FLEXS
latest
flexs
FLEXS
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
A
AAS (in module flexs.utils.sequence_utils)
action_spec() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment method)
(flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironmentMutative method)
(flexs.baselines.explorers.environments.ppo.PPOEnvironment method)
Adalead (class in flexs.baselines.explorers.adalead)
AdaptiveEnsemble (class in flexs.baselines.models.adaptive_ensemble)
adaptivity() (in module flexs.evaluate)
add_last_seq_in_trajectory() (flexs.baselines.explorers.dyna_ppo.DynaPPO method)
(flexs.baselines.explorers.dyna_ppo.DynaPPOMutative method)
(flexs.baselines.explorers.ppo.PPO method)
AdditiveAAVPackaging (class in flexs.landscapes.additive_aav_packaging)
alpha (flexs.utils.replay_buffers.PrioritizedReplayBuffer attribute)
B
BA (in module flexs.utils.sequence_utils)
batch_size() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment property)
batched() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment method)
BertGFPBrightness (class in flexs.landscapes.bert_gfp)
BO (class in flexs.baselines.explorers.bo)
build_q_network() (in module flexs.baselines.explorers.dqn)
C
calculate_log_probability() (flexs.utils.VAE_utils.VAE method)
calculate_next_q_values() (flexs.baselines.explorers.dqn.DQN method)
call() (flexs.utils.VAE_utils.Sampling method)
(flexs.utils.VAE_utils.VAEModel method)
capacity (flexs.utils.replay_buffers.SegmentTree attribute)
CbAS (class in flexs.baselines.explorers.cbas_dbas)
CMAES (class in flexs.baselines.explorers.cmaes)
CNN (class in flexs.baselines.models.cnn)
combine_with (flexs.ensemble.Ensemble attribute)
compute_max_possible() (flexs.landscapes.additive_aav_packaging.AdditiveAAVPackaging method)
compute_min_binding_energies() (flexs.landscapes.rna.RNABinding method)
construct_mutant_from_sample() (in module flexs.utils.sequence_utils)
cost (flexs.landscape.Landscape attribute)
D
DNAA (in module flexs.utils.sequence_utils)
DQN (class in flexs.baselines.explorers.dqn)
DynaPPO (class in flexs.baselines.explorers.dyna_ppo)
DynaPPOEnsemble (class in flexs.baselines.explorers.dyna_ppo)
DynaPPOEnvironment (class in flexs.baselines.explorers.environments.dyna_ppo)
DynaPPOEnvironmentMutative (class in flexs.baselines.explorers.environments.dyna_ppo)
DynaPPOMutative (class in flexs.baselines.explorers.dyna_ppo)
E
efficiency() (in module flexs.evaluate)
EI() (flexs.baselines.explorers.bo.BO method)
Ensemble (class in flexs.ensemble)
Explorer (class in flexs.explorer)
F
flexs (module)
flexs.baselines (module)
flexs.baselines.explorers (module)
flexs.baselines.explorers.adalead (module)
flexs.baselines.explorers.bo (module)
flexs.baselines.explorers.cbas_dbas (module)
flexs.baselines.explorers.cmaes (module)
flexs.baselines.explorers.dqn (module)
flexs.baselines.explorers.dyna_ppo (module)
flexs.baselines.explorers.environments (module)
flexs.baselines.explorers.environments.dyna_ppo (module)
flexs.baselines.explorers.environments.ppo (module)
flexs.baselines.explorers.genetic_algorithm (module)
flexs.baselines.explorers.ppo (module)
flexs.baselines.explorers.random (module)
flexs.baselines.models (module)
flexs.baselines.models.adaptive_ensemble (module)
flexs.baselines.models.cnn (module)
flexs.baselines.models.global_epistasis_model (module)
flexs.baselines.models.keras_model (module)
flexs.baselines.models.mlp (module)
flexs.baselines.models.noisy_abstract_model (module)
flexs.baselines.models.sklearn_models (module)
flexs.ensemble (module)
flexs.evaluate (module)
flexs.explorer (module)
flexs.landscape (module)
flexs.landscapes (module)
flexs.landscapes.additive_aav_packaging (module)
flexs.landscapes.bert_gfp (module)
