torchcell.datasets ================== .. module:: torchcell.datasets .. currentmodule:: torchcell.datasets Dataset loaders. The top level of ``torchcell.datasets`` holds the per-gene embedding datasets (sequence language-model embeddings, codon frequencies, one-hot and random baselines), which derive from the in-memory embedding base in ``torchcell.data.embedding``, and ``NodeEmbeddingBuilder``, which builds them from a configuration. The experiment datasets live in ``torchcell.datasets.scerevisiae``: one module per source publication, each reading that publication's released data, converting its records into :mod:`torchcell.datamodels` experiments and storing them in LMDB. A class decorated with :func:`~torchcell.datasets.dataset_registry.register_dataset` is added to ``dataset_registry``, the name-to-class map that ``knowledge_graphs.create_kg`` and ``knowledge_graphs.kg_manifest`` look datasets up in; the table below lists every registered class. .. contents:: Contents :local: Embedding datasets ------------------ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst NucleotideTransformerDataset FungalUpDownTransformerDataset CodonFrequencyDataset OneHotGeneDataset ProtT5Dataset GraphEmbeddingDataset Esm2Dataset CalmDataset RandomEmbeddingDataset NodeEmbeddingBuilder Dataset registry ---------------- .. currentmodule:: torchcell.datasets.dataset_registry .. autosummary:: :nosignatures: :toctree: ../generated register_dataset .. autosummary:: :nosignatures: :toctree: ../generated dataset_registry Registered *S. cerevisiae* experiment datasets ---------------------------------------------- The 52 classes in ``dataset_registry``, grouped by source module (one module per publication). .. currentmodule:: torchcell.datasets.scerevisiae .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst auesukaree2009.EnvChemgenAuesukaree2009Dataset baryshnikova2010.SmfBaryshnikova2010Dataset bloom2019.Bloom2019Dataset cachera2023.BetaxanthinCachera2023Dataset caudal2024.CaudalPanTranscriptome2024Dataset cooper2010.AminoAcidCooper2010Dataset costanzo2016.DmfCostanzo2016Dataset costanzo2016.DmiCostanzo2016Dataset costanzo2016.SmfCostanzo2016Dataset costanzo2021.EnvChemgenCostanzo2021Dataset dasilveira2014.MetaboliteDaSilveira2014Dataset hillenmeyer2008.HetHillenmeyer2008Dataset hillenmeyer2008.HomHillenmeyer2008Dataset hoepfner2014.EnvChemgenHoepfner2014Dataset kemmeren2014.MicroarrayKemmeren2014Dataset kuzmin2018.DmfKuzmin2018Dataset kuzmin2018.DmiKuzmin2018Dataset kuzmin2018.SmfKuzmin2018Dataset kuzmin2018.TmfKuzmin2018Dataset kuzmin2018.TmiKuzmin2018Dataset kuzmin2020.DmfKuzmin2020Dataset kuzmin2020.DmiKuzmin2020Dataset kuzmin2020.SmfKuzmin2020Dataset kuzmin2020.TmfKuzmin2020Dataset kuzmin2020.TmiKuzmin2020Dataset lian2019.CrisprMagicLian2019Dataset lopez2024.IsobutanolScreenLopez2024Dataset lopez2024.IsobutanolValidatedLopez2024Dataset messner2023.ProteomeMessner2023Dataset mormino2022.CrispriMormino2022Dataset mota2024.EnvChemgenMota2024Dataset mulleder2016.AminoAcidMulleder2016Dataset nadal_ribelles2025.NadalRibellesPerturbSeq2025Dataset oduibhir2014.SmfODuibhir2014Dataset ohnuki2018.ScmdOhnuki2018Dataset ohnuki2022.ScmdOhnuki2022Dataset ohya2005.ScmdOhya2005Dataset ozaydin2013.CarotenoidOzaydin2013Dataset sameith2015.DmMicroarraySameith2015Dataset sameith2015.SmMicroarraySameith2015Dataset sgd.GeneEssentialitySgdDataset smith2006.FattyAcidSmith2006Dataset smith2016.CrispriChemgenSmith2016Dataset synth_leth_db.SynthLethalityYeastSynthLethDbDataset synth_leth_db.SynthRescueYeastSynthLethDbDataset vanacloig2022.EnvChemgenVanacloig2022Dataset wildenhain2015.EnvChemgenWildenhain2015Dataset xue2025.FattyAcidXue2025Dataset yeastphenome.YeastPhenomeDataset yoshida2012.OrganicAcidYoshida2012Dataset zelezniak2018.MetaboliteZelezniak2018Dataset zelezniak2018.ProteomeZelezniak2018Dataset