Index

A

accuracy() (in module alf_core.utils.metrics.classification) acq_batch_size (alf_core.dataclasses.state.State attribute), [1] Acquisition function AcquisitionFunction (class in alf_core.optimizer.acquisition_function) activation (alf_tools.models.mlp.MLPModelConfig attribute) Active learning additional_metrics (alf_core.dataclasses.surrogate_epoch_metrics.SurrogateEpochMetrics attribute), [1] alf_core.dataclasses.candidate module alf_core.dataclasses.labelled_candidates module alf_core.dataclasses.predictions module alf_core.dataclasses.results module alf_core.dataclasses.round_metrics module alf_core.dataclasses.state module alf_core.dataclasses.surrogate_epoch_metrics module alf_core.dataset.base_dataset module alf_core.dataset.splitting_utils module alf_core.model.base_model module alf_core.model.normaliser module alf_core.optimizer.acquisition_function module alf_core.optimizer.optimizer module alf_core.optimizer.search module alf_core.oracle.oracle module alf_core.surrogate.surrogate module alf_core.tasks.base_task module alf_core.tasks.design_task module alf_core.tasks.supervised_task module alf_core.tasks.zeroshot_task module alf_core.utils.enums module alf_core.utils.metrics.acquisition_batch module alf_core.utils.metrics.aggregate module alf_core.utils.metrics.base module alf_core.utils.metrics.calibration module alf_core.utils.metrics.classification module alf_core.utils.metrics.regression module

alf_core.utils.state_logger module alf_tools.datasets.flip module alf_tools.datasets.gfp module alf_tools.datasets.proteingym module alf_tools.models.cnn module alf_tools.models.ensemble module alf_tools.models.esm2 module alf_tools.models.esm_utils.config module alf_tools.models.esm_utils.loss module alf_tools.models.esm_utils.scoring_function module alf_tools.models.gp module alf_tools.models.mlp module alf_tools.models.pyrosetta module alf_tools.models.utils.botorch_model_wrapper module alf_tools.models.utils.botorch_utils module alf_tools.models.utils.config_utils module alf_tools.models.utils.data_utils module alf_tools.optimizer.acquisition_functions.botorch_acquisition module alf_tools.optimizer.acquisition_functions.botorch_samplers module alf_tools.optimizer.acquisition_functions.core_set module alf_tools.optimizer.acquisition_functions.expected_improvement module alf_tools.optimizer.acquisition_functions.greedy module alf_tools.optimizer.acquisition_functions.thompson_sampling module alf_tools.optimizer.acquisition_functions.ucb module alf_tools.optimizer.search.botorch_continuous_search module alf_tools.optimizer.search.single_mutant_search module alf_tools.utils.constants module append() (alf_core.dataclasses.labelled_candidates.LabelledCandidates method) ard (alf_tools.models.gp.GPModelConfig attribute) ask() (alf_core.optimizer.optimizer.Optimizer method) auc_roc() (in module alf_core.utils.metrics.classification) auc_top_k() (in module alf_core.utils.metrics.aggregate)

B

backbone_learning_rate (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) base_seed (alf_tools.models.ensemble.EnsembleWrapperConfig attribute) BaseDataset (class in alf_core.dataset.base_dataset) BaseDatasetConfig (class in alf_core.dataset.base_dataset) BaseModel (class in alf_core.model.base_model) BaseSearch (class in alf_core.optimizer.search) BaseTask (class in alf_core.tasks.base_task) BaseTrainConfig (class in alf_core.model.base_model) batch_limit (alf_tools.optimizer.acquisition_functions.botorch_acquisition.BoTorchAcquisitionOptConfig attribute) batch_shape (alf_tools.models.utils.botorch_model_wrapper.BotorchModelWrapper property) batch_size (alf_tools.models.cnn.CNNTrainConfig attribute) (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) (alf_tools.models.mlp.MLPTrainConfig attribute)

batch_size_inference (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) Best-found BINARY (alf_core.utils.enums.ProblemType attribute), [1] botorch_model (alf_tools.models.gp.GPModel property) BoTorchAcquisition (class in alf_tools.optimizer.acquisition_functions.botorch_acquisition) BoTorchAcquisitionOptConfig (class in alf_tools.optimizer.acquisition_functions.botorch_acquisition) BotorchContinuousSearch (class in alf_tools.optimizer.search.botorch_continuous_search) BoTorchMCSampler (class in alf_tools.optimizer.acquisition_functions.botorch_samplers) BotorchModelWrapper (class in alf_tools.models.utils.botorch_model_wrapper) build_from_target() (in module alf_tools.models.utils.config_utils) build_kernel_fn (alf_tools.models.gp.GPModelConfig attribute)

