SeqPE: Transformer With Sequential Position Encoding
Huayang Li, Yahui Liu, Hongyu Sun, Deng Cai, Leyang Cui, Wei Bi, Peilin Zhao, Taro Watanabe · IEEE Transactions on Pattern Analysis and Machine Intelligence · 2026
Since self-attention layers in Transformers are permutation invariant by design, positional encodings must be explicitly incorporated to enable spatial understanding. However, fixed-size lookup tables used in traditional learnable position embeddings (PEs) limit extrapolation capabilities beyond pre-trained sequence lengths. Expert-designed methods such as ALiBi and RoPE, mitigate this limitation but demand extensive modifications for adapting to new modalities, underscoring fundamental challenges in adaptability and scalability. In this work, we present SeqPE, a unified and fully learnable position encoding framework that represents each $n$ndimensional position index as a symbolic sequence and employs a lightweight sequential position encoder to learn their embeddings in an end-to-end manner. To regularize SeqPE's embedding space, we introduce two complementary objectives: a contrastive objective that aligns embedding distances with a predefined positiondistance function, and a knowledge distillation loss that anchors out-of-distribution position embeddings to in-distribution teacher representations, further enhancing extrapolation performance. Experiments across language modeling, longcontext question answering, and 2D image classification demonstrate that SeqPE not only surpasses strong baselines in perplexity, exact match (EM), and accuracy-particularly under context length extrapolation-but also enables seamless generalization to multi-dimensional inputs without requiring manual architectural redesign.