Index

B

BBRBM (class in rbms.bernoulli_bernoulli.classes)

C

check_file_existence() (in module rbms.utils) clone() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) compute_energy() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.RBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) compute_energy_hiddens() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.RBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method)

compute_energy_visibles() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) compute_gradient() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) compute_log_likelihood() (in module rbms.utils) compute_weights() (in module rbms.dataset.fasta_utils)

D

decode_sequence() (in module rbms.dataset.fasta_utils)

device (rbms.classes.EBM attribute), [1]

E

EBM (class in rbms.classes), [1]

encode_sequence() (in module rbms.dataset.fasta_utils)

G

get_categorical_configurations() (in module rbms.utils) get_effective_size() (rbms.dataset.dataset_class.RBMDataset method) get_eigenvalues_history() (in module rbms.utils) get_flagged_updates() (in module rbms.utils) get_gzip_entropy() (rbms.dataset.dataset_class.RBMDataset method)

get_num_states() (rbms.dataset.dataset_class.RBMDataset method) get_num_visibles() (rbms.dataset.dataset_class.RBMDataset method) get_saved_updates() (in module rbms.utils) get_subset_labels() (in module rbms.dataset.utils) get_tokens() (in module rbms.dataset.fasta_utils)

I

import_from_fasta() (in module rbms.dataset.fasta_utils) independent_model() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) init_chains() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method)

init_parameters() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM static method) (rbms.classes.EBM static method), [1] (rbms.potts_bernoulli.classes.PBRBM static method)

L

load_FASTA() (in module rbms.dataset.load_fasta) load_HDF5() (in module rbms.dataset.load_h5)

log2cosh() (in module rbms.custom_fn) log_to_csv() (in module rbms.utils)

M

module rbms.bernoulli_bernoulli.classes rbms.bernoulli_bernoulli.functional rbms.classes, [1] rbms.const rbms.custom_fn rbms.dataset.dataset_class rbms.dataset.fasta_utils rbms.dataset.load_fasta rbms.dataset.load_h5 rbms.dataset.utils rbms.plot rbms.potts_bernoulli.classes rbms.potts_bernoulli.functional rbms.utils

N

named_parameters() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) num_hiddens() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.RBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method)

num_states() (rbms.potts_bernoulli.classes.PBRBM method) num_visibles() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method)

O

one_hot() (in module rbms.custom_fn)

P

parameters() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) PBRBM (class in rbms.potts_bernoulli.classes)

plot_hist() (in module rbms.plot) plot_image() (in module rbms.plot) plot_PCA() (in module rbms.plot) plot_scatter_labels() (in module rbms.plot)

Q

query_yes_no() (in module rbms.utils)

R

RBM (class in rbms.classes), [1] RBMDataset (class in rbms.dataset.dataset_class) rbms.bernoulli_bernoulli.classes module rbms.bernoulli_bernoulli.functional module rbms.classes module, [1] rbms.const module rbms.custom_fn module rbms.dataset.dataset_class module rbms.dataset.fasta_utils module rbms.dataset.load_fasta module

rbms.dataset.load_h5 module rbms.dataset.utils module rbms.plot module rbms.potts_bernoulli.classes module rbms.potts_bernoulli.functional module rbms.utils module ref_log_z() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) restore_rng_state() (in module rbms.utils)

S

sample_hiddens() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.RBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) sample_state() (rbms.classes.EBM method), [1] (rbms.classes.RBM method), [1]

sample_visibles() (in module rbms.bernoulli_bernoulli.functional) (in module rbms.potts_bernoulli.functional) (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method) set_named_parameters() (rbms.bernoulli_bernoulli.classes.BBRBM static method) (rbms.classes.EBM static method), [1] (rbms.potts_bernoulli.classes.PBRBM static method)

T

to() (rbms.bernoulli_bernoulli.classes.BBRBM method) (rbms.classes.EBM method), [1] (rbms.potts_bernoulli.classes.PBRBM method)

V

validate_alphabet() (in module rbms.dataset.fasta_utils)

W

write_fasta() (in module rbms.dataset.fasta_utils)