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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