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
- Downloads last month
- 14