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
- Downloads last month
- 16