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config.yaml
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# Unified configuration for scFM evaluation pipeline
# All dataset paths, model paths, and parameters are centralized here
# Model directory paths - where downloaded models are stored
model_paths:
geneformer:
model_dir: "/home/wanglinting/scFM/Download/GeneformerV2/Geneformer-V2-316M"
token_dict: "/home/wanglinting/scFM/Download/GeneformerV2/geneformer/token_dictionary_gc104M.pkl"
code_path: "/home/wanglinting/scFM/Download/GeneformerV2/geneformer"
thread_num: 4
gpu: 0
batch_size: 32
embedding_dim: 1152
genecompass:
code_path: "/home/wanglinting/LCBERT/Download/GeneCompass/genecompass"
prior_knowledge_path: "/home/wanglinting/scFM/Download/GeneCompass/prior_knowledge"
checkpoint_path: "/home/wanglinting/scFM/Download/GeneCompass/pretrained_models/GeneCompass_Base"
resources:
dict_path: "/home/wanglinting/scFM/Download/GeneCompass/scdata/dict/human_gene_median_after_filter.pickle"
token_path: "/home/wanglinting/scFM/Download/GeneCompass/scdata/dict/human_mouse_tokens.pickle"
gene_id_name_path: "/home/wanglinting/scFM/Download/GeneCompass/scdata/dict/Gene_id_name_dict1.pickle"
gene_id_path: "/home/wanglinting/scFM/Download/GeneCompass/scdata/dict/gene_id_hpromoter.pickle"
protein_coding_path: "/home/wanglinting/scFM/Download/GeneCompass/scdata/human_protein_coding.txt"
mirna_path: "/home/wanglinting/scFM/Download/GeneCompass/scdata/human_miRNA.txt"
mitochondria_path: "/home/wanglinting/scFM/Download/GeneCompass/scdata/human_mitochondria.xlsx"
gpu: 1
batch_size: 32
pooling_method: "cls"
cellplm:
module_path: "/home/wanglinting/scFM/Download/CellPLM"
pretrain_directory: "/home/wanglinting/LCBERT/Download/CellPLM/ckpt"
pretrain_version: "20231027_85M"
gpu: 2
batch_size: 2048
uce:
code_path: "/home/wanglinting/scFM/Download/UCE"
model_path: "/home/wanglinting/scFM/Download/UCE/model_files/33l_8ep_1024t_1280.torch"
gpu: 3
nlayers: 33
batch_size: 32
species: "human"
scfoundation:
code_path: "/home/wanglinting/scFM/Download/scFoundation/model"
gene_list: "/home/wanglinting/scFM/Download/scFoundation/model/OS_scRNA_gene_index.19264.tsv"
model_path: "/home/wanglinting/scFM/Download/scFoundation/model/models/models.ckpt"
gpu: 4
batch_size: 32
sccello:
transformation_script: "/home/wanglinting/scFM/Code/model-sccello/sccello/script/run_data_transformation.py"
code_path: "/home/wanglinting/scFM/Code/model-sccello/sccello"
pretrained_ckpt: "/home/wanglinting/scFM/Download/scCello/scCello-zeroshot"
gpu: 5
batch_size: 32
scgpt:
model_dir: "/home/wanglinting/scFM/Download/scGPT/model/scGPT_human"
code_path: "/home/wanglinting/scFM/Download/scGPT/scgpt"
gpu: 6
batch_size: 32
nicheformer:
model_dir: "/home/wanglinting/scFM/Download/nicheformer/nicheformer.ckpt"
technology_mean_path: "/home/wanglinting/scFM/Download/nicheformer/data/model_means/dissociated_mean_script.npy"
model_reference_path: "/home/wanglinting/scFM/Download/nicheformer/data/model_means/model.h5ad"
code_path: "/home/wanglinting/LCBERT/Download/nicheformer/src/nicheformer"
gpu: 7
batch_size: 32
max_seq_len: 1500
aux_tokens: 30
chunk_size: 1000
num_workers: 4
modality_code: 3 # dissociated
technology_dict:
"merfish": 7
"MERFISH": 7
"cosmx": 8
"NanoString digital spatial profiling": 8
"visium": 9
"10x 5' v2": 10
"10x 3' v3": 11
"10x 3' v2": 12
"10x 5' v1": 13
"10x 3' v1": 14
"10x 3' transcription profiling": 15
"10x transcription profiling": 15
"10x 5' transcription profiling": 16
"CITE-seq": 17
"Smart-seq v4": 18
species_dict:
"human": 5
"Human": 5
"mouse": 6
"Mouse": 6
"Mus musculus": 6
"Homo sapiens": 5
# Batch correction parameters
batch_correction:
batch_cells:
max_cells_per_batch: 10000
random_seed: 42
normalize: true
# Probing parameters
probing:
cv_folds: 5
test_size: 0.2
random_seed: 42
classifiers:
- logistic_regression
# Dataset configurations
datasets:
limb:
description: "Cross-species limb tissue dataset"
human_path: "/home/wanglinting/scFM/Data/CELLxGENE/limb_human.h5ad"
mouse_path: "/home/wanglinting/scFM/Data/CELLxGENE/limb_mouse.h5ad"
homology_path: "/home/wanglinting/scFM/Data/CELLxGENE/mart_export.txt"
output_data_dir: "/home/wanglinting/scFM/Data/Evaluation/limb"
output_res_dir: "/home/wanglinting/scFM/Result/limb"
batch_key: "organism"
celltype_key: "cell_type"
gene_col: "gene_symbols"
liver:
description: "Liver tissue dataset"
data_path: "/home/wanglinting/scFM/Data/CELLxGENE/liver.h5ad"
output_data_dir: "/home/wanglinting/scFM/Data/Evaluation/liver"
output_res_dir: "/home/wanglinting/scFM/Result/liver"
batch_key: "donor_id"
celltype_key: "cell_type"
gene_col: "gene_symbols"
Immune:
description: "Immune cells dataset"
data_path: "/home/wanglinting/scFM/Data/CELLxGENE/immune_cells.h5ad"
output_data_dir: "/home/wanglinting/scFM/Data/Evaluation/Immune"
output_res_dir: "/home/wanglinting/scFM/Result/Immune"
batch_key: "tissue"
celltype_key: "cell_type_level_2"
gene_col: "gene_symbols"
HLCA_assay:
description: "HLCA dataset - Assay"
data_path: "/home/wanglinting/scFM/Download/HLCA/HLCA_rawcount.h5ad"
output_data_dir: "/home/wanglinting/scFM/Data/Evaluation/HLCA_assay"
output_res_dir: "/home/wanglinting/scFM/Result/HLCA_assay"
batch_key: "assay"
celltype_key: "final_annotation"
gene_col: "original_gene_symbols"
HLCA_disease:
description: "HLCA dataset - Disease"
data_path: "/home/wanglinting/scFM/Download/HLCA/HLCA_rawcount.h5ad"
output_data_dir: "/home/wanglinting/scFM/Data/Evaluation/HLCA_disease"
output_res_dir: "/home/wanglinting/scFM/Result/HLCA_disease"
batch_key: "disease"
celltype_key: "final_annotation"
gene_col: "original_gene_symbols"
HLCA_sn:
description: "HLCA dataset - Single-nucleus"
data_path: "/home/wanglinting/scFM/Download/HLCA/HLCA_rawcount.h5ad"
output_data_dir: "/home/wanglinting/scFM/Data/Evaluation/HLCA_sn"
output_res_dir: "/home/wanglinting/scFM/Result/HLCA_sn"
batch_key: "suspension_type"
celltype_key: "final_annotation"
gene_col: "original_gene_symbols"