Survival analysis

Survival analysis connects molecular features to clinical outcomes — Kaplan-Meier curves, log-rank testing, multivariate Cox regression, and longitudinal molecular trajectories.

Uses the lifelines library for Kaplan-Meier estimation, log-rank tests, and Cox proportional hazards regression.

Prerequisites

Clinical CSV with patient_id, time_to_event_days, and event_observed columns
Optional feature CSV with molecular variables for stratification and Cox covariates
Optional longitudinal CSV for treatment timepoint trajectories

Launching the pipeline

Open the study Survival page or dispatch via API:

curl -X POST http://localhost:8001/oncology/jobs/survival \
  -H "Content-Type: application/json" \
  -d '{
    "study_id": "your-study-id",
    "parameters": {
      "clinical_path": "/path/to/clinical.csv",
      "feature_path": "/path/to/features.csv",
      "longitudinal_path": "/path/to/longitudinal.csv",
      "stratify_by": "treatment_arm",
      "cox_covariates": ["tmb", "cd8_score"]
    }
  }'

Key parameters

Parameter	Default	Purpose
`clinical_path`	—	Patient survival table
`feature_path`	—	Molecular features for stratification and Cox models
`longitudinal_path`	—	Timepoint feature trajectories
`stratify_by`	—	Column for Kaplan-Meier group stratification
`cox_covariates`	[]	Columns included in multivariate Cox regression

Outputs

Output	Description
`kaplan_meier`	Survival curve data per stratification group
`logrank`	Log-rank test statistic and p-value
`cox_regression`	Hazard ratios, confidence intervals, and p-values per covariate
`longitudinal`	Feature trajectory summaries across timepoints

The frontend Survival page renders Kaplan-Meier curves with log-rank p-values and Cox regression tables.

Typical use cases

Compare overall survival between treatment arms
Stratify survival by TMB, immune phenotype, or gene signature score
Test whether molecular features independently predict outcome in multivariate Cox models
Track CD8 score or other biomarkers across baseline and on-treatment timepoints

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