dataset property) (EnvChemgenMota2024Dataset property) (EnvChemgenVanacloig2022Dataset property) (EnvChemgenWildenhain2015Dataset property) (ExperimentDataset property) (FattyAcidSmith2006Dataset property) (FattyAcidXue2025Dataset property) (GeneEssentialitySgdDataset property) (MetaboliteDaSilveira2014Dataset property) (MetaboliteZelezniak2018Dataset property) (MicroarrayKemmeren2014Dataset property) (NadalRibellesPerturbSeq2025Dataset property) (OrganicAcidYoshida2012Dataset property) (ProteomeMessner2023Dataset property) (ProteomeZelezniak2018Dataset property) (ScmdOhnuki2018Dataset property) (ScmdOhnuki2022Dataset property) (ScmdOhya2005Dataset property) (SmfBaryshnikova2010Dataset property) (SmfCostanzo2016Dataset property) (SmfKuzmin2018Dataset property) (SmfKuzmin2020Dataset property) (SmfODuibhir2014Dataset property) (SmMicroarraySameith2015Dataset property) (SynthLethalityYeastSynthLethDbDataset property) (SynthRescueYeastSynthLethDbDataset property) (TmfKuzmin2018Dataset property) (TmfKuzmin2020Dataset property) (TmiKuzmin2018Dataset property) (TmiKuzmin2020Dataset property) (YeastPhenomeDataset property)

experiment_closure() (in module torchcell.datamodels.ontology_checks) experiment_node_id() (in module torchcell.knowledge_graphs.kg_manifest) experiment_reference_index (ExperimentDataset property) experiment_results_dir() (in module torchcell.utils) experiment_root() (in module torchcell.utils) ExperimentDataset (class in torchcell.data) ExperimentReference (class in torchcell.datamodels.schema) ExperimentReferenceIndex (class in torchcell.data) ExpressionModulationPerturbation (class in torchcell.datamodels.schema) ExpressionRangeMultiplier (class in torchcell.datamodels.schema) extract_dependencies() (in module torchcell.knowledge_graphs.supported_queries.cypher_deps) extract_systematic_gene_names() (Bloom2019Dataset static method) (ExperimentDataset static method)

F

failing (QueryResult property) fast_soft_sort() (in module torchcell.losses.multi_dim_nan_tolerant) FastSoftSort (class in torchcell.losses.multi_dim_nan_tolerant) FattyAcidSmith2006Dataset (class in torchcell.datasets.scerevisiae.smith2006) FattyAcidXue2025Adapter (class in torchcell.adapters) FattyAcidXue2025Dataset (class in torchcell.datasets.scerevisiae.xue2025) feature_types (Genome property) fetch_oed_records() (in module torchcell.metabolism.enzyme_kinetics) fetch_si_data() (in module torchcell.literature) FieldSpec (class in torchcell.provenance) file_sha256() (in module torchcell.data) FileLockHelper (class in torchcell.utils) filter_by_contained_genes() (in module torchcell.graph) filter_by_date() (in module torchcell.graph) filter_existing_edges() (in module torchcell.knowledge_graphs.incremental_import) filter_go_IGI() (in module torchcell.graph) filter_redundant_terms() (in module torchcell.graph) find_item_by_doi() (ZoteroLibrary method) finding_class (LevelResult property) findings (VerificationReport property) fingerprint() (in module torchcell.provenance) first_emitting_km() (PredictorRegistry method) fitness_gene_set() (in module torchcell.verification) FitnessExperiment (class in torchcell.datamodels.schema) FitnessExperimentReference (class in torchcell.datamodels.schema) FitnessPhenotype (class in torchcell.datamodels.schema) flush() (PubChemClient method) FluxLayer (class in torchcell.metabolism.flux_layer) FluxLayerConfig (class in torchcell.metabolism.flux_layer) FluxMetaboliteHead (class in torchcell.models.cell_graph_transformer_metabolism) FluxScalarHead (class in torchcell.models.cell_graph_transformer_metabolism) format_batch_report() (in module torchcell.knowledge_graphs.kg_manifest) format_report() (in module torchcell.knowledge_graphs.kg_manifest) format_scientific_notation() (in module torchcell.utils) format_table() (in module torchcell.knowledge_graphs.releases) forward() (AttentionalGraphAggregation method), [1], [2], [3] (AttentionConvWrapper method), [1], [2] (BufferedWeightedDistLoss method) (BufferedWeightedSupCRCell method), [1] (BufferedWeightedWassersteinLoss method) (CategoricalEntropyRegLoss method) (CellGraphTransformer method), [1] (CellGraphTransformerMetabolism method) (CombinedCELoss method) (CombinedOrdinalCELoss method) (CombinedRegressionLoss method) (COOInverseCompose method) (COOLabelBinningTransform method) (COOLabelNormalizationTransform method) (CrossAttention method) (CrossAttnHead method) (CrossGeneMixing method) (Dango method) (DangoLikeHyperSAGNN method), [1] (DangoLoss method) (DangoLossSched method) (DangoPreTrain method) (DCell method) (DCellLoss method) (DCellOpt method) (DCellRegressionSlimTask method) (DCellRegressionTask method) (DCellSubsystem method), [1] (DeepSet method) (DenoisingBlock method) (DiffusionLoss method) (EquivariantPerturbationTransform method) (FastSoftSort static method) (FluxLayer method) (FluxMetaboliteHead method) (FluxScalarHead method) (GeneInteractionAttention method) (GeneInteractionDango method), [1] (GeneInteractionDiff method) (GeneInteractionPredictor method), [1], [2] (GlobalHead method) (GraphRegularizedTransformerLayer method), [1] (HeteroCellBipartite method) (HeteroCellNSA method) (HeteroConvAggregator method), [1] (HeteroNSA method) (HeteroNSAEncoder method) (HeteroToDenseMask method) (HyperSAGNN method), [1], [2] (ICLoss method) (ICLossStd method) (InverseCompose method) (LabelBinningTransform method) (LabelNormalizationTransform method) (LinearDecoder method) (LinearUntilFlipped method) (LinearUntilUniform method) (ListMLELoss method) (LogCoshLoss method) (LowRankBilinear method) (MaskedAttentionBlock method) (MaskedGINConv method) (MaskedMultitaskLoss method) (MetabolomeVectorHead method) (MetaEmbedding method) (MleDistSupCR method) (MleWassSupCR method) (Mlp method) (MseCategoricalEntropyRegLoss method) (MSEListMLELoss method) (MultiDimNaNTolerantCELoss method) (MultiDimNaNTolerantOrdinalCELoss method) (NaNTolerantHuberLoss method) (NaNTolerantL1Loss method) (NaNTolerantLogCoshLoss method) (NaNTolerantMSELoss method) (NaNTolerantQuantileLoss method) (NodeSelfAttention method) (NSAEncoder method) (ObservedLabelEncoder method) (PairwiseGraphAggregation method), [1] (PerceiverMixing method) (PerGeneHead method) (PerMetaboliteHead method) (PerturbationGraphPropagation method) (PerturbationHead method), [1] (PointDistGraphReg method) (PreProcessor method), [1], [2], [3] (PreThenPost method) (ProductScalarHead method) (RegressionTask method), [1], [2], [3], [4] (ResponseBasisHead method) (SelfAttention method) (SelfAttentionBlock method) (SelfAttentionDeepSet method) (SelfAttentionGraphAggregation method), [1] (SimpleLinearModel method) (SimpleLinearRegressionTask method) (SinusoidalTimeEmbedding method) (StoichHypergraphConv method) (SupCR method) (WeightedDistLoss method) (WeightedMSELoss method) (WeightedSupCRCell method) (WeightedWassersteinLoss method)

forward_closure() (in module torchcell.provenance) forward_diffusion() (DiffusionDecoder method) forward_single() (GeneInteractionDango method), [1] (HeteroCellBipartite method) (HeteroCellNSA method) from_env() (LiteratureKeys class method) (LiteratureServerConfig class method) (ZoteroConfig class method) (ZoteroLibrary class method) from_pairs() (LiteratureKeys class method) from_properties() (KgRelease class method) from_stored() (ExperimentReferenceIndex class method) functional_copies() (StrainBackground method) FungalUpDownTransformer (class in torchcell.models.fungal_up_down_transformer) FungalUpDownTransformerDataset (class in torchcell.datasets)

G

G_gene (SCerevisiaeGraph property) G_genetic (SCerevisiaeGraph property) G_go (SCerevisiaeGraph property) G_physical (SCerevisiaeGraph property) G_raw (SCerevisiaeGraph property) G_regulatory (SCerevisiaeGraph property) G_string11_0_coexpression (SCerevisiaeGraph property) G_string11_0_cooccurence (SCerevisiaeGraph property) G_string11_0_database (SCerevisiaeGraph property) G_string11_0_experimental (SCerevisiaeGraph property) G_string11_0_fusion (SCerevisiaeGraph property) G_string11_0_neighborhood (SCerevisiaeGraph property) G_string12_0_coexpression (SCerevisiaeGraph property) G_string12_0_cooccurence (SCerevisiaeGraph property) G_string12_0_database (SCerevisiaeGraph property) G_string12_0_experimental (SCerevisiaeGraph property) G_string12_0_fusion (SCerevisiaeGraph property) G_string12_0_neighborhood (SCerevisiaeGraph property) G_string9_1_coexpression (SCerevisiaeGraph property) G_string9_1_cooccurence (SCerevisiaeGraph property) G_string9_1_database (SCerevisiaeGraph property) G_string9_1_experimental (SCerevisiaeGraph property) G_string9_1_fusion (SCerevisiaeGraph property) G_string9_1_neighborhood (SCerevisiaeGraph property) G_tflink (SCerevisiaeGraph property) gapped_fields() (ProvenanceGapMixin method) gate_results (VerificationReport property) gather_across_gpus() (MleDistSupCR method) (MleWassSupCR method) (PointDistGraphReg method) gather_dataset_full_records() (in module torchcell.knowledge_graphs.build_time_projection) gaussian_crps() (in module torchcell.losses.distributional) gaussian_nll() (in module torchcell.losses.distributional) GemTensors (class in torchcell.metabolism.constraints) Gene (class in torchcell.sequence) gene_attribute_table (Genome property) gene_availability() (FluxLayer method) gene_essentiality_to_fitness_experiment() (in module torchcell.datamodels.gene_essentiality_to_fitness_conversion) gene_essentiality_to_fitness_reference() (in module torchcell.datamodels.gene_essentiality_to_fitness_conversion) gene_index_map() (in module torchcell.metabolism.flux_layer) gene_set (ExperimentDataset property) (Genome property) (Neo4jCellDataset property) (YeastGEM property) gene_sets (RecordFilter attribute) gene_sets_file (RecordFilter attribute) GeneAdditionPerturbation (class in torchcell.datamodels.schema) GeneEssentialityExperiment (class in torchcell.datamodels.schema) GeneEssentialityExperimentReference (class in torchcell.datamodels.schema) GeneEssentialityPhenotype (class in torchcell.datamodels.schema) GeneEssentialitySgdAdapter (class in torchcell.adapters) GeneEssentialitySgdDataset (class in torchcell.datasets.scerevisiae.sgd) GeneEssentialityToFitnessConverter (class in torchcell.datamodels.gene_essentiality_to_fitness_conversion) GeneGraph (class in torchcell.graph) GeneInteractionAttention (class in torchcell.models.hetero_cell_bipartite_dango) GeneInteractionDango (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) GeneInteractionDiff (class in torchcell.models.hetero_cell_bipartite_dango_diff_gi) GeneInteractionExperiment (class in torchcell.datamodels.schema) GeneInteractionExperimentReference (class in torchcell.datamodels.schema) GeneInteractionPhenotype (class in torchcell.datamodels.schema) GeneInteractionPredictor (class in torchcell.models.hetero_cell_bipartite_dango) (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy)

