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Protein biomarkers can be used to characterize symptom classes, which describe the metabolic or immunodeficient state of patients during the progression of a specific disease. Recent literature has shown that machine learning methods can complement traditional clinical methods in identifying biomarkers. However, many machine learning frameworks only apply narrowly to a specific archetype or subset of diseases. In this paper, we propose a feature extractor which can discover protein biomarkers for a wide variety of classification problems. The feature extractor uses a special type of deep learning model, which discovers a latent space that allows for optimal class separation and enhanced class cluster identity. The extracted biomarkers can then be used to train highly accurate supervised learning models. We apply our methods to a dataset involving COVID-19 patients and another involving scleroderma patients, to demonstrate improved class separation and reduced false discovery rates compared to results obtained using traditional models., Competing Interests: The authors declare no competing interests., (© 2023 The Authors.)