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CLR training doesn't enter "tail" phase #49

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CLR training doesn't enter "tail" phase#49
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@csestili

Description

@csestili
csestili
opened on Oct 3, 2023

reported by @andreww136082 . he used the CLR schedule but it went through the full number of epochs for training and then didn't enter the tail phase.

config:

# Project

project:
  desc: Name of `wandb` project for tracking.
  value: sst_fold3_first

entity:
  desc: Name of `wandb` account for tracking.
  value: <username>

# Data

train_data_paths:
  desc: Paths to FASTA, BED, or NarrowPeak files for training data.
  # To use FASTA files with sequences already extracted, just put the file path.
  # To use a reference genome and a BED or NarrowPeak file with intervals, put:
  #     genome: <path to genome .fa>
  #     intervals: <path to interval .bed or .narrowPeak>
  value:
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/positive-splits/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/positive-splits/fold3/train.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/positive-splits/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/positive-splits/fold3/train.bed

    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsGLIA_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsINH_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsnonITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsGLIA_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsINH_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsnonITexc_negative/fold3/train.bed

    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsGLIA_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsINH_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsnonITexc_negative/fold3/train.bed

    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsGLIA_negative/fold3/train.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsINH_negative/fold3/train.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsITexc_negative/fold3/train.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsnonITexc_negative/fold3/train.bed

    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsGLIA_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsnonITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsGLIA_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsINH_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsnonITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsGLIA_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsINH_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsITexc_negative/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsnonITexc_negative/fold3/train.bed
    
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/negative_splits_enh_raw/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/negative_splits_enh_raw/fold3/train.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/negative_splits_enh_raw/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/negative_splits_enh_raw/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/hg38/negative_splits_gc/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rn6/negative_splits_gc/fold3/train.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rhemac10/negative_splits_gc/fold3/train.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/mm10/negative_splits_gc/fold3/train.bed
      

train_targets:
  desc: Targets corresponding to each training data path.
  # To use a constant value per file, e.g. 0 or "neg", just put the value here.
  # To extract the value from each line of a BED or NarrowPeak file, put:
  #     column: <column number>
  value:
    - 1
    - 1
    - 1
    - 1

    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0

    - 0
    - 0
    - 0
    - 0
    
    - 0
    - 0
    - 0
    - 0

    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0

    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0

val_data_paths:
  desc: Paths to FASTA, BED, or NarrowPeak files for validation data.
  value:
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/positive-splits/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/positive-splits/fold3/valid.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/positive-splits/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/positive-splits/fold3/valid.bed

    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsGLIA_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsINH_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsnonITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsGLIA_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsINH_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsnonITexc_negative/fold3/valid.bed

    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsGLIA_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsINH_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsnonITexc_negative/fold3/valid.bed

    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsGLIA_negative/fold3/valid.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsINH_negative/fold3/valid.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsITexc_negative/fold3/valid.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsnonITexc_negative/fold3/valid.bed

    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsINH_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsINH_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed

    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/negative_splits_enh_raw/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/negative_splits_enh_raw/fold3/valid.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/negative_splits_enh_raw/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/negative_splits_enh_raw/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/hg38/negative_splits_gc/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rn6/negative_splits_gc/fold3/valid.bed
    - genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rhemac10/negative_splits_gc/fold3/valid.bed
    - genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa
      intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/mm10/negative_splits_gc/fold3/valid.bed
 
val_targets:
  desc: Targets corresponding to each validation data path.
  value:
    - 1
    - 1
    - 1
    - 1

    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0

    - 0
    - 0
    - 0
    - 0
    
    - 0
    - 0
    - 0
    - 0

    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0

    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0
    - 0


targets_are_classes:
  desc: Whether to treat targets as a set of discrete classes (classification) or as continuous values (regression).
  value: true

additional_val_data_paths:
  desc: Paths to additional validation datasets. Metrics will be reported for each set separately.
  value:
      - [{genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/positive-splits/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/positive-splits/fold3/valid.bed}, 
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/positive-splits/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/positive-splits/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/negative_splits_enh_raw/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/negative_splits_enh_raw/fold3/valid.bed}, 
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/negative_splits_enh_raw/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/negative_splits_enh_raw/fold3/valid.bed}]
      
