Certain aspects of the disclosure provide systems and methods for diagnosing and treating chronic liver disease and portal vein thrombosis. In particular, methods may include measuring levels of one or more proteins, including factor V, factor VIII, protein C, protein S, D-dimer, sP-selectin, or asTF in a biological sample from a subject and determining a CLD score based on the levels of the one or more proteins, whereby, a CLD stage may be determined based on the CLD score. In some aspects, methods may include determining a PVT score based on levels of the one or more proteins in the biological sample. In some aspects, methods further include treating CLD and/or PVT.