A Mechanistic Investigation of Supervised Fine Tuning

Low-Rank Adaptation (LoRA) has emerged as a widely adopted approach for adapting large language models, yet the internal representational changes induced by LoRA fine-tuning remain insufficiently understood. In this work, we investigate the geometry of LoRA-induced representations using Sparse Autoencoders (SAEs). We introduce a delta activation framework that isolates the adapter-specific contribution to the residual stream. Using Gemma-2-9B with LoRA ranks 4, 8, 16, and 32, we train adapter-specific SAEs across multiple transformer layers and compare their learned feature spaces with pretrained SAE dictionaries. We evaluate representational alignment using cosine similarity between decoder directions, principal-angle analysis of feature subspaces, and Centered Kernel Alignment (CKA) between activation representations. Across layers and ranks, we consistently observe comparatively weak geometric alignment between LoRA-induced feature dictionaries and pretrained SAE features. Adapter-specific SAEs also reconstruct delta activations more effectively than pretrained SAEs, suggesting that LoRA updates occupy partially distinct representational structure within the residual stream. Additionally, feature density increases with rank and depth, while geometric divergence remains relatively stable across ranks. These findings provide empirical evidence that LoRA fine-tuning can induce feature structures that are not fully captured by pretrained interpretability dictionaries, with implications for mechanistic interpretability, adaptation analysis, and safety auditing of fine-tuned language models.

Safety alignment in large language models can be fragile under fine-tuning, as even benign task adaptation may increase harmful compliance. Existing defenses mainly follow two directions: they either intervene during or after fine-tuning through retraining or weight modification, which can be costly and may hurt task performance, or they use model-agnostic safety classifiers, which may miss failures specific to a given fine-tuned checkpoint. These limitations motivate a post hoc, model-specific, and non-invasive approach to safety restoration. To meet these requirements, we propose HyperSafe, a framework that restores safety behavior by generating a model-specific Safe Side Network (SSN) for each fine-tuned checkpoint. HyperSafe uses layer-wise activation fingerprints to capture how fine-tuning changes the model's inner representations. With a small set of given calibration prompts, the hypernetwork maps these fingerprints to the parameters of the \ssn{} in a single forward pass. The generated \ssn{} runs alongside the frozen fine-tuned model and performs prompt-level safety classification: harmful prompts are routed to refusal, while safe prompts are answered by the original fine-tuned model. Thus, HyperSafe requires no gradient updates, no safety data at deployment time, and no modification to the deployed model weights. We evaluate HyperSafe on two model families, Qwen2-7B and LLaMA-3-8B, across multiple safety benchmarks. HyperSafe reduces harmful response rates from 19-31% to below 1% on every held-out checkpoint, while keeping downstream task accuracy within 1% of the fine-tuned baseline on average. Code is available at https://github.com/nokronim/project-safety-remedy.

Large language models have achieved remarkable capabilities across diverse tasks, yet their internal decision-making processes remain largely opaque, limiting our ability to inspect, control, and systematically improve them. This opacity motivates a growing body of research in mechanistic interpretability, with sparse autoencoders (SAEs) emerging as one of the most promising tools for decomposing model activations into sparse, interpretable feature representations. We introduce Qwen-Scope, an open-source suite of SAEs built on the Qwen model family, comprising 14 groups of SAEs across 7 model variants from the Qwen3 and Qwen3.5 series, covering both dense and mixture-of-expert architectures. Built on top of these SAEs, we show that SAEs can go beyond post-hoc analysis to serve as practical interfaces for model development along four directions: (i) inference-time steering, where SAE feature directions control language, concepts, and preferences without modifying model weights; (ii) evaluation analysis, where activated SAE features provide a representation-level proxy for benchmark redundancy and capability coverage; (iii) data-centric workflows, where SAE features support multilingual toxicity classification and safety-oriented data synthesis; and (iv) post-training optimization, where SAE-derived signals are incorporated into supervised fine-tuning and reinforcement learning objectives to mitigate undesirable behaviors such as code-switching and repetition. Together, these results demonstrate that SAEs can serve not only as post-hoc analysis tools, but also as reusable representation-level interfaces for diagnosing, controlling, evaluating, and improving large language models. By open-sourcing Qwen-Scope, we aim to support mechanistic research and accelerate practical workflows that connect model internals to downstream behavior.