In this work, we study the problem of computing a maximum common contraction of two vertex-labeled graphs, i.e. how to make them identical by contracting as little edges as possible in the two graphs. We study the problem from a parameterized complexity point of view, using parameters such as the maximum degree, the degeneracy, the clique-width or treewidth of the input graphs as well as the number of allowed contractions. We put this complexity in perspective with that of the labeled contractibility problem, i.e determining whether a labeled graph is a contraction of another. Surprisingly, our results indicate very little difference between these problems in terms of parameterized complexity status. We only prove their status to differ when parameterizing by both the degeneracy and the number of allowed contractions, showing W[1]-hardness of the maximum common contraction problem in this case, whereas the contractibility problem is FPT.

In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations connect the space of all phylogenetic networks on the same set of leaves, even if we forbid contractions that create cycles. This allows to define an operational distance on this space, as the minimum number of contractions and expansions required to transform one network into another. We highlight the difference between this distance and the computation of the maximum common contraction between two networks. Given its ability to outline a common structure between them, which can provide valuable biological insights, we study the algorithmic aspects of the latter. We first prove that computing a maximum common contraction between two networks is NP-hard, even when the maximum degree, the size of the common contraction, or the number of leaves is bounded. We also provide lower bounds to the problem based on the Exponential-Time Hypothesis. Nonetheless, we do provide a polynomial-time algorithm for weakly-galled trees, a generalization of galled trees.

MOTIVATION: Noncoding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature of molecular function. Consequently, within an RNA functional family, secondary structures are generally more evolutionarily conserved than sequences. Conversely, homologous RNA families grouped within an RNA clan share ancestors but typically exhibit structural differences. Inferring the evolution of RNA structures within RNA families and clans is crucial for gaining insights into functional adaptations over time and providing clues about the Ancient RNA World Hypothesis. RESULTS: We introduce the median problem and the small parsimony problem for ncRNA families, where secondary structures are represented as leaf-labeled trees. We utilize the Robinson-Foulds (RF) tree distance, which corresponds to a specific edit distance between RNA trees, and a new metric called the Internal-Leafset (IL) distance. While the RF tree distance compares sets of leaves descending from internal nodes of two RNA trees, the IL distance compares the collection of leaf-children of internal nodes. The latter is better at capturing differences in structural elements of RNAs than the RF distance, which is more focused on base pairs. We also consider a more general tree edit distance that allows the mapping of base pairs that are not perfectly aligned. We study the theoretical complexity of the median problem and the small parsimony problem under the three distance metrics and various biologically relevant constraints, and we present polynomial-time maximum parsimony algorithms for solving some versions of the problems. Our algorithms are applied to ncRNA families from the RFAM database, illustrating their practical utility. AVAILABILITY AND IMPLEMENTATION: https://github.com/bmarchand/rna\_small\_parsimony.

Budget Minimization is a scheduling problem with precedence constraints, i.e., a scheduling problem on a partially ordered set of jobs $(N, \unlhd)$. A job $j \in N$ is available for scheduling, if all jobs $i \in N$ with $i \unlhd j$ are completed. Further, each job $j \in N$ is assigned real valued costs $c_{j}$, which can be negative or positive. A schedule is an ordering $j_{1}, \dots, j_{\vert N \vert}$ of all jobs in $N$. The budget of a schedule is the external investment needed to complete all jobs, i.e., it is $\max_{l \in \{0, \dots, \vert N \vert \} } \sum_{1 \le k \le l} c_{j_{k}}$. The goal is to find a schedule with minimum budget. Rafiey et al. (2015) showed that Budget Minimization is NP-hard following from a reduction from a molecular folding problem. We extend this result and prove that it is NP-hard to $α(N)$-approximate the minimum budget even on bipartite partial orders. We present structural insights that lead to arguably simpler algorithms and extensions of the results by Rafiey et al. (2015). In particular, we show that there always exists an optimal solution that partitions the set of jobs and schedules each subset independently of the other jobs. We use this structural insight to derive polynomial-time algorithms that solve the problem to optimality on series-parallel and convex bipartite partial orders.