      - [{genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/positive-splits/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/positive-splits/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/positive-splits/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/positive-splits/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsnonITexc_negative/fold3/valid.bed},

      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsnonITexc_negative/fold3/valid.bed},
      
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsINH_negative/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsnonITexc_negative/fold3/valid.bed},

      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed}]
      


      - [{genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/positive-splits/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/positive-splits/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/positive-splits/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/positive-splits/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/hg38/negative_splits_gc/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rn6/negative_splits_gc/fold3/valid.bed}, 
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rhemac10/negative_splits_gc/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/mm10/negative_splits_gc/fold3/valid.bed}]
      


      - [{genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/positive-splits/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/hg38/negative_splits_enh_raw/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/Human_Cortex_hg38_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/hg38/negatives/HumanHerring_Cortex_hg38_SSTvsnonITexc_negative/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanGenome/hg38.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/hg38/negative_splits_gc/fold3/valid.bed}]

      - [{genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/positive-splits/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rn6/negative_splits_enh_raw/fold3/valid.bed}, 
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rn6/negatives/Rat_Cortex_rn6_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/RatGenome/rn6.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rn6/negative_splits_gc/fold3/valid.bed}]

      - [{genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/positive-splits/fold3/valid.bed}, 
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/rhemac10/negative_splits_enh_raw/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsINH_negative/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/rheMac10/negatives/Macaque_Cortex_rheMac10_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /home/bnphan/resources/genomes/rheMac10/rheMac10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/rhemac10/negative_splits_gc/fold3/valid.bed}]
      
      - [{genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/positive-splits/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected/SST/mm10/negative_splits_enh_raw/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseAlzheimers_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseBICCN_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsGLIA_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsINH_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cortex-SNAIL/bed/SST/mm10/negatives/MouseLareau_Cortex_mm10_SSTvsnonITexc_negative/fold3/valid.bed},
      {genome: /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseGenome/mm10.fa, intervals: /projects/pfenninggroup/machineLearningForComputationalBiology/Cortex_Cell-TACIT/data/tidy_data/Cell-TACIT_Corrected_500/SST/mm10/negative_splits_gc/fold3/valid.bed}]

additional_val_targets:
  desc: Targets corresponding to additional validation paths.
  value:
    - [1, 1, 1, 1, 0, 0, 0, 0]
    - [1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
    - [1, 1, 1, 1, 0, 0, 0, 0]
    - [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
    - [1, 0, 0, 0, 0, 0, 0]
    - [1, 0, 0, 0, 0, 0, 0]
    - [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]

# Training

batch_size:
  desc: Batch size for training and validation.
  value: 100

num_epochs:
  desc: Number of training epochs.
  value: 25

metric_pos_label:
  desc: Positive label to use for binary metrics.
  value: 1

early_stopping_callbacks:
  desc: Callbacks to use for early stopping. Use arguments as in tf.keras.callbacks.EarlyStopping.
  value:
    - monitor: val_auprc
      patience: 5
      verbose: 1
      mode: max

use_exact_val_metrics:
  desc: If true, use exact validation metrics during training (requires loading whole validation set into RAM). If false, use a close approximation (+/- ~2%) that streams the validation set without loading into RAM.
  value: true

use_reverse_complement:
  desc: If true, add reverse complement sequences to the training set, doubling the training set size.
  value: true

class_weight:
  desc: Scheme to weight the loss function according to the class.
  allowed_values: ['none', 'reciprocal', 'proportional']
  value: proportional

