---
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