GeneMultiGraph (class in torchcell.graph) GenePerturbation (class in torchcell.datamodels.schema) generate_batch_masks() (GPUEdgeMaskGenerator method) generate_batch_masks_vectorized() (GPUEdgeMaskGenerator method) generate_citation_key() (in module torchcell.literature) generate_simulated_data() (in module torchcell.viz.fitness) (in module torchcell.viz.genetic_interaction_score) generate_simulated_data_with_nan() (in module torchcell.viz.fitness) (in module torchcell.viz.genetic_interaction_score) generate_single_mask() (GPUEdgeMaskGenerator method) GeneSet (class in torchcell.sequence) Genome (class in torchcell.sequence) GenomicSpan (class in torchcell.datamodels.schema) Genotype (class in torchcell.datamodels.schema) GenotypeAggregator (class in torchcell.data) get() (ExperimentDataset method) (Neo4jCellDataset method) (QueryRegistry method) get_activation() (in module torchcell.models.hetero_cell_bipartite_dango_gi) get_base_title() (Visualization method) get_bin_info() (COOLabelBinningTransform method) (LabelBinningTransform method) get_buffer_samples() (BufferedWeightedDistLoss method) (BufferedWeightedSupCRCell method), [1] (BufferedWeightedWassersteinLoss method) get_buffer_weight() (AdaptiveWeighting method), [1] get_chr_from_description() (in module torchcell.sequence) get_data_by_type() (CellAdapter method) get_edges() (CellAdapter method) get_init_graphs() (Neo4jCellDataset method) get_lr() (CosineAnnealingWarmupRestarts method) get_memory_reduction_factor() (CellAdapter method) get_memory_usage() (GPUEdgeMaskGenerator method) get_nodes() (CellAdapter method) get_norm_layer() (in module torchcell.models.hetero_cell_bipartite_dango) (in module torchcell.models.hetero_cell_bipartite_dango_gi) (in module torchcell.models.hetero_cell_bipartite_dango_gi_lazy) (in module torchcell.models.hetero_cell_nsa_retry) get_num_workers() (in module torchcell.knowledge_graphs.create_kg) (in module torchcell.knowledge_graphs.create_scerevisiae_kg) (in module torchcell.knowledge_graphs.create_scerevisiae_kg_small) (in module torchcell.knowledge_graphs.gene_interactions_scerevisae_kg) get_or_compute() (SignalCache method) get_parser() (BuildCommand method) get_seq() (Genome method) get_single_item() (ExperimentDataset method) get_temperature() (TemperatureScheduler method), [1] get_timing_summary() (in module torchcell.profiling) get_timings() (in module torchcell.profiling) GlobalHead (class in torchcell.models.equivariant_cell_graph_transformer) go_to_genes (SCerevisiaeGraph property) GPUEdgeMaskGenerator (class in torchcell.models.gpu_edge_mask_generator) graph_labels() (in module torchcell.knowledge_graphs.supported_queries.check) graph_schema() (in module torchcell.datamodels.ontology_checks) graph_schema_from_yaml() (in module torchcell.knowledge_graphs.kg_manifest) GraphEmbeddingDataset (class in torchcell.datasets) GraphLabels (class in torchcell.knowledge_graphs.supported_queries.check) GraphRecoveryVisualization (class in torchcell.viz.graph_recovery) GraphRegularizedTransformerLayer (class in torchcell.models.cell_graph_transformer) (class in torchcell.models.equivariant_cell_graph_transformer) GraphSchemaEntry (class in torchcell.knowledge_graphs.kg_manifest)

H

HaplotypeBlock (class in torchcell.datamodels.schema) has_breaking (ImpactReport property) has_duplicate_edge_risk (ReferenceAnalysis property) has_gene_perturbations (ExperimentDataset attribute) has_impact (ImpactReport property) HashableProvenanceGapMixin (class in torchcell.datamodels.schema) HeadOntologyError (class in torchcell.knowledge_graphs.head_ontology) HeadOntologyMirror (class in torchcell.knowledge_graphs.head_ontology) HeteroCellBipartite (class in torchcell.models.hetero_cell_bipartite_dango) HeteroCellNSA (class in torchcell.models.hetero_cell_nsa_retry) HeteroConvAggregator (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) HeterologousPathway (class in torchcell.metabolism.pathway)

HeteroNSA (class in torchcell.nn.hetero_nsa) HeteroNSAEncoder (class in torchcell.nn.hetero_nsa) HeteroToDenseMask (class in torchcell.transforms.hetero_to_dense_mask) heterozygous_deletion_functional_copies() (in module torchcell.datamodels.schema) HeterozygousDeletionPerturbation (class in torchcell.datamodels.schema) HetHillenmeyer2008Adapter (class in torchcell.adapters) HetHillenmeyer2008Dataset (class in torchcell.datasets.scerevisiae.hillenmeyer2008) HomHillenmeyer2008Adapter (class in torchcell.adapters) HomHillenmeyer2008Dataset (class in torchcell.datasets.scerevisiae.hillenmeyer2008) hp (RegressionTask property) human_bytes() (in module torchcell.paper.tables) HyperSAGNN (class in torchcell.models.cell_graph_transformer) (class in torchcell.models.dango) (class in torchcell.models.equivariant_cell_graph_transformer)

I

ICLoss (class in torchcell.losses.isomorphic_cell_loss) ICLossStd (class in torchcell.losses.isomorphic_cell_loss) identified (CompoundIdentityResolution property) identity_sha256() (in module torchcell.datamodels.identity) ImpactReport (class in torchcell.provenance) inchikey_from_smiles() (in module torchcell.datamodels.compound_identity) IncidenceSubgraphRepresentation (class in torchcell.data) IncompatibleReleaseError (class in torchcell.knowledge_graphs.releases) incremental_import_call() (in module torchcell.knowledge_graphs.incremental_import) incremental_node_header() (in module torchcell.knowledge_graphs.incremental_import) IncrementalImportPlan (class in torchcell.knowledge_graphs.incremental_import) independent_balance_rows() (in module torchcell.metabolism.constraints) index (CellDataModule property) index_by_uniprot() (in module torchcell.metabolism.enzyme_kinetics) index_details (CellDataModule property) IndexSplit (class in torchcell.datamodules) init_lr() (CosineAnnealingWarmupRestarts method) init_wandb_artifact() (Visualization method) initialize_model() (CalmDataset method) (CodonFrequencyDataset method) (Esm2Dataset method) (FungalUpDownTransformerDataset method) (GraphEmbeddingDataset method) (NucleotideTransformerDataset method) (OneHotGeneDataset method) (ProtT5Dataset method) (RandomEmbeddingDataset method)

instance_bytes() (in module torchcell.paper.tables) inverse() (COOLabelBinningTransform method) (COOLabelNormalizationTransform method) (LabelBinningTransform method) (LabelNormalizationTransform method) InverseCompose (class in torchcell.transforms.regression_to_classification) is_any_deletion_gene_index (Neo4jCellDataset property) is_any_perturbed_gene_index (Neo4jCellDataset property) is_bijective (PhenotypeLabelMap property) is_empty (AdapterDrift property) is_fully_characterized (Media property) is_fully_sourced (StrainBackground property) is_open_finding (LevelResult property) is_sourced (BackgroundAllele property) IsobutanolScreenLopez2024Adapter (class in torchcell.adapters) IsobutanolScreenLopez2024Dataset (class in torchcell.datasets.scerevisiae.lopez2024) IsobutanolValidatedLopez2024Adapter (class in torchcell.adapters) IsobutanolValidatedLopez2024Dataset (class in torchcell.datasets.scerevisiae.lopez2024) isolated_graph_node_classes() (in module torchcell.datamodels.ontology_checks) isotonic_l2_pav() (in module torchcell.losses.multi_dim_nan_tolerant) items() (GeneMultiGraph method)

J

join_key_audit() (in module torchcell.datamodels.ontology_checks)

JoinKeyCensus (class in torchcell.datamodels.ontology_checks)

K

KanMxDeletionPerturbation (class in torchcell.datamodels.schema) KcatPredictor (class in torchcell.metabolism.parameters) keys() (GeneMultiGraph method) KgBuildManifest (class in torchcell.knowledge_graphs.kg_manifest) KgDatasetEntry (class in torchcell.knowledge_graphs.kg_manifest)

KgEvent (class in torchcell.knowledge_graphs.kg_manifest) KgRelease (class in torchcell.knowledge_graphs.releases) KgReleaseSnapshot (class in torchcell.knowledge_graphs.release_snapshot) KineticKind (class in torchcell.metabolism.enzyme_kinetics) KineticRetrieval (class in torchcell.metabolism.enzyme_kinetics) KineticSource (class in torchcell.metabolism.enzyme_kinetics)