# Optimization

optimizer:
  desc: Weight optimization algorithm to use.
  allowed_values: ['sgd', 'adam']
  value: sgd

optimizer_args:
  desc: Arguments for optimizer.
  value:
    #beta_1: 0.9
    #beta_2: 0.999

lr_schedule:
  desc: Learning rate schedule to use.
  allowed_values: ['cyclic', 'exponential']
  value: cyclic

lr_cyc_scale_fn:
  desc: Scaling function for each cycle of cyclic LR schedule.
  allowed_values: ['triangular', 'triangular2']
  value: triangular2

clr_tail_epochs:
  desc: Int >= 0. Number of epochs to fine-tune model following cyclic LR training. Learning rate will decrease linearly from lr_init to lr_init / 10.
  value: 10

lr_init:
  desc: Initial learning rate.
  value: 0.0025661823297004364

lr_max:
  desc: Maximum learning rate for cyclic LR schedule.
  value: 0.49633379653263104

lr_exp_decay_per_epoch:
  desc: Float in [0, 1]. Decay per epoch, for exponential LR schedule.
  value: 0.95

lr_cyc_num_cycles:
  desc: Float > 0. Number of cycles, for cyclic LR schedule.
  value: 1.0

momentum_schedule:
  desc: Momentum schedule to use.
  allowed_values: ['constant', 'cyclic']
  value: cyclic

momentum_base:
  desc: Minimum momentum for cyclic momentum schedule.
  value: 0.867629166936401

momentum_max:
  desc: Maximum momentum for cyclic momentum schedule.
  value: 0.9872919477284136

# Initialization

kernel_initializer:
  desc: Initializer for kernel weights.
  # `identifier` can be any Keras initializer string. See https://keras.io/api/layers/initializers/
  # `args` is an optional mapping of keyword arguments and values for this identifier, e.g.
  # identifier: he_normal
  # args:
  #   seed: 0
  value:
    identifier: glorot_uniform

bias_initializer:
  desc: Initializer for bias weights.
  value:
    identifier: zeros

# Regularization

l2_reg_conv:
  desc: Strength of L2 regularization for each convolutional layer.
  value: 1.e-4

l2_reg_dense:
  desc: Strength of L2 regularization for each dense layer.
  value: 1.e-4

l2_reg_final:
  desc: Strength of L2 regularization for the final (output) dense layer.
  value: 1.e-4

dropout_rate_conv:
  desc: Float in [0, 1]. Rate for dropout after each convolutional layer.
  value: 0.3

dropout_rate_dense:
  desc: Float in [0, 1]. Rate for dropout after each dense layer.
  value: 0.25

# Architecture

num_conv_layers:
  desc: Number of 1D convolutional layers. Each is followed by a dropout layer.
  value: 6

conv_filters:
  desc: Number of filters in each convolutional layer.
  value: 500

conv_width:
  desc: Width of 1D convolutional kernels.
  value: 13

conv_stride:
  desc: Stride of convolutional layers.
  value: 1

max_pool_size:
  desc: Width of max pooling partitions.
  value: 26

max_pool_stride:
  desc: Stride of max pooling layer.
  value: 26

num_dense_layers:
  desc: Number of dense layers, not including the final layer. Each is followed by a dropout layer.
  value: 1

dense_filters:
  desc: Number of filters in dense layer.
  value: 300

# Interpretation

interp_model_path:
  desc: Path to model to interpret.
  value: /home/csestili/models/model-5layer.h5

shap_num_bg:
  desc: Number of background samples to use for SHAP model interpretation. Taken from training set.
  value: 20

shap_num_fg:
  desc: Number of foreground samples to use for SHAP model interpretation. Taken from positive subset of validation set.
  value: 5

shap_pos_label:
  desc: Positive label to use for SHAP model interpretation.
  value: 1

modisco_normalization:
  desc: Normalization method to use for importance scores.
  allowed_values: ['none', 'pointwise', 'gkm_explain']
  value: gkm_explain

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