Datasets:
row_id string | series_id string | day int64 | host_model string | abx_drug string | abx_exposure_index float64 | host_stress_index float64 | symptom_score int64 | expected_symptom_score int64 | symptom_nonresponse_vs_expected int64 | urine_culture_cfu_mL int64 | expected_urine_cfu_mL int64 | urine_cfu_persistence_vs_expected int64 | urine_leukocyte_esterase int64 | expected_leukocyte_esterase int64 | le_nonresponse_vs_expected int64 | uti_coherence_index float64 | later_uti_recurrence_flag int64 | assay_method string | source_type string | uti_recurrence_risk_signal int64 | earliest_uti_recurrence_risk int64 | notes string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ABXCS003-TR-0001 | S1 | 0 | human_sim | nitrofurantoin | 0.1 | 0.2 | 8 | 8 | 0 | 100,000 | 100,000 | 0 | 3 | 3 | 0 | 0.9 | 0 | urine_panel | simulated | 0 | 0 | baseline |
ABXCS003-TR-0002 | S1 | 2 | human_sim | nitrofurantoin | 0.9 | 0.9 | 5 | 5 | 0 | 12,000 | 15,000 | -3,000 | 2 | 2 | 0 | 0.86 | 0 | urine_panel | simulated | 0 | 0 | tracks expected |
ABXCS003-TR-0003 | S1 | 3 | human_sim | nitrofurantoin | 0.9 | 0.9 | 5 | 3 | 2 | 20,000 | 5,000 | 15,000 | 2 | 1 | 1 | 0.35 | 0 | urine_panel | simulated | 0 | 0 | first coherence loss |
ABXCS003-TR-0004 | S1 | 4 | human_sim | nitrofurantoin | 0.9 | 0.9 | 5 | 2 | 3 | 18,000 | 1,500 | 16,500 | 2 | 1 | 1 | 0.3 | 0 | urine_panel | simulated | 1 | 1 | onset |
ABXCS003-TR-0005 | S1 | 14 | human_sim | nitrofurantoin | 0.9 | 0.9 | 6 | 0 | 6 | 80,000 | 0 | 80,000 | 3 | 0 | 3 | 0.2 | 1 | urine_panel | simulated | 1 | 0 | recurrence later |
ABXCS003-TR-0006 | S2 | 0 | human_sim | trimethoprim | 0.1 | 0.2 | 7 | 7 | 0 | 80,000 | 80,000 | 0 | 3 | 3 | 0 | 0.9 | 0 | urine_panel | simulated | 0 | 0 | baseline |
ABXCS003-TR-0007 | S2 | 3 | human_sim | trimethoprim | 0.9 | 0.8 | 2 | 2 | 0 | 1,000 | 1,500 | -500 | 0 | 1 | -1 | 0.84 | 0 | urine_panel | simulated | 0 | 0 | clearing |
ABXCS003-TR-0008 | S2 | 7 | human_sim | trimethoprim | 0.9 | 0.8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.83 | 0 | urine_panel | simulated | 0 | 0 | resolved |
ABXCS003-TR-0009 | S3 | 0 | human_sim | nitrofurantoin | 0.9 | 0.9 | 1 | 1 | 0 | 100,000 | 100,000 | 0 | 3 | 3 | 0 | 0.9 | 1 | urine_panel | simulated | 0 | 0 | symptoms low baseline |
ABXCS003-TR-0010 | S4 | 4 | human_sim | nitrofurantoin | 0.3 | 0.9 | 5 | 2 | 3 | 18,000 | 1,500 | 16,500 | 2 | 1 | 1 | 0.3 | 1 | urine_panel | simulated | 0 | 0 | exposure low |
ABX-CS-003 UTI Recurrence Prediction
Purpose
Predict UTI recurrence from early coherence loss during treatment.
Core pattern
- host_stress_index high
- abx_exposure_index high
- uti_coherence_index drops
- urine_cfu_persistence_vs_expected stays high
- symptom_nonresponse_vs_expected stays high
- later_uti_recurrence_flag appears
Files
- data/train.csv
- data/test.csv
- scorer.py
Schema
Each row is one timepoint in a within series UTI course.
Required columns
- row_id
- series_id
- day
- host_model
- abx_drug
- abx_exposure_index
- host_stress_index
- symptom_score
- expected_symptom_score
- symptom_nonresponse_vs_expected
- urine_culture_cfu_mL
- expected_urine_cfu_mL
- urine_cfu_persistence_vs_expected
- urine_leukocyte_esterase
- expected_leukocyte_esterase
- le_nonresponse_vs_expected
- uti_coherence_index
- later_uti_recurrence_flag
- assay_method
- source_type
- uti_recurrence_risk_signal
- earliest_uti_recurrence_risk
Labels
uti_recurrence_risk_signal
- 1 for rows at or after first confirmed risk onset
earliest_uti_recurrence_risk
- 1 only for the first onset row in that series
Scorer logic in v1
- exclude series where baseline symptoms are already low
- candidate onset point
- abx_exposure_index at least 0.80
- host_stress_index at least 0.80
- uti_coherence_index at most 0.40
- urine_cfu_persistence_vs_expected at least 12000
- symptom_nonresponse_vs_expected at least 2.0
- for two consecutive points
- ignore one point contamination spike then clean
- confirmation
- later_uti_recurrence_flag equals 1 later in series
Evaluation
Run
- python scorer.py --path data/test.csv
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