Stability-Based Machine Learning Identifies a Minimal Two-Protein Serum Signature for Early Silicosis

Background: The early diagnosis of silicosis, an irreversible fibrotic lung disease, is challenged by the low sensitivity of current radiological methods in early-stage disease and their susceptibility to interobserver variability. Consequently, a pressing need exists for noninvasive, objective biomarkers to facilitate timely detection and intervention. Methods: We employed a multistage study design comprising a discovery cohort (57 Stage I silicosis patients, 57 matched controls) and an independent, unmatched validation cohort (40 patients, 40 controls). Serum protein profiles were generated using Olink targeted proteomics. We utilized a rigorous, stability-based machine learning framework, which integrated Lasso, Random Forest, and SVM-RFE algorithms over 100 iterations, to perform feature selection and identify a robust biomarker signature from the discovery cohort. Based on the selected features, a logistic regression model was subsequently constructed, and its performance was evaluated using both internal and external validation. Results: Our discovery strategy identified a two-protein signature comprising IL8 and CCL3. This signature demonstrated excellent diagnostic performance in the discovery cohort, achieving a cross-validation AUC of 0.986 (95% CI: 0.975–1.000). Importantly, the model’s robustness was confirmed in the heterogeneous validation cohort, where it achieved an outstanding AUC of 0.973 (95% CI: 0.936–1.000), with 95.0% specificity and 77.5% sensitivity. Bioinformatic analysis revealed that decreased serum levels of IL8 and CCL3 were associated with silicosis, providing novel diagnostic biomarkers and highlighting a complex, paradoxical shift in circulating chemokines during early-stage disease.