Index

_

__init__() (Aggregate method) (Alphabet method) (BaseFit method) (BaseLoss method) (BaseRound method) (Batch method) (Binding method) (BindingOptim method) (BoundRound method) (BoundUnsaturatedRound method) (Call method) (Codon method) (Component method) (Contribution method) (Conv0d method) (Conv1d method) (Cooperativity method) (CountBatch method) (CountTable method) (DNA method) (EmptyLayerSpec method) (EvenSampler method) (Experiment method) (ExponentialRound method) (Fit method) (InitialRound method) (Layer method) (LayerSpec method) (LengthManager method) (LogFit method) (Loss method) (MaxPool1d method) (MaxPool1dSpec method) (Mode method) (ModeKey method) (ModuleLayer method) (ModuleSpec method) (MultiExperimentLoss method) (MultiRoundMSLELoss method) (MultitaskLoader method) (NonSpecific method) (Optimizer method) (Pad method) (PadSpec method) (Protein method) (PSAM method) (RhoGammaRound method) (RNA method) (Roll method) (RollSpec method) (Round method) (Spacing method) (Spec method) (Step method) (Table method) (TModuleList method) (TParameterDict method) (TParameterList method) (Transform method) (UnboundRound method)

_blocking (Component attribute) _cache_fun (Component attribute) _caches (Component attribute) _layers (LayerSpec attribute) _modes (Layer attribute)

A

activity_heuristic() (Aggregate method) aggregate (BoundRound attribute) (BoundUnsaturatedRound attribute) Aggregate (class in pyprobound.aggregate) aggregate (ExponentialRound attribute) (RhoGammaRound attribute) (Round attribute) (UnboundRound attribute)

alphabet (Alphabet attribute) Alphabet (class in pyprobound.alphabets) alphabet (Codon attribute) (DNA attribute) (Protein attribute) (RNA attribute) ancestry (BindingOptim attribute), [1] avg_pool1d() (in module pyprobound.utils)

B

BaseFit (class in pyprobound.fitting) BaseLoss (class in pyprobound.loss) BaseRound (class in pyprobound.rounds) Batch (class in pyprobound.table) batchlen() (Batch method) (CountBatch method) betaln() (in module pyprobound.utils) betas (PSAM attribute)

bias_bin (Conv1d property) (Cooperativity property) bias_mode (Conv1d property) (Cooperativity property) Binding (class in pyprobound.base) binding (Contribution attribute) BindingOptim (class in pyprobound.base) BoundRound (class in pyprobound.rounds) BoundUnsaturatedRound (class in pyprobound.rounds)

C

cache() (Transform class method) Call (class in pyprobound.base) calls (Step attribute), [1] ceil_div() (in module pyprobound.utils) ceil_mode (MaxPool1dSpec property) check_length_consistency() (Component method) (Conv0d method) (Conv1d method) (Cooperativity method) (Layer method) (Mode method) (Optimizer method) clear_cache() (in module pyprobound.utils) cmpt (Call attribute), [1] Codon (class in pyprobound.alphabets) collate_batch_fn() (in module pyprobound.table) Component (class in pyprobound.base) components() (Aggregate method) (BaseLoss method) (BaseRound method) (Component method) (Contribution method) (Cooperativity method) (Experiment method) (InitialRound method) (Layer method) (LayerSpec method) (Mode method) (Round method) (Spacing method) (Spec method)

Contribution (class in pyprobound.aggregate) contribution() (in module pyprobound.plotting) contributions (Aggregate attribute) Conv0d (class in pyprobound.layers.conv0d) Conv1d (class in pyprobound.layers.conv1d) Cooperativity (class in pyprobound.cooperativity) cooperativity() (in module pyprobound.plotting) count_kmers() (in module pyprobound.utils) CountBatch (class in pyprobound.table) counts_per_round (CountTable attribute) (Experiment property) CountTable (class in pyprobound.table)

D

dataloaders (MultitaskLoader attribute)

dilation (PSAM property) DNA (class in pyprobound.alphabets)

