The document discusses shortcomings of traditional statistical analysis of molecular biomarker data and advocates for a biology-driven approach. It proposes building active knowledge repositories focused on specific diseases or areas by extracting relevant molecular entities and pathways from databases, literature mining, and integrating experimental molecular profiling data. The repositories would parameterize biological relationships to form statistical models and generate hypotheses to guide biomarker study design and drive multivariate data analysis in a hypothesis-testing framework.