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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