learnMSA
User Guide:
Input/output and general control
Protein Language Model Integration
Training
Initialize with existing MSA
Visualization
API Reference:
API Reference
learnMSA
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
add_block_separator_to_msa (learnMSA.config.input_output.InputOutputConfig attribute)
advanced (learnMSA.Configuration attribute)
AdvancedConfig (class in learnMSA.config.advanced)
aligner_threads (learnMSA.config.advanced.AdvancedConfig attribute)
auto_crop (learnMSA.config.training.TrainingConfig attribute)
auto_crop_scale (learnMSA.config.training.TrainingConfig attribute)
B
batch_size (learnMSA.config.training.TrainingConfig attribute)
C
cluster_seq_id (learnMSA.config.training.TrainingConfig attribute)
conditionally_independent (learnMSA.config.language_model.LanguageModelConfig attribute)
Configuration (class in learnMSA)
convert (learnMSA.config.input_output.InputOutputConfig attribute)
crop (learnMSA.config.training.TrainingConfig attribute)
cuda_visible_devices (learnMSA.config.input_output.InputOutputConfig attribute)
D
decoding_mode (learnMSA.config.training.TrainingConfig attribute)
dirichlet_mix_comp_count (learnMSA.config.training.TrainingConfig attribute)
dist_out (learnMSA.config.advanced.AdvancedConfig attribute)
E
emb_file (learnMSA.config.input_output.InputOutputConfig attribute)
embedding_prior_components (learnMSA.config.language_model.LanguageModelConfig attribute)
epochs (learnMSA.config.training.TrainingConfig attribute)
extract_num_model() (learnMSA.config.training.TrainingConfig class method)
F
format (learnMSA.config.input_output.InputOutputConfig attribute)
from_msa (learnMSA.config.init_msa.InitMSAConfig attribute)
G
global_factor (learnMSA.config.init_msa.InitMSAConfig attribute)
H
hit_alignment_mode (learnMSA.config.training.TrainingConfig attribute)
hmm (learnMSA.Configuration attribute)
hmm_prior (learnMSA.Configuration attribute)
I
id_string() (learnMSA.config.language_model.LanguageModelConfig method)
indexed_data (learnMSA.config.training.TrainingConfig attribute)
init_msa (learnMSA.Configuration attribute)
initial_distance (learnMSA.config.advanced.AdvancedConfig attribute)
InitMSAConfig (class in learnMSA.config.init_msa)
input_file (learnMSA.config.input_output.InputOutputConfig attribute)
input_format (learnMSA.config.input_output.InputOutputConfig attribute)
input_output (learnMSA.Configuration attribute)
InputOutputConfig (class in learnMSA.config.input_output)
insert_expectation (learnMSA.config.language_model.LanguageModelConfig attribute)
insert_variance (learnMSA.config.language_model.LanguageModelConfig attribute)
insertion_aligner (learnMSA.config.advanced.AdvancedConfig attribute)
inverse_gamma_alpha (learnMSA.config.language_model.LanguageModelConfig attribute)
inverse_gamma_beta (learnMSA.config.language_model.LanguageModelConfig attribute)
J
jit_compile (learnMSA.config.advanced.AdvancedConfig attribute)
L
L2_insert (learnMSA.config.language_model.LanguageModelConfig attribute)
L2_match (learnMSA.config.language_model.LanguageModelConfig attribute)
language_model (learnMSA.config.language_model.LanguageModelConfig attribute)
(learnMSA.Configuration attribute)
LanguageModelConfig (class in learnMSA.config.language_model)
learning_rate (learnMSA.config.training.TrainingConfig attribute)
len_mul (learnMSA.config.training.TrainingConfig attribute)
length_init (learnMSA.config.training.TrainingConfig attribute)
length_init_quantile (learnMSA.config.training.TrainingConfig attribute)
load_model (learnMSA.config.input_output.InputOutputConfig attribute)
logo_gif (learnMSA.config.visualization.VisualizationConfig attribute)
M
match_expectations (learnMSA.config.language_model.LanguageModelConfig attribute)
match_threshold (learnMSA.config.init_msa.InitMSAConfig attribute)
match_variance (learnMSA.config.language_model.LanguageModelConfig attribute)
max_iterations (learnMSA.config.training.TrainingConfig attribute)
max_seq_model_select (learnMSA.config.training.TrainingConfig attribute)
min_surgery_seqs (learnMSA.config.training.TrainingConfig attribute)
model_config (learnMSA.config.advanced.AdvancedConfig attribute)
(learnMSA.config.init_msa.InitMSAConfig attribute)
(learnMSA.config.input_output.InputOutputConfig attribute)
(learnMSA.config.language_model.LanguageModelConfig attribute)
(learnMSA.config.training.TrainingConfig attribute)
(learnMSA.config.visualization.VisualizationConfig attribute)
(learnMSA.Configuration attribute)
model_criterion (learnMSA.config.training.TrainingConfig attribute)
model_post_init() (learnMSA.config.training.TrainingConfig method)
N
