ClarusC64/ABX-RM-015_visa_stepwise_cell_wall_thickening-v0.1

ABX-RM-015 Vancomycin Intermediate Stepwise

Purpose

Detect stepwise cell wall thickening consistent with VISA emergence.

Core pattern

• —Staphylococcus aureus
• —vancomycin exposure
• —wallthicknessnm increases through sequential step events
• —MIC enters VISA range later
• —autolysisraterel drops during remodeling

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
• —wallthicknessnm
• —wallthicknessdelta_nm
• —autolysisraterel
• —micvancomg_L
• —visamiclowermgL
• —visamicuppermgL
• —media
• —assay_method
• —source_type
• —visastepwisesignal
• —earliestvisastep

Labels

• —visastepwisesignal
• —1 for rows at or after the first detected stepwise thickening point

• —earliestvisastep
• —1 only for the first detected stepwise row in that series

Scorer logic in v1

• —Staphylococcus aureus only
• —vancomycin only
• —baseline must be below VISA range
• —detect thickening steps
• —stress_index at least 0.80
• —wallthicknessdelta_nm at least 4 nm
• —at least 2 step events
• —require MIC later enters VISA range
• —require autolysis drop at first step
• —avoid large early MIC jumps

Evaluation

Run

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