2025/08/08 by Jonas S. Almeida, Almeida, Jonas S, D. Russ +15
Biochemistry, Genetics and Molecular Biology · Materials Science · Social Sciences · #Artificial Intelligence (cs.AI) #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Mathematics #Fractal and DNA sequence analysis #Language and cultural evolution #Machine Learning (cs.LG) #Numerical Analysis (math.NA) #Quantitative Methods (q-bio.QM) #Quasicrystal Structures and Properties
paper · pdf · doi:10.48550/arxiv.2508.06641
openalex publication_date 2025/08/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Motivation: With the advent of Language Models using Transformers, popularized by ChatGPT, there is a renewed interest in exploring encoding procedures that numerically represent symbolic sequences at multiple scales and embedding dimensions. The challenge that encoding addresses is the need for mechanisms that uniquely retain contextual information about the succession of individual symbols, which can then be modeled by nonlinear formulations such as neural networks. Context: Universal Sequence Maps(USM) are iterated functions that bijectively encode symbolic sequences onto embedded numerical spaces. USM is composed of two Chaos Game Representations (CGR), iterated forwardly and backwardly, that can be projected into the frequency domain (FCGR). The corresponding USM coordinates can be used to compute a Chebyshev distance metric as well as k-mer frequencies, without having to recompute the embedded numeric coordinates, and, paradoxically, allowing for non-integers values of k. Results: This report advances the bijective fractal encoding by Universal Sequence Maps (USM) by resolving seeding biases affecting the iterated process. The resolution had two results, the first expected, the second an intriguing outcome: 1) full reconciliation of numeric positioning with sequence identity; and 2) uncovering the nature of USM as an efficient numeric process converging towards a steady state sequence embedding solution. We illustrate these results for genomic sequences because of the convenience of a planar representation defined by an alphabet with only 4 tokens (the 4 nucleotides). Nevertheless, the application to alphabet of arbitrary cardinality was found to be straightforward.