no_aa (learnMSA.config.training.TrainingConfig attribute)
no_sequence_weights (learnMSA.config.training.TrainingConfig attribute)
num_model (learnMSA.config.training.TrainingConfig property)
O
one_dnn_opts (learnMSA.config.advanced.AdvancedConfig attribute)
only_embeddings (learnMSA.config.language_model.LanguageModelConfig attribute)
only_matches (learnMSA.config.training.TrainingConfig attribute)
output_file (learnMSA.config.input_output.InputOutputConfig attribute)
P
plm_cache_dir (learnMSA.config.language_model.LanguageModelConfig attribute)
plot (learnMSA.config.visualization.VisualizationConfig attribute)
plot_head (learnMSA.config.visualization.VisualizationConfig attribute)
pre_training_checkpoint (learnMSA.config.training.TrainingConfig attribute)
pseudocounts (learnMSA.config.init_msa.InitMSAConfig attribute)
R
reset_branch_lengths (learnMSA.config.advanced.AdvancedConfig attribute)
reset_emissions_after_surgery (learnMSA.config.training.TrainingConfig attribute)
reset_evo_model (learnMSA.config.advanced.AdvancedConfig attribute)
reset_transitions_after_surgery (learnMSA.config.training.TrainingConfig attribute)
S
save_emb (learnMSA.config.input_output.InputOutputConfig attribute)
save_model (learnMSA.config.input_output.InputOutputConfig attribute)
scores (learnMSA.config.input_output.InputOutputConfig attribute)
scoring_model_activation (learnMSA.config.language_model.LanguageModelConfig attribute)
scoring_model_dim (learnMSA.config.language_model.LanguageModelConfig attribute)
scoring_model_suffix (learnMSA.config.language_model.LanguageModelConfig attribute)
seeded (learnMSA.config.init_msa.InitMSAConfig attribute)
serialize_model() (learnMSA.config.training.TrainingConfig method)
skip_training (learnMSA.config.training.TrainingConfig attribute)
struct_file (learnMSA.config.input_output.InputOutputConfig attribute)
structure (learnMSA.Configuration attribute)
subset_ids (learnMSA.config.input_output.InputOutputConfig attribute)
surgery_checkpoints (learnMSA.config.training.TrainingConfig attribute)
surgery_del (learnMSA.config.training.TrainingConfig attribute)
surgery_ins (learnMSA.config.training.TrainingConfig attribute)
surgery_quantile (learnMSA.config.training.TrainingConfig attribute)
T
temperature (learnMSA.config.language_model.LanguageModelConfig attribute)
temperature_mode (learnMSA.config.language_model.LanguageModelConfig attribute)
tokens_per_batch (learnMSA.config.training.TrainingConfig attribute)
trainable_insertions (learnMSA.config.training.TrainingConfig attribute)
training (learnMSA.Configuration attribute)
TrainingConfig (class in learnMSA.config.training)
tree (learnMSA.Configuration attribute)
U
unaligned_insertions (learnMSA.config.training.TrainingConfig attribute)
use_L2 (learnMSA.config.language_model.LanguageModelConfig attribute)
use_language_model (learnMSA.config.language_model.LanguageModelConfig attribute)
use_noise (learnMSA.config.training.TrainingConfig attribute)
use_prior (learnMSA.config.training.TrainingConfig attribute)
V
validate_crop() (learnMSA.config.training.TrainingConfig class method)
validate_cuda_devices() (learnMSA.config.input_output.InputOutputConfig class method)
validate_epochs() (learnMSA.config.training.TrainingConfig class method)
validate_format() (learnMSA.config.input_output.InputOutputConfig class method)
validate_input_format() (learnMSA.config.input_output.InputOutputConfig class method)
validate_language_model() (learnMSA.config.language_model.LanguageModelConfig class method)
validate_learning_rate() (learnMSA.config.training.TrainingConfig class method)
validate_length_init() (learnMSA.config.training.TrainingConfig class method)
validate_max_iterations() (learnMSA.config.training.TrainingConfig class method)
validate_nonnegative_floats() (learnMSA.config.language_model.LanguageModelConfig class method)
validate_positive_floats() (learnMSA.config.language_model.LanguageModelConfig class method)
(learnMSA.config.training.TrainingConfig class method)
validate_positive_ints() (learnMSA.config.language_model.LanguageModelConfig class method)
validate_quantiles() (learnMSA.config.advanced.AdvancedConfig class method)
(learnMSA.config.init_msa.InitMSAConfig class method)
(learnMSA.config.training.TrainingConfig class method)
variance_init (learnMSA.config.language_model.LanguageModelConfig attribute)
verbose (learnMSA.config.input_output.InputOutputConfig attribute)
visualization (learnMSA.Configuration attribute)
VisualizationConfig (class in learnMSA.config.visualization)
W
warn_batch_size_ignored() (learnMSA.config.training.TrainingConfig method)
work_dir (learnMSA.config.input_output.InputOutputConfig attribute)