L

l0_structural() (in module torchcell.verification) l1_completeness() (in module torchcell.verification) l1_count() (in module torchcell.verification) l1_provenance_gaps() (in module torchcell.verification) l2_cross_method() (in module torchcell.verification) l2_value_fidelity() (in module torchcell.verification) l3_convention() (in module torchcell.verification) l4_cross_source() (in module torchcell.verification) label_df (Neo4jCellDataset property) label_width() (COOLabelBinningTransform method) LabelBinningTransform (class in torchcell.transforms.regression_to_classification) LabelNormalizationTransform (class in torchcell.transforms.regression_to_classification) lambda_values (DangoPreTrain property) Lane (class in torchcell.paper.ontology_svg) lane_back_edges() (in module torchcell.datamodels.ontology_checks) lane_members() (OntologyGraph method) lane_membership() (in module torchcell.datamodels.ontology_checks) lane_of() (in module torchcell.database.browser_style) lane_roots() (OntologyGraph method) laplace_crps() (in module torchcell.losses.distributional) Layout (class in torchcell.paper.ontology_svg) LazySubgraphRepresentation (class in torchcell.data) len() (ExperimentDataset method) (Neo4jCellDataset method) Level (class in torchcell.verification) LevelResult (class in torchcell.verification) levels_covered (VerificationReport property) Lian2019Adapter (class in torchcell.adapters) library_available() (in module torchcell.verification) LinearDecoder (class in torchcell.models.hetero_cell_bipartite_dango_diff_gi) LinearUntilFlipped (class in torchcell.losses.dango) LinearUntilUniform (class in torchcell.losses.dango) link_verified() (in module torchcell.data) list_collections() (ZoteroLibrary method) list_databases() (in module torchcell.knowledge_graphs.releases) list_databases_bounded() (in module torchcell.knowledge_graphs.releases) ListMLELoss (class in torchcell.losses.list_mle) ListMLEMetric (class in torchcell.trainers.neo_regression) LiteratureKeys (class in torchcell.literature) LiteratureServerConfig (class in torchcell.literature) live_dataset_counts() (in module torchcell.knowledge_graphs.kg_manifest)

live_experiment_ids() (in module torchcell.knowledge_graphs.kg_manifest) live_neo4j_version() (in module torchcell.knowledge_graphs.kg_manifest) lmdb_fingerprint() (in module torchcell.paper.tables) load() (QueryRegistry class method) (SignalCache class method) load_cellpose_model() (in module torchcell.sga) load_closures() (in module torchcell.knowledge_graphs.release_snapshot) load_default_surface() (in module torchcell.provenance) load_gene_sets() (in module torchcell.knowledge_graphs.subset) load_graph() (SCerevisiaeGraph method) load_manifest() (in module torchcell.knowledge_graphs.kg_manifest) load_measured_concentrations() (in module torchcell.metabolism.parameters) load_mirror_record() (in module torchcell.knowledge_graphs.head_ontology) load_mirrored_records() (in module torchcell.metabolism.enzyme_kinetics) load_model() (Esm2 method) (FungalUpDownTransformer method) (NucleotideModel method) (NucleotideTransformer method) (PeptideModel method) (ProtT5 method) load_raw() (Neo4jCellDataset static method) load_report() (in module torchcell.knowledge_graphs.kg_manifest) load_snapshot() (in module torchcell.knowledge_graphs.release_snapshot) load_snapshots() (in module torchcell.knowledge_graphs.release_snapshot) load_surface() (in module torchcell.provenance) load_surface_from_sources() (in module torchcell.provenance) load_swissprot() (in module torchcell.metabolism.parameters) load_thermo_table() (in module torchcell.metabolism.constraints) load_timings() (in module torchcell.knowledge_graphs.build_time_projection) loader_closure() (in module torchcell.provenance) loader_relpath() (in module torchcell.knowledge_graphs.kg_manifest) loader_schema_deps() (in module torchcell.provenance) LoaderImpact (class in torchcell.provenance) local_bottleneck_score() (VisGraphDegen static method) log_method_table() (CellAdapter method) log_metrics() (VisGraphDegen method) log_sample_metrics() (Visualization method) LogCoshLoss (class in torchcell.losses.logcosh) loss() (DiffusionDecoder method) (DistHead method) LowRankBilinear (class in torchcell.models.equivariant_cell_graph_transformer)

M

make_dist_head() (in module torchcell.losses.distributional) make_zotero_client() (in module torchcell.literature) Manifest (class in torchcell.literature) ManifestPinMismatchError (class in torchcell.data) MarkerDeletionPerturbation (class in torchcell.datamodels.schema) mask() (ExperimentReferenceIndex method) masked_mean() (in module torchcell.losses.distributional) MaskedAttentionBlock (class in torchcell.nn.masked_attention_block) MaskedGINConv (class in torchcell.nn.masked_gin_conv) MaskedMultitaskLoss (class in torchcell.models.equivariant_cell_graph_transformer) matches() (RecordFilter method) materialize() (Neo4jCellDataset static method) MatingType (class in torchcell.datamodels.schema) MAX_HEIGHT_MM (in module torchcell.utils) max_sequence_size (Esm2 property) (FungalUpDownTransformer property) (NucleotideModel property) (NucleotideTransformer property) (PeptideModel property) (ProtT5 property) MeanDeletionPerturbation (class in torchcell.datamodels.schema) MeanExperimentDeduplicator (class in torchcell.data) measured_gene_universe() (in module torchcell.verification) MeasurementType (class in torchcell.datamodels.schema) mechanism_so (BackgroundAllele property) Media (class in torchcell.datamodels.schema) media_base_issues() (in module torchcell.datamodels.ontology_checks) media_derivation_issues() (in module torchcell.datamodels.ontology_checks) media_identity() (in module torchcell.datamodels.identity) media_library_compound_issues() (in module torchcell.datamodels.ontology_checks) media_to_bounds() (in module torchcell.metabolism.media) MediaBaseIssue (class in torchcell.datamodels.ontology_checks) MediaBounds (class in torchcell.metabolism.media) MediaBoundsDiff (class in torchcell.metabolism.media) MediaComponent (class in torchcell.datamodels.schema) MediaComponentRole (class in torchcell.datamodels.schema) MediaDerivationIssue (class in torchcell.datamodels.ontology_checks) MemberlessReactionError (class in torchcell.metabolism.yeast_GEM) merge_layout() (in module torchcell.sga) message() (MaskedGINConv method) (StoichHypergraphConv method) metabolite_gene_set() (in module torchcell.verification) MetaboliteDaSilveira2014Adapter (class in torchcell.adapters) MetaboliteDaSilveira2014Dataset (class in torchcell.datasets.scerevisiae.dasilveira2014) MetaboliteExperiment (class in torchcell.datamodels.schema) MetaboliteExperimentReference (class in torchcell.datamodels.schema) MetabolitePhenotype (class in torchcell.datamodels.schema) MetaboliteSpec (class in torchcell.metabolism.pathway) MetaboliteZelezniak2018Adapter (class in torchcell.adapters) MetaboliteZelezniak2018Dataset (class in torchcell.datasets.scerevisiae.zelezniak2018) MetabolomeVectorHead (class in torchcell.models.cell_graph_transformer_metabolism) MetaEmbedding (class in torchcell.models.dango) MicroarrayExpressionExperiment (class in torchcell.datamodels.schema) MicroarrayExpressionExperimentReference (class in torchcell.datamodels.schema) MicroarrayExpressionPhenotype (class in torchcell.datamodels.schema) MicroarrayKemmeren2014Adapter (class in torchcell.adapters) MicroarrayKemmeren2014Dataset (class in torchcell.datasets.scerevisiae.kemmeren2014) mirror_oed_slice() (in module torchcell.metabolism.enzyme_kinetics) mismatch_positions() (in module torchcell.sequence) MleDistSupCR (class in torchcell.losses.mle_dist_supcr) MleWassSupCR (class in torchcell.losses.mle_wasserstein) Mlp (class in torchcell.models.mlp) mm_to_in() (in module torchcell.utils) model (YeastGEM property) model_config (AdapterContribution attribute) (AdapterDrift attribute) (AdapterNodeSite attribute) (AdapterRate attribute) (AdapterTiming attribute) (AdmissionReport attribute) (AllelePerturbation attribute) (AlleleSpec attribute) (BackfillReport attribute) (BackgroundAllele attribute) (BarcodedKanMxDeletionPerturbation attribute) (BatchAdmissionReport attribute) (BiologicPerturbation attribute) (BuildManifest attribute) (BuildTimeProjection attribute) (ByGenotype attribute) (CalibrationTimings attribute) (CalMorphExperiment attribute) (CalMorphExperimentReference attribute) (CalMorphPhenotype attribute) (Caption attribute) (Card attribute) (CarrierGapCensus attribute) (CatalyticUnits attribute) (Cell attribute) (CellposeSegConfig attribute) (CheckReport attribute) (Column attribute) (CompartmentParameters attribute) (ComponentResolution attribute) (CompositionEdge attribute) (Compound attribute) (CompoundIdentityIssue attribute) (CompoundIdentityRecord attribute) (CompoundIdentityResolution attribute) (Concentration attribute) (ConditionalAllelePerturbation attribute) (ConstructedOrf attribute) (ConversionEntry attribute) (ConversionMap attribute) (CopyNumberVariantPerturbation attribute) (CrisprActivationPerturbation attribute) (CrisprConstruct attribute) (CrisprDeletionPerturbation attribute) (CrisprInterferencePerturbation attribute) (CsvGroup attribute) (CultureEnvironment attribute) (CultureFormat attribute) (CuratedRow attribute) (CurationDirective attribute) (DampPerturbation attribute) (DataModuleIndex attribute) (DataModuleIndexDetails attribute) (DatasetCheck attribute) (DatasetDrift attribute) (DatasetSignalRecord attribute) (DatasetSize attribute) (DatasetSplit attribute) (DeletionPerturbation attribute) (DnaSelectionResult attribute) (DnaWindowResult attribute) (EngineeredCopyNumberPerturbation attribute) (Environment attribute) (EnvironmentCompoundCollision attribute) (EnvironmentPerturbation attribute) (EnvironmentPhysicalPerturbation attribute) (EnvironmentResponseExperiment attribute) (EnvironmentResponseExperimentReference attribute) (EnvironmentResponsePhenotype attribute) (ExchangeBound attribute) (ExchangeIndex attribute) (ExistingEdgeFilter attribute) (Experiment attribute) (ExperimentReference attribute) (ExperimentReferenceIndex attribute) (ExpressionModulationPerturbation attribute) (ExpressionRangeMultiplier attribute) (FitnessExperiment attribute) (FitnessExperimentReference attribute) (FitnessPhenotype attribute) (FluxLayerConfig attribute) (GemTensors attribute) (GeneAdditionPerturbation attribute) (GeneEssentialityExperiment attribute) (GeneEssentialityExperimentReference attribute) (GeneEssentialityPhenotype attribute) (GeneGraph attribute) (GeneInteractionExperiment attribute) (GeneInteractionExperimentReference attribute) (GeneInteractionPhenotype attribute) (GeneMultiGraph attribute) (GenePerturbation attribute) (GenomicSpan attribute) (Genotype attribute) (GraphLabels attribute) (GraphSchemaEntry attribute) (HaplotypeBlock attribute) (HashableProvenanceGapMixin attribute) (HeadOntologyMirror attribute) (HeterologousPathway attribute) (HeterozygousDeletionPerturbation attribute) (ImpactReport attribute) (IncrementalImportPlan attribute) (IndexSplit attribute) (JoinKeyCensus attribute) (KanMxDeletionPerturbation attribute) (KgBuildManifest attribute) (KgDatasetEntry attribute) (KgEvent attribute) (KgRelease attribute) (KgReleaseSnapshot attribute) (KineticRetrieval attribute) (Lane attribute) (Layout attribute) (LevelResult attribute) (LiteratureKeys attribute) (LiteratureServerConfig attribute) (LoaderImpact attribute) (Manifest attribute) (MarkerDeletionPerturbation attribute) (MeanDeletionPerturbation attribute) (Media attribute) (MediaBaseIssue attribute) (MediaBounds attribute) (MediaBoundsDiff attribute) (MediaComponent attribute) (MediaDerivationIssue attribute) (MetaboliteExperiment attribute) (MetaboliteExperimentReference attribute) (MetabolitePhenotype attribute) (MetaboliteSpec attribute) (MicroarrayExpressionExperiment attribute) (MicroarrayExpressionExperimentReference attribute) (MicroarrayExpressionPhenotype attribute) (ModelStrict attribute) (ModelStrictArbitrary attribute) (NatMxDeletionPerturbation attribute) (NaturalGeneAbsencePerturbation attribute) (NaturalGenePresencePerturbation attribute) (Neo4jConnectionSettings attribute) (NodeRule attribute) (NormalizationConfig attribute) (OedKineticRecord attribute) (OntologyClass attribute) (OntologyField attribute) (OntologyGraph attribute) (OptionalTraversal attribute) (PaperTable attribute) (ParameterTable attribute) (ParsedGenome attribute) (Phenotype attribute) (PhenotypeLabelMap attribute) (PlateSegResult attribute) (PreCulture attribute) (PredictorRegistry attribute) (PresenceAbsencePerturbation attribute) (PropertyMismatch attribute) (ProteinAbundanceExperiment attribute) (ProteinAbundanceExperimentReference attribute) (ProteinAbundancePhenotype attribute) (Provenance attribute) (ProvenanceGap attribute) (ProvenanceGapCensus attribute) (ProvenanceGapMixin attribute) (PseudobulkExpressionExperiment attribute) (PseudobulkExpressionExperimentReference attribute) (PseudobulkExpressionPhenotype attribute) (PubChemProperty attribute) (Publication attribute) (QueryDependencies attribute) (QueryDrift attribute) (QueryRegistry attribute) (QueryResult attribute) (ReactionSpec attribute) (RecordFilter attribute) (ReferenceAnalysis attribute) (ReferenceGenome attribute) (ReferenceIndex attribute) (RelationshipRule attribute) (ReleaseCompatibility attribute) (ReleaseDataset attribute) (ReleaseDiff attribute) (ResolvedKineticParameter attribute) (RNASeqExpressionExperiment attribute) (RNASeqExpressionExperimentReference attribute) (RNASeqExpressionPhenotype attribute) (Row attribute) (ScoreReport attribute) (SeedNodeStyle attribute) (SeedState attribute) (SegregantGenotype attribute) (SegregantGrowthExperiment attribute) (SegregantGrowthExperimentReference attribute) (SegregantParent attribute) (SequencePerturbation attribute) (SequenceVariantPerturbation attribute) (ServedDatabase attribute) (ServedDrift attribute) (SgaAllelePerturbation attribute) (SgaDampPerturbation attribute) (SgaKanMxDeletionPerturbation attribute) (SgaNatMxDeletionPerturbation attribute) (SgaSuppressorAllelePerturbation attribute) (SgaTsAllelePerturbation attribute) (SignalCache attribute) (SmallMoleculePerturbation attribute) (SnapshotDataset attribute) (SnapshotEvent attribute) (Solvent attribute) (SOTerm attribute) (SourcedValue attribute) (StaleResult attribute) (StatDerivation attribute) (StrainBackground attribute) (StrainConstruction attribute) (StrainEnvironmentResponseExperiment attribute) (StrainEnvironmentResponseExperimentReference attribute) (StrainReferenceGenome attribute) (StrainScore attribute) (SubsetConfig attribute) (SupersetCheck attribute) (SupersetLineage attribute) (SupportedQuery attribute) (SuppressorAllelePerturbation attribute) (SymbolChange attribute) (SymbolDrift attribute) (SyntheticLethalityExperiment attribute) (SyntheticLethalityExperimentReference attribute) (SyntheticLethalityPhenotype attribute) (SyntheticRescueExperiment attribute) (SyntheticRescueExperimentReference attribute) (SyntheticRescuePhenotype attribute) (TableCoverage attribute) (Temperature attribute) (ThermoTable attribute) (TsAllelePerturbation attribute) (UptakePolicy attribute) (VerificationReport attribute) (VisualScoreExperiment attribute) (VisualScoreExperimentReference attribute) (VisualScorePhenotype attribute) (ZoteroConfig attribute)

