Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | antibiotic_name string | antibiotic_class string | exposure_index float64 | mic_mg_L float64 | pae_hours float64 | media string | assay_method string | source_type string | pae_loss_signal int64 | earliest_pae_loss int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXPD003-TR-0001 | S1 | 0 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 1 | 0.03 | 3.5 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | baseline PAE |
ABXPD003-TR-0002 | S1 | 24 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 1.1 | 0.03 | 3.4 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | stable |
ABXPD003-TR-0003 | S1 | 48 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 1.05 | 0.03 | 3.3 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | stable |
ABXPD003-TR-0004 | S2 | 0 | Klebsiella pneumoniae | KP-CLIN021 | ceftriaxone | 3rd_gen_cephalosporin | 1 | 0.5 | 2.8 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | baseline PAE |
ABXPD003-TR-0005 | S2 | 24 | Klebsiella pneumoniae | KP-CLIN021 | ceftriaxone | 3rd_gen_cephalosporin | 1 | 0.5 | 2.6 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | small drop |
ABXPD003-TR-0006 | S2 | 48 | Klebsiella pneumoniae | KP-CLIN021 | ceftriaxone | 3rd_gen_cephalosporin | 1.05 | 0.5 | 1.3 | CAMHB | pae_regrowth_delay | simulated | 1 | 1 | PAE halves before MIC changes |
ABXPD003-TR-0007 | S2 | 72 | Klebsiella pneumoniae | KP-CLIN021 | ceftriaxone | 3rd_gen_cephalosporin | 1.1 | 0.5 | 1.1 | CAMHB | pae_regrowth_delay | simulated | 1 | 0 | continued low PAE |
ABXPD003-TR-0008 | S3 | 0 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 1 | 1 | 2.2 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | baseline |
ABXPD003-TR-0009 | S3 | 24 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 1 | 1 | 0.2 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | likely measurement issue |
ABXPD003-TR-0010 | S3 | 48 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 1 | 1 | 2.1 | CAMHB | pae_regrowth_delay | simulated | 0 | 0 | snap back supports error |
ABX-PD-003: Post-Antibiotic Effect Loss
This dataset tests early resistance signals that appear before MIC changes.
The signal is loss of the post-antibiotic effect.
PAE is the duration of growth suppression after drug removal.
Files
- data/train.csv
- data/test.csv
- scorer.py
Schema
Each row is one timepoint in a longitudinal series.
Required columns
- row_id
- series_id
- timepoint_h
- organism
- strain_id
- antibiotic_name
- antibiotic_class
- exposure_index
- mic_mg_L
- pae_hours
- media
- assay_method
- source_type
- pae_loss_signal
- earliest_pae_loss
Labels
pae_loss_signal
- 1 for rows at or after meaningful PAE loss
earliest_pae_loss
- 1 only for the first detected row in that series
Evaluation
Run
- python scorer.py --path data/test.csv
The scorer reports
- series level F1 for pae_loss_signal
- earliest loss hits and misses
- measurement spike flags
Notes
The scorer avoids a common mistake.
It does not call resistance when exposure collapses.
It also flags spike and snap PAE values as likely measurement artifacts.
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