E

embed() (Alphabet method) EmptyLayerSpec (class in pyprobound.layers.layer) enrichment_plotter() (in module pyprobound.plotting) EvenSampler (class in pyprobound.table) expected_log_aggregate() (Aggregate method) expected_log_contribution() (Contribution method)

expected_log_score() (Binding method) expected_sequence() (Binding method) (Cooperativity method) (Mode method) Experiment (class in pyprobound.experiment) ExponentialRound (class in pyprobound.rounds)

F

Fit (class in pyprobound.fitting) fit() (Fit method) (LogFit method) fix_gauge() (PSAM method) floor_div() (in module pyprobound.utils) forward() (Aggregate method) (BaseLoss method) (BaseRound method) (Contribution method) (Conv0d method) (Conv1d method) (Cooperativity method) (Experiment method) (MaxPool1d method) (Mode method) (ModuleLayer method) (Pad method) (Roll method) (Spec method) (Transform method)

free_protein() (Experiment method) freeze() (Component method) from_binding() (Aggregate class method) (ExponentialRound class method) (RhoGammaRound class method) (Round class method) from_nonspecific() (Conv0d class method) (Mode class method) from_psam() (Conv1d class method) (Mode class method) from_round() (ExponentialRound class method) (UnboundRound class method) from_spec() (MaxPool1d class method) (ModuleLayer class method) (Pad class method) (Roll class method) frozen_positions() (PSAM static method) fun (Call attribute), [1]

G

gamma (RhoGammaRound attribute) get_bias() (PSAM method) get_dataframe() (in module pyprobound.table) get_dirichlet() (PSAM method) get_encoding (Alphabet attribute) (Codon attribute) (DNA attribute) (Protein attribute) (RNA attribute) get_filter() (PSAM method) get_fit_final() (in module pyprobound.external) get_index (Alphabet attribute) (Codon attribute) (DNA attribute) (Protein attribute) (RNA attribute) get_information() (PSAM method) get_inv_encoding (Alphabet attribute)

get_log_posbias() (Conv0d method) (Conv1d method) get_log_spacing() (Cooperativity method) (Spacing method) get_log_spacing_diagonals() (Cooperativity method) get_log_spacing_matrix() (Cooperativity method) (Spacing method) get_ordinal() (in module pyprobound.utils) get_padding_layers() (in module pyprobound.layers.pad) get_parameter_string() (Optimizer method) get_setup_string() (BaseFit method) (BaseLoss method) (CountTable method) (Optimizer method) (Table method) get_split_size() (in module pyprobound.utils) get_train_sequential() (Optimizer method) greedy (Step attribute), [1] greedy_search() (Optimizer method)

H

heatmap_plotter() (in module pyprobound.plotting)

I

import_hocomoco() (in module pyprobound.external) import_jaspar() (in module pyprobound.external) import_motif_central() (in module pyprobound.external) in_channels (Layer property) (LayerSpec property) (LengthManager property) (Mode property) (ModeKey property) in_len() (Layer method) (LengthManager method) (MaxPool1dSpec method) (Mode method) (ModeKey method) (ModuleSpec method) (NonSpecific method) (PadSpec method) (PSAM method) (RollSpec method)

InitialRound (class in pyprobound.rounds) input_shape (CountTable property) (Layer property) (Mode property) (Table property) insert() (TModuleList method) (TParameterList method) intercept (BaseFit attribute) (Fit attribute) (LogFit attribute)

K

kd_consistency() (in module pyprobound.plotting) keff_consistency() (in module pyprobound.plotting) kernel_size (MaxPool1dSpec property) (PSAM property)

key() (Binding method) (Cooperativity method) (Mode method) kmer_enrichment() (in module pyprobound.plotting) kwargs (Call attribute), [1]

L

Layer (class in pyprobound.layers.layer) layer_spec (Layer attribute) layers (Mode attribute) LayerSpec (class in pyprobound.layers.layer) left (PadSpec property) left_flank (CountTable attribute) (Table attribute) (Table property) left_flank_length (CountTable attribute) (Table attribute) (Table property) length_specific_bias (Conv1d property) (Cooperativity property) LengthManager (class in pyprobound.layers.layer) lengths() (Layer method) library_concentration (BaseRound property) line_plotter() (in module pyprobound.plotting) log1mexp() (in module pyprobound.utils) log_activity (Contribution attribute) log_aggregate() (BaseFit method) (BaseRound method) (InitialRound method) (Round method) log_cumulative_enrichment() (BaseRound method) log_delta (ExponentialRound attribute)

