ClarusC64/ABX-RM-013_ribosomal_protection_timing-v0.1

ABX-RM-013 Ribosomal Protection Timing

Purpose

Detect early ribosomal protection activity that precedes MIC crossing a resistant cutoff.

Core pattern

• —stress_index high
• —ribosomalprotectionrel rises above a threshold
• —translationoutputrel rebounds vs prior timepoint
• —MIC stays below resistantmiccutoffmgL during the early window
• —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
• —stress_index
• —ribosomalprotectionrel
• —translationoutputrel
• —growthraterel
• —micdrugmg_L
• —resistantmiccutoffmgL
• —media
• —assay_method
• —source_type
• —riboprotectionsignal
• —earliestriboprotection

Labels

• —riboprotectionsignal
• —1 for rows at or after the first confirmed protection point

• —earliestriboprotection
• —1 only for the first detected protection row in that series

Scorer logic in v1

• —baseline is timepoint 0
• —candidate protection point
• —stress_index at least 0.80
• —ribosomalprotectionrel at least 1.50
• —translationoutputrel rebound of at least 0.20 vs previous timepoint
• —MIC below cutoff and at most 2x baseline
• —exclude ribosomal_protection spike then reversal artifacts
• —confirmation
• —later MIC crosses resistant cutoff

Evaluation

Run

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