Getting Started

The benchmark has two main entry points:

• array-based benchmarking via gene_calling_benchmark.benchmark_from_arrays()

• annotation-file benchmarking via gene_calling_benchmark.benchmark_from_gff()

Use the array API when your training or inference pipeline already produces integer label arrays. Use the GFF/GTF pipeline when you want the benchmark to handle parsing, transcript pairing, array construction, and aggregation.

Both entry points are anchored to an explicit annotation mode (EXON_INTRON or UTR_CDS_INTRON). Read Annotation Modes first — it explains what the positive labels mean, how evaluation scopes work, and which metrics each mode unlocks.

Ready-made reference datasets can be downloaded on demand from the registry — see Datasets.

• Annotation Modes
• Datasets
• Array Benchmark
• Online W&B Logging
• Method Comparison
• GFF/GTF Benchmark