Smoother
Basics
Installation
Basic usage
General spatial loss design
Tutorials
Quick start
Data imputation using a hidden Markov random field with the spatial prior
Deconvolution of human brain cortical layers using spatially aware NNLS
Dimensionality reduction using spatially aware autoencoders
Joint analysis of single-cell and spatial data using SpatialVAE
API Reference
smoother
Smoother
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Y
_
_check_swm_stats() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
_data (smoother.models.reduction._spae.AutoEncoderClass attribute)
(smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction.SpatialPCA attribute)
_data_splitter_cls (smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction._spmultivi.SpatialMULTIVI attribute)
(smoother.models.reduction._spvae.SpatialVAE attribute)
(smoother.models.reduction.SpatialANVI attribute)
(smoother.models.reduction.SpatialMULTIVI attribute)
(smoother.models.reduction.SpatialVAE attribute)
_deconv_torch() (in module smoother.models.deconv)
_dwls_loss() (in module smoother.models.deconv)
_get_cost_matrix() (in module smoother.visualization)
_gram_schmidt() (smoother.models.reduction._sppca.SpatialPCA method)
(smoother.models.reduction.SpatialPCA method)
_init_with_svd() (smoother.models.reduction._sppca.SpatialPCA method)
(smoother.models.reduction.SpatialPCA method)
_model_summary_string (smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction._spmultivi.SpatialMULTIVI attribute)
(smoother.models.reduction._spvae.SpatialVAE attribute)
(smoother.models.reduction.SpatialANVI attribute)
(smoother.models.reduction.SpatialMULTIVI attribute)
(smoother.models.reduction.SpatialVAE attribute)
_module_cls (smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction._spmultivi.SpatialMULTIVI attribute)
(smoother.models.reduction._spvae.SpatialVAE attribute)
(smoother.models.reduction.SpatialANVI attribute)
(smoother.models.reduction.SpatialMULTIVI attribute)
(smoother.models.reduction.SpatialVAE attribute)
_mono_exp() (in module smoother.utils)
_nu_svr_loss() (in module smoother.models.deconv)
_num_spot (smoother.losses.TopLoss attribute)
_pca() (in module smoother.utils)
_reduce_dim_ae() (smoother.models.reduction._spae.AutoEncoderClass class method)
_sanity_check() (smoother.losses.SpatialLoss method)
(smoother.SpatialLoss method)
_standardize_inv_cov() (in module smoother.weights)
_train_runner_cls (smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction.SpatialANVI attribute)
_training_plan_cls (smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction.SpatialANVI attribute)
_z_score() (in module smoother.utils)
A
add_gamma_noises() (in module smoother.simulation.utils)
align_clusters() (in module smoother.visualization)
AutoEncoderClass (class in smoother.models.reduction._spae)
B
betti_prior (smoother.losses.TopLoss attribute)
betti_priors (smoother.losses.TopLoss attribute)
broadcast_labels() (in module smoother.models.reduction._utils)
C
C (smoother.models.deconv.NuSVRConvex attribute)
,
[1]
(smoother.models.deconv.NuSVRTorch attribute)
,
[1]
cal_counts_ct() (in module smoother.simulation.utils)
cal_membership_value() (in module smoother.simulation.histology)
calc_corr_decay_stats() (smoother.losses.SpatialLoss method)
(smoother.SpatialLoss method)
calc_feature_similarity() (in module smoother.utils)
calc_feature_similarity_sparse() (in module smoother.utils)
calc_histology_similarity() (in module smoother.utils)
calc_histology_similarity_sparse() (in module smoother.utils)
