Transformers Are Born Biased: Structural Inductive Biases at Random Initialization and Their Practical Consequences

Abstract: Transformers underpin modern LLMs and are commonly assumed to be behaviorally unstructured at random initialization, with all meaningful preferences emerging only through large-scale training. We challenge this assumption by showing that randomly initialized transformers already exhibit strong and systematic structural biases. In particular, untrained models display extreme token preferences: across random input sequences, certain tokens are predicted with probabilities orders of magnitude larger. We provide a mechanistic explanation for this phenomenon by dissecting the transformer architecture at initialization. We show that extreme token preference arises from a contraction of token representations along a random seed-dependent direction. This contraction is driven by two interacting forces: (i) asymmetric nonlinear activations in MLP sublayers induce global (inter-sequence) representation concentration, and (ii) self-attention further amplifies this effect through local (intra-sequence) aggregation. Together, these mechanisms align hidden representations along a direction determined solely by the random initialization, producing highly non-uniform next-token predictions. Beyond mechanistic insight, we demonstrate that these initialization-induced biases persist throughout training, forming a stable and intrinsic model identity. Leveraging this property, we introduce SeedPrint, a fingerprinting method that can reliably distinguish models that differ only in their random initialization, even after extensive training and under substantial distribution shift. Finally, we identify a fundamental positional discrepancy inherent to the attention mechanism's intra-sequence contraction that is causally linked to the attention-sink phenomenon. This discovery provides a principled explanation for the emergence of sinks and offers a pathway for their control.