Preference alignment has substantially improved the observable behavior of large language models, yet it remains unclear what alignment changes internally. Aligned systems still fail under jailbreaks, prompt injection, and retrieval-time corruption, suggesting behavior-level evaluation alone is incomplete. Post-training should leave measurable traces in internal computation. We ask: when an instruction-tuned (IT) model becomes a preference-aligned (PA) model, what geometric structure changes, where do those changes concentrate, and how selectively do they vary across concepts, prompts, and model families? We introduce MENTIS, a geometry-first framework for measuring alignment-induced internal reorganization in paired checkpoints. MENTIS compares IT and PA models using a primary layerwise covariance-based torsion norm (T1), a secondary spectral torsion diagnostic (T2), and an Energy-Radiance-Activation measure (ERA) for depth localization. Across four 7-8B model pairs on LITMUS, our study reveals that alignment-induced change is selective rather than uniform: normative concepts exhibit larger torsion shifts than factual concepts on average; torsion is negatively correlated with contextual entropy; and peak effects localize to architecture-specific mid-to-late layers. The same pattern appears across word-level, prompt-level, and model-level analyses. These results suggest preference alignment leaves structured, depth-localized geometric signatures in internal computation beyond what behavior-level evaluation alone can reveal.
Post-training alignment algorithms are predominantly evaluated as black boxes, obscuring how they reshape language models' internal computations. We present a systematic mechanistic analysis of six preference-optimization methods: PPO, DPO, SimPO, ORPO, GRPO, and KTO across three open-weight model families. By integrating layer-wise linear probing, Sparse Autoencoders, and crosscoders, we localize preference representations and quantify alignment-induced geometric transformations in latent space. We find that preference signals consistently concentrate in early--mid or mid--late layers, but different objectives induce qualitatively distinct representational shifts. KTO and GRPO enhance linear separability through constructive feature sharing and sparse, high-salience recruitment. In contrast, DPO and ORPO degrade separability via non-constructive geometric rotation and feature attenuation, while PPO and SimPO largely preserve baseline geometry. These transformations exhibit architecture-dependent variability, demonstrating that behavioral alignment does not imply uniform internal restructuring. Our findings establish alignment as a heterogeneous intervention, motivate standardized feature-level auditing for safety and interpretability, and highlight the need for mechanism-aware optimization objectives.
Large language models are commonly aligned through supervised fine-tuning, yet little is known about how their internal representations evolve during this process. We study alignment dynamics using persistent homology by tracking the topology of activation spaces throughout fine-tuning. Across four transformer language models ranging from 1B to 7B parameters and three alignment objectives corresponding to helpful, harmless, and mixed training data, we find that the majority of topological reorganization occurs during the earliest stages of training. A dense checkpoint analysis reveals a transient peak in topological activity followed by rapid stabilization. We further show that different alignment objectives induce distinguishable topological trajectories, while instruction-tuned and pretrained models exhibit qualitatively different patterns of evolution. Our results suggest that persistent homology provides a complementary perspective on alignment, revealing representation-level changes that are not apparent from behavioral metrics alone.
Various language domains have undergone remarkable changes in recent years; these shifts are largely attributed to the advent of Large Language Models and their misalignment with natural language usage. These misalignments are thought to partly originate in the preference-learning stage, e.g. Reinforcement Learning from Human Feedback, which generally makes models more useful but simultaneously may introduce systematic lexical bias. In terms of lexical behavior, this is visible in a model's preference for certain formats or the overuse of words (delve, furthermore), even when such patterns are not present in base model outputs. Research on lexical misalignment induced during preference training is constrained by reliance on manual curation. We address this, by introducing the Triangulated Preference Shift score, a metric that triangulates between human gold standards, base models, and instruct variants to isolate shifts induced specifically by preference learning, without manual curation. We provide data across six model families, anchor the results in the literature, and illustrate the general approach's utility by analyzing whether preference learning shifts models toward what could be interpreted as a "language of prestige". The metric provides an initial automated method to quantify behavioral shifts attributable to preference tuning, and thus, may help inform model alignment and development of trustworthy AI.
Xiaoyang Ming, Jose Hernandez, Thomas Stephan Juzek