calc_weights_dist() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
calc_weights_knn() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
check_positive_definite() (smoother.ContrastiveSpatialLoss method)
(smoother.losses.ContrastiveSpatialLoss method)
clr_stable() (in module smoother.visualization)
cluster_and_plot_celltype_props() (in module smoother.visualization)
cluster_features() (in module smoother.visualization)
conc_cir() (in module smoother.simulation.gp)
confidences (smoother.losses.SpatialLoss attribute)
(smoother.SpatialLoss attribute)
config (smoother.SpatialWeightMatrix attribute)
,
[1]
(smoother.weights.SpatialWeightMatrix attribute)
,
[1]
ContrastiveSpatialLoss (class in smoother)
(class in smoother.losses)
coordinate_to_weights_dist_dense() (in module smoother.weights)
coordinate_to_weights_dist_sparse() (in module smoother.weights)
coordinate_to_weights_knn_dense() (in module smoother.weights)
coordinate_to_weights_knn_sparse() (in module smoother.weights)
coords_xy (smoother.losses.TopLoss attribute)
,
[1]
create_spatial_adata() (in module smoother.simulation.utils)
D
decode() (smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._spae.SpatialAutoEncoder method)
(smoother.models.reduction.SpatialAutoEncoder method)
decoder (smoother.models.reduction._spae.SpatialAutoEncoder attribute)
(smoother.models.reduction.SpatialAutoEncoder attribute)
deconv() (smoother.models.deconv.DeconvModelConvex method)
(smoother.models.deconv.DeconvModelTorch method)
deconv_configs (smoother.models.deconv.DeconvModelConvex attribute)
,
[1]
(smoother.models.deconv.DeconvModelTorch attribute)
,
[1]
deconv_time (smoother.models.deconv.DeconvModelConvex attribute)
,
[1]
(smoother.models.deconv.DeconvModelTorch attribute)
,
[1]
DeconvModel (class in smoother.models.deconv)
DeconvModelConvex (class in smoother.models.deconv)
DeconvModelTorch (class in smoother.models.deconv)
diag_block_mat_boolindex() (in module smoother.simulation.utils)
diag_sp_inv_cov (smoother.models.reduction._spanvi.SPANVAE attribute)
(smoother.models.reduction._spmultivi.SPMULTIVAE attribute)
(smoother.models.reduction._spvae.SPVAE attribute)
dim_in (smoother.models.deconv.DeconvModelConvex attribute)
,
[1]
(smoother.models.deconv.DeconvModelTorch attribute)
,
[1]
dim_out (smoother.models.deconv.DeconvModelConvex attribute)
,
[1]
(smoother.models.deconv.DeconvModelTorch attribute)
,
[1]
dr_configs (smoother.models.reduction._spae.AutoEncoderClass attribute)
(smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction.SpatialPCA attribute)
dr_logs (smoother.models.reduction._spae.AutoEncoderClass attribute)
(smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction._spmultivi.SpatialMULTIVI attribute)
(smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction._spvae.SpatialVAE attribute)
(smoother.models.reduction.SpatialANVI attribute)
(smoother.models.reduction.SpatialMULTIVI attribute)
(smoother.models.reduction.SpatialPCA attribute)
(smoother.models.reduction.SpatialVAE attribute)
DWLS() (in module smoother.models.deconv)
DWLSConvex (class in smoother.models.deconv)
DWLSTorch (class in smoother.models.deconv)
E
encode() (smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._spae.SpatialAutoEncoder method)
(smoother.models.reduction.SpatialAutoEncoder method)
encoder (smoother.models.reduction._spae.SpatialAutoEncoder attribute)
(smoother.models.reduction.SpatialAutoEncoder attribute)
epsilon (smoother.models.deconv.LogNormRegTorch attribute)
,
[1]
(smoother.models.deconv.NuSVRConvex attribute)
,
[1]
(smoother.models.deconv.NuSVRTorch attribute)
