Life sciences · Preprint
arXiv · November 3, 2026
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Pervasive Capability Degradation (PCD) refers to the phenomenon in which supervised fine-tuning (SFT), while adapting a large language model (LLM) to a target task, often erodes the general capabilities acquired during pre-training. Prevailing explanations attribute PCD to macroscopic distribution shift and therefore lack microscopic manipulability, leaving existing mitigation methods without a complete theoretical foundation. In this paper, we first develop a bottom-up geometric theory of PCD grounded in feature interference under superposition: narrow-domain SFT data disrupt the almost-orthogonal feature structure formed during pre-training, and the resulting interference drives activations across decision hyperplanes in the output Laguerre-Voronoi geometry, flipping predictions on general tasks. This theory unifies existing methods into six paradigms and reveals both the source of their efficacy and their theoretical limits. We then prove that cross-entropy under one-hot supervision cannot resolve PCD on its own, and accordingly propose the AEGIS loss, which directly constrains the drift of activation margins along all competing token directions, thereby decoupling interference suppression from task adaptation. Across 3 model families and 14 SFT tasks, AEGIS outperforms representative methods of every paradigm on target tasks and pervasive capabilities simultaneously, at only about 1.3 times the computational cost of standard SFT. Its generality, scalability, and mechanistic interpretability offer a new perspective on fully resolving PCD.