row_id string | series_id string | exposure_rank int64 | organism string | strain_id string | antibiotic_name string | antibiotic_class string | cmax_mg_L float64 | ctr_min_mg_L float64 | mic_mg_L float64 | cmax_mic_ratio float64 | cfu0_log10 float64 | cfu24_log10 float64 | kill_24_log10 float64 | media string | assay_method string | source_type string | cmax_mic_failure_signal int64 | earliest_failure int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXPD007-TR-0001 | S1 | 1 | Escherichia coli | EC-ATCC25922 | gentamicin | aminoglycoside | 8 | 1.2 | 0.5 | 16 | 7.2 | 5.7 | 1.5 | CAMHB | cmax_time_kill | simulated | 0 | 0 | baseline |
ABXPD007-TR-0002 | S1 | 2 | Escherichia coli | EC-ATCC25922 | gentamicin | aminoglycoside | 12 | 1.3 | 0.5 | 24 | 7.2 | 4.9 | 2.3 | CAMHB | cmax_time_kill | simulated | 0 | 0 | improves |
ABXPD007-TR-0003 | S1 | 3 | Escherichia coli | EC-ATCC25922 | gentamicin | aminoglycoside | 18 | 1.4 | 0.5 | 36 | 7.2 | 4.2 | 3 | CAMHB | cmax_time_kill | simulated | 0 | 0 | improves |
ABXPD007-TR-0004 | S2 | 1 | Pseudomonas aeruginosa | PA-CLIN204 | tobramycin | aminoglycoside | 10 | 1 | 1 | 10 | 7.3 | 5.4 | 1.9 | CAMHB | cmax_time_kill | simulated | 0 | 0 | baseline |
ABXPD007-TR-0005 | S2 | 2 | Pseudomonas aeruginosa | PA-CLIN204 | tobramycin | aminoglycoside | 16 | 1 | 1 | 16 | 7.3 | 5.35 | 1.95 | CAMHB | cmax_time_kill | simulated | 1 | 1 | cmax up kill flat |
ABXPD007-TR-0006 | S2 | 3 | Pseudomonas aeruginosa | PA-CLIN204 | tobramycin | aminoglycoside | 22 | 1.1 | 1 | 22 | 7.3 | 5.55 | 1.75 | CAMHB | cmax_time_kill | simulated | 1 | 0 | cmax up kill worse |
ABXPD007-TR-0007 | S3 | 1 | Staphylococcus aureus | SA-ATCC29213 | daptomycin | lipopeptide | 25 | 5 | 0.5 | 50 | 6.9 | 4.9 | 2 | CAMHB | cmax_time_kill | simulated | 0 | 0 | baseline |
ABXPD007-TR-0008 | S3 | 2 | Staphylococcus aureus | SA-ATCC29213 | daptomycin | lipopeptide | 35 | 5.2 | 0.5 | 70 | 6.9 | 4.2 | 2.7 | CAMHB | cmax_time_kill | simulated | 0 | 0 | improves |
ABXPD007-TR-0009 | S3 | 3 | Staphylococcus aureus | SA-ATCC29213 | daptomycin | lipopeptide | 45 | 5.3 | 0.5 | 90 | 6.9 | 4.25 | 2.65 | CAMHB | cmax_time_kill | simulated | 0 | 0 | small variance |
ABXPD007-TR-0010 | S4 | 1 | Klebsiella pneumoniae | KP-CLIN333 | amikacin | aminoglycoside | 20 | 0.3 | 2 | 10 | 7.1 | 6.3 | 0.8 | CAMHB | cmax_time_kill | simulated | 0 | 0 | single row control |
license: mit language: - en pretty_name: ABX-PD-007 Cmax/MIC Coherence Failure tags: - antibiotics - pharmacodynamics - pkpd - resistance - tabular task_categories: - tabular-classification size_categories: - n<1k
ABX-PD-007: Cmax/MIC Coherence Failure
This dataset tests when peak concentration stops predicting bacterial killing.
The expected pattern is simple.
Higher Cmax/MIC should produce more 24h killing.
Failure is when Cmax/MIC rises but killing does not improve.
The scorer requires maintained trough levels.
It avoids false calls when levels are not maintained.
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
- cmax_mg_L
- ctr_min_mg_L
- mic_mg_L
- cmax_mic_ratio
- cfu0_log10
- cfu24_log10
- kill_24_log10
- media
- assay_method
- source_type
- cmax_mic_failure_signal
- earliest_failure
Labels
cmax_mic_failure_signal
- 1 for rows at or after failure
earliest_failure
- 1 only for the first detected row in that series
Evaluation
Run
- python scorer.py --path data/test.csv
The scorer
- checks ratio consistency
- detects failure when ratio rises but kill does not
- requires maintained levels using ctr_min_mg_L
- avoids series with unstable baseline inoculum
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