,
[1]
estimate_confidence() (smoother.losses.SpatialLoss method)
(smoother.SpatialLoss method)
estimate_decay_rate() (in module smoother.utils)
extract_features_from_image() (in module smoother.simulation.histology)
F
final_sanity_check() (smoother.models.deconv.DeconvModelTorch method)
(smoother.models.deconv.LinearRegressionTorch method)
(smoother.models.deconv.NuSVRTorch method)
(smoother.models.impute.ImputeTorch method)
fixed_obs (smoother.models.impute.ImputeModel attribute)
,
[1]
forward() (smoother.ContrastiveSpatialLoss method)
(smoother.losses.ContrastiveSpatialLoss method)
(smoother.losses.SpatialLoss method)
(smoother.losses.TopLoss method)
(smoother.models.deconv.LinearRegressionTorch method)
(smoother.models.impute.ImputeTorch method)
(smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._sppca.SpatialPCA method)
(smoother.models.reduction.SpatialPCA method)
(smoother.SpatialLoss method)
from_rna_model() (smoother.models.reduction._spae.SpatialAutoEncoder class method)
(smoother.models.reduction._spanvi.SpatialANVI class method)
(smoother.models.reduction._sppca.SpatialPCA class method)
(smoother.models.reduction._spvae.SpatialVAE class method)
(smoother.models.reduction.SpatialANVI class method)
(smoother.models.reduction.SpatialAutoEncoder class method)
(smoother.models.reduction.SpatialPCA class method)
(smoother.models.reduction.SpatialVAE class method)
from_sc_model() (smoother.models.reduction._spmultivi.SpatialMULTIVI class method)
(smoother.models.reduction.SpatialMULTIVI class method)
from_scanpy() (smoother.models.reduction._sppca.SpatialPCA class method)
(smoother.models.reduction.SpatialPCA class method)
from_vae() (smoother.models.reduction._spanvi.SPANVAE class method)
(smoother.models.reduction._spmultivi.SPMULTIVAE class method)
(smoother.models.reduction._spvae.SPVAE class method)
G
generate_grid() (in module smoother.simulation.gp)
get_abundances() (in module smoother.simulation.gp)
get_abundances_circ() (in module smoother.simulation.gp)
get_abundances_hist() (in module smoother.simulation.gp)
get_features_matrix() (in module smoother.simulation.histology)
get_histology_vector() (in module smoother.utils)
get_inv_cov() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
get_latent_representation() (smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._sppca.SpatialPCA method)
(smoother.models.reduction.SpatialPCA method)
get_max_epochs_heuristic() (in module smoother.models.reduction._utils)
get_model_loss() (smoother.models.deconv.DeconvModel method)
(smoother.models.deconv.DeconvModelConvex method)
(smoother.models.deconv.LinearRegressionConvex method)
(smoother.models.deconv.LinearRegressionTorch method)
get_model_loss_fn() (smoother.models.deconv.DWLSTorch method)
(smoother.models.deconv.LinearRegressionTorch method)
(smoother.models.deconv.LogNormRegTorch method)
(smoother.models.deconv.NuSVRTorch method)
get_neighbor_quantile_value_by_k() (in module smoother.utils)
get_orth_loss() (smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._spae.SpatialAutoEncoder method)
(smoother.models.reduction.SpatialAutoEncoder method)
get_props() (smoother.models.deconv.DeconvModel method)
(smoother.models.deconv.DeconvModelConvex method)
(smoother.models.deconv.LinearRegressionConvex method)
(smoother.models.deconv.LinearRegressionTorch method)
get_recon_loss() (smoother.models.impute.ImputeConvex method)
(smoother.models.impute.ImputeModel method)
(smoother.models.impute.ImputeTorch method)
(smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._spae.SpatialAutoEncoder method)
