ClarusC64/ABX-RM-003_efflux_pump_activation_cascade-v0.1

ABX-RM-003 Efflux Pump Activation Cascade

Purpose

Detect a coherent rise in efflux expression that occurs before MIC shifts.

Core pattern

• efflux_expression_rel rises across multiple timepoints
• mic_drug_mg_L stays near baseline during the rise
• mic_drug_mg_L rises later

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
• efflux_system
• efflux_expression_rel
• drug_name
• mic_drug_mg_L
• media
• assay_method
• source_type
• efflux_cascade_signal
• earliest_efflux_cascade

Labels

• efflux_cascade_signal

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

• earliest_efflux_cascade

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

Scorer logic in v1

• baseline is timepoint 0
• cascade detection
  • two consecutive expression increases
  • each step at least 1.25x
  • total at least 2.5x vs baseline
  • MIC during the rise no more than 2x baseline
  • exclude spike and snapback artifacts
• confirmation
  • later MIC reaches at least 4x baseline

Evaluation

Run

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