Datasets:
row_id
string | series_id
string | timepoint_h
int64 | organism
string | strain_id
string | drug_name
string | stress_index
float64 | cw_mod_index
float64 | wall_thickness_nm
int64 | growth_rate_rel
float64 | mic_drug_mg_L
float64 | resistant_mic_cutoff_mg_L
float64 | media
string | assay_method
string | source_type
string | cw_progression_signal
int64 | earliest_cw_progression
int64 | notes
string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM012-TR-0001
|
S1
| 0
|
Staphylococcus aureus
|
SA-CLIN101
|
vancomycin
| 0.1
| 0.1
| 22
| 1
| 1
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 0
| 0
|
baseline
|
ABXRM012-TR-0002
|
S1
| 12
|
Staphylococcus aureus
|
SA-CLIN101
|
vancomycin
| 0.85
| 0.18
| 26
| 0.3
| 1
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 0
| 0
|
stress growth drops
|
ABXRM012-TR-0003
|
S1
| 24
|
Staphylococcus aureus
|
SA-CLIN101
|
vancomycin
| 0.9
| 0.32
| 31
| 0.55
| 1
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 1
| 1
|
progression starts MIC stable
|
ABXRM012-TR-0004
|
S1
| 48
|
Staphylococcus aureus
|
SA-CLIN101
|
vancomycin
| 0.9
| 0.48
| 36
| 0.6
| 2
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 1
| 0
|
continues
|
ABXRM012-TR-0005
|
S1
| 72
|
Staphylococcus aureus
|
SA-CLIN101
|
vancomycin
| 0.9
| 0.62
| 41
| 0.7
| 16
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 1
| 0
|
MIC crosses later
|
ABXRM012-TR-0006
|
S2
| 0
|
Enterococcus faecium
|
EF-CLIN220
|
daptomycin
| 0.1
| 0.12
| 24
| 1
| 1
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 0
| 0
|
baseline
|
ABXRM012-TR-0007
|
S2
| 24
|
Enterococcus faecium
|
EF-CLIN220
|
daptomycin
| 0.85
| 0.16
| 25
| 0.7
| 1
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 0
| 0
|
small change no event
|
ABXRM012-TR-0008
|
S2
| 48
|
Enterococcus faecium
|
EF-CLIN220
|
daptomycin
| 0.9
| 0.18
| 26
| 0.65
| 1
| 8
|
CAMHB
|
cell_wall_panel
|
simulated
| 0
| 0
|
stable
|
ABXRM012-TR-0009
|
S3
| 0
|
Pseudomonas aeruginosa
|
PA-CLIN330
|
piperacillin
| 0.1
| 0.1
| 18
| 1
| 2
| 16
|
CAMHB
|
cell_wall_panel
|
simulated
| 0
| 0
|
baseline
|
ABXRM012-TR-0010
|
S3
| 12
|
Pseudomonas aeruginosa
|
PA-CLIN330
|
piperacillin
| 0.9
| 0.85
| 19
| 0.4
| 2
| 16
|
CAMHB
|
cell_wall_panel
|
simulated
| 0
| 0
|
one point only keep v1 strict
|
ABX-RM-012 Cell Wall Modification Progression
Purpose
Detect accumulating cell wall modification before MIC crosses a resistant cutoff and before treatment failure.
Core pattern
- stress_index high
- cw_mod_index climbs and continues climbing
- growth_rate_rel rebounds while MIC stays below cutoff
- later MIC crosses resistant_mic_cutoff_mg_L
Files
- data/train.csv
- data/test.csv
- scorer.py
Schema
Each row is one timepoint in a within strain series.
Required columns
- row_id
- series_id
- timepoint_h
- organism
- strain_id
- drug_name
- stress_index
- cw_mod_index
- wall_thickness_nm
- growth_rate_rel
- mic_drug_mg_L
- resistant_mic_cutoff_mg_L
- media
- assay_method
- source_type
- cw_progression_signal
- earliest_cw_progression
Labels
cw_progression_signal
- 1 for rows at or after the first confirmed progression point
earliest_cw_progression
- 1 only for the first detected progression row in that series
Scorer logic in v1
- baseline is timepoint 0
- candidate progression point
- stress_index at least 0.80
- cw_mod_index at least 0.30
- next timepoint cw_mod_index increases by 0.10 or more
- growth_rate_rel rebound of at least 0.20 vs previous timepoint
- MIC below cutoff and at most 2x baseline
- exclude cw_mod_index spike then reversal artifacts
- confirmation
- later MIC crosses resistant cutoff
Evaluation
Run
- python scorer.py --path data/test.csv
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