ModelStrict (class in torchcell.datamodels.pydant) ModelStrict.Config (class in torchcell.datamodels.pydant) ModelStrictArbitrary (class in torchcell.datamodels.pydant) ModelStrictArbitrary.Config (class in torchcell.datamodels.pydant) module torchcell.adapters torchcell.data torchcell.database torchcell.datamodels torchcell.datamodules torchcell.datasets torchcell.graph torchcell.knowledge_graphs torchcell.literature torchcell.loader torchcell.losses torchcell.metabolism torchcell.models torchcell.nn torchcell.ontology torchcell.paper torchcell.profiling torchcell.provenance torchcell.scheduler torchcell.sequence torchcell.sga torchcell.trainers torchcell.transforms torchcell.utils torchcell.verification torchcell.viz molecular_weight_table() (in module torchcell.metabolism.parameters) MonotonicParameter (class in torchcell.losses.multi_dim_nan_tolerant) Mormino2022Adapter (class in torchcell.adapters) MseCategoricalEntropyRegLoss (class in torchcell.losses.multi_dim_nan_tolerant) MSEListMLELoss (class in torchcell.trainers.neo_regression) MultiDimNaNTolerantCELoss (class in torchcell.losses.multi_dim_nan_tolerant) MultiDimNaNTolerantOrdinalCELoss (class in torchcell.losses.multi_dim_nan_tolerant)

N

n_blocks (SegregantGenotype property) n_components (MediaBounds property) n_datasets (KgRelease property) n_differences (MediaBoundsDiff property) n_existing (ExistingEdgeFilter property) n_perturbations (RecordFilter attribute) n_resolved (MediaBounds property) NadalRibellesPerturbSeq2025Adapter (class in torchcell.adapters) NadalRibellesPerturbSeq2025Dataset (class in torchcell.datasets.scerevisiae.nadal_ribelles2025) name_property_url() (in module torchcell.datamodels.compound_identity_curate) name_query (CurationDirective property) names (SchemaSurface property) NaNTolerantHuberLoss (class in torchcell.losses.multi_dim_nan_tolerant) NaNTolerantL1Loss (class in torchcell.losses.multi_dim_nan_tolerant) NaNTolerantLogCoshLoss (class in torchcell.losses.multi_dim_nan_tolerant) NaNTolerantMSELoss (class in torchcell.losses.multi_dim_nan_tolerant) NaNTolerantQuantileLoss (class in torchcell.losses.multi_dim_nan_tolerant) NatMxDeletionPerturbation (class in torchcell.datamodels.schema) NaturalGeneAbsencePerturbation (class in torchcell.datamodels.schema) NaturalGenePresencePerturbation (class in torchcell.datamodels.schema) neo4j_connection_settings() (in module torchcell.database.connection) Neo4jCellDataset (class in torchcell.data) Neo4jConnectionSettings (class in torchcell.database.connection) next_version() (in module torchcell.knowledge_graphs.releases) node_layers_forward() (DeepSet method) (SelfAttentionDeepSet method)

node_rules() (in module torchcell.database.browser_style) NodeEmbeddingBuilder (class in torchcell.datasets) NodeRule (class in torchcell.database.browser_style) NodeSelfAttention (class in torchcell.nn.masked_attention_block) NormalizationConfig (class in torchcell.sga) normalize() (COOLabelNormalizationTransform method) (LabelNormalizationTransform method) normalize_accumulation_schedule() (in module torchcell.trainers.int_hetero_cell) normalize_compound_name() (in module torchcell.datamodels.compound_identity) normalize_plate() (in module torchcell.sga) NSAEncoder (class in torchcell.nn.nsa_encoder) NucleotideModel (class in torchcell.models.llm) NucleotideTransformer (class in torchcell.models.nucleotide_transformer) NucleotideTransformerDataset (class in torchcell.datasets) null_space_basis() (in module torchcell.metabolism.constraints) num_parameters (CellGraphTransformer property), [1] (CellGraphTransformerMetabolism property) (Dango property) (DCell property) (DCellOpt property) (GeneInteractionDango property), [1] (GeneInteractionDiff property) (HeteroCellBipartite property) (HeteroCellNSA property)

