Multi-Scale Reversible Chaos Game Representation: A Unified Framework for Sequence Classification

TL;DR

This paper introduces MS-RCGR, a reversible, multi-scale geometric encoding framework for biological sequences that improves classification performance across machine learning, vision, and hybrid models.

Contribution

MS-RCGR is a novel, reversible, multi-resolution encoding method that unifies different sequence analysis paradigms and enhances classification accuracy.

Findings

MS-RCGR features improve classification across all tested paradigms.

Hybrid models with language embeddings and MS-RCGR outperform individual methods.

Reversibility ensures no information loss during sequence transformation.

Abstract

Biological classification with interpretability remains a challenging task. For this, we introduce a novel encoding framework, Multi-Scale Reversible Chaos Game Representation (MS-RCGR), that transforms biological sequences into multi-resolution geometric representations with guaranteed reversibility. Unlike traditional sequence encoding methods, MS-RCGR employs rational arithmetic and hierarchical k-mer decomposition to generate scale-invariant features that preserve complete sequence information while enabling diverse analytical approaches. Our framework bridges three distinct paradigms for sequence analysis: (1) traditional machine learning using extracted geometric features, (2) computer vision models operating on CGR-generated images, and (3) hybrid approaches combining protein language model embeddings with CGR features. Through comprehensive experiments on synthetic DNA and protein datasets encompassing seven distinct sequence classes, we demonstrate that MS-RCGR features consistently enhance classification performance across all paradigms. Notably, our hybrid approach combining pre-trained language model embeddings (ESM2, ProtT5) with MS-RCGR features achieves superior performance compared to either method alone. The reversibility property of our encoding ensures no information loss during transformation, while multi-scale analysis captures patterns ranging from individual nucleotides to complex motif structures. Our results indicate that MS-RCGR provides a flexible, interpretable, and high-performing foundation for biological sequence analysis.