Datasets:
row_id
string | series_id
string | timepoint_h
int64 | organism
string | strain_id
string | drug_name
string | persister_frac
float64 | kill_log10
float64 | exposure_index
float64 | mic_drug_mg_L
float64 | media
string | assay_method
string | source_type
string | persister_wave_signal
int64 | earliest_persister_wave
int64 | notes
string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM008-TR-0001
|
S1
| 0
|
Escherichia coli
|
EC-CLIN101
|
ciprofloxacin
| 0.01
| 0
| 0
| 0.25
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
baseline
|
ABXRM008-TR-0002
|
S1
| 6
|
Escherichia coli
|
EC-CLIN101
|
ciprofloxacin
| 0.02
| 1.8
| 1
| 0.25
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
kill rising
|
ABXRM008-TR-0003
|
S1
| 12
|
Escherichia coli
|
EC-CLIN101
|
ciprofloxacin
| 0.15
| 2
| 2
| 0.25
|
CAMHB
|
persister_assay
|
simulated
| 1
| 1
|
wave onset
|
ABXRM008-TR-0004
|
S1
| 24
|
Escherichia coli
|
EC-CLIN101
|
ciprofloxacin
| 0.18
| 2
| 3
| 0.25
|
CAMHB
|
persister_assay
|
simulated
| 1
| 0
|
plateau persists
|
ABXRM008-TR-0005
|
S2
| 0
|
Staphylococcus aureus
|
SA-CLIN220
|
vancomycin
| 0.01
| 0
| 0
| 1
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
baseline
|
ABXRM008-TR-0006
|
S2
| 12
|
Staphylococcus aureus
|
SA-CLIN220
|
vancomycin
| 0.02
| 1
| 1
| 1
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
no wave
|
ABXRM008-TR-0007
|
S2
| 24
|
Staphylococcus aureus
|
SA-CLIN220
|
vancomycin
| 0.03
| 1.6
| 2
| 1
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
kill continues
|
ABXRM008-TR-0008
|
S3
| 0
|
Pseudomonas aeruginosa
|
PA-CLIN330
|
tobramycin
| 0.01
| 0
| 0
| 1
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
baseline
|
ABXRM008-TR-0009
|
S3
| 6
|
Pseudomonas aeruginosa
|
PA-CLIN330
|
tobramycin
| 0.35
| 0.8
| 1
| 1
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
spike candidate
|
ABXRM008-TR-0010
|
S3
| 12
|
Pseudomonas aeruginosa
|
PA-CLIN330
|
tobramycin
| 0.02
| 1.7
| 2
| 1
|
CAMHB
|
persister_assay
|
simulated
| 0
| 0
|
snapback artifact
|
ABX-RM-008 Persister Cell Synchronization
Purpose
Detect coordinated rises in persister fraction that coincide with kill curve plateaus while MIC stays stable.
Core pattern
- persister_frac crosses a wave threshold and stays elevated
- kill_log10 gain collapses to a plateau
- mic_drug_mg_L stays near baseline
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
- persister_frac
- kill_log10
- exposure_index
- mic_drug_mg_L
- media
- assay_method
- source_type
- persister_wave_signal
- earliest_persister_wave
Labels
persister_wave_signal
- 1 for rows at or after the first detected wave onset
earliest_persister_wave
- 1 only for the first detected wave row in that series
Scorer logic in v1
- baseline is timepoint 0
- candidate wave onset at time t when
- persister_frac at least 0.12
- persister_frac remains at least 0.12 at the next timepoint
- kill_log10 gain vs previous timepoint at most 0.20
- MIC during the wave window at most 2x baseline
- exclude spike then snapback artifacts
Evaluation
Run
- python scorer.py --path data/test.csv
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