(smoother.models.reduction.SpatialAutoEncoder method)
get_reconstruction_loss_protein() (in module smoother.models.reduction._spmultivi)
get_results() (smoother.models.impute.ImputeConvex method)
(smoother.models.impute.ImputeModel method)
(smoother.models.impute.ImputeTorch method)
get_sp_loss() (smoother.models.deconv.DeconvModel method)
(smoother.models.deconv.DeconvModelConvex method)
(smoother.models.deconv.LinearRegressionConvex method)
(smoother.models.deconv.LinearRegressionTorch method)
(smoother.models.impute.ImputeConvex method)
(smoother.models.impute.ImputeModel method)
(smoother.models.impute.ImputeTorch method)
(smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._spae.SpatialAutoEncoder method)
(smoother.models.reduction.SpatialAutoEncoder method)
get_top_loss() (smoother.models.deconv.DeconvModelTorch method)
(smoother.models.deconv.LinearRegressionTorch method)
grouped_obs_mean() (in module smoother.simulation.utils)
I
ilr_stable() (in module smoother.visualization)
ImageContainer (in module smoother.simulation.histology)
impute() (smoother.models.impute.ImputeConvex method)
(smoother.models.impute.ImputeTorch method)
impute_configs (smoother.models.impute.ImputeModel attribute)
,
[1]
impute_flag (smoother.models.impute.ImputeConvex attribute)
(smoother.models.impute.ImputeModel attribute)
(smoother.models.impute.ImputeTorch attribute)
impute_time (smoother.models.impute.ImputeModel attribute)
,
[1]
ImputeConvex (class in smoother.models.impute)
ImputeModel (class in smoother.models.impute)
ImputeTorch (class in smoother.models.impute)
init_params_ (smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction._spmultivi.SpatialMULTIVI attribute)
(smoother.models.reduction._spvae.SpatialVAE attribute)
(smoother.models.reduction.SpatialANVI attribute)
(smoother.models.reduction.SpatialMULTIVI attribute)
(smoother.models.reduction.SpatialVAE attribute)
init_with_lr_sol() (smoother.models.deconv.DeconvModelTorch method)
(smoother.models.deconv.LinearRegressionTorch method)
inv_cov (smoother.losses.SpatialLoss attribute)
(smoother.SpatialLoss attribute)
inv_cov_2d_sp (smoother.losses.SpatialLoss attribute)
(smoother.SpatialLoss attribute)
inv_covs (smoother.SpatialWeightMatrix attribute)
,
[1]
(smoother.weights.SpatialWeightMatrix attribute)
,
[1]
iterate() (in module smoother.models.reduction._utils)
K
kernel() (in module smoother.simulation.gp)
kl_loss() (in module smoother.losses)
kl_loss_scipy() (in module smoother.losses)
L
l_orth_loss (smoother.models.reduction._spae.AutoEncoderClass attribute)
l_sp_loss (smoother.models.reduction._spae.AutoEncoderClass attribute)
(smoother.models.reduction._spanvi.SPANVAE attribute)
(smoother.models.reduction._spmultivi.SPMULTIVAE attribute)
(smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction._spvae.SPVAE attribute)
(smoother.models.reduction.SpatialPCA attribute)
lambda_spatial_loss (smoother.models.deconv.LinearRegressionConvex attribute)
lib_size (smoother.models.reduction._spae.SpatialAutoEncoder attribute)
(smoother.models.reduction.SpatialAutoEncoder attribute)
LinearRegression() (in module smoother.models.deconv)
LinearRegressionConvex (class in smoother.models.deconv)
LinearRegressionTorch (class in smoother.models.deconv)
list_w_row (smoother.models.deconv.LinearRegressionConvex attribute)
load_adata() (smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._sppca.SpatialPCA method)
(smoother.models.reduction.SpatialPCA method)
logger (in module smoother.models.reduction._spanvi)
LogNormReg() (in module smoother.models.deconv)
