Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | drug_name string | drug_class string | stress_index float64 | gyrA_mut_frac float64 | parC_mut_frac float64 | mutation_burden float64 | mic_drug_mg_L float64 | resistant_mic_cutoff_mg_L float64 | sequencing_depth int64 | assay_method string | source_type string | mutation_cascade_signal int64 | earliest_mutation_cascade int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM014-TR-0001 | S1 | 0 | Escherichia coli | EC-CLIN101 | ciprofloxacin | fluoroquinolone | 0.1 | 0 | 0 | 0 | 0.25 | 4 | 2,000 | deep_amplicon | simulated | 0 | 0 | baseline |
ABXRM014-TR-0002 | S1 | 6 | Escherichia coli | EC-CLIN101 | ciprofloxacin | fluoroquinolone | 0.85 | 0.12 | 0 | 0.12 | 0.25 | 4 | 2,000 | deep_amplicon | simulated | 0 | 0 | gyrA begins |
ABXRM014-TR-0003 | S1 | 12 | Escherichia coli | EC-CLIN101 | ciprofloxacin | fluoroquinolone | 0.9 | 0.28 | 0.02 | 0.3 | 0.5 | 4 | 2,000 | deep_amplicon | simulated | 1 | 1 | parC starts after gyrA lead |
ABXRM014-TR-0004 | S1 | 24 | Escherichia coli | EC-CLIN101 | ciprofloxacin | fluoroquinolone | 0.9 | 0.4 | 0.1 | 0.5 | 1 | 4 | 2,000 | deep_amplicon | simulated | 1 | 0 | cascade continues MIC still low |
ABXRM014-TR-0005 | S1 | 48 | Escherichia coli | EC-CLIN101 | ciprofloxacin | fluoroquinolone | 0.9 | 0.65 | 0.35 | 1 | 16 | 4 | 2,000 | deep_amplicon | simulated | 1 | 0 | MIC crosses later |
ABXRM014-TR-0006 | S2 | 0 | Escherichia coli | EC-CLIN220 | ciprofloxacin | fluoroquinolone | 0.1 | 0 | 0 | 0 | 0.25 | 4 | 2,000 | deep_amplicon | simulated | 0 | 0 | baseline |
ABXRM014-TR-0007 | S2 | 24 | Escherichia coli | EC-CLIN220 | ciprofloxacin | fluoroquinolone | 0.6 | 0.05 | 0 | 0.05 | 0.25 | 4 | 2,000 | deep_amplicon | simulated | 0 | 0 | stress too low |
ABXRM014-TR-0008 | S3 | 0 | Klebsiella pneumoniae | KP-CLIN330 | levofloxacin | fluoroquinolone | 0.1 | 0 | 0 | 0 | 0.5 | 8 | 1,800 | deep_amplicon | simulated | 0 | 0 | baseline |
ABXRM014-TR-0009 | S3 | 12 | Klebsiella pneumoniae | KP-CLIN330 | levofloxacin | fluoroquinolone | 0.9 | 0.05 | 0.3 | 0.35 | 0.5 | 8 | 1,800 | deep_amplicon | simulated | 0 | 0 | parC without gyrA lead |
ABXRM014-TR-0010 | S4 | 0 | Escherichia coli | EC-CLIN600 | ceftriaxone | beta_lactam | 0.9 | 0.2 | 0.1 | 0.3 | 0.25 | 4 | 1,500 | deep_amplicon | simulated | 0 | 0 | wrong drug class |
ABX-RM-014 DNA Gyrase Mutation Cascade
Purpose
Detect staged gyrA then parC mutation accumulation under fluoroquinolone stress before MIC crosses a resistant cutoff.
Core pattern
- stress_index high
- gyrA_mut_frac rises first
- parC_mut_frac follows
- MIC stays below resistant_mic_cutoff_mg_L during early cascade
- 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
- drug_class
- stress_index
- gyrA_mut_frac
- parC_mut_frac
- mutation_burden
- mic_drug_mg_L
- resistant_mic_cutoff_mg_L
- sequencing_depth
- assay_method
- source_type
- mutation_cascade_signal
- earliest_mutation_cascade
Labels
mutation_cascade_signal
- 1 for rows at or after the first confirmed cascade point
earliest_mutation_cascade
- 1 only for the first detected cascade row in that series
Scorer logic in v1
- fluoroquinolone only
- baseline is timepoint 0
- candidate cascade point
- stress_index at least 0.80
- gyrA_mut_frac at least 0.20
- parC_mut_frac at least 0.03
- MIC below cutoff and at most 2x baseline
- exclude gyrA spike then reversal artifacts
- do not allow parC to lead gyrA
- confirmation
- later MIC crosses resistant cutoff
Evaluation
Run
- python scorer.py --path data/test.csv
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