C

Calibration Candidate (class in alf_core.dataclasses.candidate) candidate_pool (alf_core.dataset.base_dataset.BaseDataset property) candidates (alf_core.dataclasses.labelled_candidates.LabelledCandidates attribute), [1] candidates_to_tensor() (in module alf_tools.models.utils.botorch_utils) check_inputs() (in module alf_core.utils.metrics.base) check_variance_validity() (in module alf_core.utils.metrics.base) ClassificationMetricRegistry (class in alf_core.utils.metrics.base) cleanup() (alf_core.model.base_model.BaseModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.mlp.MLPModel method) CNNModel (class in alf_tools.models.cnn) CNNModelConfig (class in alf_tools.models.cnn) CNNTrainConfig (class in alf_tools.models.cnn)

compute_aggregate_metrics() (in module alf_core.utils.metrics.aggregate) compute_experiment_summary() (in module alf_core.utils.metrics.aggregate) compute_metrics() (alf_core.dataclasses.results.Results method) compute_pll() (in module alf_tools.models.esm_utils.scoring_function) compute_recall() (in module alf_core.utils.metrics.acquisition_batch) compute_regret() (in module alf_core.utils.metrics.acquisition_batch) compute_supervised_loss() (in module alf_tools.models.esm_utils.loss) config (alf_tools.datasets.flip.FLIP attribute) CoreSet (class in alf_tools.optimizer.acquisition_functions.core_set) Coverage coverage() (in module alf_core.utils.metrics.regression) cross_validation (alf_tools.datasets.proteingym.ProteinGymConfig attribute), [1] cross_validation_fold (alf_tools.datasets.proteingym.ProteinGymConfig attribute), [1] cross_validation_type (alf_tools.datasets.proteingym.ProteinGymConfig attribute), [1] custom_featurizer (alf_tools.models.gp.FeaturizerConfig attribute)

D

data (alf_core.dataclasses.candidate.Candidate attribute), [1] (alf_core.dataclasses.labelled_candidates.LabelledCandidates property) Dataset dataset (alf_core.dataclasses.state.State attribute), [1] DatasetSearch (class in alf_core.optimizer.search) DesignTask (class in alf_core.tasks.design_task)

determine_num_classes() (alf_core.dataset.base_dataset.BaseDataset method) dms_name (alf_tools.datasets.proteingym.ProteinGymConfig attribute), [1] dms_type (alf_tools.datasets.proteingym.ProteinGymConfig attribute), [1] dropout (alf_tools.models.cnn.CNNModelConfig attribute) (alf_tools.models.mlp.MLPModelConfig attribute) dropout_seed (alf_tools.models.mlp.MLPModelConfig attribute) dtype (alf_tools.models.gp.GPTrainConfig attribute)

E

early_stopping_delta (alf_tools.models.gp.GPTrainConfig attribute) early_stopping_patience (alf_tools.models.gp.GPTrainConfig attribute) ECE embed() (alf_tools.models.esm2.ESM2Model method) empirical_dist (alf_core.dataclasses.predictions.Predictions attribute), [1] EnsembleWrapper (class in alf_tools.models.ensemble) EnsembleWrapperConfig (class in alf_tools.models.ensemble)

epoch (alf_core.dataclasses.surrogate_epoch_metrics.SurrogateEpochMetrics attribute), [1] ESM2Model (class in alf_tools.models.esm2) ESM2ModelConfig (class in alf_tools.models.esm_utils.config) ESM2TrainConfig (class in alf_tools.models.esm_utils.config) evaluate() (alf_core.oracle.oracle.Oracle method) (alf_core.tasks.base_task.BaseTask method) expected_calibration_error() (in module alf_core.utils.metrics.calibration) ExpectedImprovement (class in alf_tools.optimizer.acquisition_functions.expected_improvement)

