DeepBenchBioData 🖥️🧬

DeepBenchBioData is a Nextflow-based pipeline for cross-species gene expression benchmarking, promoter-sequence profiling, gene-pair labeling, sequence encoding, and deep learning model training/evaluation.

Pipeline

main_full_pipeline.nf runs the full workflow:

1. data exploration before normalization
2. normalization benchmarking
3. profiling benchmarking, with optional promoter-alignment comparison
4. labeled gene-pair generation
5. promoter-sequence encoding and train/validation/test splitting
6. model training and evaluation

Requirements

• Nextflow
• A Micromamba/Conda environment named environment_tfm
• The input expression table, promoter alignment, and human/mouse promoter FASTA files
• Execution from the repository root

Before running the pipeline, load the environment with micromamba activate environment_tfm.

Inputs

Parameter	Description
--input	Tabular gene expression dataset.
--name	Run name used for metadata and output naming.
--promoter	Promoter alignment path supplied to the run.
--human_fasta	Human promoter FASTA file.
--mouse_fasta	Mouse promoter FASTA file.
--labeling	Strategy used to label gene pairs.
--split_mode	Train/validation/test split strategy.
--val_frac, --test_frac	Validation and test-set fractions.
--n_pos, --n_neg	Number of positive and negative gene pairs.
Model parameters	Training hyperparameters passed to the model step.

Runnable example

nextflow run main_full_pipeline.nf   -c conf/full_pipeline.config   -profile local   --input data/new_expression_data.txt   --name my_results --promoter data/kinases_promoter_alignment   --outdir results/my_results  --human_fasta data/promoter_kinases_human.fasta   --mouse_fasta data/promoter_kinases_mouse.fasta   --labeling rank_labeling  --split_mode anti_leakage   --val_frac 0.15   --test_frac 0.15   --n_pos 10000   --n_neg 8000   --epochs 40 --small_kernel_size 6 --medium_kernel_size 10 --large_kernel_size 20 --dropout 0.1 --learning_rate 0.0005 --weight_decay 0 

Outputs

With the example above, outputs are written under results/my_results/:

• data_exploration/: exploratory outputs before and after normalization
• normalization/: normalization benchmark results and selected method
• profiling/: profiling benchmark results and selected metric
• labeling/: labeled gene-pair tables
• encoding/: encoded sequences and train/validation/test splits
• model/: trained model and evaluation outputs
• nextflow_reports/: trace, timeline, report, and DAG files

Repository layout

Path	Purpose
main_full_pipeline.nf	Full pipeline entry point.
conf/full_pipeline.config	Default parameters and execution profiles.
workflows/	Workflow definitions.
modules/local/	Nextflow process modules.
bin/	Python wrappers called by Nextflow.
lib/	Core Python implementation.
envs/environment_tfm.yml	Environment definition.
data/	Example input data and promoter files.

Adding New Metrics

The benchmarking framework is easily extensible.

To add a new normalization method:

1. Implement the normalization function in lib/normalization.py.
2. Add the function name to the NORMALIZATION_METHODS list.

To add a new profiling metric:

1. Implement the metric function in lib/profiling_functions.py.
2. Register the function in:
   • INTERNAL_METRICS if it is a gene-wise metric (computed independently for each species).
   • EXTERNAL_METRICS if it is a pair-wise metric (computed directly between species).