Datasets:
metadata
license: mit
language:
- en
pretty_name: ABX-RM-005 Target Modification Penetration
tags:
- antibiotics
- resistance
- target-modification
- population-genetics
- tabular
task_categories:
- tabular-classification
size_categories:
- n<1k
ABX-RM-005 Target Modification Penetration
Purpose
Detect when target modified mutants spread through the population before the MIC crosses a resistant cutoff.
Core pattern
- mutant_frac_target_mod rises
- MIC stays below resistant cutoff during early rise
- later MIC crosses resistant_mic_cutoff_mg_L
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
- target_gene
- mutation_id
- mutant_frac_target_mod
- mic_drug_mg_L
- resistant_mic_cutoff_mg_L
- media
- assay_method
- source_type
- penetration_signal
- earliest_penetration
Labels
penetration_signal
- 1 for rows at or after the first confirmed penetration timepoint
earliest_penetration
- 1 only for the first detected penetration row
Scorer logic in v1
- baseline is timepoint 0
- candidate penetration event
- mutant_frac_target_mod at least 0.20
- MIC still below resistant cutoff
- MIC at most 2x baseline at penetration moment
- exclude spike then snapback artifacts
- confirmation
- later timepoint reaches MIC at or above resistant cutoff
Evaluation
Run
- python scorer.py --path data/test.csv