flexs.landscapes.rna (module)
flexs.landscapes.rosetta (module)
flexs.landscapes.tf_binding (module)
flexs.model (module)
flexs.types (module)
flexs.utils (module)
flexs.utils.replay_buffers (module)
flexs.utils.sequence_utils (module)
flexs.utils.VAE_utils (module)
forward() (flexs.baselines.explorers.dqn.Q_Network method)
G
generate() (flexs.utils.VAE_utils.VAE method)
(flexs.utils.VAE_utils.VAEModel method)
generate_random_mutant() (in module flexs.utils.sequence_utils)
generate_random_sequences() (in module flexs.utils.sequence_utils)
generate_single_mutants() (in module flexs.utils.sequence_utils)
GeneticAlgorithm (class in flexs.baselines.explorers.genetic_algorithm)
get_action_and_mutant() (flexs.baselines.explorers.dqn.DQN method)
get_cached_fitness() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment method)
get_fitness() (flexs.landscape.Landscape method)
get_folding_energy() (flexs.landscapes.rosetta.RosettaFolding method)
get_state_string() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironmentMutative method)
(flexs.baselines.explorers.environments.ppo.PPOEnvironment method)
gfp_wt_sequence (flexs.landscapes.bert_gfp.BertGFPBrightness attribute)
,
[1]
GlobalEpistasisModel (class in flexs.baselines.models.global_epistasis_model)
GPR_BO (class in flexs.baselines.explorers.bo)
I
initialize_data_structures() (flexs.baselines.explorers.bo.BO method)
(flexs.baselines.explorers.dqn.DQN method)
K
KerasModel (class in flexs.baselines.models.keras_model)
L
Landscape (class in flexs.landscape)
LandscapeAsModel (class in flexs.model)
LinearRegression (class in flexs.baselines.models.sklearn_models)
LogisticRegression (class in flexs.baselines.models.sklearn_models)
M
max_priority (flexs.utils.replay_buffers.PrioritizedReplayBuffer attribute)
min() (flexs.utils.replay_buffers.MinSegmentTree method)
min_tree (flexs.utils.replay_buffers.PrioritizedReplayBuffer attribute)
MinSegmentTree (class in flexs.utils.replay_buffers)
MLP (class in flexs.baselines.models.mlp)
Model (class in flexs.model)
models (flexs.ensemble.Ensemble attribute)
N
name (flexs.landscape.Landscape attribute)
NoisyAbstractModel (class in flexs.baselines.models.noisy_abstract_model)
O
observation_spec() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment method)
(flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironmentMutative method)
(flexs.baselines.explorers.environments.ppo.PPOEnvironment method)
one_hot_to_string() (in module flexs.utils.sequence_utils)
operate() (flexs.utils.replay_buffers.SegmentTree method)
operation (flexs.utils.replay_buffers.SegmentTree attribute)
P
pick_action() (flexs.baselines.explorers.bo.BO method)
(flexs.baselines.explorers.dqn.DQN method)
PPO (class in flexs.baselines.explorers.ppo)
PPOEnvironment (class in flexs.baselines.explorers.environments.ppo)
PrioritizedReplayBuffer (class in flexs.utils.replay_buffers)
propose_sequences() (flexs.baselines.explorers.adalead.Adalead method)
(flexs.baselines.explorers.bo.BO method)
(flexs.baselines.explorers.bo.GPR_BO method)
(flexs.baselines.explorers.cbas_dbas.CbAS method)
(flexs.baselines.explorers.cmaes.CMAES method)
(flexs.baselines.explorers.dqn.DQN method)
(flexs.baselines.explorers.dyna_ppo.DynaPPO method)
(flexs.baselines.explorers.dyna_ppo.DynaPPOMutative method)
(flexs.baselines.explorers.genetic_algorithm.GeneticAlgorithm method)
(flexs.baselines.explorers.ppo.PPO method)
(flexs.baselines.explorers.random.Random method)
(flexs.explorer.Explorer method)
propose_sequences_via_greedy() (flexs.baselines.explorers.bo.GPR_BO method)
propose_sequences_via_thompson() (flexs.baselines.explorers.bo.GPR_BO method)
propose_sequences_via_ucb() (flexs.baselines.explorers.bo.GPR_BO method)