F

f1() (in module alf_core.utils.metrics.classification) fc_hidden_dim (alf_tools.models.cnn.CNNModelConfig attribute) feature_dim (alf_tools.models.gp.GPModel attribute) features (alf_core.dataclasses.candidate.Candidate attribute), [1] featurise() (alf_core.model.base_model.BaseModel method) (alf_core.surrogate.surrogate.Surrogate method) (alf_tools.models.cnn.CNNModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.esm2.ESM2Model method) (alf_tools.models.gp.GPModel method) (alf_tools.models.mlp.MLPModel method) (alf_tools.models.pyrosetta.PyRosetta method) featurizer_type (alf_tools.models.gp.FeaturizerConfig attribute) FeaturizerConfig (class in alf_tools.models.gp)

FileStateLogger (class in alf_core.utils.state_logger) fit() (alf_core.model.normaliser.InputNormaliser method) (alf_core.model.normaliser.InputStandardiser method) (alf_core.model.normaliser.OutputStandardiser method) (alf_core.surrogate.surrogate.Surrogate method) flatten_one_hot (alf_tools.models.gp.FeaturizerConfig attribute) FLIP (class in alf_tools.datasets.flip) flip_dataset (alf_tools.datasets.flip.FLIPConfig attribute), [1] flip_split (alf_tools.datasets.flip.FLIPConfig attribute), [1] FLIPConfig (class in alf_tools.datasets.flip) force_download (alf_tools.datasets.proteingym.ProteinGymConfig attribute), [1] forward() (alf_tools.models.cnn.SequenceCNN method) (alf_tools.models.mlp.MLP method) fraction (alf_tools.models.ensemble.SubsampleConfig attribute) freeze_backbone (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute)

G

GeneratorSearch (class in alf_core.optimizer.search) get_bounds_tensor() (in module alf_tools.models.utils.botorch_utils) get_epoch_metrics() (alf_core.model.base_model.BaseModel method) (alf_tools.models.cnn.CNNModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.esm2.ESM2Model method) (alf_tools.models.gp.GPModel method) (alf_tools.models.mlp.MLPModel method) get_hyperparameters() (alf_tools.models.gp.GPModel method) get_metrics() (alf_core.dataset.base_dataset.BaseDataset method) (alf_core.optimizer.optimizer.Optimizer method) (alf_core.optimizer.search.BaseSearch method) (alf_core.optimizer.search.DatasetSearch method) (alf_core.oracle.oracle.Oracle method) (alf_core.utils.metrics.base.ClassificationMetricRegistry method) (alf_core.utils.metrics.base.RegressionMetricRegistry method) (alf_tools.optimizer.search.botorch_continuous_search.BotorchContinuousSearch method)

get_sampler() (alf_tools.optimizer.acquisition_functions.botorch_samplers.BoTorchMCSampler method) get_top_k() (alf_core.dataclasses.labelled_candidates.LabelledCandidates method) get_training_summary_metrics() (alf_core.model.base_model.BaseModel method) (alf_core.surrogate.surrogate.Surrogate method) (alf_tools.models.cnn.CNNModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.esm2.ESM2Model method) (alf_tools.models.gp.GPModel method) (alf_tools.models.mlp.MLPModel method) (alf_tools.models.pyrosetta.PyRosetta method) GFP (class in alf_tools.datasets.gfp) gp_model (alf_tools.models.gp.GPModel attribute) GPModel (class in alf_tools.models.gp) GPModelConfig (class in alf_tools.models.gp) GPTrainConfig (class in alf_tools.models.gp) Greedy (class in alf_tools.optimizer.acquisition_functions.greedy)

H

hidden_dims (alf_tools.models.mlp.MLPModelConfig attribute)

history (alf_core.dataclasses.state.State attribute), [1] hit_rate() (in module alf_core.utils.metrics.regression)

I

InputNormaliser (class in alf_core.model.normaliser) InputStandardiser (class in alf_core.model.normaliser) intra_batch_diversity() (in module alf_core.utils.metrics.acquisition_batch) inverse_transform() (alf_core.model.normaliser.InputNormaliser method) (alf_core.model.normaliser.InputStandardiser method) (alf_core.model.normaliser.OutputStandardiser method)

is_fitted (alf_core.model.normaliser.InputNormaliser property) (alf_core.model.normaliser.InputStandardiser property) (alf_core.model.normaliser.OutputStandardiser property)

K

kernel_size (alf_tools.models.cnn.CNNModelConfig attribute)

kernel_type (alf_tools.models.gp.GPModelConfig attribute)

