Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | drug_name string | stress_index float64 | wall_thickness_nm int64 | wall_thickness_delta_nm int64 | autolysis_rate_rel float64 | mic_vanco_mg_L float64 | visa_mic_lower_mg_L float64 | visa_mic_upper_mg_L float64 | media string | assay_method string | source_type string | visa_stepwise_signal int64 | earliest_visa_step int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM015-TR-0001 | S1 | 0 | Staphylococcus aureus | SA-CLIN101 | vancomycin | 0.1 | 22 | 0 | 1 | 1 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 0 | 0 | baseline VSSA |
ABXRM015-TR-0002 | S1 | 12 | Staphylococcus aureus | SA-CLIN101 | vancomycin | 0.85 | 26 | 4 | 0.8 | 1 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 0 | 0 | first thickening step MIC stable |
ABXRM015-TR-0003 | S1 | 24 | Staphylococcus aureus | SA-CLIN101 | vancomycin | 0.9 | 31 | 5 | 0.65 | 2 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 1 | 1 | second step MIC rising not VISA yet |
ABXRM015-TR-0004 | S1 | 48 | Staphylococcus aureus | SA-CLIN101 | vancomycin | 0.9 | 36 | 5 | 0.55 | 4 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 1 | 0 | enters VISA range |
ABXRM015-TR-0005 | S1 | 72 | Staphylococcus aureus | SA-CLIN101 | vancomycin | 0.9 | 40 | 4 | 0.45 | 8 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 1 | 0 | upper VISA |
ABXRM015-TR-0006 | S2 | 0 | Staphylococcus aureus | SA-CLIN220 | vancomycin | 0.1 | 23 | 0 | 1 | 1 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 0 | 0 | baseline |
ABXRM015-TR-0007 | S2 | 24 | Staphylococcus aureus | SA-CLIN220 | vancomycin | 0.85 | 25 | 2 | 0.95 | 1 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 0 | 0 | minor change no steps |
ABXRM015-TR-0008 | S2 | 48 | Staphylococcus aureus | SA-CLIN220 | vancomycin | 0.9 | 26 | 1 | 0.92 | 1 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 0 | 0 | stable |
ABXRM015-TR-0009 | S3 | 0 | Enterococcus faecium | EF-CLIN330 | vancomycin | 0.9 | 28 | 0 | 0.8 | 4 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 0 | 0 | wrong organism |
ABXRM015-TR-0010 | S4 | 0 | Staphylococcus aureus | SA-CLIN600 | linezolid | 0.9 | 28 | 0 | 0.8 | 1 | 4 | 8 | CAMHB | cell_wall_panel | simulated | 0 | 0 | wrong drug |
ABX-RM-015 Vancomycin Intermediate Stepwise
Purpose
Detect stepwise cell wall thickening consistent with VISA emergence.
Core pattern
- Staphylococcus aureus
- vancomycin exposure
- wall_thickness_nm increases through sequential step events
- MIC enters VISA range later
- autolysis_rate_rel drops during remodeling
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
- wall_thickness_nm
- wall_thickness_delta_nm
- autolysis_rate_rel
- mic_vanco_mg_L
- visa_mic_lower_mg_L
- visa_mic_upper_mg_L
- media
- assay_method
- source_type
- visa_stepwise_signal
- earliest_visa_step
Labels
visa_stepwise_signal
- 1 for rows at or after the first detected stepwise thickening point
earliest_visa_step
- 1 only for the first detected stepwise row in that series
Scorer logic in v1
- Staphylococcus aureus only
- vancomycin only
- baseline must be below VISA range
- detect thickening steps
- stress_index at least 0.80
- wall_thickness_delta_nm at least 4 nm
- at least 2 step events
- require MIC later enters VISA range
- require autolysis drop at first step
- avoid large early MIC jumps
Evaluation
Run
- python scorer.py --path data/test.csv
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