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kundajelab
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encode-chrombpnet-DNASE-T-helper-2-cell-ENCSR000EQI-ENCSR745WFF

chrombpnet
encode
chromatin-accessibility
DNASE
t-helper
hg38
Model card Files
xet
 Community
encode-chrombpnet-DNASE-T-helper-2-cell-ENCSR000EQI-ENCSR745WFF
File size: 2,400 Bytes
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{
    "cmd": "train",
    "genome": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference//hg38.genome.fa",
    "chrom_sizes": "/scratch/groups/akundaje/anusri/chromatin_atlas/reference//chrom.sizes",
    "input_bam_file": null,
    "input_fragment_file": null,
    "input_tagalign_file": null,
    "bigwig": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE//ENCSR000EQI//preprocessing/bigWigs/ENCSR000EQI.bigWig",
    "output_dir": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR000EQI//chrombpnet_model_feb15_fold_4/chrombpnet_model/",
    "data_type": "DNASE",
    "peaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR000EQI//chrombpnet_model_feb15_fold_4/chrombpnet_model/auxiliary/ENCSR000EQI_filtered.peaks.bed",
    "nonpeaks": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR000EQI//chrombpnet_model_feb15_fold_4/chrombpnet_model/auxiliary/ENCSR000EQI_filtered.nonpeaks.bed",
    "chr_fold_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/splits/fold_4.json",
    "outlier_threshold": 0.9999,
    "ATAC_ref_path": null,
    "DNASE_ref_path": null,
    "num_samples": 10000,
    "inputlen": 2114,
    "outputlen": 1000,
    "seed": 1234,
    "epochs": 50,
    "early_stop": 5,
    "learning_rate": 0.001,
    "trackables": [
        "logcount_predictions_loss",
        "loss",
        "logits_profile_predictions_loss",
        "val_logcount_predictions_loss",
        "val_loss",
        "val_logits_profile_predictions_loss"
    ],
    "architecture_from_file": "/home/groups/akundaje/anusri/simg/chrombpnet_latest/chrombpnet/chrombpnet/training/models/chrombpnet_with_bias_model.py",
    "file_prefix": "ENCSR000EQI",
    "html_prefix": "./",
    "bias_model_path": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR000EQI//chrombpnet_model_feb15_fold_0/bias_model/models/ENCSR000EQI_bias.h5",
    "negative_sampling_ratio": 0.1,
    "filters": 512,
    "n_dilation_layers": 8,
    "max_jitter": 500,
    "batch_size": 64,
    "output_prefix": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR000EQI//chrombpnet_model_feb15_fold_4/chrombpnet_model/models/ENCSR000EQI_chrombpnet",
    "chr": "chr10",
    "pwm_width": 24,
    "params": "/scratch/groups/akundaje/anusri/chromatin_atlas/DNASE/ENCSR000EQI//chrombpnet_model_feb15_fold_4/chrombpnet_model/logs/ENCSR000EQI_chrombpnet_model_params.tsv"
}