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config.yaml
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config.yaml
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#----------------------------------- Global ------------------------------------
use:
- hyperparam
- hvg
- benchmark
- benchmark_noprep
- prior_corrupt
- prior_alt
- subsample
dataset:
Chen-2019:
rna: ../data/dataset/Chen-2019-RNA.h5ad
atac: ../data/dataset/Chen-2019-ATAC.h5ad
frags2rna: ../data/dataset/Chen-2019-FRAGS2RNA.h5ad # Sham file
paired: true
Ma-2020:
rna: ../data/dataset/Ma-2020-RNA.h5ad
atac: ../data/dataset/Ma-2020-ATAC.h5ad
frags2rna: ../data/dataset/Ma-2020-FRAGS2RNA.h5ad
paired: true
10x-Multiome-Pbmc10k:
rna: ../data/dataset/10x-Multiome-Pbmc10k-RNA.h5ad
atac: ../data/dataset/10x-Multiome-Pbmc10k-ATAC.h5ad
frags2rna: ../data/dataset/10x-Multiome-Pbmc10k-FRAGS2RNA.h5ad
paired: true
Muto-2021:
rna: ../data/dataset/Muto-2021-RNA.h5ad
atac: ../data/dataset/Muto-2021-ATAC.h5ad
frags2rna: ../data/dataset/Muto-2021-FRAGS2RNA.h5ad
paired: false
Yao-2021:
rna: ../data/dataset/Yao-2021-RNA.h5ad
atac: ../data/dataset/Yao-2021-ATAC.h5ad
frags2rna: ../data/dataset/Yao-2021-FRAGS2RNA.h5ad
paired: false
timeout: 24h
#-------------------------- Hyperparameter stability ---------------------------
hyperparam:
data:
prior:
gene_region: combined
extend_range: 0
corrupt_rate: 0.0
corrupt_seed: 0
method:
GLUE:
dim:
default: 50
choices:
- 10
- 30
- 50
- 100
- 200
alt_dim:
default: 100
choices:
- 30
- 50
- 100
- 200
- 400
hidden_depth:
default: 2
choices:
- 0
- 1
- 2
- 3
- 4
hidden_dim:
default: 256
choices:
- 64
- 128
- 256
- 512
- 1024
dropout:
default: 0.2
choices:
- 0.0
- 0.1
- 0.2
- 0.3
- 0.5
lam_graph:
default: 0.02
choices:
- 0.001
- 0.005
- 0.02
- 0.1
- 0.5
lam_align:
default: 0.05
choices:
- 0.002
- 0.01
- 0.05
- 0.2
- 1.0
neg_samples:
default: 10
choices:
- 2
- 5
- 10
- 20
- 50
seed: 4
#----------------------- Highly variable gene stability ------------------------
hvg:
data:
hvg:
- 500
- 1000
- 2000
- 4000
- 8000
prior:
gene_region: combined
extend_range: 0
corrupt_rate: 0.0
corrupt_seed: 0
method:
GLUE:
dim: 50
alt_dim: 100
hidden_depth: 2
hidden_dim: 256
dropout: 0.2
lam_graph: 0.02
lam_align: 0.05
neg_samples: 10
seed: 8
#---------------------------------- Benchmark ----------------------------------
benchmark:
data:
prior:
gene_region: combined
extend_range: 0
corrupt_rate: 0.0
corrupt_seed: 0
method:
UnionCom:
Pamona:
MMD_MA:
iNMF:
iNMF_FiG:
LIGER:
LIGER_FiG:
Harmony:
bindSC:
CCA_anchor:
GLUE:
dim: 50
alt_dim: 100
hidden_depth: 2
hidden_dim: 256
dropout: 0.2
lam_graph: 0.02
lam_align: 0.05
neg_samples: 10
seed: 8
benchmark_noprep:
data:
prior:
gene_region: combined
extend_range: 0
corrupt_rate: 0.0
corrupt_seed: 0
method:
UnionCom:
Pamona:
MMD_MA:
iNMF:
iNMF_FiG:
LIGER:
LIGER_FiG:
Harmony:
bindSC:
CCA_anchor:
GLUE:
dim: 50
alt_dim: 0
hidden_depth: 2
hidden_dim: 256
dropout: 0.2
lam_graph: 0.02
lam_align: 0.05
neg_samples: 10
seed: 8
#------------------------------ Prior robustness -------------------------------
prior_corrupt:
data:
prior:
gene_region: combined
extend_range: 0
corrupt_rate:
- 0.2
- 0.4
- 0.6
- 0.8
- 0.9
- 1.0
corrupt_seed: 8
method:
iNMF:
LIGER:
Harmony:
bindSC:
CCA_anchor:
GLUE:
dim: 50
alt_dim: 100
hidden_depth: 2
hidden_dim: 256
dropout: 0.2
lam_graph: 0.02
lam_align: 0.05
neg_samples: 10
seed: 1
prior_alt:
data:
prior:
gene_region:
- combined
- promoter
extend_range:
- 0
- 150000
corrupt_rate: 0.0
corrupt_seed: 0
method:
iNMF:
LIGER:
Harmony:
bindSC:
CCA_anchor:
GLUE:
dim: 50
alt_dim: 100
hidden_depth: 2
hidden_dim: 256
dropout: 0.2
lam_graph: 0.02
lam_align: 0.05
neg_samples: 10
seed: 8
#------------------------------- Subsample data --------------------------------
subsample:
data:
subsample_size:
- 250
- 500
- 1000
- 2000
- 4000
- 8000
subsample_seed: 8
prior:
gene_region: combined
extend_range: 0
corrupt_rate: 0.0
corrupt_seed: 0
method:
UnionCom:
Pamona:
MMD_MA:
iNMF:
iNMF_FiG:
LIGER:
LIGER_FiG:
Harmony:
bindSC:
CCA_anchor:
GLUE:
dim: 50
alt_dim: 100
hidden_depth: 2
hidden_dim: 256
dropout: 0.2
lam_graph: 0.02
lam_align: 0.05
neg_samples: 10
seed: 1
#----------------------------- Feature consistency -----------------------------
feature:
data:
prior:
gene_region: combined
extend_range: 0
corrupt_rate: 0.0
corrupt_seed: 0
method:
GLUE:
dim: 50
alt_dim: 100
hidden_depth: 2
hidden_dim: 256
dropout: 0.2
lam_graph: 0.02
lam_align: 0.05
neg_samples: 10
seed: 8