L

label_dtype (alf_core.model.base_model.BaseTrainConfig attribute) LabelledCandidates (class in alf_core.dataclasses.labelled_candidates) labels (alf_core.dataclasses.labelled_candidates.LabelledCandidates attribute), [1] learning_rate (alf_core.model.base_model.BaseTrainConfig attribute) (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) (alf_tools.models.gp.GPTrainConfig attribute) (alf_tools.models.mlp.MLPTrainConfig attribute) lengthscale_constraint (alf_tools.models.gp.GPModelConfig attribute) lengthscale_prior (alf_tools.models.gp.GPModelConfig attribute) likelihood (alf_tools.models.gp.GPModel attribute) load_dataset() (alf_core.dataset.base_dataset.BaseDataset method) (alf_tools.datasets.flip.FLIP method) (alf_tools.datasets.gfp.GFP method) (alf_tools.datasets.proteingym.ProteinGym method)

log() (alf_core.utils.state_logger.FileStateLogger method) (alf_core.utils.state_logger.StateLogger method) (alf_core.utils.state_logger.TerminalStateLogger method) log_frequency (alf_core.model.base_model.BaseTrainConfig attribute) (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) (alf_tools.models.mlp.MLPTrainConfig attribute) log_summary() (alf_core.utils.state_logger.FileStateLogger method) (alf_core.utils.state_logger.StateLogger method) (alf_core.utils.state_logger.TerminalStateLogger method) loss_fn (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute)

M

make_input_transform() (in module alf_core.model.normaliser) mask_probability (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) mask_splitting (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) mask_tokens() (in module alf_tools.models.esm_utils.loss) matern_nu (alf_tools.models.gp.GPModelConfig attribute) max_attempts (alf_tools.models.gp.GPTrainConfig attribute) max_candidate_pool (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] max_grad_norm (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) max_length (alf_tools.models.esm_utils.config.ESM2ModelConfig attribute) maxiter (alf_tools.optimizer.acquisition_functions.botorch_acquisition.BoTorchAcquisitionOptConfig attribute) mean_type (alf_tools.models.gp.GPModelConfig attribute) means (alf_core.dataclasses.predictions.Predictions attribute), [1] member_seeds (alf_tools.models.ensemble.EnsembleWrapperConfig attribute) metrics (alf_core.dataclasses.round_metrics.RoundMetrics attribute), [1] metrics_history (alf_core.dataclasses.state.State attribute), [1] MLP (class in alf_tools.models.mlp) MLPModel (class in alf_tools.models.mlp) MLPModelConfig (class in alf_tools.models.mlp) MLPTrainConfig (class in alf_tools.models.mlp) Modality modality (alf_core.dataclasses.candidate.Candidate attribute), [1] (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] Modality (class in alf_core.dataclasses.candidate) mode (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) Model model_config (alf_core.dataset.base_dataset.BaseDatasetConfig attribute) (alf_tools.datasets.flip.FLIPConfig attribute) (alf_tools.datasets.proteingym.ProteinGymConfig attribute) model_id (alf_tools.models.esm_utils.config.ESM2ModelConfig attribute) model_seed (alf_tools.models.mlp.MLPModelConfig attribute) ModelProtocolSearch (class in alf_core.optimizer.search) module alf_core.dataclasses.candidate alf_core.dataclasses.labelled_candidates alf_core.dataclasses.predictions alf_core.dataclasses.results alf_core.dataclasses.round_metrics alf_core.dataclasses.state alf_core.dataclasses.surrogate_epoch_metrics alf_core.dataset.base_dataset alf_core.dataset.splitting_utils alf_core.model.base_model alf_core.model.normaliser alf_core.optimizer.acquisition_function alf_core.optimizer.optimizer alf_core.optimizer.search alf_core.oracle.oracle alf_core.surrogate.surrogate alf_core.tasks.base_task alf_core.tasks.design_task alf_core.tasks.supervised_task alf_core.tasks.zeroshot_task alf_core.utils.enums alf_core.utils.metrics.acquisition_batch alf_core.utils.metrics.aggregate alf_core.utils.metrics.base alf_core.utils.metrics.calibration alf_core.utils.metrics.classification alf_core.utils.metrics.regression alf_core.utils.state_logger alf_tools.datasets.flip alf_tools.datasets.gfp alf_tools.datasets.proteingym alf_tools.models.cnn alf_tools.models.ensemble alf_tools.models.esm2 alf_tools.models.esm_utils.config alf_tools.models.esm_utils.loss alf_tools.models.esm_utils.scoring_function alf_tools.models.gp alf_tools.models.mlp alf_tools.models.pyrosetta alf_tools.models.utils.botorch_model_wrapper alf_tools.models.utils.botorch_utils alf_tools.models.utils.config_utils alf_tools.models.utils.data_utils alf_tools.optimizer.acquisition_functions.botorch_acquisition alf_tools.optimizer.acquisition_functions.botorch_samplers alf_tools.optimizer.acquisition_functions.core_set alf_tools.optimizer.acquisition_functions.expected_improvement alf_tools.optimizer.acquisition_functions.greedy alf_tools.optimizer.acquisition_functions.thompson_sampling alf_tools.optimizer.acquisition_functions.ucb alf_tools.optimizer.search.botorch_continuous_search alf_tools.optimizer.search.single_mutant_search alf_tools.utils.constants

