Algorithmica
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Listing Even Cycles Faster than the Submodular-Width Barrier
arXiv:2605.30564v1 Announce Type: new Abstract: A classic result of Alon, Yuster, and Zwick (AYZ, Algorithmica 1997) shows that all $2k$-cycles in an $m$-edge graph can be listed in $\tilde O(m^{2-1/k}+t)$ time, where $t$ is the output size. This bound underlies the {\em submodular width} of Marx (JACM 2013) and the PANDA framework of Abo Khamis, Ngo, and Suciu (PODS 2017), which extend AYZ to arbitrary conjunctive queries with degree constraints. A central open question is whether...
Revisiting $O(n \log \log n)$ chaining for anchored edit distance
arXiv:2606.03929v1 Announce Type: new Abstract: Colinear chaining is a classical heuristic for sequence alignment: it enables scalable genome comparison and is a main component of many state-of-the-art read mappers based on seed-chain-extend. The earliest $O(n \log \log n)$ time algorithms by Eppstein et al. (J. ACM, 1992) chained $n$ fragments between two sequences $T$ and $Q$ while minimizing a gap cost based on the diagonal distance $\Delta_{\text{diag}}$ between consecutive fragments.
An Optimal Algorithm for Binary Closest String
arXiv:2605.31417v1 Announce Type: new Abstract: We revisit the Binary Closest String problem, which asks, given a set of binary strings $X \subseteq \{0, 1\}^n$, to compute a string minimizing the maximum Hamming distance to $X$. A long line of work has focused on parameterized algorithms with respect to the optimal distance $d$, yielding a sequence of improvements from $O^*(d^d)$ through $O^*(16^d)$, $O^*(9.513^d)$, $O^*(8^d)$, $O^*(6.731^d)$ to the current best-known running time of...