O

ObservedLabelEncoder (class in torchcell.models.equivariant_cell_graph_transformer) ocr_artifact() (in module torchcell.literature) ocr_pdf() (in module torchcell.literature) OedKineticRecord (class in torchcell.metabolism.enzyme_kinetics) of() (TableCoverage class method) offline (BackfillReport property) ok (ReleaseCompatibility property) on_test_epoch_end() (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method), [1], [2], [3] (SimpleLinearRegressionTask method) on_test_epoch_start() (RegressionTask method), [1], [2] on_train_end() (DCellRegressionSlimTask method) (DCellRegressionTask method) (SimpleLinearRegressionTask method) on_train_epoch_end() (DCellRegressionSlimTask method) (DCellRegressionTask method) (DiffusionRegressionTask method) (RegressionTask method), [1], [2], [3], [4] (SimpleLinearRegressionTask method) on_train_epoch_start() (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method), [1], [2], [3] (SimpleLinearRegressionTask method) on_train_start() (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method) (SimpleLinearRegressionTask method) on_validation_epoch_end() (DCellRegressionSlimTask method) (DCellRegressionTask method) (DiffusionRegressionTask method) (RegressionTask method), [1], [2], [3], [4] (SimpleLinearRegressionTask method) on_validation_epoch_start() (RegressionTask method), [1], [2], [3] one_hot_encode_gene() (OneHotGeneDataset method) OneHotGeneDataset (class in torchcell.datasets) OntologyClass (class in torchcell.paper.ontology_graph) OntologyField (class in torchcell.paper.ontology_graph) OntologyGraph (class in torchcell.paper.ontology_graph) open_findings (VerificationReport property) open_gaps (Media property) OptionalTraversal (class in torchcell.datamodels.ontology_checks) OrfHistoryRelation (class in torchcell.datamodels.schema) OrganicAcidYoshida2012Adapter (class in torchcell.adapters) OrganicAcidYoshida2012Dataset (class in torchcell.datasets.scerevisiae.yoshida2012) organism (AminoAcidCooper2010Dataset attribute) (AminoAcidMulleder2016Dataset attribute) (BetaxanthinCachera2023Dataset attribute) (Bloom2019Dataset attribute) (CarotenoidOzaydin2013Dataset attribute) (CaudalPanTranscriptome2024Dataset attribute) (CrispriChemgenSmith2016Dataset attribute) (CrispriMormino2022Dataset attribute) (CrisprMagicLian2019Dataset attribute) (DmfCostanzo2016Dataset attribute) (DmfKuzmin2018Dataset attribute) (DmfKuzmin2020Dataset attribute) (DmiCostanzo2016Dataset attribute) (DmiKuzmin2018Dataset attribute) (DmiKuzmin2020Dataset attribute) (DmMicroarraySameith2015Dataset attribute) (EnvChemgenAuesukaree2009Dataset attribute) (EnvChemgenCostanzo2021Dataset attribute) (EnvChemgenHoepfner2014Dataset attribute) (EnvChemgenMota2024Dataset attribute) (EnvChemgenVanacloig2022Dataset attribute) (EnvChemgenWildenhain2015Dataset attribute) (ExperimentDataset attribute) (FattyAcidSmith2006Dataset attribute) (FattyAcidXue2025Dataset attribute) (GeneEssentialitySgdDataset attribute) (HetHillenmeyer2008Dataset attribute) (HomHillenmeyer2008Dataset attribute) (IsobutanolScreenLopez2024Dataset attribute) (IsobutanolValidatedLopez2024Dataset attribute) (MetaboliteDaSilveira2014Dataset attribute) (MetaboliteZelezniak2018Dataset attribute) (MicroarrayKemmeren2014Dataset attribute) (NadalRibellesPerturbSeq2025Dataset attribute) (OrganicAcidYoshida2012Dataset attribute) (ProteomeMessner2023Dataset attribute) (ProteomeZelezniak2018Dataset attribute) (ScmdOhnuki2018Dataset attribute) (ScmdOhnuki2022Dataset attribute) (ScmdOhya2005Dataset attribute) (SmfBaryshnikova2010Dataset attribute) (SmfCostanzo2016Dataset attribute) (SmfKuzmin2018Dataset attribute) (SmfKuzmin2020Dataset attribute) (SmfODuibhir2014Dataset attribute) (SmMicroarraySameith2015Dataset attribute) (SynthLethalityYeastSynthLethDbDataset attribute) (SynthRescueYeastSynthLethDbDataset attribute) (TmfKuzmin2018Dataset attribute) (TmfKuzmin2020Dataset attribute) (TmiKuzmin2018Dataset attribute) (TmiKuzmin2020Dataset attribute) (YeastPhenomeDataset attribute)

orphan_models() (in module torchcell.datamodels.ontology_checks)

P

package_checkout() (in module torchcell.knowledge_graphs.releases) package_label() (in module torchcell.knowledge_graphs.releases) package_tag_at_ref() (in module torchcell.knowledge_graphs.kg_manifest) package_version_at_ref() (in module torchcell.knowledge_graphs.kg_manifest) package_version_from_source() (in module torchcell.knowledge_graphs.kg_manifest) pair_package_tag() (in module torchcell.knowledge_graphs.release_snapshot) paired (ReleaseCompatibility property) PairwiseGraphAggregation (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) panel_label() (in module torchcell.utils) PANEL_WIDTHS_MM (in module torchcell.utils) PAPER_RC (in module torchcell.utils) PaperTable (class in torchcell.paper.tables) param_dim (DistHead property) ParameterProvenance (class in torchcell.metabolism.parameters) ParameterTable (class in torchcell.metabolism.parameters) parse_catalytic_units() (in module torchcell.metabolism.constraints) parse_genome() (CalmDataset static method) (CodonFrequencyDataset static method) (Esm2Dataset static method) (FungalUpDownTransformerDataset static method) (NucleotideTransformerDataset static method) (OneHotGeneDataset static method) (ProtT5Dataset static method) (RandomEmbeddingDataset static method) (SCerevisiaeGraph static method) parse_line() (in module torchcell.datamodels.compound_identity_curate) parse_n_experiments() (in module torchcell.knowledge_graphs.kg_manifest) ParsedGenome (class in torchcell.sequence) partial_path (CalmDataset property) (RandomEmbeddingDataset property) pascal_label() (in module torchcell.knowledge_graphs.supported_queries.check) passed (VerificationReport property) pdf_attachments() (ZoteroLibrary method) pending_source_review() (in module torchcell.datamodels.strain_background) PeptideModel (class in torchcell.models.llm) PerceiverMixing (class in torchcell.models.equivariant_cell_graph_transformer) PerGeneHead (class in torchcell.models.equivariant_cell_graph_transformer) PerMetaboliteHead (class in torchcell.models.equivariant_cell_graph_transformer) persisted_value() (in module torchcell.database.browser_style) Perturbation (class in torchcell.data) perturbation_count_index (Neo4jCellDataset property) perturbation_types (Genotype property) PerturbationGraphPropagation (class in torchcell.models.equivariant_cell_graph_transformer) PerturbationHead (class in torchcell.models.cell_graph_transformer) (class in torchcell.models.equivariant_cell_graph_transformer) perturbed_gene_names (Genotype property) perturbed_gene_pool() (in module torchcell.models.cell_graph_transformer_metabolism) perturbed_gene_set() (in module torchcell.verification) Phenotype (class in torchcell.datamodels.schema) phenotype_descriptor() (in module torchcell.paper.tables) phenotype_info (Aggregator property) (Neo4jCellDataset property) phenotype_label_index (Neo4jCellDataset property) phenotype_label_map() (in module torchcell.datamodels.ontology_checks) PhenotypeLabelMap (class in torchcell.datamodels.ontology_checks) PhysicalFactor (class in torchcell.datamodels.schema) pinball() (in module torchcell.losses.distributional) pit() (DistHead method) pit_ks() (in module torchcell.losses.distributional) pit_values() (in module torchcell.losses.distributional) PlateSegResult (class in torchcell.sga) plot_attention_diagnostics() (TransformerDiagnostics method) plot_bipartite_network() (in module torchcell.metabolism.yeast_GEM) plot_correlations() (Visualization method) plot_distribution() (Visualization method) plot_edge_mass_alignment() (GraphRecoveryVisualization method) plot_edge_recovery_per_graph() (GraphRecoveryVisualization method) plot_edge_recovery_precision() (GraphRecoveryVisualization method) plot_edge_recovery_recall() (GraphRecoveryVisualization method) plot_full_network() (in module torchcell.metabolism.yeast_GEM) plot_graph_info_summary() (GraphRecoveryVisualization method) PLOT_PALETTE (in module torchcell.utils) PLOT_PALETTE_FILL (in module torchcell.utils) PLOT_PALETTE_NAMES (in module torchcell.utils) plot_random_network() (in module torchcell.metabolism.yeast_GEM) plot_reaction_map() (in module torchcell.metabolism.yeast_GEM) plot_umap() (Visualization method) point() (DistHead method) PointDistGraphReg (class in torchcell.losses.point_dist_graph_reg) post_process() (in module torchcell.data) PreCulture (class in torchcell.datamodels.schema) PreCultureSource (class in torchcell.datamodels.schema) predict() (KcatPredictor method) PredictorRegistry (class in torchcell.metabolism.parameters) prepare_incremental_import() (in module torchcell.knowledge_graphs.incremental_import) preprocess_calmorph_data() (ScmdOhnuki2018Dataset method) (ScmdOhya2005Dataset method) preprocess_raw() (AminoAcidCooper2010Dataset method) (AminoAcidMulleder2016Dataset method) (BetaxanthinCachera2023Dataset method) (Bloom2019Dataset method) (CarotenoidOzaydin2013Dataset method) (CaudalPanTranscriptome2024Dataset method) (CrispriChemgenSmith2016Dataset method) (CrispriMormino2022Dataset method) (CrisprMagicLian2019Dataset method) (DmfCostanzo2016Dataset method) (DmfKuzmin2018Dataset method) (DmfKuzmin2020Dataset method) (DmiCostanzo2016Dataset method) (DmiKuzmin2018Dataset method) (DmiKuzmin2020Dataset method) (DmMicroarraySameith2015Dataset method) (EnvChemgenAuesukaree2009Dataset method) (EnvChemgenCostanzo2021Dataset method) (EnvChemgenHoepfner2014Dataset method) (EnvChemgenMota2024Dataset method) (EnvChemgenVanacloig2022Dataset method) (EnvChemgenWildenhain2015Dataset method) (ExperimentDataset method) (FattyAcidSmith2006Dataset method) (FattyAcidXue2025Dataset method) (GeneEssentialitySgdDataset method) (MetaboliteDaSilveira2014Dataset method) (MetaboliteZelezniak2018Dataset method) (MicroarrayKemmeren2014Dataset method) (NadalRibellesPerturbSeq2025Dataset method) (OrganicAcidYoshida2012Dataset method) (ProteomeMessner2023Dataset method) (ProteomeZelezniak2018Dataset method) (ScmdOhnuki2018Dataset method) (ScmdOhnuki2022Dataset method) (ScmdOhya2005Dataset method) (SmfBaryshnikova2010Dataset method) (SmfCostanzo2016Dataset method) (SmfKuzmin2018Dataset method) (SmfKuzmin2020Dataset method) (SmfODuibhir2014Dataset method) (SmMicroarraySameith2015Dataset method) (SynthLethalityYeastSynthLethDbDataset method) (SynthRescueYeastSynthLethDbDataset method) (TmfKuzmin2018Dataset method) (TmfKuzmin2020Dataset method) (TmiKuzmin2018Dataset method) (TmiKuzmin2020Dataset method) (YeastPhenomeDataset method)

