Abstract: A method for diagnosing a subject with one or more of hepatocellular carcinoma (HCC), chronic liver disease, colorectal liver metastases (CRLM), and pulmonary hypertension is described. The method includes obtaining a breath sample from a subject, analyzing the breath sample obtained from the subject to determine one or more breath metabolite abundance values, inputting one or more of the breath metabolite abundance values into a machine-learning-model, and assigning a clinical parameter to the subject representing the likelihood that the subject has one or more of HCC, chronic liver disease, CRLM, and pulmonary hypertension.