MOLECULE (alf_core.dataclasses.candidate.Modality attribute) monte_carlo_ranking() (in module alf_core.utils.metrics.regression) mse() (in module alf_core.utils.metrics.regression) MULTICLASS (alf_core.utils.enums.ProblemType attribute), [1] mutate_and_relax() (alf_tools.models.pyrosetta.PyRosetta method)

N

n_mc_passes (alf_tools.models.mlp.MLPModelConfig attribute) n_members (alf_tools.models.ensemble.EnsembleWrapperConfig attribute) name (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] nll_gaussian() (in module alf_core.utils.metrics.regression) noise_constraint (alf_tools.models.gp.GPModelConfig attribute) noise_prior (alf_tools.models.gp.GPModelConfig attribute) nonnegative (alf_tools.optimizer.acquisition_functions.botorch_acquisition.BoTorchAcquisitionOptConfig attribute) norm (alf_tools.models.mlp.MLPModelConfig attribute)

normalise_inputs_strategy (alf_core.model.base_model.BaseTrainConfig attribute) (alf_tools.models.gp.GPTrainConfig attribute) num_conv_layers (alf_tools.models.cnn.CNNModelConfig attribute) num_epochs (alf_tools.models.cnn.CNNTrainConfig attribute) (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) (alf_tools.models.mlp.MLPTrainConfig attribute) num_filters (alf_tools.models.cnn.CNNModelConfig attribute) num_iterations (alf_tools.models.gp.GPTrainConfig attribute) num_outputs (alf_tools.models.utils.botorch_model_wrapper.BotorchModelWrapper property)

O

Offline Online Optimizer optimizer (alf_tools.models.mlp.MLPTrainConfig attribute) Optimizer (class in alf_core.optimizer.optimizer) optimizer_type (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) (alf_tools.models.gp.GPTrainConfig attribute)

Oracle (class in alf_core.oracle.oracle) output_dim (alf_core.model.base_model.BaseModel attribute) (alf_tools.models.esm_utils.config.ESM2TrainConfig attribute) outputscale_prior (alf_tools.models.gp.GPModelConfig attribute) OutputStandardiser (class in alf_core.model.normaliser)

P

pairwise_xent() (in module alf_core.utils.metrics.regression) pearson() (in module alf_core.utils.metrics.regression) pooling (alf_tools.models.esm_utils.config.ESM2ModelConfig attribute) posterior() (alf_tools.models.utils.botorch_model_wrapper.BotorchModelWrapper method) Precision precision() (in module alf_core.utils.metrics.classification) predict() (alf_core.model.base_model.BaseModel method) (alf_core.surrogate.surrogate.Surrogate method) (alf_tools.models.cnn.CNNModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.esm2.ESM2Model method) (alf_tools.models.gp.GPModel method) (alf_tools.models.mlp.MLPModel method) (alf_tools.models.pyrosetta.PyRosetta method) predictions (alf_core.dataclasses.results.Results attribute), [1]

Predictions (class in alf_core.dataclasses.predictions) predictions_to_posterior() (in module alf_tools.models.utils.botorch_utils) problem_type (alf_core.dataclasses.results.Results attribute), [1] (alf_core.dataclasses.state.State property) (alf_core.dataset.base_dataset.BaseDatasetConfig attribute) (alf_core.model.base_model.BaseModel attribute) (alf_tools.datasets.flip.FLIPConfig attribute) (alf_tools.datasets.proteingym.ProteinGymConfig attribute) (alf_tools.models.gp.GPModel attribute) ProblemType (class in alf_core.utils.enums) ProteinGym (class in alf_tools.datasets.proteingym) ProteinGymConfig (class in alf_tools.datasets.proteingym) ProtocolSearch (class in alf_core.optimizer.search) provides_joint_posterior (alf_tools.models.utils.botorch_model_wrapper.BotorchModelWrapper property) PyRosetta (class in alf_tools.models.pyrosetta)