log_depth (BaseRound attribute) (BoundRound attribute) (BoundUnsaturatedRound attribute) (ExponentialRound attribute) (RhoGammaRound attribute) (Round attribute) (UnboundRound attribute) log_enrichment() (BaseRound method) (BoundRound method) (BoundUnsaturatedRound method) (ExponentialRound method) (InitialRound method) (RhoGammaRound method) (UnboundRound method) log_hill (Cooperativity attribute) (Mode attribute) log_posbias (Conv0d attribute) (Conv1d attribute) (Cooperativity attribute) log_spacing (Spacing attribute) log_target_concentration (Aggregate attribute) LogFit (class in pyprobound.fitting) logo() (in module pyprobound.plotting) logomaker_plotter() (in module pyprobound.plotting) Loss (class in pyprobound.loss)

M

max_embedding_size() (Component method) (Conv0d method) (Conv1d method) (Cooperativity method) max_input_length (Layer property) (Mode property) max_length (RollSpec property) max_num_windows (Spacing property) max_read_length (CountTable property) (Table property) MaxPool1d (class in pyprobound.layers.maxpool) MaxPool1dSpec (class in pyprobound.layers.maxpool) merge_binding_optim() (BindingOptim method) min_input_length (Layer property) (Mode property) min_read_length (CountTable property) (Table property) Mode (class in pyprobound.mode) mode_a (Cooperativity attribute) mode_b (Cooperativity attribute) mode_key_a (Spacing attribute) mode_key_b (Spacing attribute) ModeKey (class in pyprobound.layers.layer) module pyprobound pyprobound.aggregate pyprobound.alphabets pyprobound.base pyprobound.containers pyprobound.cooperativity pyprobound.experiment pyprobound.external pyprobound.fitting pyprobound.layers pyprobound.layers.conv0d pyprobound.layers.conv1d pyprobound.layers.layer pyprobound.layers.maxpool pyprobound.layers.module pyprobound.layers.pad pyprobound.layers.psam pyprobound.layers.roll pyprobound.loss pyprobound.mode pyprobound.optimizer pyprobound.plotting pyprobound.rounds pyprobound.table pyprobound.utils

ModuleLayer (class in pyprobound.layers.module) ModuleSpec (class in pyprobound.layers.module) MultiExperimentLoss (class in pyprobound.loss) MultiRoundMSLELoss (class in pyprobound.loss) MultitaskLoader (class in pyprobound.table)

N

n_strands (Cooperativity property) (PSAM property) (Spacing property) negloglik (Loss attribute), [1]

negloglik() (BaseFit method) (BaseLoss method) (MultiExperimentLoss method) (MultiRoundMSLELoss method) NonSpecific (class in pyprobound.layers.conv0d)

O

obs_pred() (BaseFit method) (Fit method) (LogFit method) observed_rounds (Experiment attribute) optim_procedure() (Aggregate method) (BaseRound method) (Component method) (Cooperativity method) (Mode method) Optimizer (class in pyprobound.optimizer) out_channel_indexing (Conv1d property) out_channels (Conv1d property) (Layer property) (LayerSpec property) (LengthManager property) (Mode property) (ModeKey property)

out_len() (Layer method) (LengthManager method) (MaxPool1dSpec method) (Mode method) (ModeKey method) (ModuleSpec method) (NonSpecific method) (PadSpec method) (PSAM method) (RollSpec method)

P

Pad (class in pyprobound.layers.pad) PadSpec (class in pyprobound.layers.pad) pairwise_distance (PSAM property) pairwise_embed() (Alphabet method) pairwise_plotter() (in module pyprobound.plotting) parse_probound_aggregate() (in module pyprobound.external) parse_probound_alphabet() (in module pyprobound.external) parse_probound_interactions() (in module pyprobound.external) parse_probound_model() (in module pyprobound.external) parse_probound_modes() (in module pyprobound.external) parse_probound_psam() (in module pyprobound.external) parse_probound_rounds() (in module pyprobound.external) parse_probound_tables() (in module pyprobound.external) plot() (Fit method) (LogFit method) plot_ticks() (in module pyprobound.plotting) posbias() (in module pyprobound.plotting) print() (Optimizer method) probe_enrichment() (in module pyprobound.plotting) Protein (class in pyprobound.alphabets) PSAM (class in pyprobound.layers.psam) pyprobound module pyprobound.aggregate module pyprobound.alphabets module pyprobound.base module pyprobound.containers module pyprobound.cooperativity module pyprobound.experiment module

