Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | antibiotic_name string | antibiotic_class string | drug_conc_mg_L float64 | cfu_log10 float64 | media string | assay_method string | source_type string | biphasic_signal int64 | earliest_transition int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXPD002-TR-0001 | S1 | 0 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 2 | 7.2 | CAMHB | time_kill | simulated | 0 | 0 | baseline |
ABXPD002-TR-0002 | S1 | 2 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 2 | 5.7 | CAMHB | time_kill | simulated | 0 | 0 | fast kill continues |
ABXPD002-TR-0003 | S1 | 6 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 2 | 4.3 | CAMHB | time_kill | simulated | 0 | 0 | kill continues |
ABXPD002-TR-0004 | S1 | 24 | Escherichia coli | EC-ATCC25922 | meropenem | carbapenem | 2 | 3.8 | CAMHB | time_kill | simulated | 0 | 0 | monotone kill |
ABXPD002-TR-0005 | S2 | 0 | Klebsiella pneumoniae | KP-CLIN011 | ceftriaxone | 3rd_gen_cephalosporin | 16 | 7.1 | CAMHB | time_kill | simulated | 1 | 0 | baseline |
ABXPD002-TR-0006 | S2 | 2 | Klebsiella pneumoniae | KP-CLIN011 | ceftriaxone | 3rd_gen_cephalosporin | 16 | 5.8 | CAMHB | time_kill | simulated | 1 | 0 | fast kill |
ABXPD002-TR-0007 | S2 | 6 | Klebsiella pneumoniae | KP-CLIN011 | ceftriaxone | 3rd_gen_cephalosporin | 16 | 5.6 | CAMHB | time_kill | simulated | 1 | 1 | plateau begins |
ABXPD002-TR-0008 | S2 | 24 | Klebsiella pneumoniae | KP-CLIN011 | ceftriaxone | 3rd_gen_cephalosporin | 16 | 6.2 | CAMHB | time_kill | simulated | 1 | 0 | regrowth |
ABXPD002-TR-0009 | S3 | 0 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 8 | 6.9 | CAMHB | time_kill | simulated | 1 | 0 | baseline |
ABXPD002-TR-0010 | S3 | 2 | Staphylococcus aureus | SA-ATCC29213 | vancomycin | glycopeptide | 8 | 5.9 | CAMHB | time_kill | simulated | 1 | 1 | transition to slow kill |
ABX-PD-002: Kill Curve Biphasic Detection
This dataset tests whether you can detect biphasic kill curves.
A biphasic curve has
- fast early kill
- a transition to slow kill or plateau
- plateau persistence or regrowth
You must detect the transition point.
Files
- data/train.csv
- data/test.csv
- scorer.py
Schema
Each row is one timepoint in a longitudinal time kill series.
Required columns
- row_id
- series_id
- timepoint_h
- organism
- strain_id
- antibiotic_name
- antibiotic_class
- drug_conc_mg_L
- cfu_log10
- media
- assay_method
- source_type
- biphasic_signal
- earliest_transition
Labels
biphasic_signal
- 1 for series that show biphasic dynamics
- 0 for monotone kill or exposure loss artifacts
earliest_transition
- 1 only for the first row where the curve shifts from fast kill to slow kill or plateau
- 0 otherwise
Evaluation
Run
- python scorer.py --path data/test.csv
The scorer reports
- series level F1 for biphasic_signal
- transition hits and misses
- flags for exposure loss cases
Notes
The scorer separates two failure types
- biphasic dynamics under stable drug concentration
- regrowth driven by drug concentration drop
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