PairAlign: A Framework for Sequence Tokenization via Self-Alignment with Applications to Audio Tokenization

Many operations on sensory data -- comparison, memory, retrieval, and reasoning -- are naturally expressed over discrete symbolic structures. In language this interface is given by tokens; in audio, it must be learned. Existing audio tokenizers rely on quantization, clustering, or codec reconstruction, assigning tokens locally, so sequence consistency, compactness, length control, termination, and edit similarity are rarely optimized directly. We introduce PairAlign, a framework for compact audio tokenization through sequence-level self-alignment. PairAlign treats tokenization as conditional sequence generation: an encoder maps speech to a continuous condition, and an autoregressive decoder generates tokens from BOS, learning token identity, order, length, and EOS placement. Given two content-preserving views, each view's sequence is trained to be likely under the other's representation, while unrelated examples provide competing sequences. This gives a scalable surrogate for edit-distance preservation while discouraging many-to-one collapse. PairAlign starts from VQ-style tokenization and refines it with EMA-teacher targets, cross-paired teacher forcing, prefix corruption, likelihood contrast, and length control. On 3-second speech, PairAlign learns compact, non-degenerate sequences with broad vocabulary usage and strong cross-view consistency. On TIMIT retrieval, it preserves edit-distance search while reducing archive token count by 55%. A continuous-sweep probe shows lower local overlap than a dense geometric tokenizer, but stronger length control and bounded edit trajectories under 100 ms shifts. PairAlign is a sequence-symbolic predictive learner: like JEPA-style objectives, it predicts an abstract target from another view as a learned variable-length symbolic sequence, not a continuous latent.