ClarusC64/ABX-RM-014_dna_gyrase_mutation_cascade-v0.1

ABX-RM-014 DNA Gyrase Mutation Cascade

Purpose

Detect staged gyrA then parC mutation accumulation under fluoroquinolone stress before MIC crosses a resistant cutoff.

Core pattern

• —stress_index high
• —gyrAmutfrac rises first
• —parCmutfrac follows
• —MIC stays below resistantmiccutoffmgL during early cascade
• —later MIC crosses resistantmiccutoffmgL

Files

• —data/train.csv
• —data/test.csv
• —scorer.py

Schema

Each row is one timepoint in a within strain series.

Required columns

• —row_id
• —series_id
• —timepoint_h
• —organism
• —strain_id
• —drug_name
• —drug_class
• —stress_index
• —gyrAmutfrac
• —parCmutfrac
• —mutation_burden
• —micdrugmg_L
• —resistantmiccutoffmgL
• —sequencing_depth
• —assay_method
• —source_type
• —mutationcascadesignal
• —earliestmutationcascade

Labels

• —mutationcascadesignal
• —1 for rows at or after the first confirmed cascade point

• —earliestmutationcascade
• —1 only for the first detected cascade row in that series

Scorer logic in v1

• —fluoroquinolone only
• —baseline is timepoint 0
• —candidate cascade point
• —stress_index at least 0.80
• —gyrAmutfrac at least 0.20
• —parCmutfrac at least 0.03
• —MIC below cutoff and at most 2x baseline
• —exclude gyrA spike then reversal artifacts
• —do not allow parC to lead gyrA
• —confirmation
• —later MIC crosses resistant cutoff

Evaluation

Run

• —python scorer.py --path data/test.csv