formalization-pipeline

What problem does it solve?

Convert qualitative ME/CFS pathophysiology prose into rigorous, evidence-linked formal models (causal DAGs, EPC event chains, and ODE-ready quantitative models) with explicit uncertainty quantification so researchers and clinicians can evaluate, compare, and derive testable predictions without manual synthesis.

Core Features & Use Cases

• Evidence extraction & inventory: harvest causal claims, citations, sample sizes, effect sizes, and assign overall certainty scores for each claim.
• Causal DAG construction: generate weighted DAGs with feedback-loop detection, contradiction reports, and TikZ/LaTeX figures for manuscript inclusion.
• EPC & ODE readiness: build EPC event chains with detection criteria and timings, and prepare ODE parameter files when quantitative data permit.
• Validation & integration: run consistency and sensitivity checks, produce validation reports, and integrate models and annotated prose into the main document.
• Use case: formalize the PEM cascade from Part 2 into a DAG + EPC at level 2 to produce diagrams, evidence YAML, and a narrative summary for chapter integration.

Quick Start

Run the formalization-pipeline for "PEM cascade" at level 2 to produce an evidence inventory, a weighted causal DAG, and EPC summaries ready for document integration.