PreProcessor (class in torchcell.models.hetero_cell_bipartite_dango) (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) (class in torchcell.models.hetero_cell_nsa_retry) PresenceAbsencePerturbation (class in torchcell.datamodels.schema) PreThenPost (class in torchcell.losses.dango) pretrained_LLM (class in torchcell.models.llm) print_ontology_structure() (in module torchcell.ontology) print_ontology_summary() (in module torchcell.ontology) print_schema_mappings() (in module torchcell.ontology) print_timing_summary() (in module torchcell.profiling) process() (Aggregator method) (AminoAcidCooper2010Dataset method) (AminoAcidMulleder2016Dataset method) (BetaxanthinCachera2023Dataset method) (Bloom2019Dataset method) (CalmDataset method) (CarotenoidOzaydin2013Dataset method) (CaudalPanTranscriptome2024Dataset method) (CodonFrequencyDataset method) (Converter method) (CrispriChemgenSmith2016Dataset method) (CrispriMormino2022Dataset method) (CrisprMagicLian2019Dataset method) (DCellGraphProcessor method) (Deduplicator method) (DmfCostanzo2016Dataset method) (DmfKuzmin2018Dataset method) (DmfKuzmin2020Dataset method) (DmiCostanzo2016Dataset method) (DmiKuzmin2018Dataset method) (DmiKuzmin2020Dataset method) (DmMicroarraySameith2015Dataset method) (EnvChemgenAuesukaree2009Dataset method) (EnvChemgenCostanzo2021Dataset method) (EnvChemgenHoepfner2014Dataset method) (EnvChemgenMota2024Dataset method) (EnvChemgenVanacloig2022Dataset method) (EnvChemgenWildenhain2015Dataset method) (Esm2Dataset method) (ExperimentDataset method) (FattyAcidSmith2006Dataset method) (FattyAcidXue2025Dataset method) (FungalUpDownTransformerDataset method) (GeneEssentialitySgdDataset method) (GraphEmbeddingDataset method) (IncidenceSubgraphRepresentation method) (IsobutanolScreenLopez2024Dataset method) (IsobutanolValidatedLopez2024Dataset method) (LazySubgraphRepresentation method) (MetaboliteDaSilveira2014Dataset method) (MetaboliteZelezniak2018Dataset method) (MicroarrayKemmeren2014Dataset method) (NadalRibellesPerturbSeq2025Dataset method) (Neo4jCellDataset method) (NucleotideTransformerDataset method) (OneHotGeneDataset method) (OrganicAcidYoshida2012Dataset method) (Perturbation method) (ProteomeMessner2023Dataset method) (ProteomeZelezniak2018Dataset method) (ProtT5Dataset method) (RandomEmbeddingDataset method) (ScmdOhnuki2018Dataset method) (ScmdOhnuki2022Dataset method) (ScmdOhya2005Dataset method) (SmfBaryshnikova2010Dataset method) (SmfCostanzo2016Dataset method) (SmfKuzmin2018Dataset method) (SmfKuzmin2020Dataset method) (SmfODuibhir2014Dataset method) (SmMicroarraySameith2015Dataset method) (SubgraphRepresentation method) (SynthLethalityYeastSynthLethDbDataset method) (SynthRescueYeastSynthLethDbDataset method) (TmfKuzmin2018Dataset method) (TmfKuzmin2020Dataset method) (TmiKuzmin2018Dataset method) (TmiKuzmin2020Dataset method) (Unperturbed method) (YeastPhenomeDataset method) processed_file_names (DmfKuzmin2020Dataset property) (DmiKuzmin2020Dataset property) (ExperimentDataset property) (GraphEmbeddingDataset property) (Neo4jCellDataset property) (SmfKuzmin2018Dataset property) (SmfKuzmin2020Dataset property) (SynthLethalityYeastSynthLethDbDataset property) (SynthRescueYeastSynthLethDbDataset property) (TmfKuzmin2020Dataset property) (TmiKuzmin2020Dataset property) product_ids() (HeterologousPathway method) ProductScalarHead (class in torchcell.models.cell_graph_transformer_metabolism) project_build_time() (in module torchcell.knowledge_graphs.build_time_projection) properties_by_cids() (PubChemClient method) property_by_name() (PubChemClient method) PropertyMismatch (class in torchcell.datamodels.ontology_checks) ProteinAbundanceExperiment (class in torchcell.datamodels.schema) ProteinAbundanceExperimentReference (class in torchcell.datamodels.schema) ProteinAbundancePhenotype (class in torchcell.datamodels.schema) ProteomeMessner2023Adapter (class in torchcell.adapters) ProteomeMessner2023Dataset (class in torchcell.datasets.scerevisiae.messner2023) ProteomeZelezniak2018Adapter (class in torchcell.adapters) ProteomeZelezniak2018Dataset (class in torchcell.datasets.scerevisiae.zelezniak2018) ProtT5 (class in torchcell.models.protT5) ProtT5Dataset (class in torchcell.datasets) Provenance (class in torchcell.verification) provenance_gap_census() (in module torchcell.verification) provenance_gap_level_result() (in module torchcell.verification) ProvenanceGap (class in torchcell.verification) ProvenanceGapCensus (class in torchcell.verification) ProvenanceGapMixin (class in torchcell.datamodels.schema) ProvenanceGapReason (class in torchcell.verification) PseudobulkExpressionExperiment (class in torchcell.datamodels.schema) PseudobulkExpressionExperimentReference (class in torchcell.datamodels.schema) PseudobulkExpressionPhenotype (class in torchcell.datamodels.schema) PubChemClient (class in torchcell.datamodels.compound_identity_curate) PubChemProperty (class in torchcell.datamodels.compound_identity_curate) Publication (class in torchcell.datamodels.schema) pubmed_for() (OedKineticRecord method)

Q

quantify_plate_image() (in module torchcell.sga) quantify_plate_image_cellpose() (in module torchcell.sga) query_drifts() (in module torchcell.knowledge_graphs.supported_queries.check) query_existing_edges() (in module torchcell.knowledge_graphs.incremental_import)

QueryDependencies (class in torchcell.knowledge_graphs.supported_queries.registry) QueryDrift (class in torchcell.knowledge_graphs.supported_queries.check) QueryRegistry (class in torchcell.knowledge_graphs.supported_queries.registry) QueryResult (class in torchcell.knowledge_graphs.supported_queries.check)

R

RandomEmbeddingDataset (class in torchcell.datasets) raw_file_names (AminoAcidCooper2010Dataset property) (AminoAcidMulleder2016Dataset property) (BetaxanthinCachera2023Dataset property) (Bloom2019Dataset property) (CarotenoidOzaydin2013Dataset property) (CaudalPanTranscriptome2024Dataset property) (CrispriChemgenSmith2016Dataset property) (CrispriMormino2022Dataset property) (CrisprMagicLian2019Dataset property) (DmfCostanzo2016Dataset property) (DmfKuzmin2018Dataset property) (DmfKuzmin2020Dataset property) (DmiCostanzo2016Dataset property) (DmiKuzmin2018Dataset property) (DmiKuzmin2020Dataset property) (DmMicroarraySameith2015Dataset property) (EnvChemgenAuesukaree2009Dataset property) (EnvChemgenCostanzo2021Dataset property) (EnvChemgenHoepfner2014Dataset property) (EnvChemgenMota2024Dataset property) (EnvChemgenVanacloig2022Dataset property) (EnvChemgenWildenhain2015Dataset property) (ExperimentDataset property) (FattyAcidSmith2006Dataset property) (FattyAcidXue2025Dataset property) (GeneEssentialitySgdDataset property) (MetaboliteDaSilveira2014Dataset property) (MetaboliteZelezniak2018Dataset property) (MicroarrayKemmeren2014Dataset property) (NadalRibellesPerturbSeq2025Dataset property) (Neo4jCellDataset property) (OrganicAcidYoshida2012Dataset property) (ProteomeMessner2023Dataset property) (ProteomeZelezniak2018Dataset property) (ScmdOhnuki2018Dataset property) (ScmdOhnuki2022Dataset property) (ScmdOhya2005Dataset property) (SmfBaryshnikova2010Dataset property) (SmfCostanzo2016Dataset property) (SmfKuzmin2018Dataset property) (SmfKuzmin2020Dataset property) (SmfODuibhir2014Dataset property) (SmMicroarraySameith2015Dataset property) (SynthLethalityYeastSynthLethDbDataset property) (SynthRescueYeastSynthLethDbDataset property) (TmfKuzmin2018Dataset property) (TmfKuzmin2020Dataset property) (TmiKuzmin2018Dataset property) (TmiKuzmin2020Dataset property) (YeastPhenomeDataset property) RawSha256MismatchError (class in torchcell.data) reaction_availability() (FluxLayer method) reaction_map (YeastGEM property) reaction_potential() (FluxLayer method) ReactionSpec (class in torchcell.metabolism.pathway) read_cid_list() (in module torchcell.datamodels.compound_identity_curate) read_echo_picklist() (in module torchcell.sga) read_first_record() (in module torchcell.paper.tables) read_frontmatter() (in module torchcell.paper.tables) read_gitter_dat() (in module torchcell.sga) read_json_with_lock() (FileLockHelper class method) read_name_list() (in module torchcell.datamodels.compound_identity_curate) read_release() (in module torchcell.knowledge_graphs.releases) recommend_volume() (in module torchcell.sga) record_admission() (in module torchcell.knowledge_graphs.kg_manifest) record_batch_admission() (in module torchcell.knowledge_graphs.kg_manifest) record_path() (in module torchcell.knowledge_graphs.head_ontology) RecordFilter (class in torchcell.knowledge_graphs.subset) reference_class (AminoAcidCooper2010Dataset property) (AminoAcidMulleder2016Dataset property) (BetaxanthinCachera2023Dataset property) (Bloom2019Dataset property) (CarotenoidOzaydin2013Dataset property) (CaudalPanTranscriptome2024Dataset property) (CrispriChemgenSmith2016Dataset property) (CrispriMormino2022Dataset property) (CrisprMagicLian2019Dataset property) (DmfCostanzo2016Dataset property) (DmfKuzmin2018Dataset property) (DmfKuzmin2020Dataset property) (DmiCostanzo2016Dataset property) (DmiKuzmin2018Dataset property) (DmiKuzmin2020Dataset property) (DmMicroarraySameith2015Dataset property) (EnvChemgenAuesukaree2009Dataset property) (EnvChemgenCostanzo2021Dataset property) (EnvChemgenHoepfner2014Dataset property) (EnvChemgenMota2024Dataset property) (EnvChemgenVanacloig2022Dataset property) (EnvChemgenWildenhain2015Dataset property) (ExperimentDataset property) (FattyAcidSmith2006Dataset property) (FattyAcidXue2025Dataset property) (GeneEssentialitySgdDataset property) (MetaboliteDaSilveira2014Dataset property) (MetaboliteZelezniak2018Dataset property) (MicroarrayKemmeren2014Dataset property) (NadalRibellesPerturbSeq2025Dataset property) (OrganicAcidYoshida2012Dataset property) (ProteomeMessner2023Dataset property) (ProteomeZelezniak2018Dataset property) (ScmdOhnuki2018Dataset property) (ScmdOhnuki2022Dataset property) (ScmdOhya2005Dataset property) (SmfBaryshnikova2010Dataset property) (SmfCostanzo2016Dataset property) (SmfKuzmin2018Dataset property) (SmfKuzmin2020Dataset property) (SmfODuibhir2014Dataset property) (SmMicroarraySameith2015Dataset property) (SynthLethalityYeastSynthLethDbDataset property) (SynthRescueYeastSynthLethDbDataset property) (TmfKuzmin2018Dataset property) (TmfKuzmin2020Dataset property) (TmiKuzmin2018Dataset property) (TmiKuzmin2020Dataset property) (YeastPhenomeDataset property)

