Longitudinal ophthalmic imaging analysis is an essential step for prognosis prediction in ophthalmic diseases. However, AI-assisted prognosis models are challenged by follow-up sequences, which tend to be sparse, irregularly sampled, and incomplete. Although advanced prognosis modeling methods, especially for the methods based on neural controlled differential equations (NCDEs), provide a principled continuous-time framework for sparse and irregular longitudinal data. Unfortunately, two major concerns remain unsolved in clinical follow-up modeling. First, the smooth latent dynamics of standard NCDEs is poorly matched to abrupt pathological changes induced by therapeutic intervention, lesion recurrence, or long follow-up gaps. Second, numerical integration over long horizons can accumulate errors, which will produce unstable latent trajectories and weakened class discrimination. To address these challenges, we propose ImProNCDE, an impulse-corrected NCDE framework with prototype learning for longitudinal ophthalmic prognosis prediction. To capture abrupt pathological changes beyond smooth latent dynamics, ImProNCDE introduces Residual Impulse Calibration (RIC), which injects residual-based impulse corrections at visit times and then recalibrates the latent state when observations deviate from continuous predictions. To further mitigate error accumulation over long horizons, we introduce a Prototype-guided Trajectory Stabilizer (PTS), which aims to attract latent trajectories toward learnable prognosis prototypes to reduce class overlap and which ultimately improves long-horizon stability. Experiments on multiple private and public longitudinal ophthalmic datasets (totalling over 1206 samples) show that ImProNCDE outperforms existing SOTA methods focusing on sequence modeling.

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