pyprobound.external module pyprobound.fitting module pyprobound.layers module pyprobound.layers.conv0d module pyprobound.layers.conv1d module pyprobound.layers.layer module pyprobound.layers.maxpool module pyprobound.layers.module module pyprobound.layers.pad module pyprobound.layers.psam module pyprobound.layers.roll module pyprobound.loss module pyprobound.mode module pyprobound.optimizer module pyprobound.plotting module pyprobound.rounds module pyprobound.table module pyprobound.utils module

R

reference_round (BaseRound attribute) (BoundRound attribute) (BoundUnsaturatedRound attribute) (ExponentialRound attribute) (RhoGammaRound attribute) (Round attribute) (UnboundRound attribute) regularization (Loss attribute), [1] regularization() (BaseLoss method) (MultiExperimentLoss method) reload() (Component method) (Optimizer method) reload_from_state_dict() (Component method) repeat_round() (in module pyprobound.rounds) rho (RhoGammaRound attribute)

RhoGammaRound (class in pyprobound.rounds) right (PadSpec property) right_flank (CountTable attribute) (Table attribute) (Table property) right_flank_length (CountTable attribute) (Table attribute) (Table property) RNA (class in pyprobound.alphabets) Roll (class in pyprobound.layers.roll) RollSpec (class in pyprobound.layers.roll) Round (class in pyprobound.rounds) rounds (Experiment attribute) run_one_epoch() (Optimizer method) run_step() (Optimizer method)

S

sample_counts() (in module pyprobound.table) sample_dataframe() (in module pyprobound.table) save() (Component method) (Optimizer method) scale (BaseFit attribute) (Fit attribute) (LogFit attribute) score() (BaseFit method) (in module pyprobound.table) score_dense() (Conv1d method) score_onehot() (Conv1d method) score_reverse (PSAM property) score_windows() (Binding method) (Cooperativity method) (Mode method)

seqs (CountBatch attribute), [1] (CountTable attribute) set_contribution() (Contribution method) set_flank_length() (CountTable method) (Table method) shift_heuristic() (PSAM method) Spacing (class in pyprobound.cooperativity) spacing (Cooperativity attribute) spacing() (in module pyprobound.plotting) Spec (class in pyprobound.base) Step (class in pyprobound.base) steps (BindingOptim attribute), [1]

T

Table (class in pyprobound.table) target (CountBatch attribute), [1] (CountTable attribute) TModuleList (class in pyprobound.containers) TParameterDict (class in pyprobound.containers) TParameterList (class in pyprobound.containers) train_sequential() (Optimizer method)

train_simultaneous() (Optimizer method) train_until_convergence() (Optimizer method) Transform (class in pyprobound.base) transforms (BaseLoss attribute) (MultiExperimentLoss attribute) (MultiRoundMSLELoss attribute) translate() (Alphabet method)

U

UnboundRound (class in pyprobound.rounds) unfreezable (Aggregate attribute) (BaseRound attribute) (Component attribute), [1] (Contribution attribute) (Conv0d attribute) (Conv1d attribute) (Cooperativity attribute) (ExponentialRound attribute) (Mode attribute) (PSAM attribute) (RhoGammaRound attribute) (Spacing attribute) unfreeze() (Aggregate method) (BaseRound method) (Component method) (Contribution method) (Conv0d method) (Conv1d method) (Cooperativity method) (ExponentialRound method) (Mode method) (ModuleSpec method) (PSAM method) (RhoGammaRound method) (Spacing method)

update_binding_optim() (Conv0d method) (Conv1d method) (Layer method) (PSAM method) (Spacing method) (Spec method) update_footprint() (PSAM method) update_input_length() (Conv0d method) (Conv1d method) (Layer method) update_params() (PSAM method) update_read_length() (Mode method) (Optimizer method)