Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | drug_name string | target_gene string | mutation_id string | mutant_frac_target_mod float64 | mic_drug_mg_L float64 | resistant_mic_cutoff_mg_L float64 | media string | assay_method string | source_type string | penetration_signal int64 | earliest_penetration int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM005-TR-0001 | S1 | 0 | Staphylococcus aureus | SA-CLIN101 | rifampicin | rpoB | rpoB_S531L | 0 | 0.03 | 1 | CAMHB | amplicon_seq | simulated | 0 | 0 | baseline |
ABXRM005-TR-0002 | S1 | 12 | Staphylococcus aureus | SA-CLIN101 | rifampicin | rpoB | rpoB_S531L | 0.05 | 0.03 | 1 | CAMHB | amplicon_seq | simulated | 0 | 0 | early low level |
ABXRM005-TR-0003 | S1 | 24 | Staphylococcus aureus | SA-CLIN101 | rifampicin | rpoB | rpoB_S531L | 0.22 | 0.06 | 1 | CAMHB | amplicon_seq | simulated | 1 | 1 | penetration before phenotype |
ABXRM005-TR-0004 | S1 | 48 | Staphylococcus aureus | SA-CLIN101 | rifampicin | rpoB | rpoB_S531L | 0.55 | 4 | 1 | CAMHB | amplicon_seq | simulated | 1 | 0 | phenotype emerges |
ABXRM005-TR-0005 | S2 | 0 | Escherichia coli | EC-CLIN220 | ciprofloxacin | gyrA | gyrA_S83L | 0 | 0.25 | 1 | CAMHB | amplicon_seq | simulated | 0 | 0 | baseline |
ABXRM005-TR-0006 | S2 | 24 | Escherichia coli | EC-CLIN220 | ciprofloxacin | gyrA | gyrA_S83L | 0.04 | 0.25 | 1 | CAMHB | amplicon_seq | simulated | 0 | 0 | stable |
ABXRM005-TR-0007 | S2 | 48 | Escherichia coli | EC-CLIN220 | ciprofloxacin | gyrA | gyrA_S83L | 0.06 | 0.25 | 1 | CAMHB | amplicon_seq | simulated | 0 | 0 | no penetration |
ABXRM005-TR-0008 | S3 | 0 | Streptococcus pneumoniae | SP-CLIN330 | penicillin | pbp2x | pbp2x_T338A | 0 | 0.06 | 2 | CAMHB | amplicon_seq | simulated | 0 | 0 | baseline |
ABXRM005-TR-0009 | S3 | 12 | Streptococcus pneumoniae | SP-CLIN330 | penicillin | pbp2x | pbp2x_T338A | 0.85 | 0.06 | 2 | CAMHB | amplicon_seq | simulated | 0 | 0 | spike candidate |
ABXRM005-TR-0010 | S3 | 24 | Streptococcus pneumoniae | SP-CLIN330 | penicillin | pbp2x | pbp2x_T338A | 0.02 | 0.06 | 2 | CAMHB | amplicon_seq | simulated | 0 | 0 | snapback artifact |
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
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