Q

query() (alf_core.dataset.base_dataset.BaseDataset method)

R

rank_coverage() (in module alf_core.utils.metrics.regression) rank_expected_calibration_error() (in module alf_core.utils.metrics.calibration) rank_width() (in module alf_core.utils.metrics.regression) raw_dataset (alf_core.dataset.base_dataset.BaseDataset property) Recall recall() (in module alf_core.utils.metrics.classification) register() (alf_core.utils.metrics.base.ClassificationMetricRegistry method) (alf_core.utils.metrics.base.RegressionMetricRegistry method) register_classification_metric() (in module alf_core.utils.metrics.classification) register_no_variance_required() (in module alf_core.utils.metrics.regression) register_requires_variance() (in module alf_core.utils.metrics.regression) REGRESSION (alf_core.utils.enums.ProblemType attribute), [1] RegressionMetricRegistry (class in alf_core.utils.metrics.base) Regret regret_ucb_alpha() (in module alf_core.utils.metrics.regression) regret_ucb_alpha_sweep() (in module alf_core.utils.metrics.regression) relax_local() (alf_tools.models.pyrosetta.PyRosetta method) relax_structure() (alf_tools.models.pyrosetta.PyRosetta method)

remove() (alf_core.dataclasses.labelled_candidates.LabelledCandidates method) replace (alf_tools.models.ensemble.SubsampleConfig attribute) repr_layer (alf_tools.models.esm_utils.config.ESM2ModelConfig attribute) require_min_samples() (in module alf_core.utils.metrics.base) residual_pearson() (in module alf_core.utils.metrics.regression) residual_spearman() (in module alf_core.utils.metrics.regression) resolve_botorch_model() (in module alf_tools.models.utils.botorch_model_wrapper) Results (class in alf_core.dataclasses.results) round (alf_core.dataclasses.round_metrics.RoundMetrics attribute), [1] (alf_core.dataclasses.state.State attribute), [1] round_metrics (alf_core.dataclasses.state.State attribute), [1] round_predictions (alf_core.dataclasses.state.State attribute), [1] RoundMetrics (class in alf_core.dataclasses.round_metrics) run() (alf_core.tasks.base_task.BaseTask method) (alf_core.tasks.design_task.DesignTask method) (alf_core.tasks.supervised_task.SupervisedTask method) (alf_core.tasks.zeroshot_task.ZeroShotTask method) run_initial_train_round() (alf_core.tasks.design_task.DesignTask method)

S

sample() (alf_core.model.base_model.BaseModel method) (alf_tools.models.cnn.CNNModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.esm2.ESM2Model method) (alf_tools.models.gp.GPModel method) (alf_tools.models.mlp.MLPModel method) (alf_tools.models.pyrosetta.PyRosetta method) sample_around_best (alf_tools.optimizer.acquisition_functions.botorch_acquisition.BoTorchAcquisitionOptConfig attribute) sample_around_best_sigma (alf_tools.optimizer.acquisition_functions.botorch_acquisition.BoTorchAcquisitionOptConfig attribute) save_splits() (alf_core.dataset.base_dataset.BaseDataset method) Search function SearchProtocol (class in alf_core.optimizer.search) seed (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] (alf_tools.models.esm_utils.config.ESM2ModelConfig attribute) seeds (alf_tools.models.ensemble.EnsembleWrapperConfig attribute) (alf_tools.models.ensemble.SubsampleConfig attribute) SEQUENCE (alf_core.dataclasses.candidate.Modality attribute) SequenceCNN (class in alf_tools.models.cnn) set_metadata() (alf_core.dataset.base_dataset.BaseDataset method) setup() (alf_core.dataset.base_dataset.BaseDataset method) (alf_core.model.base_model.BaseModel method) (alf_core.surrogate.surrogate.Surrogate method) (alf_core.tasks.base_task.BaseTask method) (alf_tools.models.cnn.CNNModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.gp.GPModel method)