pwm_to_boltzmann_weights() (in module flexs.utils.VAE_utils)
Q
Q_Network (class in flexs.baselines.explorers.dqn)
q_network_loss() (flexs.baselines.explorers.dqn.DQN method)
R
r2_weights() (in module flexs.baselines.models.adaptive_ensemble)
Random (class in flexs.baselines.explorers.random)
RandomForest (class in flexs.baselines.models.sklearn_models)
registry() (in module flexs.landscapes.additive_aav_packaging)
(in module flexs.landscapes.rna)
(in module flexs.landscapes.rosetta)
(in module flexs.landscapes.tf_binding)
ReplayBuffer (class in flexs.utils.replay_buffers)
reset() (flexs.baselines.explorers.bo.GPR_BO method)
retrieve() (flexs.utils.replay_buffers.SumSegmentTree method)
RNAA (in module flexs.utils.sequence_utils)
RNABinding (class in flexs.landscapes.rna)
RNAFolding (class in flexs.landscapes.rna)
robustness() (in module flexs.evaluate)
RosettaFolding (class in flexs.landscapes.rosetta)
run() (flexs.explorer.Explorer method)
S
sample() (flexs.baselines.explorers.dqn.DQN method)
sample_actions() (flexs.baselines.explorers.bo.BO method)
sample_batch() (flexs.utils.replay_buffers.PrioritizedReplayBuffer method)
(flexs.utils.replay_buffers.ReplayBuffer method)
Sampling (class in flexs.utils.VAE_utils)
SegmentTree (class in flexs.utils.replay_buffers)
sequence_density() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment method)
(flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironmentMutative method)
set_fitness_model_to_gt() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment method)
(flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironmentMutative method)
SklearnClassifier (class in flexs.baselines.models.sklearn_models)
SklearnModel (class in flexs.baselines.models.sklearn_models)
SklearnRegressor (class in flexs.baselines.models.sklearn_models)
store() (flexs.utils.replay_buffers.PrioritizedReplayBuffer method)
(flexs.utils.replay_buffers.ReplayBuffer method)
string_to_one_hot() (in module flexs.utils.sequence_utils)
sum() (flexs.utils.replay_buffers.SumSegmentTree method)
sum_tree (flexs.utils.replay_buffers.PrioritizedReplayBuffer attribute)
SumSegmentTree (class in flexs.utils.replay_buffers)
T
TFBinding (class in flexs.landscapes.tf_binding)
Thompson_sample() (flexs.baselines.explorers.bo.BO static method)
time_step_spec() (flexs.baselines.explorers.environments.dyna_ppo.DynaPPOEnvironment method)
train() (flexs.baselines.explorers.dyna_ppo.DynaPPOEnsemble method)
(flexs.baselines.models.adaptive_ensemble.AdaptiveEnsemble method)
(flexs.baselines.models.keras_model.KerasModel method)
(flexs.baselines.models.noisy_abstract_model.NoisyAbstractModel method)
(flexs.baselines.models.sklearn_models.SklearnModel method)
(flexs.ensemble.Ensemble method)
(flexs.model.LandscapeAsModel method)
(flexs.model.Model method)
train_actor() (flexs.baselines.explorers.dqn.DQN method)
train_model() (flexs.utils.VAE_utils.VAE method)
train_models() (flexs.baselines.explorers.bo.BO method)
train_step() (flexs.utils.VAE_utils.VAEModel method)
training (flexs.baselines.explorers.dqn.Q_Network attribute)
tree (flexs.utils.replay_buffers.SegmentTree attribute)
tree_ptr (flexs.utils.replay_buffers.PrioritizedReplayBuffer attribute)
U
UCB() (flexs.baselines.explorers.bo.BO static method)
update_priorities() (flexs.utils.replay_buffers.PrioritizedReplayBuffer method)
V
VAE (class in flexs.utils.VAE_utils)
VAEModel (class in flexs.utils.VAE_utils)
W
wild_type (flexs.landscapes.additive_aav_packaging.AdditiveAAVPackaging attribute)
wt_pose (flexs.landscapes.rosetta.RosettaFolding attribute)
Read the Docs
v: latest
Versions
latest
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds