Datasets:
row_id string | series_id string | day int64 | host_model string | abx_drug string | plasma_conc_mg_L float64 | expected_plasma_conc_mg_L float64 | plasma_conc_deviation float64 | abscess_conc_mg_L float64 | expected_abscess_conc_mg_L float64 | abscess_conc_deviation float64 | abscess_to_plasma_ratio float64 | expected_abscess_to_plasma_ratio float64 | ratio_drop_vs_expected float64 | crp_mg_L int64 | expected_crp_mg_L int64 | crp_nonresponse_vs_expected int64 | abx_exposure_index float64 | severity_index float64 | iaai_coherence_index float64 | later_source_control_or_persistent_abscess_flag int64 | assay_method string | source_type string | iaai_failure_signal int64 | earliest_iaai_failure int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXCS004-TR-0001 | S1 | 0 | human_sim | piperacillin_tazobactam | 30 | 30 | 0 | 6 | 6 | 0 | 0.2 | 0.2 | 0 | 220 | 220 | 0 | 0.1 | 0.9 | 0.9 | 0 | abscess_pk_inflammation_panel | simulated | 0 | 0 | baseline |
ABXCS004-TR-0002 | S1 | 1 | human_sim | piperacillin_tazobactam | 31 | 30.5 | 0.5 | 6 | 6.1 | -0.1 | 0.19 | 0.2 | 0.01 | 180 | 185 | -5 | 0.9 | 0.9 | 0.86 | 0 | abscess_pk_inflammation_panel | simulated | 0 | 0 | tracks expected |
ABXCS004-TR-0003 | S1 | 2 | human_sim | piperacillin_tazobactam | 30.5 | 30.2 | 0.3 | 3 | 6 | -3 | 0.1 | 0.2 | 0.1 | 175 | 150 | 25 | 0.9 | 0.9 | 0.35 | 0 | abscess_pk_inflammation_panel | simulated | 0 | 0 | first penetration loss |
ABXCS004-TR-0004 | S1 | 3 | human_sim | piperacillin_tazobactam | 30.2 | 30 | 0.2 | 2.8 | 5.9 | -3.1 | 0.09 | 0.2 | 0.11 | 170 | 130 | 40 | 0.9 | 0.9 | 0.3 | 0 | abscess_pk_inflammation_panel | simulated | 1 | 1 | onset |
ABXCS004-TR-0005 | S1 | 5 | human_sim | piperacillin_tazobactam | 30 | 29.8 | 0.2 | 2 | 5.6 | -3.6 | 0.07 | 0.19 | 0.12 | 190 | 90 | 100 | 0.9 | 0.9 | 0.2 | 1 | abscess_pk_inflammation_panel | simulated | 1 | 0 | source control later |
ABXCS004-TR-0006 | S2 | 0 | human_sim | ertapenem | 25 | 25 | 0 | 5 | 5 | 0 | 0.2 | 0.2 | 0 | 160 | 160 | 0 | 0.1 | 0.8 | 0.9 | 0 | abscess_pk_inflammation_panel | simulated | 0 | 0 | baseline |
ABXCS004-TR-0007 | S2 | 2 | human_sim | ertapenem | 25.5 | 25.2 | 0.3 | 5.2 | 5.1 | 0.1 | 0.2 | 0.2 | 0 | 120 | 120 | 0 | 0.9 | 0.8 | 0.84 | 0 | abscess_pk_inflammation_panel | simulated | 0 | 0 | improves |
ABXCS004-TR-0008 | S2 | 4 | human_sim | ertapenem | 25.2 | 25 | 0.2 | 5 | 5 | 0 | 0.2 | 0.2 | 0 | 70 | 70 | 0 | 0.9 | 0.8 | 0.83 | 0 | abscess_pk_inflammation_panel | simulated | 0 | 0 | resolves |
ABXCS004-TR-0009 | S3 | 0 | human_sim | piperacillin_tazobactam | 30 | 30 | 0 | 6 | 6 | 0 | 0.2 | 0.2 | 0 | 220 | 220 | 0 | 0.9 | 0.9 | 0.9 | 1 | abscess_pk_inflammation_panel | simulated | 0 | 0 | no failure shown |
ABXCS004-TR-0010 | S4 | 3 | human_sim | piperacillin_tazobactam | 30.2 | 30 | 0.2 | 2.8 | 5.9 | -3.1 | 0.09 | 0.2 | 0.11 | 170 | 130 | 40 | 0.9 | 0.3 | 0.3 | 1 | abscess_pk_inflammation_panel | simulated | 0 | 0 | severity low |
ABX-CS-004 Intra-abdominal Infection Failure
Purpose
Detect abscess penetration failure when abscess exposure stops tracking systemic exposure and clinical inflammation fails to improve.
Core pattern
- severity_index high
- abx_exposure_index high
- iaai_coherence_index drops
- ratio_drop_vs_expected stays high
- crp_nonresponse_vs_expected stays high
- later_source_control_or_persistent_abscess_flag appears
Files
- data/train.csv
- data/test.csv
- scorer.py
Schema
Each row is one timepoint in a within series intra-abdominal infection course.
Required columns
- row_id
- series_id
- day
- host_model
- abx_drug
- plasma_conc_mg_L
- expected_plasma_conc_mg_L
- plasma_conc_deviation
- abscess_conc_mg_L
- expected_abscess_conc_mg_L
- abscess_conc_deviation
- abscess_to_plasma_ratio
- expected_abscess_to_plasma_ratio
- ratio_drop_vs_expected
- crp_mg_L
- expected_crp_mg_L
- crp_nonresponse_vs_expected
- abx_exposure_index
- severity_index
- iaai_coherence_index
- later_source_control_or_persistent_abscess_flag
- assay_method
- source_type
- iaai_failure_signal
- earliest_iaai_failure
Labels
iaai_failure_signal
- 1 for rows at or after first confirmed failure onset
earliest_iaai_failure
- 1 only for the first onset row in that series
Scorer logic in v1
- require abscess measurement in series
- candidate onset point
- abx_exposure_index at least 0.80
- severity_index at least 0.80
- iaai_coherence_index at most 0.40
- ratio_drop_vs_expected at least 0.08
- crp_nonresponse_vs_expected at least 30
- for two consecutive points
- ignore one point abscess sample artifact then recovery
- confirmation
- later_source_control_or_persistent_abscess_flag equals 1 later in series
Evaluation
Run
- python scorer.py --path data/test.csv
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