Breaking the Block: Preserving Data Continuity to Train Superior SAEs for Instruct Models

Sparse Autoencoders (SAEs) are a cornerstone of mechanistic interpretability. Existing training methods inherit the Block Training paradigm from LLM pre-training, which introduces destructive gradient noise in instruct models due to attention leakage from unrelated contexts. Using GSNR analysis, we theoretically characterize this issue and propose Finetuning-aligned Sequential Training (FAST), a sequential training paradigm specifically designed for instruct models. FAST aligns SAE training with the data distribution and activation patterns of instruct models, substantially improving both reconstruction fidelity and feature interpretability. Experimental results show that FAST achieves higher GSNR, a significantly lower log-scaled MSE of 0.6468 compared to the baseline's 5.1985, and a near-zero Delta Loss (-0.51% to 0.37%). Moreover, on Llama-3.2-3B-it, FAST produces 21.1% high-quality features, substantially outperforming baseline methods that achieve 7.0% and 10.2%. We further find that intervening on special token activations through SAEs can improve generation quality, revealing new opportunities for fine-grained control. Our codes are available as open source at https://github.com/Geaming2002/FAST.