LogNormRegTorch (class in smoother.models.deconv)
loss() (smoother.models.reduction._spanvi.SPANVAE method)
(smoother.models.reduction._spmultivi.SPMULTIVAE method)
(smoother.models.reduction._spvae.SPVAE method)
loss_mode (smoother.models.deconv.NuSVRConvex attribute)
,
[1]
(smoother.models.deconv.NuSVRTorch attribute)
,
[1]
lower_bound (smoother.ContrastiveSpatialLoss attribute)
(smoother.losses.ContrastiveSpatialLoss attribute)
lr (smoother.models.deconv.LinearRegressionTorch attribute)
M
max_weights (smoother.models.deconv.DWLSConvex attribute)
,
[1]
(smoother.models.deconv.DWLSTorch attribute)
,
[1]
model_loss_exp (smoother.models.deconv.LinearRegressionConvex attribute)
model_name (smoother.models.deconv.DeconvModelConvex attribute)
,
[1]
(smoother.models.deconv.DeconvModelTorch attribute)
,
[1]
(smoother.models.deconv.DWLSConvex attribute)
(smoother.models.deconv.DWLSTorch attribute)
(smoother.models.deconv.LogNormRegTorch attribute)
(smoother.models.deconv.NNLSConvex attribute)
(smoother.models.deconv.NNLSTorch attribute)
(smoother.models.deconv.NuSVRConvex attribute)
(smoother.models.deconv.NuSVRTorch attribute)
module
smoother
smoother.losses
smoother.models
smoother.models.deconv
smoother.models.impute
smoother.models.reduction
smoother.models.reduction._spae
smoother.models.reduction._spanvi
smoother.models.reduction._spmultivi
smoother.models.reduction._sppca
smoother.models.reduction._spvae
smoother.models.reduction._utils
smoother.simulation
smoother.simulation.gp
smoother.simulation.histology
smoother.simulation.utils
smoother.utils
smoother.visualization
smoother.weights
module (smoother.models.reduction._spanvi.SpatialANVI attribute)
(smoother.models.reduction._spmultivi.SpatialMULTIVI attribute)
(smoother.models.reduction._spvae.SpatialVAE attribute)
(smoother.models.reduction.SpatialANVI attribute)
(smoother.models.reduction.SpatialMULTIVI attribute)
(smoother.models.reduction.SpatialVAE attribute)
N
n_all (smoother.models.impute.ImputeModel attribute)
,
[1]
n_feature (smoother.models.impute.ImputeModel attribute)
,
[1]
(smoother.models.reduction._spae.AutoEncoderClass attribute)
(smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction.SpatialPCA attribute)
n_latent (smoother.models.reduction._spae.AutoEncoderClass attribute)
(smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction.SpatialPCA attribute)
n_missing (smoother.models.impute.ImputeModel attribute)
,
[1]
n_obs (smoother.models.impute.ImputeModel attribute)
,
[1]
neg2pos_ratio (smoother.ContrastiveSpatialLoss attribute)
(smoother.losses.ContrastiveSpatialLoss attribute)
NNLS() (in module smoother.models.deconv)
NNLSConvex (class in smoother.models.deconv)
NNLSTorch (class in smoother.models.deconv)
nonneg (smoother.models.deconv.DeconvModelConvex attribute)
,
[1]
(smoother.models.deconv.DeconvModelTorch attribute)
,
[1]
(smoother.models.deconv.DWLSConvex attribute)
(smoother.models.deconv.DWLSTorch attribute)
(smoother.models.deconv.LinearRegressionConvex attribute)
(smoother.models.deconv.LinearRegressionTorch attribute)
(smoother.models.deconv.LogNormRegTorch attribute)
(smoother.models.deconv.NNLSConvex attribute)
(smoother.models.deconv.NNLSTorch attribute)
(smoother.models.deconv.NuSVRConvex attribute)
(smoother.models.deconv.NuSVRTorch attribute)
(smoother.models.impute.ImputeModel attribute)
,
[1]
normalize_minmax() (in module smoother.utils)
nu (smoother.models.deconv.NuSVRConvex attribute)
,
[1]
(smoother.models.deconv.NuSVRTorch attribute)
,
[1]
num_perm (smoother.ContrastiveSpatialLoss attribute)
