Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | antibiotic_name string | antibiotic_class string | drug_trough_mg_L float64 | mic_mg_L float64 | media string | assay_method string | source_type string | resistance_signal int64 | earliest_signal int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXPD001-TR-0001 | S1 | 0 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 1.2 | 0.03 | CAMHB | broth_microdilution | simulated | 0 | 0 | baseline stable |
ABXPD001-TR-0002 | S1 | 24 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 2 | 0.03 | CAMHB | broth_microdilution | simulated | 0 | 0 | trough up MIC stable |
ABXPD001-TR-0003 | S1 | 48 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 2.1 | 0.03 | CAMHB | broth_microdilution | simulated | 0 | 0 | stable |
ABXPD001-TR-0004 | S2 | 0 | Klebsiella pneumoniae | KP-CLIN001 | ceftriaxone | 3rd_gen_cephalosporin | 18 | 0.5 | CAMHB | broth_microdilution | simulated | 0 | 0 | baseline |
ABXPD001-TR-0005 | S2 | 24 | Klebsiella pneumoniae | KP-CLIN001 | ceftriaxone | 3rd_gen_cephalosporin | 20 | 0.5 | CAMHB | broth_microdilution | simulated | 0 | 0 | stable coverage |
ABXPD001-TR-0006 | S2 | 48 | Klebsiella pneumoniae | KP-CLIN001 | ceftriaxone | 3rd_gen_cephalosporin | 19 | 2 | CAMHB | broth_microdilution | simulated | 1 | 1 | first MIC rise breaks coverage |
ABXPD001-TR-0007 | S2 | 72 | Klebsiella pneumoniae | KP-CLIN001 | ceftriaxone | 3rd_gen_cephalosporin | 22 | 4 | CAMHB | broth_microdilution | simulated | 1 | 0 | continued resistance |
ABXPD001-TR-0008 | S3 | 0 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 12 | 1 | CAMHB | broth_microdilution | simulated | 0 | 0 | baseline |
ABXPD001-TR-0009 | S3 | 24 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 14 | 16 | CAMHB | broth_microdilution | simulated | 0 | 0 | unit or read error spike |
ABXPD001-TR-0010 | S3 | 48 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 13 | 1 | CAMHB | broth_microdilution | simulated | 0 | 0 | snap back supports error |
ABX-PD-001: MIC Coherence Decay
This dataset tests early resistance detection.
You detect the first time MIC stops tracking drug exposure.
Core idea
You track
- drug trough concentration in mg/L
- MIC in mg/L
- ratio = trough / MIC
You flag resistance when
- MIC rises fast
- trough stays stable or rises
- ratio drops hard
You avoid false alarms from
- PK failure where trough collapses
- measurement spikes that snap back
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
- drug_trough_mg_L
- mic_mg_L
- media
- assay_method
- source_type
- resistance_signal
- earliest_signal
Labels
resistance_signal
- 1 for rows at or after emergence
- 0 otherwise
earliest_signal
- 1 only for the first detected row in that series
- 0 otherwise
Evaluation
Run
- python scorer.py --path data/test.csv
The scorer reports
- F1 for resistance_signal
- earliest signal hits and misses
- PK failure flags
- measurement spike flags
Notes on realism
This v0.1 seed includes
- stable controls
- clear emergence
- slow drift emergence
- trough drop cases
- spike and snap cases
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