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
- Downloads last month
- 26