Where Decoder Cosine Similarity Fails for SAE Feature Flow Discovery

Foundation models are increasingly adapted through fine-tuning, model editing, and alignment procedures while retaining previously acquired capabilities. Understanding the internal computations that support these adaptations is therefore becoming increasingly important for continual model evolution. Sparse autoencoders (SAEs) provide interpretable feature dictionaries for residual-stream activations and sublayer outputs, but it remains unclear how state features and update features interact to produce downstream residual features. In this work, we focus on MLP updates as a first test case. We construct a transition atlas of triples sk + uj rightarrow tℓ, where a residual-state feature and an MLP-update feature jointly predict a target residual feature, and validate candidate triples by ablating the decoded update feature. In a 20M-token Pythia-160M L7 rightarrow L8 run, we find 38,125 strong ablation-effect transitions, but 88.0% have both state-target and update-target decoder cosine similarity below 0.7. As a preliminary cross-model check, a run of 20M-token Gemma-3-4B L21 rightarrow L22 causally validates only the top 30,000 ranked candidate triples by ablating the decoded update feature, and 53.6% of strong-effect triples have both state-target and update-target decoder cosine similarity below 0.7. The Gemma result is directionally consistent with Pythia, but weaker, since update-target cosine recovers many of the strongest Gemma effects and the run is not a full-atlas causal validation. Ultimately, our results suggest that feature flow atlases can serve as diagnostics of representation-update mechanisms and thereby inform tools for steering model updates. Future work will validate more complex patterns across layers, models, and SAE families.