Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | drug_name string | resistant_subpop_frac float64 | mic_drug_mg_L float64 | resistant_mic_cutoff_mg_L float64 | media string | assay_method string | source_type string | hetero_shift_signal int64 | earliest_hetero_shift int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM007-TR-0001 | S1 | 0 | Klebsiella pneumoniae | KP-CLIN101 | colistin | 0.01 | 0.5 | 4 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | baseline |
ABXRM007-TR-0002 | S1 | 12 | Klebsiella pneumoniae | KP-CLIN101 | colistin | 0.04 | 0.5 | 4 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | minor rise |
ABXRM007-TR-0003 | S1 | 24 | Klebsiella pneumoniae | KP-CLIN101 | colistin | 0.18 | 1 | 4 | CAMHB | pap_heteroresistance | simulated | 1 | 1 | minor threshold crossed |
ABXRM007-TR-0004 | S1 | 48 | Klebsiella pneumoniae | KP-CLIN101 | colistin | 0.72 | 8 | 4 | CAMHB | pap_heteroresistance | simulated | 1 | 0 | dominance and MIC crosses |
ABXRM007-TR-0005 | S2 | 0 | Staphylococcus aureus | SA-CLIN220 | vancomycin | 0.02 | 1 | 8 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | baseline |
ABXRM007-TR-0006 | S2 | 24 | Staphylococcus aureus | SA-CLIN220 | vancomycin | 0.03 | 1 | 8 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | stable |
ABXRM007-TR-0007 | S2 | 48 | Staphylococcus aureus | SA-CLIN220 | vancomycin | 0.05 | 1 | 8 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | no shift |
ABXRM007-TR-0008 | S3 | 0 | Acinetobacter baumannii | AB-CLIN330 | imipenem | 0.01 | 0.5 | 8 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | baseline |
ABXRM007-TR-0009 | S3 | 12 | Acinetobacter baumannii | AB-CLIN330 | imipenem | 0.9 | 0.5 | 8 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | spike candidate |
ABXRM007-TR-0010 | S3 | 24 | Acinetobacter baumannii | AB-CLIN330 | imipenem | 0.02 | 0.5 | 8 | CAMHB | pap_heteroresistance | simulated | 0 | 0 | snapback artifact |
ABX-RM-007 Heteroresistance Population Shift
Purpose
Detect growth of a minor resistant subpopulation before it becomes dominant and before MIC crosses the resistant cutoff.
Core pattern
- resistant_subpop_frac crosses a minor threshold
- MIC stays below resistant_mic_cutoff_mg_L at that time
- later resistant_subpop_frac becomes dominant
- 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
- resistant_subpop_frac
- mic_drug_mg_L
- resistant_mic_cutoff_mg_L
- media
- assay_method
- source_type
- hetero_shift_signal
- earliest_hetero_shift
Labels
hetero_shift_signal
- 1 for rows at or after the first confirmed shift point
earliest_hetero_shift
- 1 only for the first detected shift row in that series
Scorer logic in v1
- baseline is timepoint 0
- candidate early shift point
- resistant_subpop_frac at least 0.20
- MIC at most 2x baseline
- MIC still below resistant cutoff
- exclude spike then snapback artifacts
- confirmation
- later resistant_subpop_frac reaches at least 0.70
- later MIC crosses resistant cutoff
Evaluation
Run
- python scorer.py --path data/test.csv
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