Combinatorial alphabet-dependent bounds for insdel codes

Abstract: Error-correcting codes resilient to synchronization errors such as insertions and deletions are known as insdel codes. Due to their important applications in DNA storage and computational biology, insdel codes have recently become a focal point of research in coding theory. In this paper, we present several new combinatorial upper and lower bounds on the maximum size of $q$-ary insdel codes. Our main upper bound is a sphere-packing bound obtained by solving a linear programming (LP) problem. It improves upon previous results for cases when the distance $d$ or the alphabet size $q$ is large. Our first lower bound is derived from a connection between insdel codes and matchings in special hypergraphs. This lower bound, together with our upper bound, shows that for fixed block length $n$ and edit distance $d$, when $q$ is sufficiently large, the maximum size of insdel codes is $ \frac{q^{n-\frac{d}{2}+1}}{{n\choose \frac{d}{2}-1}}(1 \pm o(1))$. The second lower bound refines Alon et al.'s recent logarithmic improvement on Levenshtein's GV-type bound and extends its applicability to large $q$ and $d$.