torchcell.trainers ================== .. module:: torchcell.trainers .. currentmodule:: torchcell.trainers PyTorch Lightning training tasks. The package exports the regression task (:class:`~torchcell.trainers.neo_regression.RegressionTask`), a simple linear baseline, and two DCell tasks. The ``fit_int_*`` and ``int_*`` modules hold the tasks used by individual experiments and are imported by module path from the experiment scripts. Every class below is listed under the module that defines it. .. contents:: Contents :local: ``dcell_regression`` -------------------- Lightning training task for DCell graph-based fitness regression. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst dcell_regression.DCellRegressionTask ``dcell_regression_slim`` ------------------------- Slim Lightning trainer for DCell regression with subsystem and root metrics. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst dcell_regression_slim.DCellRegressionSlimTask ``int_dango`` ------------- Lightning training task for the DANGO genetic-interaction regression model. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst int_dango.RegressionTask ``int_dcell`` ------------- Lightning training module for DCell gene-interaction regression. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst int_dcell.RegressionTask ``int_hetero_cell`` ------------------- Lightning regression tasks for heterogeneous-cell gene interaction models. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst int_hetero_cell.RegressionTask int_hetero_cell.DiffusionRegressionTask Functions ~~~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated int_hetero_cell.scheduler_type int_hetero_cell.normalize_accumulation_schedule int_hetero_cell.accumulation_steps ``int_transformer_cell`` ------------------------ Lightning training module for the transformer cell gene-interaction model. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst int_transformer_cell.RegressionTask ``neo_regression`` ------------------ Lightning regression trainer with MSE/ListMLE losses and correlation metrics. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst neo_regression.ListMLEMetric neo_regression.MSEListMLELoss neo_regression.RegressionTask ``simple_linear_regression`` ---------------------------- Lightning task for simple linear regression on graph perturbation data. Classes ~~~~~~~ .. autosummary:: :nosignatures: :toctree: ../generated :template: autosummary/class.rst simple_linear_regression.SimpleLinearRegressionTask