ReferenceAnalysis (class in torchcell.knowledge_graphs.incremental_import) ReferenceGenome (class in torchcell.datamodels.schema) ReferenceIndex (class in torchcell.data) refs_of() (Neo4jCellDataset method) register_dataset() (in module torchcell.datasets.dataset_registry) registry_path() (in module torchcell.knowledge_graphs.supported_queries.registry) RegressionTask (class in torchcell.trainers.int_dango) (class in torchcell.trainers.int_dcell) (class in torchcell.trainers.int_hetero_cell) (class in torchcell.trainers.int_transformer_cell) (class in torchcell.trainers.neo_regression) RelationshipRule (class in torchcell.database.browser_style) release_from_manifest() (in module torchcell.knowledge_graphs.releases) release_id() (in module torchcell.knowledge_graphs.releases) ReleaseCompatibility (class in torchcell.knowledge_graphs.releases) ReleaseDataset (class in torchcell.knowledge_graphs.releases) ReleaseDiff (class in torchcell.knowledge_graphs.releases) render() (in module torchcell.database.browser_style) (NodeRule method) (RelationshipRule method) render_schematic_svg() (in module torchcell.paper.ontology_svg) render_seed_js() (in module torchcell.database.browser_style) render_svg() (in module torchcell.paper.ontology_svg) replace() (QueryRegistry method) repo_root() (in module torchcell.utils) REPRESENTATION_DISPLAY_NAMES (in module torchcell.utils) require_no_aggregation_norm() (in module torchcell.models.hetero_cell_bipartite_dango_gi) require_paired() (in module torchcell.knowledge_graphs.releases) required (FieldSpec property) reset_attention_diagnostics() (RegressionTask method) reset_edge_recovery_accumulators() (RegressionTask method) reset_parameters() (DangoPreTrain method) (StoichHypergraphConv method) reset_timings() (in module torchcell.profiling) resolve_component() (in module torchcell.metabolism.media) resolve_compound_identity() (in module torchcell.datamodels.compound_identity) resolve_compound_identity_from_smiles() (in module torchcell.datamodels.compound_identity) resolve_database() (in module torchcell.knowledge_graphs.releases) resolve_dataset_class() (in module torchcell.database.build_dataset_lmdb) resolve_gene_name_comprehensive() (MicroarrayKemmeren2014Dataset method) resolve_kcat_table() (in module torchcell.metabolism.parameters) resolve_label_type() (in module torchcell.transforms.regression_to_classification) resolve_lmdb() (in module torchcell.paper.signal) resolve_orientation() (in module torchcell.sga) resolve_parameter() (in module torchcell.metabolism.enzyme_kinetics) resolve_pointers() (in module torchcell.datamodels.interned_constant) resolve_snapshot() (in module torchcell.knowledge_graphs.supported_queries.check) resolved_compound() (in module torchcell.datamodels.compound_identity) ResolvedKineticParameter (class in torchcell.metabolism.enzyme_kinetics) ResponseBasisHead (class in torchcell.models.equivariant_cell_graph_transformer) ResponseCategory (class in torchcell.datamodels.schema) restated() (in module torchcell.datamodels.media) results() (SharedRecordRules method) reversible_mask (GemTensors property) RNASeqExpressionExperiment (class in torchcell.datamodels.schema) RNASeqExpressionExperimentReference (class in torchcell.datamodels.schema) RNASeqExpressionPhenotype (class in torchcell.datamodels.schema) roman_to_int() (in module torchcell.sequence) Row (class in torchcell.paper.tables) row_count (OntologyClass property) run_check() (in module torchcell.knowledge_graphs.supported_queries.check)

S

sample() (DiffusionDecoder method) (GeneInteractionDiff method) (LinearDecoder method) samples() (DistHead method) SampleUnit (class in torchcell.datamodels.schema) sanity_check_metabolic_networks() (in module torchcell.metabolism.yeast_GEM) save() (QueryRegistry method) (SignalCache method) save_and_log_figure() (GraphRecoveryVisualization method) (TransformerDiagnostics method) (Visualization method) save_graph() (SCerevisiaeGraph method) save_manifest() (in module torchcell.knowledge_graphs.kg_manifest) savefig_true_size_svg() (in module torchcell.utils) SCerevisiaeGraph (class in torchcell.graph) scheduler_type() (in module torchcell.trainers.int_hetero_cell) schema_enums() (in module torchcell.datamodels.ontology_checks) schema_is_a() (in module torchcell.knowledge_graphs.supported_queries.check) schema_models() (in module torchcell.datamodels.ontology_checks) schema_node_labels() (in module torchcell.database.browser_style) SchemaSurface (class in torchcell.provenance) scientific() (in module torchcell.paper.tables) ScmdOhnuki2018Adapter (class in torchcell.adapters) ScmdOhnuki2018Dataset (class in torchcell.datasets.scerevisiae.ohnuki2018) ScmdOhnuki2022Adapter (class in torchcell.adapters) ScmdOhnuki2022Dataset (class in torchcell.datasets.scerevisiae.ohnuki2022) ScmdOhya2005Adapter (class in torchcell.adapters) ScmdOhya2005Dataset (class in torchcell.datasets.scerevisiae.ohya2005) score_plate() (in module torchcell.sga) score_table() (in module torchcell.sga) ScoreReport (class in torchcell.sga) seed_state() (in module torchcell.database.browser_style) SeedNodeStyle (class in torchcell.database.browser_style) SeedState (class in torchcell.database.browser_style) SegregantGenotype (class in torchcell.datamodels.schema) SegregantGrowthExperiment (class in torchcell.datamodels.schema) SegregantGrowthExperimentReference (class in torchcell.datamodels.schema) SegregantParent (class in torchcell.datamodels.schema) select_indices() (in module torchcell.knowledge_graphs.subset) selected_composite() (in module torchcell.knowledge_graphs.supported_queries.check) SelfAttention (class in torchcell.models.self_attention_deep_set) SelfAttentionBlock (class in torchcell.nn.self_attention_block) SelfAttentionDeepSet (class in torchcell.models.self_attention_deep_set) SelfAttentionGraphAggregation (class in torchcell.models.hetero_cell_bipartite_dango_gi) (class in torchcell.models.hetero_cell_bipartite_dango_gi_lazy) SequencePerturbation (class in torchcell.datamodels.schema) SequenceVariantPerturbation (class in torchcell.datamodels.schema) serialize() (in module torchcell.datamodels.compound_identity_curate) served_nodes_unchanged_by() (GraphSchemaEntry method) ServedDatabase (class in torchcell.knowledge_graphs.releases) ServedDrift (class in torchcell.knowledge_graphs.kg_manifest) set_layers_forward() (DeepSet method) (SelfAttentionDeepSet method) setup() (CellDataModule method) (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method) (SimpleLinearRegressionTask method) SgaAllelePerturbation (class in torchcell.datamodels.schema) SgaDampPerturbation (class in torchcell.datamodels.schema) SgaKanMxDeletionPerturbation (class in torchcell.datamodels.schema) SgaNatMxDeletionPerturbation (class in torchcell.datamodels.schema) SgaSuppressorAllelePerturbation (class in torchcell.datamodels.schema) SgaTsAllelePerturbation (class in torchcell.datamodels.schema) sha256_file() (in module torchcell.verification) shared_rule_results() (in module torchcell.verification) SharedRecordRules (class in torchcell.verification) SignalCache (class in torchcell.paper.tables) SimpleLinearModel (class in torchcell.models.linear) SimpleLinearRegressionTask (class in torchcell.trainers.simple_linear_regression) SinusoidalTimeEmbedding (class in torchcell.models.diffusion_decoder) skip_lookup (CurationDirective property) skipped (BackfillReport property) SmallMoleculePerturbation (class in torchcell.datamodels.schema) SmfBaryshnikova2010Adapter (class in torchcell.adapters) SmfBaryshnikova2010Dataset (class in torchcell.datasets.scerevisiae.baryshnikova2010) SmfCostanzo2016Adapter (class in torchcell.adapters)

SmfCostanzo2016Dataset (class in torchcell.datasets.scerevisiae.costanzo2016) SmfKuzmin2018Adapter (class in torchcell.adapters) SmfKuzmin2018Dataset (class in torchcell.datasets.scerevisiae.kuzmin2018) SmfKuzmin2020Adapter (class in torchcell.adapters) SmfKuzmin2020Dataset (class in torchcell.datasets.scerevisiae.kuzmin2020) SmfODuibhir2014Adapter (class in torchcell.adapters) SmfODuibhir2014Dataset (class in torchcell.datasets.scerevisiae.oduibhir2014) Smith2006Adapter (class in torchcell.adapters) Smith2016Adapter (class in torchcell.adapters) SmMicroarraySameith2015Adapter (class in torchcell.adapters) SmMicroarraySameith2015Dataset (class in torchcell.datasets.scerevisiae.sameith2015) snapshot_from_manifest() (in module torchcell.knowledge_graphs.release_snapshot) snapshot_paths() (in module torchcell.knowledge_graphs.release_snapshot) SnapshotDataset (class in torchcell.knowledge_graphs.release_snapshot) SnapshotEvent (class in torchcell.knowledge_graphs.release_snapshot) Solvent (class in torchcell.datamodels.schema) sort_perturbations() (Genotype class method) SOTerm (class in torchcell.datamodels.schema) source_for() (UptakePolicy method) source_path() (SourcedValue method) SOURCED (EvidenceTier attribute) sourced_value_fields() (in module torchcell.datamodels.ontology_checks) SourcedValue (class in torchcell.verification) split_blocks() (in module torchcell.knowledge_graphs.supported_queries.cypher_deps) split_dataset_args() (in module torchcell.knowledge_graphs.kg_manifest) split_experiment_dump() (in module torchcell.datamodels.interned_constant) StaleResult (class in torchcell.provenance) stamp_manifest() (in module torchcell.knowledge_graphs.releases) standard_allele() (in module torchcell.datamodels.strain_background) standard_background() (in module torchcell.datamodels.strain_background) standard_reaction_delta_g() (GemTensors method) StatDerivation (class in torchcell.verification) stated_name (Media property) status_rows() (in module torchcell.knowledge_graphs.releases) step() (CosineAnnealingWarmupRestarts method) StoichHypergraphConv (class in torchcell.nn.stoichiometric_hypergraph_conv) strain_background_identity() (in module torchcell.datamodels.identity) StrainBackground (class in torchcell.datamodels.schema) StrainConstruction (class in torchcell.datamodels.schema) StrainEnvironmentResponseExperiment (class in torchcell.datamodels.schema) StrainEnvironmentResponseExperimentReference (class in torchcell.datamodels.schema) StrainReferenceGenome (class in torchcell.datamodels.schema) StrainScore (class in torchcell.sga) stream_gzip_signal() (in module torchcell.paper.tables) strip_comments() (in module torchcell.knowledge_graphs.supported_queries.cypher_deps) strip_string_prefix() (SCerevisiaeGraph method) stylesheet_sha256() (in module torchcell.database.browser_style) SubgraphRepresentation (class in torchcell.data) subset_dataset() (in module torchcell.knowledge_graphs.subset) SubsetConfig (class in torchcell.knowledge_graphs.build_time_projection) summary() (VerificationReport method) SupCR (class in torchcell.losses.multi_dim_nan_tolerant) superset_check() (in module torchcell.knowledge_graphs.kg_manifest) SupersetCheck (class in torchcell.knowledge_graphs.kg_manifest) SupersetLineage (class in torchcell.knowledge_graphs.kg_manifest) supported_edge_methods (CellAdapter property) supported_node_methods (CellAdapter property) SupportedQuery (class in torchcell.knowledge_graphs.supported_queries.registry) SuppressorAllelePerturbation (class in torchcell.datamodels.schema) surface_at_ref() (in module torchcell.knowledge_graphs.kg_manifest) surface_in_worktree() (in module torchcell.knowledge_graphs.kg_manifest) SymbolChange (class in torchcell.provenance) SymbolDrift (class in torchcell.provenance) synonyms_url() (in module torchcell.datamodels.compound_identity_curate) synthetic_lethality_to_fitness_experiment() (in module torchcell.datamodels.synthetic_lethality_to_fitness_conversion) synthetic_lethality_to_fitness_reference() (in module torchcell.datamodels.synthetic_lethality_to_fitness_conversion) SyntheticLethalityExperiment (class in torchcell.datamodels.schema) SyntheticLethalityExperimentReference (class in torchcell.datamodels.schema) SyntheticLethalityPhenotype (class in torchcell.datamodels.schema) SyntheticLethalityToFitnessConverter (class in torchcell.datamodels.synthetic_lethality_to_fitness_conversion) SyntheticRescueExperiment (class in torchcell.datamodels.schema) SyntheticRescueExperimentReference (class in torchcell.datamodels.schema) SyntheticRescuePhenotype (class in torchcell.datamodels.schema) SynthLethalityYeastSynthLethDbAdapter (class in torchcell.adapters) SynthLethalityYeastSynthLethDbDataset (class in torchcell.datasets.scerevisiae.synth_leth_db) SynthRescueYeastSynthLethDbAdapter (class in torchcell.adapters) SynthRescueYeastSynthLethDbDataset (class in torchcell.datasets.scerevisiae.synth_leth_db) systematic_gene_names (Genotype property)

