A Layer-wise Analysis of Supervised Fine-Tuning

The cosine similarity between a large language model's hidden activations before and after Supervised Fine-Tuning (SFT) remains very high. This, at first glance, suggests that SFT leaves the model's activation geometry largely undisturbed. However, projecting both sets of activations through a Sparse Autoencoder (SAE) pretrained on the base model reveals that the underlying sparse latents diverge significantly. We introduce a novel investigative pipeline which utilizes these pretrained SAEs as a high-resolution diagnostic tool to mechanistically investigate the drivers of this representational divergence. Through our analytical pipeline, we discover task-specific and layer-specific distributions of the precise semantic features that are systematically altered during supervised fine-tuning. We additionally identify a layer-wise update profile specific to safety alignment. All code, experimental scripts, and analysis files associated with this work are publicly available at: https://github.com/ruhzi/sae-investigation.

Supervised fine-tuning (SFT) is a common first stage of LLM post-training, teaching the model to follow instructions and shaping its behavior as a helpful assistant. At the same time, SFT may harm the fundamental capabilities of an LLM, particularly after long pretraining: a phenomenon known as catastrophic overtraining (Springer et al., 2025). To understand overtraining, we first investigate catastrophic forgetting in finetuning through the lens of implicit regularization of the learning rate. For models trained to the same SFT loss, we identify how the learning rate mediates optimization: finetuning with large and small steps converges to qualitatively different models. Next, we link forgetting to overtraining: learning rate decay increases the sharpness of the pretrained model, which in turn exacerbates catastrophic forgetting during SFT, leading to overtraining. Our findings paint a picture of the overtraining mechanism in LLMs and broadly contribute to the understanding of the interplay between optimization dynamics during pretraining and finetuning.

Every supervised fine-tuning run forces the same chain of decisions, such as learning rate, batch size, LoRA or full fine-tuning, how many epochs, which optimiser, and what data to feed the model. Each of these is typically rediscovered from scratch for every new model and dataset. Here we measure them under one instrument: a sweep that varies one lever at a time, and spans dense and mixture-of-experts models in two families (Qwen3 and Llama), on four real-world customer SFT datasets, for both LoRA and full fine-tuning. These datasets give a controlled testbed: each task carries an evaluation built with the customer, and its training data is produced by iterative supervised fine-tuning that refines model outputs until they pass that evaluation, so the supervised target is internally consistent and the task judge we report against is the criterion the data was built to satisfy. We ask how the optimal learning rate and batch size move with model scale, family, and data, and whether one selection rule transfers across them; what LoRA trades against full fine-tuning, and how its rank and alpha set what the adapter can learn; whether validation loss (or other metrics, such as loss landscape flatness) faithfully ranks downstream quality; whether post-training gains scale with model size and data volume, on a model ladder extended through mixtures-of-experts to 235B parameters; how many epochs to train before general instruction-following erodes; and whether a geometry-aware optimiser improves on AdamW. Each recommendation is paired with a measure of its uncertainty.