Datasets:

ClarusC64
/

ABX-CS-010_icu_pharmacodynamics_collapse-v0.1

row_id string	series_id string	day int64	host_model string	icu_day_index int64	organism string	infection_site string	abx_drug string	exposure_index float64	expected_exposure_index float64	exposure_shortfall_vs_expected float64	severity_index float64	bacterial_burden_index float64	expected_burden_index float64	burden_persistence_vs_expected float64	lactate_mmol_L float64	expected_lactate_mmol_L float64	lactate_nonresponse_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	icu_pd_coherence_index float64	later_resistant_isolate_or_escalation_or_death_flag int64	assay_method string	source_type string	icu_pd_collapse_signal int64	earliest_icu_pd_collapse int64	notes string
ABXCS010-TR-0001	S1	0	human_sim	1	P_aeruginosa	ventilator_pneumonia	meropenem	0.1	0.1	0	0.95	0.9	0.9	0	4.2	4.2	0	0.2	0.2	0	1	1	0	0.9	0	icu_pd_panel	simulated	0	0	baseline
ABXCS010-TR-0002	S1	1	human_sim	2	P_aeruginosa	ventilator_pneumonia	meropenem	0.9	0.9	0	0.95	0.7	0.7	0	3.6	3.6	0	0.25	0.25	0	1	1	0	0.86	0	icu_pd_panel	simulated	0	0	tracks expected
ABXCS010-TR-0003	S1	2	human_sim	3	P_aeruginosa	ventilator_pneumonia	meropenem	0.9	0.9	0	0.95	0.72	0.5	0.22	3.5	3	0.5	0.55	0.3	0.25	1	1	0	0.35	0	icu_pd_panel	simulated	0	0	first collapse signal
ABXCS010-TR-0004	S1	3	human_sim	4	P_aeruginosa	ventilator_pneumonia	meropenem	0.9	0.9	0	0.95	0.75	0.35	0.4	3.6	2.6	1	0.62	0.32	0.3	1	1	0	0.3	0	icu_pd_panel	simulated	1	1	onset
ABXCS010-TR-0005	S1	5	human_sim	6	P_aeruginosa	ventilator_pneumonia	meropenem	0.9	0.9	0	0.95	0.8	0.1	0.7	4	2	2	0.78	0.35	0.43	4	1	3	0.2	1	icu_pd_panel	simulated	1	0	later resistant or escalation
ABXCS010-TR-0006	S2	0	human_sim	1	E_coli	urosepsis	piperacillin_tazobactam	0.1	0.1	0	0.85	0.8	0.8	0	3	3	0	0.2	0.2	0	0.25	0.25	0	0.9	0	icu_pd_panel	simulated	0	0	baseline
ABXCS010-TR-0007	S2	2	human_sim	3	E_coli	urosepsis	piperacillin_tazobactam	0.9	0.9	0	0.85	0.3	0.4	-0.1	1.8	2	-0.2	0.22	0.22	0	0.25	0.25	0	0.84	0	icu_pd_panel	simulated	0	0	improves
ABXCS010-TR-0008	S2	4	human_sim	5	E_coli	urosepsis	piperacillin_tazobactam	0.9	0.9	0	0.85	0.1	0.1	0	1.2	1.2	0	0.2	0.2	0	0.25	0.25	0	0.83	0	icu_pd_panel	simulated	0	0	resolves
ABXCS010-TR-0009	S3	0	human_sim	1	K_pneumoniae	abdominal_sepsis	meropenem	0.9	0.9	0	0.95	0.9	0.9	0	4.2	4.2	0	0.2	0.2	0	1	1	0	0.9	1	icu_pd_panel	simulated	0	0	baseline only
ABXCS010-TR-0010	S4	3	human_sim	4	P_aeruginosa	ventilator_pneumonia	meropenem	0.3	0.9	0.6	0.95	0.75	0.35	0.4	3.6	2.6	1	0.62	0.32	0.3	1	1	0	0.3	1	icu_pd_panel	simulated	0	0	exposure low ignore

ABX-CS-010 ICU Pharmacodynamics Collapse

Purpose

Detect early ICU pharmacodynamics collapse when exposure looks adequate but response fails and tolerance rises before MIC shift, leading to resistance emergence patterns.

Core pattern

severity_index high
exposure_index adequate
icu_pd_coherence_index drops
burden_persistence_vs_expected stays high
lactate_nonresponse_vs_expected stays high
tolerance_rise_vs_expected stays high
later_resistant_isolate_or_escalation_or_death_flag appears

Files

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

Schema

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

Required columns

row_id
series_id
day
host_model
icu_day_index
organism
infection_site
abx_drug
exposure_index
expected_exposure_index
exposure_shortfall_vs_expected
severity_index
bacterial_burden_index
expected_burden_index
burden_persistence_vs_expected
lactate_mmol_L
expected_lactate_mmol_L
lactate_nonresponse_vs_expected
tolerance_index
expected_tolerance_index
tolerance_rise_vs_expected
mic_mg_L
expected_mic_mg_L
mic_rise_vs_expected
icu_pd_coherence_index
later_resistant_isolate_or_escalation_or_death_flag
assay_method
source_type
icu_pd_collapse_signal
earliest_icu_pd_collapse

Labels

icu_pd_collapse_signal
- 1 for rows at or after first confirmed collapse onset
earliest_icu_pd_collapse
- 1 only for the first onset row in that series

Scorer logic in v1

candidate onset point
- severity_index at least 0.85
- exposure_index at least 0.80
- icu_pd_coherence_index at most 0.40
- burden_persistence_vs_expected at least 0.20
- lactate_nonresponse_vs_expected at least 0.70
- tolerance_rise_vs_expected at least 0.20
- for two consecutive points
- ignore one point lactate spike then return to expected
confirmation
- later_resistant_isolate_or_escalation_or_death_flag equals 1 later in series

Evaluation

Run

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

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Number of rows:

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18.4 kB