T

TableCoverage (class in torchcell.metabolism.constraints) take_action() (BuildCommand method) taus (DistHead property) TCDB (class in torchcell.database.tcdb) Temperature (class in torchcell.datamodels.schema) temperature_identity() (in module torchcell.datamodels.identity) TemperatureScheduler (class in torchcell.losses.mle_dist_supcr) (class in torchcell.losses.mle_wasserstein) TemperatureUnit (class in torchcell.datamodels.schema) test_bipartite_attributes() (in module torchcell.metabolism.yeast_GEM) test_dataloader() (CellDataModule method) test_step() (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method), [1], [2], [3], [4] (SimpleLinearRegressionTask method) tex_escape() (in module torchcell.paper.tables) tex_spec() (Column method) ThermoMode (class in torchcell.metabolism.constraints) ThermoTable (class in torchcell.metabolism.constraints) thresholds (MultiDimNaNTolerantOrdinalCELoss property) time_method() (in module torchcell.profiling) TmfKuzmin2018Adapter (class in torchcell.adapters) TmfKuzmin2018Dataset (class in torchcell.datasets.scerevisiae.kuzmin2018) TmfKuzmin2020Adapter (class in torchcell.adapters) TmfKuzmin2020Dataset (class in torchcell.datasets.scerevisiae.kuzmin2020) TmiKuzmin2018Adapter (class in torchcell.adapters) TmiKuzmin2018Dataset (class in torchcell.datasets.scerevisiae.kuzmin2018) TmiKuzmin2020Adapter (class in torchcell.adapters) TmiKuzmin2020Dataset (class in torchcell.datasets.scerevisiae.kuzmin2020) to_latex() (PaperTable method) to_markdown() (PaperTable method) to_properties() (KgRelease method) torchcell.adapters module torchcell.data module torchcell.database module torchcell.datamodels module torchcell.datamodules module torchcell.datasets module torchcell.graph module

torchcell.knowledge_graphs module torchcell.literature module torchcell.loader module torchcell.losses module torchcell.metabolism module torchcell.models module torchcell.nn module torchcell.ontology module torchcell.paper module torchcell.profiling module torchcell.provenance module torchcell.scheduler module torchcell.sequence module torchcell.sga module torchcell.trainers module torchcell.transforms module torchcell.utils module torchcell.verification module torchcell.viz module train_dataloader() (CellDataModule method) training_step() (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method), [1], [2], [3], [4] (SimpleLinearRegressionTask method) transform_item() (ExperimentDataset method) TransformerDiagnostics (class in torchcell.viz.transformer_diagnostics) TsAllelePerturbation (class in torchcell.datamodels.schema) turnover() (FluxLayer method)

U

UncertaintyType (class in torchcell.datamodels.schema) uniprot_for_genes() (in module torchcell.metabolism.parameters) unit_for() (OedKineticRecord method) Unperturbed (class in torchcell.data) unresolved_names (MediaBounds property)

update() (ListMLEMetric method) update_buffer() (BufferedWeightedDistLoss method) (BufferedWeightedSupCRCell method), [1] (BufferedWeightedWassersteinLoss method) update_json_with_lock() (FileLockHelper class method) UptakePolicy (class in torchcell.metabolism.media)

V

v (DistHead property) val_dataloader() (CellDataModule method) VALID_MODEL_NAMES (FungalUpDownTransformer attribute) validate_aerobicity() (Environment class method) validate_calmorph() (CalMorphPhenotype class method) validate_copy_number_positive() (CopyNumberVariantPerturbation class method) (EngineeredCopyNumberPerturbation class method) (NaturalGenePresencePerturbation class method) validate_cv() (CalMorphPhenotype class method) validate_data() (ReferenceIndex class method) validate_dilution_rate() (Environment class method) validate_dispersion() (PseudobulkExpressionPhenotype class method) validate_dropout_roles_unique() (Media class method) validate_expression_direction() (ExpressionModulationPerturbation class method) validate_fields() (Phenotype method) validate_fitness() (FitnessPhenotype class method) (GeneInteractionPhenotype class method) validate_gene_set() (ParsedGenome class method) validate_genes_in_graph() (GeneGraph class method) validate_label_fields() (Phenotype method) validate_matching_keys() (MicroarrayExpressionPhenotype method) (RNASeqExpressionPhenotype method) validate_mechanism_so_id() (CopyNumberVariantPerturbation class method) (EngineeredCopyNumberPerturbation class method) (ExpressionModulationPerturbation class method) (PresenceAbsencePerturbation class method) (SequencePerturbation class method) validate_metabolite_level() (MetabolitePhenotype method) validate_n_cells() (PseudobulkExpressionPhenotype class method) validate_n_samples() (EnvironmentResponsePhenotype class method) (FitnessPhenotype class method) (GeneInteractionPhenotype class method) validate_pert_gene_name() (GenePerturbation class method) validate_protein_abundance() (ProteinAbundancePhenotype method) validate_provenance() (GenePerturbation class method) validate_provenance_gaps() (ProvenanceGapMixin method) validate_query() (in module torchcell.knowledge_graphs.supported_queries.check) validate_response() (EnvironmentResponsePhenotype class method) validate_so_id() (SOTerm class method)

validate_state() (Media class method) (PresenceAbsencePerturbation class method) validate_sys_gene_name() (CopyNumberVariantPerturbation class method) (GeneAdditionPerturbation class method) (GenePerturbation class method) (NaturalGeneAbsencePerturbation class method) (NaturalGenePresencePerturbation class method) validate_visual_score() (VisualScorePhenotype method) validation_step() (DCellRegressionSlimTask method) (DCellRegressionTask method) (RegressionTask method), [1], [2], [3], [4] (SimpleLinearRegressionTask method) value_for() (OedKineticRecord method) value_surface_at_ref() (in module torchcell.knowledge_graphs.kg_manifest) value_surface_drift() (in module torchcell.knowledge_graphs.kg_manifest) value_surface_from_sources() (in module torchcell.knowledge_graphs.kg_manifest) value_surface_in_worktree() (in module torchcell.knowledge_graphs.kg_manifest) values() (GeneMultiGraph method) VerificationReport (class in torchcell.verification) verified_constant() (in module torchcell.datamodels.interned_constant) verify_expression_dataset() (in module torchcell.verification) verify_fitness_dataset() (in module torchcell.verification) verify_head_ontology() (in module torchcell.knowledge_graphs.head_ontology) verify_metabolite_dataset() (in module torchcell.verification) verify_morphology_dataset() (in module torchcell.verification) verify_raw_files() (in module torchcell.data) verify_sha256() (in module torchcell.data) verify_visual_score_dataset() (in module torchcell.verification) version (YeastGEM attribute) VisGraphDegen (class in torchcell.viz.visual_graph_degen) visibility (ExperimentDataset attribute) visual_score_gene_set() (in module torchcell.verification) Visualization (class in torchcell.viz.visual_regression) visualize_model_outputs() (Visualization method) VisualScoreExperiment (class in torchcell.datamodels.schema) VisualScoreExperimentReference (class in torchcell.datamodels.schema) VisualScorePhenotype (class in torchcell.datamodels.schema) volume_assay_metrics() (in module torchcell.sga) volume_position_confound() (in module torchcell.sga)

W

WeightedDistLoss (class in torchcell.losses.multi_dim_nan_tolerant) WeightedMSELoss (class in torchcell.losses.multi_dim_nan_tolerant) WeightedSupCRCell (class in torchcell.losses.multi_dim_nan_tolerant) WeightedWassersteinLoss (class in torchcell.losses.mle_wasserstein) well_to_rowcol() (in module torchcell.sga) window() (Gene method) window_five_prime() (Gene method) window_three_prime() (Gene method) with_file_lock() (FileLockHelper class method)

with_zotero_retry() (in module torchcell.literature) worker_function() (CpuExperimentLoaderMultiprocessing static method) write_build_manifest() (in module torchcell.provenance) write_incremental_headers() (in module torchcell.knowledge_graphs.incremental_import) write_json_with_lock() (FileLockHelper class method) write_manifest() (in module torchcell.literature) write_release() (in module torchcell.knowledge_graphs.releases) write_snapshot() (in module torchcell.knowledge_graphs.release_snapshot) write_verified() (in module torchcell.data)

Y

YeastGEM (class in torchcell.metabolism.yeast_GEM)

YeastPhenomeDataset (class in torchcell.datasets.scerevisiae.yeastphenome)

Z

zfactor() (in module torchcell.sga) ZoteroConfig (class in torchcell.literature)

ZoteroLibrary (class in torchcell.literature) Zygosity (class in torchcell.datamodels.schema)