Datasets:
row_id string | series_id string | exposure_rank int64 | organism string | strain_id string | antibiotic_name string | antibiotic_class string | ft_greater_mic_frac float64 | mic_mg_L float64 | cfu0_log10 float64 | cfu24_log10 float64 | kill_24_log10 float64 | media string | assay_method string | source_type string | threshold_drift_signal int64 | earliest_drift int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXPD008-TR-0001 | S1 | 1 | Escherichia coli | EC-ATCC25922 | piperacillin_tazobactam | beta_lactam | 0.35 | 1 | 7.2 | 6.2 | 1 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | baseline |
ABXPD008-TR-0002 | S1 | 2 | Escherichia coli | EC-ATCC25922 | piperacillin_tazobactam | beta_lactam | 0.5 | 1 | 7.2 | 5.6 | 1.6 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | improves |
ABXPD008-TR-0003 | S1 | 3 | Escherichia coli | EC-ATCC25922 | piperacillin_tazobactam | beta_lactam | 0.7 | 1 | 7.2 | 4.9 | 2.3 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | improves |
ABXPD008-TR-0004 | S2 | 1 | Klebsiella pneumoniae | KP-CLIN190 | ceftriaxone | beta_lactam | 0.4 | 0.5 | 7.1 | 5.2 | 1.9 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | baseline |
ABXPD008-TR-0005 | S2 | 2 | Klebsiella pneumoniae | KP-CLIN190 | ceftriaxone | beta_lactam | 0.55 | 0.5 | 7.1 | 5.15 | 1.95 | CAMHB | ftmic_time_kill | simulated | 1 | 1 | ftmic up kill flat |
ABXPD008-TR-0006 | S2 | 3 | Klebsiella pneumoniae | KP-CLIN190 | ceftriaxone | beta_lactam | 0.7 | 0.5 | 7.1 | 5.3 | 1.8 | CAMHB | ftmic_time_kill | simulated | 1 | 0 | ftmic up kill worse |
ABXPD008-TR-0007 | S3 | 1 | Staphylococcus aureus | SA-CLIN701 | cefazolin | beta_lactam | 0.45 | 0.5 | 6.9 | 5.6 | 1.3 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | baseline |
ABXPD008-TR-0008 | S3 | 2 | Staphylococcus aureus | SA-CLIN701 | cefazolin | beta_lactam | 0.6 | 0.5 | 6.9 | 5 | 1.9 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | improves |
ABXPD008-TR-0009 | S3 | 3 | Staphylococcus aureus | SA-CLIN701 | cefazolin | beta_lactam | 0.75 | 0.5 | 6.9 | 5.05 | 1.85 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | small variance |
ABXPD008-TR-0010 | S4 | 1 | Pseudomonas aeruginosa | PA-CLIN404 | cefepime | beta_lactam | 0.55 | 2 | 7.3 | 6.9 | 0.4 | CAMHB | ftmic_time_kill | simulated | 0 | 0 | single row control |
ABX-PD-008: Time Above MIC Threshold Drift
This dataset tests when the required fT>MIC rises before obvious clinical failure.
The expected pattern is simple.
Higher fT>MIC should produce more 24h killing.
Drift is when fT>MIC rises but killing does not improve.
Files
- data/train.csv
- data/test.csv
- scorer.py
Schema
Each row is one exposure condition in an ordered series.
Required columns
- row_id
- series_id
- exposure_rank
- organism
- strain_id
- antibiotic_name
- antibiotic_class
- ft_greater_mic_frac
- mic_mg_L
- cfu0_log10
- cfu24_log10
- kill_24_log10
- media
- assay_method
- source_type
- threshold_drift_signal
- earliest_drift
Labels
threshold_drift_signal
- 1 for rows at or after drift
earliest_drift
- 1 only for the first detected row in that series
Evaluation
Run
- python scorer.py --path data/test.csv
The scorer
- detects drift when fT>MIC rises but killing does not
- requires exposure to be maintained
- avoids false calls when baseline inoculum varies too much
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