Abstract: The exemplified intrinsic phase space tomography methods and systems facilitate the analysis and evaluation of complex, quasi-periodic system by generating computed phase-space tomographic images as a representation of the dynamics of the quasi-periodic cardiac systems. The computed phase-space tomographic images can be presented to a physician to assist in the assessment of presence or non-presence of disease. In some embodiments, the phase space tomographic images are used as input to a trained neural network classifier configured to assess for presence or non-presence of significant coronary artery disease.