ClarusC64/ABX-RM-011_metabolic_bypass_activation-v0.1

ABX-RM-011 Metabolic Bypass Activation

Purpose

Detect bypass pathway activation under stress before MIC crosses a resistant cutoff.

Core pattern

• —stress_index high
• —primaryfluxrel drops
• —bypass_share rises
• —growthraterel rebounds while MIC stays below cutoff
• —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
• —primary_pathway
• —bypass_pathway
• —stress_index
• —primaryfluxrel
• —bypassfluxrel
• —bypass_share
• —growthraterel
• —micdrugmg_L
• —resistantmiccutoffmgL
• —media
• —assay_method
• —source_type
• —bypassactivationsignal
• —earliestbypassactivation

Labels

• —bypassactivationsignal
• —1 for rows at or after the first confirmed bypass activation point

• —earliestbypassactivation
• —1 only for the first detected bypass activation row in that series

Scorer logic in v1

• —baseline is timepoint 0
• —candidate bypass activation point
• —stress_index at least 0.80
• —primaryfluxrel at most 0.45
• —bypass_share at least 0.80
• —growthraterel rebound of at least 0.20 vs previous step
• —MIC below cutoff and at most 2x baseline
• —exclude bypass_share spike then snapback artifacts
• —confirmation
• —later MIC crosses resistant cutoff

Evaluation

Run

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