config.json

{
    "schic_directory" : "/directory/of/higashi/imputed/maps",
    "label_info": {
        "path":"/path/to/label_info.pickle",
        "cell_type_key": "cell type key in label_info.pickle"
    },
    "data_directory" : "/directory/to/save/scghost/outputs/",
    "chromosomes" : {
        "1" : {
            "adj" : "chr1_sparse_adj.npy",
            "imputed" : "chr1_exp1_nbr_5_impute.hdf5",
            "integer" : 1
        },
        "2" : {
            "adj" : "chr2_sparse_adj.npy",
            "imputed" : "chr2_exp1_nbr_5_impute.hdf5",
            "integer" : 2
        },
        "3" : {
            "adj" : "chr3_sparse_adj.npy",
            "imputed" : "chr3_exp1_nbr_5_impute.hdf5",
            "integer" : 3
        },
        "4" : {
            "adj" : "chr4_sparse_adj.npy",
            "imputed" : "chr4_exp1_nbr_5_impute.hdf5",
            "integer" : 4
        },
        "5" : {
            "adj" : "chr5_sparse_adj.npy",
            "imputed" : "chr5_exp1_nbr_5_impute.hdf5",
            "integer" : 5
        },
        "6" : {
            "adj" : "chr6_sparse_adj.npy",
            "imputed" : "chr6_exp1_nbr_5_impute.hdf5",
            "integer" : 6
        },
        "7" : {
            "adj" : "chr7_sparse_adj.npy",
            "imputed" : "chr7_exp1_nbr_5_impute.hdf5",
            "integer" : 7
        },
        "8" : {
            "adj" : "chr8_sparse_adj.npy",
            "imputed" : "chr8_exp1_nbr_5_impute.hdf5",
            "integer" : 8
        },
        "9" : {
            "adj" : "chr9_sparse_adj.npy",
            "imputed" : "chr9_exp1_nbr_5_impute.hdf5",
            "integer" : 9
        },
        "10" : {
            "adj" : "chr10_sparse_adj.npy",
            "imputed" : "chr10_exp1_nbr_5_impute.hdf5",
            "integer" : 10
        },
        "11" : {
            "adj" : "chr11_sparse_adj.npy",
            "imputed" : "chr11_exp1_nbr_5_impute.hdf5",
            "integer" : 11
        },
        "12" : {
            "adj" : "chr12_sparse_adj.npy",
            "imputed" : "chr12_exp1_nbr_5_impute.hdf5",
            "integer" : 12
        },
        "13" : {
            "adj" : "chr13_sparse_adj.npy",
            "imputed" : "chr13_exp1_nbr_5_impute.hdf5",
            "integer" : 13
        },
        "14" : {
            "adj" : "chr14_sparse_adj.npy",
            "imputed" : "chr14_exp1_nbr_5_impute.hdf5",
            "integer" : 14
        },
        "15" : {
            "adj" : "chr15_sparse_adj.npy",
            "imputed" : "chr15_exp1_nbr_5_impute.hdf5",
            "integer" : 15
        },
        "16" : {
            "adj" : "chr16_sparse_adj.npy",
            "imputed" : "chr16_exp1_nbr_5_impute.hdf5",
            "integer" : 16
        },
        "17" : {
            "adj" : "chr17_sparse_adj.npy",
            "imputed" : "chr17_exp1_nbr_5_impute.hdf5",
            "integer" : 17
        },
        "18" : {
            "adj" : "chr18_sparse_adj.npy",
            "imputed" : "chr18_exp1_nbr_5_impute.hdf5",
            "integer" : 18
        },
        "19" : {
            "adj" : "chr19_sparse_adj.npy",
            "imputed" : "chr19_exp1_nbr_5_impute.hdf5",
            "integer" : 19
        },
        "20" : {
            "adj" : "chr20_sparse_adj.npy",
            "imputed" : "chr20_exp1_nbr_5_impute.hdf5",
            "integer" : 20
        },
        "21" : {
            "adj" : "chr21_sparse_adj.npy",
            "imputed" : "chr21_exp1_nbr_5_impute.hdf5",
            "integer" : 21
        },
        "22" : {
            "adj" : "chr22_sparse_adj.npy",
            "imputed" : "chr22_exp1_nbr_5_impute.hdf5",
            "integer" : 22
        }
    },
    "chrom_sizes" : "data/hg38.chrom.sizes",
    "chrom_indices" : null,
    "embeddings_path" : "/path/to/exp1_0_origin.npy",
    "higashi_scab_path" : "/path/to/higashi/scAB.hdf5",
    "cell_type" : null,
    "random_walk" : {
        "num_walks" : 50,
        "ignore_top" : 0.02,
        "top_percentile" : 0.25
    },
    "eps": 1e-8,
    "num_clusters" : 5,
    "batch_size" : 16,
    "epochs" : 5,
    "resolution" : 500000,
    "neighbor_contacts" : false,
    "nearest_neighbor_override" : null,
    "gpu_uniques" : true,
    "cluster_gpu_caching" : true,
    "kmeans_init" : 1
}