Datasets:

ClarusC64
/

ABX-CS-006_device_associated_infection_persistence-v0.1

row_id string	series_id string	day int64	host_model string	device_type string	organism string	abx_drug string	abx_exposure_index float64	severity_index float64	device_site_burden_index float64	expected_burden_index float64	burden_persistence_vs_expected float64	biofilm_activity_index float64	expected_biofilm_activity_index float64	biofilm_rise_vs_expected float64	tolerance_index float64	expected_tolerance_index float64	tolerance_rise_vs_expected float64	mic_mg_L float64	expected_mic_mg_L float64	mic_rise_vs_expected float64	device_coherence_index float64	later_device_removal_or_persistent_positive_or_resistant_isolate_flag int64	assay_method string	source_type string	device_infection_persistence_signal int64	earliest_device_infection_persistence int64	notes string
ABXCS006-TE-0001	S5	0	human_sim	central_line	Staph_aureus	vancomycin	0.1	0.9	0.9	0.9	0	0.2	0.2	0	0.2	0.2	0	1	1	0	0.9	0	device_infection_panel	simulated	0	0	baseline
ABXCS006-TE-0002	S5	3	human_sim	central_line	Staph_aureus	vancomycin	0.9	0.9	0.72	0.5	0.22	0.45	0.3	0.15	0.55	0.3	0.25	1	1	0	0.35	0	device_infection_panel	simulated	0	0	first signal
ABXCS006-TE-0003	S5	4	human_sim	central_line	Staph_aureus	vancomycin	0.9	0.9	0.74	0.35	0.39	0.55	0.32	0.23	0.62	0.32	0.3	1	1	0	0.3	0	device_infection_panel	simulated	1	1	onset
ABXCS006-TE-0004	S5	7	human_sim	central_line	Staph_aureus	vancomycin	0.9	0.9	0.8	0.1	0.7	0.7	0.35	0.35	0.78	0.35	0.43	2	1	1	0.2	1	device_infection_panel	simulated	1	0	resistant later
ABXCS006-TE-0005	S6	0	human_sim	urinary_catheter	E_coli	ceftriaxone	0.1	0.8	0.8	0.8	0	0.2	0.2	0	0.2	0.2	0	0.25	0.25	0	0.9	0	device_infection_panel	simulated	0	0	baseline
ABXCS006-TE-0006	S6	3	human_sim	urinary_catheter	E_coli	ceftriaxone	0.9	0.8	0.9	0.45	0.45	0.22	0.22	0	0.22	0.22	0	0.25	0.25	0	0.3	0	device_infection_panel	simulated	0	0	one point burden spike
ABXCS006-TE-0007	S6	6	human_sim	urinary_catheter	E_coli	ceftriaxone	0.9	0.8	0.1	0.1	0	0.2	0.2	0	0.2	0.2	0	0.25	0.25	0	0.83	0	device_infection_panel	simulated	0	0	recovery
ABXCS006-TE-0008	S7	4	human_sim	central_line	Staph_aureus	vancomycin	0.3	0.9	0.74	0.35	0.39	0.55	0.32	0.23	0.62	0.32	0.3	1	1	0	0.3	1	device_infection_panel	simulated	0	0	exposure low ignore
ABXCS006-TE-0009	S8	4	human_sim	central_line	Staph_aureus	vancomycin	0.9	0.3	0.74	0.35	0.39	0.55	0.32	0.23	0.62	0.32	0.3	1	1	0	0.3	1	device_infection_panel	simulated	0	0	severity low ignore
ABXCS006-TE-0010	S9	0	human_sim	prosthetic_joint	Staph_epidermidis	rifampin_combo	0.9	0.9	0.9	0.9	0	0.2	0.2	0	0.2	0.2	0	0.5	0.5	0	0.9	1	device_infection_panel	simulated	0	0	baseline only

ABX-CS-006 Device-Associated Infection Persistence

Purpose

Detect device infection persistence and predictable resistance pattern formation driven by biofilm and rising tolerance before MIC shift.

Core pattern

severity_index high
abx_exposure_index high
device_coherence_index drops
burden_persistence_vs_expected stays high
biofilm_rise_vs_expected stays high
tolerance_rise_vs_expected stays high
later_device_removal_or_persistent_positive_or_resistant_isolate_flag appears

Files

data/train.csv
data/test.csv
scorer.py

Schema

Each row is one timepoint in a within series device infection course.

Required columns

row_id
series_id
day
host_model
device_type
organism
abx_drug
abx_exposure_index
severity_index
device_site_burden_index
expected_burden_index
burden_persistence_vs_expected
biofilm_activity_index
expected_biofilm_activity_index
biofilm_rise_vs_expected
tolerance_index
expected_tolerance_index
tolerance_rise_vs_expected
mic_mg_L
expected_mic_mg_L
mic_rise_vs_expected
device_coherence_index
later_device_removal_or_persistent_positive_or_resistant_isolate_flag
assay_method
source_type
device_infection_persistence_signal
earliest_device_infection_persistence

Labels

device_infection_persistence_signal
- 1 for rows at or after first confirmed persistence onset
earliest_device_infection_persistence
- 1 only for the first onset row in that series

Scorer logic in v1

candidate onset point
- abx_exposure_index at least 0.80
- severity_index at least 0.80
- device_coherence_index at most 0.40
- burden_persistence_vs_expected at least 0.20
- biofilm_rise_vs_expected at least 0.15
- tolerance_rise_vs_expected at least 0.20
- for two consecutive points
- ignore one point burden spike then recovery
confirmation
- later_device_removal_or_persistent_positive_or_resistant_isolate_flag equals 1 later in series

Evaluation

Run

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

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14.9 kB

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