(smoother.losses.ContrastiveSpatialLoss attribute)
NuSVR() (in module smoother.models.deconv)
NuSVRConvex (class in smoother.models.deconv)
NuSVRTorch (class in smoother.models.deconv)
O
obj (smoother.models.deconv.DeconvModelConvex attribute)
P
pdfn (smoother.losses.TopLoss attribute)
,
[1]
plot_celltype_props() (in module smoother.visualization)
plot_similarity_cdf() (in module smoother.utils)
plot_similarity_decay() (in module smoother.utils)
plot_spatial() (in module smoother.simulation.gp)
plot_spatial_clusters() (in module smoother.visualization)
prior (smoother.losses.SpatialLoss attribute)
,
[1]
(smoother.SpatialLoss attribute)
,
[1]
problem (smoother.models.deconv.DeconvModelConvex attribute)
Q
quadratic_loss() (in module smoother.losses)
quantile_feature_similarity_decay() (in module smoother.utils)
quantile_feature_similarity_neighbor() (in module smoother.utils)
R
random_gp() (in module smoother.simulation.gp)
recon_loss_exp (smoother.models.impute.ImputeConvex attribute)
,
[1]
reduce() (smoother.models.reduction._spae.AutoEncoderClass method)
(smoother.models.reduction._sppca.SpatialPCA method)
(smoother.models.reduction.SpatialPCA method)
reshape_coefs() (smoother.losses.TopLoss method)
rho (smoother.losses.SpatialLoss attribute)
,
[1]
(smoother.SpatialLoss attribute)
,
[1]
S
sample_cell_indices() (in module smoother.simulation.utils)
sample_circ() (in module smoother.simulation.gp)
sample_gp() (in module smoother.simulation.gp)
sample_hist() (in module smoother.simulation.gp)
scale_by_expr() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
scale_by_histology() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
scale_by_identity() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
scale_by_similarity() (smoother.SpatialWeightMatrix method)
(smoother.weights.SpatialWeightMatrix method)
set_lambda_only() (smoother.models.deconv.LinearRegressionConvex method)
set_model_loss() (smoother.models.deconv.DWLSConvex method)
(smoother.models.deconv.LinearRegressionConvex method)
(smoother.models.deconv.NuSVRConvex method)
set_params() (smoother.models.deconv.DeconvModelConvex method)
(smoother.models.deconv.DeconvModelTorch method)
(smoother.models.deconv.LinearRegressionConvex method)
(smoother.models.deconv.LinearRegressionTorch method)
(smoother.models.deconv.NuSVRConvex method)
(smoother.models.impute.ImputeModel method)
set_params_online_update() (in module smoother.models.reduction._utils)
set_recon_loss() (smoother.models.impute.ImputeConvex method)
set_sp_loss() (smoother.models.deconv.LinearRegressionConvex method)
(smoother.models.impute.ImputeConvex method)
set_variables() (smoother.models.impute.ImputeConvex method)
(smoother.models.impute.ImputeModel method)
(smoother.models.impute.ImputeTorch method)
setup_args (smoother.models.reduction._spae.SpatialAutoEncoder attribute)
(smoother.models.reduction.SpatialAutoEncoder attribute)
smooth_by_neighbors() (in module smoother.simulation.utils)
smoother
module
smoother.losses
module
smoother.models
module
smoother.models.deconv
module
smoother.models.impute
module
smoother.models.reduction
module
smoother.models.reduction._spae
module
smoother.models.reduction._spanvi
module
smoother.models.reduction._spmultivi
module
smoother.models.reduction._sppca
module
smoother.models.reduction._spvae
module
smoother.models.reduction._utils
module
smoother.simulation
module
smoother.simulation.gp
module
smoother.simulation.histology
module
smoother.simulation.utils
module
smoother.utils
module
smoother.visualization
module
smoother.weights
