The phase manifold should be approximated circle rather than ellipse which is your plotting function not set to ax.axis('equal'). https://github.com/sebastianstarke/AI4Animation/blob/8f3c418a46647a3c29a3c3d2e6ec03115c42c702/AI4Animation/SIGGRAPH_2022/PyTorch/PAE/Plotting.py#L32