Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | porin_marker string | porin_mean_rel float64 | porin_cv float64 | low_porin_frac float64 | permeability_index_rel float64 | mic_cefepime_mg_L float64 | media string | assay_method string | source_type string | porin_sync_signal int64 | earliest_porin_sync int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM004-TR-0001 | S1 | 0 | Escherichia coli | EC-CLIN101 | OmpF | 1 | 0.55 | 0.1 | 1 | 0.5 | CAMHB | flow_porins | simulated | 0 | 0 | baseline |
ABXRM004-TR-0002 | S1 | 12 | Escherichia coli | EC-CLIN101 | OmpF | 0.85 | 0.5 | 0.15 | 0.9 | 0.5 | CAMHB | flow_porins | simulated | 0 | 0 | small shift |
ABXRM004-TR-0003 | S1 | 24 | Escherichia coli | EC-CLIN101 | OmpF | 0.55 | 0.3 | 0.45 | 0.65 | 0.5 | CAMHB | flow_porins | simulated | 1 | 1 | sync begins before MIC |
ABXRM004-TR-0004 | S1 | 48 | Escherichia coli | EC-CLIN101 | OmpF | 0.5 | 0.28 | 0.52 | 0.6 | 2 | CAMHB | flow_porins | simulated | 1 | 0 | MIC rises later |
ABXRM004-TR-0005 | S2 | 0 | Klebsiella pneumoniae | KP-CLIN220 | OmpK36 | 1 | 0.5 | 0.12 | 1 | 1 | CAMHB | flow_porins | simulated | 0 | 0 | baseline |
ABXRM004-TR-0006 | S2 | 24 | Klebsiella pneumoniae | KP-CLIN220 | OmpK36 | 0.92 | 0.48 | 0.16 | 0.95 | 1 | CAMHB | flow_porins | simulated | 0 | 0 | no sync |
ABXRM004-TR-0007 | S2 | 48 | Klebsiella pneumoniae | KP-CLIN220 | OmpK36 | 0.9 | 0.46 | 0.18 | 0.93 | 1 | CAMHB | flow_porins | simulated | 0 | 0 | no sync |
ABXRM004-TR-0008 | S3 | 0 | Enterobacter cloacae | EN-CLIN330 | OmpC | 1 | 0.6 | 0.1 | 1 | 0.5 | CAMHB | flow_porins | simulated | 0 | 0 | baseline |
ABXRM004-TR-0009 | S3 | 12 | Enterobacter cloacae | EN-CLIN330 | OmpC | 0.2 | 0.62 | 0.8 | 0.4 | 0.5 | CAMHB | flow_porins | simulated | 0 | 0 | spike candidate |
ABXRM004-TR-0010 | S3 | 24 | Enterobacter cloacae | EN-CLIN330 | OmpC | 0.95 | 0.58 | 0.12 | 0.98 | 0.5 | CAMHB | flow_porins | simulated | 0 | 0 | snapback artifact |
ABX-RM-004 Porin Loss Synchronization
Purpose
Detect a coordinated shift toward low porin states across the population before MIC shifts.
Core pattern
- low_porin_frac rises
- porin_cv drops
- permeability_index_rel drops
- mic_cefepime_mg_L stays near baseline during the shift
- mic_cefepime_mg_L rises later
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
- porin_marker
- porin_mean_rel
- porin_cv
- low_porin_frac
- permeability_index_rel
- mic_cefepime_mg_L
- media
- assay_method
- source_type
- porin_sync_signal
- earliest_porin_sync
Labels
porin_sync_signal
- 1 for rows at or after the first confirmed synchronization point
earliest_porin_sync
- 1 only for the first detected synchronization row in that series
Scorer logic in v1
- baseline is timepoint 0
- candidate synchronization event
- low_porin_frac rises by 0.30 or more
- porin_cv drops by 0.15 or more
- permeability_index_rel drops by 20 percent or more
- MIC during the shift no more than 2x baseline
- exclude spike then snapback artifacts
- confirmation
- later MIC reaches at least 4x baseline
Evaluation
Run
- python scorer.py --path data/test.csv
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