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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