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ClarusC64
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ABX-CT-005_resistance_suppression_failure-v0.1

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combination-therapy

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train · 10 rows

row_id string	series_id string	timepoint_h int64	organism string	strain_id string	drug_a string	drug_b string	stress_index float64	combo_exposure_index float64	resistant_subpop_frac float64	resistant_subpop_growth_rate float64	monoA_mic_mg_L float64	monoB_mic_mg_L float64	monoA_resistant_cutoff_mg_L float64	monoB_resistant_cutoff_mg_L float64	later_combo_failure_flag int64	media string	assay_method string	source_type string	suppression_failure_signal int64	earliest_suppression_failure int64	notes string
ABXCT005-TR-0001	S1	0	Escherichia coli	EC-CLIN101	cefepime	amikacin	0.1	0.1	0.001	0	1	2	16	64	0	CAMHB	resistant_subpop_plating	simulated	0	0	baseline low
ABXCT005-TR-0002	S1	12	Escherichia coli	EC-CLIN101	cefepime	amikacin	0.9	0.85	0.003	0	1	2	16	64	0	CAMHB	resistant_subpop_plating	simulated	0	0	suppressed
ABXCT005-TR-0003	S1	24	Escherichia coli	EC-CLIN101	cefepime	amikacin	0.9	0.9	0.02	0.017	1	2	16	64	0	CAMHB	resistant_subpop_plating	simulated	0	0	rise begins
ABXCT005-TR-0004	S1	36	Escherichia coli	EC-CLIN101	cefepime	amikacin	0.9	0.9	0.06	0.04	2	2	16	64	0	CAMHB	resistant_subpop_plating	simulated	1	1	confirmed onset mono still low
ABXCT005-TR-0005	S1	72	Escherichia coli	EC-CLIN101	cefepime	amikacin	0.9	0.9	0.2	0.14	32	2	16	64	1	CAMHB	resistant_subpop_plating	simulated	1	0	later failure monoA crosses
ABXCT005-TR-0006	S2	0	Pseudomonas aeruginosa	PA-CLIN220	piperacillin_tazobactam	ciprofloxacin	0.1	0.1	0.001	0	2	0.25	64	4	0	CAMHB	resistant_subpop_plating	simulated	0	0	baseline
ABXCT005-TR-0007	S2	24	Pseudomonas aeruginosa	PA-CLIN220	piperacillin_tazobactam	ciprofloxacin	0.9	0.9	0.004	0.003	2	0.25	64	4	0	CAMHB	resistant_subpop_plating	simulated	0	0	still suppressed
ABXCT005-TR-0008	S2	48	Pseudomonas aeruginosa	PA-CLIN220	piperacillin_tazobactam	ciprofloxacin	0.9	0.9	0.006	0.002	2	0.25	64	4	0	CAMHB	resistant_subpop_plating	simulated	0	0	no failure
ABXCT005-TR-0009	S3	0	Klebsiella pneumoniae	KP-CLIN330	meropenem	amikacin	0.1	0.85	0.05	0	0.5	4	8	64	0	CAMHB	resistant_subpop_plating	simulated	0	0	baseline resistant subpop already high
ABXCT005-TR-0010	S4	0	Staphylococcus aureus	SA-CLIN600	vancomycin	rifampin	0.3	0.9	0.02	0	1	0.03	8	1	0	CAMHB	resistant_subpop_plating	simulated	0	0	stress low

ABX-CT-005 Resistance Suppression Failure

Purpose

Detect when a combination stops suppressing resistant subpopulations.

Core pattern

stress_index high
combo_exposure_index high
resistant_subpop_frac rises and keeps rising
mono MICs stay below cutoffs at onset
later_combo_failure_flag appears later in the series

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_a
drug_b
stress_index
combo_exposure_index
resistant_subpop_frac
resistant_subpop_growth_rate
monoA_mic_mg_L
monoB_mic_mg_L
monoA_resistant_cutoff_mg_L
monoB_resistant_cutoff_mg_L
later_combo_failure_flag
media
assay_method
source_type
suppression_failure_signal
earliest_suppression_failure

Labels

suppression_failure_signal
- 1 for rows at or after first detected suppression failure
earliest_suppression_failure
- 1 only for the first detected row in that series

Scorer logic in v1

baseline resistant_subpop_frac must be low
candidate failure point
- stress_index at least 0.80
- combo_exposure_index at least 0.80
- resistant_subpop_frac at least 0.05
- resistant_subpop_frac increases again at next timepoint
- mono MICs below cutoffs at onset
confirmation
- later_combo_failure_flag equals 1 later in series

Evaluation

Run

python scorer.py --path data/test.csv

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