shuffle() (alf_core.dataclasses.labelled_candidates.LabelledCandidates method) SingleMutantSearch (class in alf_tools.optimizer.search.single_mutant_search) sort() (alf_core.dataclasses.labelled_candidates.LabelledCandidates method) Spearman correlation spearman() (in module alf_core.utils.metrics.regression) special_tokens_mask() (in module alf_tools.models.esm_utils.loss) split_dataset() (in module alf_core.dataset.splitting_utils) split_low_vs_high() (in module alf_core.dataset.splitting_utils) split_random() (in module alf_core.dataset.splitting_utils) split_stratified() (in module alf_core.dataset.splitting_utils) split_type (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] standardise_outputs (alf_core.model.base_model.BaseTrainConfig attribute) (alf_tools.models.gp.GPTrainConfig attribute) State (class in alf_core.dataclasses.state) StateLogger (class in alf_core.utils.state_logger) subsample (alf_tools.models.ensemble.EnsembleWrapperConfig attribute) SubsampleConfig (class in alf_tools.models.ensemble) SupervisedTask (class in alf_core.tasks.supervised_task) Surrogate surrogate (alf_core.dataclasses.state.State attribute), [1] Surrogate (class in alf_core.surrogate.surrogate) SurrogateEpochMetrics (class in alf_core.dataclasses.surrogate_epoch_metrics)

T

TABULAR (alf_core.dataclasses.candidate.Modality attribute) targets (alf_core.dataclasses.results.Results attribute), [1] Task tell() (alf_core.optimizer.optimizer.Optimizer method) tensor_to_candidates() (in module alf_tools.models.utils.botorch_utils) TerminalStateLogger (class in alf_core.utils.state_logger) test_dataset (alf_core.dataset.base_dataset.BaseDataset property) test_ratio (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] ThompsonSampling (class in alf_tools.optimizer.acquisition_functions.thompson_sampling) to_dataframe() (alf_core.dataclasses.labelled_candidates.LabelledCandidates method) (alf_core.dataclasses.predictions.Predictions method) to_metrics_dict() (alf_core.dataclasses.surrogate_epoch_metrics.SurrogateEpochMetrics method) to_serializable() (alf_core.dataclasses.candidate.Candidate method) top_k_max() (in module alf_core.utils.metrics.regression) top_k_mean() (in module alf_core.utils.metrics.regression) train() (alf_core.model.base_model.BaseModel method) (alf_tools.models.cnn.CNNModel method) (alf_tools.models.ensemble.EnsembleWrapper method) (alf_tools.models.esm2.ESM2Model method) (alf_tools.models.gp.GPModel method) (alf_tools.models.mlp.MLPModel method) (alf_tools.models.pyrosetta.PyRosetta method)

train_dataset (alf_core.dataset.base_dataset.BaseDataset property) train_loss (alf_core.dataclasses.surrogate_epoch_metrics.SurrogateEpochMetrics attribute), [1] train_ratio (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] train_x (alf_tools.models.gp.GPModel attribute) train_y (alf_tools.models.gp.GPModel attribute) training_history (alf_core.dataclasses.round_metrics.RoundMetrics attribute), [1] training_metrics (alf_tools.models.gp.GPModel attribute) transform() (alf_core.model.normaliser.InputNormaliser method) (alf_core.model.normaliser.InputStandardiser method) (alf_core.model.normaliser.OutputStandardiser method) transform_data() (in module alf_tools.models.utils.data_utils)

U

UCB (class in alf_tools.optimizer.acquisition_functions.ucb)

update() (alf_core.dataclasses.state.State method) update_splits() (alf_core.dataset.base_dataset.BaseDataset method)

V

val_loss (alf_core.dataclasses.surrogate_epoch_metrics.SurrogateEpochMetrics attribute), [1] validate_config() (alf_core.dataset.base_dataset.BaseDatasetConfig method) (alf_tools.datasets.flip.FLIPConfig method)

validation_dataset (alf_core.dataset.base_dataset.BaseDataset property) validation_frac (alf_core.dataset.base_dataset.BaseDatasetConfig attribute), [1] variances (alf_core.dataclasses.predictions.Predictions attribute), [1]

W

weight_decay (alf_tools.models.mlp.MLPTrainConfig attribute)

width() (in module alf_core.utils.metrics.regression)

Z

ZeroShotTask (class in alf_core.tasks.zeroshot_task)