module
sp_loss_as_kl (smoother.models.reduction._spanvi.SPANVAE attribute)
(smoother.models.reduction._spmultivi.SPMULTIVAE attribute)
(smoother.models.reduction._spvae.SPVAE attribute)
sp_loss_exp (smoother.models.impute.ImputeConvex attribute)
SPANVAE (class in smoother.models.reduction._spanvi)
sparse_quadratic_loss() (in module smoother.losses)
sparse_weights_to_inv_cov() (in module smoother.weights)
spatial_loss (smoother.models.reduction._spae.AutoEncoderClass attribute)
(smoother.models.reduction._spanvi.SPANVAE attribute)
(smoother.models.reduction._spmultivi.SPMULTIVAE attribute)
(smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction._spvae.SPVAE attribute)
(smoother.models.reduction.SpatialPCA attribute)
spatial_loss_all (smoother.models.impute.ImputeModel attribute)
,
[1]
spatial_loss_exp (smoother.models.deconv.LinearRegressionConvex attribute)
(smoother.models.impute.ImputeConvex attribute)
spatial_weights (smoother.losses.SpatialLoss attribute)
,
[1]
(smoother.SpatialLoss attribute)
,
[1]
SpatialANVI (class in smoother.models.reduction)
(class in smoother.models.reduction._spanvi)
SpatialAutoEncoder (class in smoother.models.reduction)
(class in smoother.models.reduction._spae)
SpatialLoss (class in smoother)
(class in smoother.losses)
SpatialMULTIVI (class in smoother.models.reduction)
(class in smoother.models.reduction._spmultivi)
SpatialPCA (class in smoother.models.reduction)
(class in smoother.models.reduction._sppca)
SpatialVAE (class in smoother.models.reduction)
(class in smoother.models.reduction._spvae)
SpatialWeightMatrix (class in smoother)
(class in smoother.weights)
SPMULTIVAE (class in smoother.models.reduction._spmultivi)
SPVAE (class in smoother.models.reduction._spvae)
standardize_cov (smoother.losses.SpatialLoss attribute)
,
[1]
(smoother.SpatialLoss attribute)
,
[1]
swm (smoother.SpatialWeightMatrix attribute)
,
[1]
(smoother.weights.SpatialWeightMatrix attribute)
,
[1]
swm_scaled (smoother.SpatialWeightMatrix attribute)
,
[1]
(smoother.weights.SpatialWeightMatrix attribute)
,
[1]
T
topfn (smoother.losses.TopLoss attribute)
,
[1]
TopLoss (class in smoother.losses)
train() (smoother.models.reduction._spanvi.SpatialANVI method)
(smoother.models.reduction._spmultivi.SpatialMULTIVI method)
(smoother.models.reduction._spvae.SpatialVAE method)
(smoother.models.reduction.SpatialANVI method)
(smoother.models.reduction.SpatialMULTIVI method)
(smoother.models.reduction.SpatialVAE method)
U
U (smoother.models.reduction._sppca.SpatialPCA attribute)
(smoother.models.reduction.SpatialPCA attribute)
use_bias (smoother.models.deconv.DeconvModelTorch attribute)
,
[1]
(smoother.models.deconv.LinearRegressionConvex attribute)
(smoother.models.deconv.LinearRegressionTorch attribute)
use_sparse (smoother.losses.SpatialLoss attribute)
,
[1]
(smoother.SpatialLoss attribute)
,
[1]
V
var_all (smoother.models.impute.ImputeConvex attribute)
(smoother.models.impute.ImputeModel attribute)
,
[1]
(smoother.models.impute.ImputeTorch attribute)
var_missing (smoother.models.impute.ImputeConvex attribute)
(smoother.models.impute.ImputeModel attribute)
,
[1]
(smoother.models.impute.ImputeTorch attribute)
var_obs (smoother.models.impute.ImputeConvex attribute)
(smoother.models.impute.ImputeModel attribute)
,
[1]
(smoother.models.impute.ImputeTorch attribute)
W
warm_start (smoother.models.deconv.LinearRegressionConvex attribute)
weights (smoother.models.deconv.LinearRegressionConvex attribute)
weights_to_inv_cov() (in module smoother.weights)
Y
y_obs (smoother.models.impute.ImputeModel attribute)
,
[1]