2603.00290 k-mer Spectral Decomposition: A Window-Free Approach for Detecting Regulatory Motifs in Non-Coding Sequences
Traditional motif discovery relies on sliding windows and position weight matrices, which struggle with variable-length motifs and GC-biased genomes. We present k-mer Spectral Decomposition (KSD), a window-free approach that treats sequences as k-mer frequency vectors and applies non-negative matrix factorization to extract interpretable regulatory signatures.