Datasets:
row_id
string | series_id
string | timepoint_h
int64 | organism
string | strain_id
string | drug_name
string | target_gene
string | mutation_id
string | mutant_frac_target_mod
float64 | mic_drug_mg_L
float64 | resistant_mic_cutoff_mg_L
float64 | media
string | assay_method
string | source_type
string | penetration_signal
int64 | earliest_penetration
int64 | notes
string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXRM005-TR-0001
|
S1
| 0
|
Staphylococcus aureus
|
SA-CLIN101
|
rifampicin
|
rpoB
|
rpoB_S531L
| 0
| 0.03
| 1
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
baseline
|
ABXRM005-TR-0002
|
S1
| 12
|
Staphylococcus aureus
|
SA-CLIN101
|
rifampicin
|
rpoB
|
rpoB_S531L
| 0.05
| 0.03
| 1
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
early low level
|
ABXRM005-TR-0003
|
S1
| 24
|
Staphylococcus aureus
|
SA-CLIN101
|
rifampicin
|
rpoB
|
rpoB_S531L
| 0.22
| 0.06
| 1
|
CAMHB
|
amplicon_seq
|
simulated
| 1
| 1
|
penetration before phenotype
|
ABXRM005-TR-0004
|
S1
| 48
|
Staphylococcus aureus
|
SA-CLIN101
|
rifampicin
|
rpoB
|
rpoB_S531L
| 0.55
| 4
| 1
|
CAMHB
|
amplicon_seq
|
simulated
| 1
| 0
|
phenotype emerges
|
ABXRM005-TR-0005
|
S2
| 0
|
Escherichia coli
|
EC-CLIN220
|
ciprofloxacin
|
gyrA
|
gyrA_S83L
| 0
| 0.25
| 1
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
baseline
|
ABXRM005-TR-0006
|
S2
| 24
|
Escherichia coli
|
EC-CLIN220
|
ciprofloxacin
|
gyrA
|
gyrA_S83L
| 0.04
| 0.25
| 1
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
stable
|
ABXRM005-TR-0007
|
S2
| 48
|
Escherichia coli
|
EC-CLIN220
|
ciprofloxacin
|
gyrA
|
gyrA_S83L
| 0.06
| 0.25
| 1
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
no penetration
|
ABXRM005-TR-0008
|
S3
| 0
|
Streptococcus pneumoniae
|
SP-CLIN330
|
penicillin
|
pbp2x
|
pbp2x_T338A
| 0
| 0.06
| 2
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
baseline
|
ABXRM005-TR-0009
|
S3
| 12
|
Streptococcus pneumoniae
|
SP-CLIN330
|
penicillin
|
pbp2x
|
pbp2x_T338A
| 0.85
| 0.06
| 2
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
spike candidate
|
ABXRM005-TR-0010
|
S3
| 24
|
Streptococcus pneumoniae
|
SP-CLIN330
|
penicillin
|
pbp2x
|
pbp2x_T338A
| 0.02
| 0.06
| 2
|
CAMHB
|
amplicon_seq
|
simulated
| 0
| 0
|
snapback artifact
|
ABX-RM-005 Target Modification Penetration
Purpose
Detect when target modified mutants spread through the population before the MIC crosses a resistant cutoff.
Core pattern
- mutant_frac_target_mod rises
- MIC stays below resistant cutoff during early rise
- 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
- target_gene
- mutation_id
- mutant_frac_target_mod
- mic_drug_mg_L
- resistant_mic_cutoff_mg_L
- media
- assay_method
- source_type
- penetration_signal
- earliest_penetration
Labels
penetration_signal
- 1 for rows at or after the first confirmed penetration timepoint
earliest_penetration
- 1 only for the first detected penetration row
Scorer logic in v1
- baseline is timepoint 0
- candidate penetration event
- mutant_frac_target_mod at least 0.20
- MIC still below resistant cutoff
- MIC at most 2x baseline at penetration moment
- exclude spike then snapback artifacts
- confirmation
- later timepoint reaches MIC at or above resistant cutoff
Evaluation
Run
- python scorer.py --path data/test.csv
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