Datasets:
row_id string | series_id string | timepoint_h int64 | organism string | strain_id string | drug_name string | reg_network string | stress_index float64 | regulator_activity_rel float64 | expected_activity_rel float64 | decoupling_error float64 | mic_drug_mg_L float64 | resistant_mic_cutoff_mg_L float64 | media string | assay_method string | source_type string | rewiring_signal int64 | earliest_rewiring int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM010-TR-0001 | S1 | 0 | Escherichia coli | EC-CLIN101 | ceftriaxone | RpoS_sigmaS | 0.1 | 1 | 1 | 0 | 0.25 | 2 | CAMHB | rna_seq_signature | simulated | 0 | 0 | baseline |
ABXRM010-TR-0002 | S1 | 6 | Escherichia coli | EC-CLIN101 | ceftriaxone | RpoS_sigmaS | 0.85 | 1.3 | 1.6 | 0.3 | 0.25 | 2 | CAMHB | rna_seq_signature | simulated | 0 | 0 | stress rises normal tracking |
ABXRM010-TR-0003 | S1 | 12 | Escherichia coli | EC-CLIN101 | ceftriaxone | RpoS_sigmaS | 0.9 | 0.8 | 1.8 | 1 | 0.25 | 2 | CAMHB | rna_seq_signature | simulated | 1 | 1 | decoupling starts |
ABXRM010-TR-0004 | S1 | 24 | Escherichia coli | EC-CLIN101 | ceftriaxone | RpoS_sigmaS | 0.9 | 0.75 | 1.8 | 1.05 | 0.5 | 2 | CAMHB | rna_seq_signature | simulated | 1 | 0 | decoupling persists MIC still low |
ABXRM010-TR-0005 | S1 | 48 | Escherichia coli | EC-CLIN101 | ceftriaxone | RpoS_sigmaS | 0.9 | 0.7 | 1.8 | 1.1 | 8 | 2 | CAMHB | rna_seq_signature | simulated | 1 | 0 | MIC crosses later |
ABXRM010-TR-0006 | S2 | 0 | Staphylococcus aureus | SA-CLIN220 | vancomycin | WalKR | 0.1 | 1 | 1 | 0 | 1 | 8 | CAMHB | rna_seq_signature | simulated | 0 | 0 | baseline |
ABXRM010-TR-0007 | S2 | 24 | Staphylococcus aureus | SA-CLIN220 | vancomycin | WalKR | 0.85 | 1.4 | 1.55 | 0.15 | 1 | 8 | CAMHB | rna_seq_signature | simulated | 0 | 0 | tracks expectation |
ABXRM010-TR-0008 | S2 | 48 | Staphylococcus aureus | SA-CLIN220 | vancomycin | WalKR | 0.9 | 1.5 | 1.6 | 0.1 | 1 | 8 | CAMHB | rna_seq_signature | simulated | 0 | 0 | no rewiring |
ABXRM010-TR-0009 | S3 | 0 | Pseudomonas aeruginosa | PA-CLIN330 | meropenem | AmpR_beta_lactam | 0.1 | 1 | 1 | 0 | 0.5 | 8 | CAMHB | rna_seq_signature | simulated | 0 | 0 | baseline |
ABXRM010-TR-0010 | S3 | 12 | Pseudomonas aeruginosa | PA-CLIN330 | meropenem | AmpR_beta_lactam | 0.9 | 0.1 | 1.7 | 1.6 | 0.5 | 8 | CAMHB | rna_seq_signature | simulated | 0 | 0 | one point only keep v1 strict |
ABX-RM-010 Regulatory Network Rewiring
Purpose
Detect sustained decoupling between expected stress regulation and measured regulator activity before MIC crosses a resistant cutoff.
Core pattern
- stress_index high
- decoupling_error stays high across consecutive timepoints
- MIC stays below resistant_mic_cutoff_mg_L during the decoupling window
- 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
- reg_network
- stress_index
- regulator_activity_rel
- expected_activity_rel
- decoupling_error
- mic_drug_mg_L
- resistant_mic_cutoff_mg_L
- media
- assay_method
- source_type
- rewiring_signal
- earliest_rewiring
Labels
rewiring_signal
- 1 for rows at or after the first confirmed rewiring point
earliest_rewiring
- 1 only for the first detected rewiring row in that series
Scorer logic in v1
- baseline is timepoint 0
- candidate rewiring point
- stress_index at least 0.80
- decoupling_error at least 0.90 at two consecutive timepoints
- MIC at that point below cutoff and at most 2x baseline
- exclude decoupling spike then snapback artifacts
- confirmation
- later MIC crosses resistant cutoff
Evaluation
Run
- python scorer.py --path data/test.csv
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