Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the network itself, have been well studied. However, not all networks are tree-based. Francis-Semple-Steel (2018) thus introduced several indices to measure the deviation of rooted binary phylogenetic networks $N$ from being tree-based, such as the minimum number $\delta^\ast(N)$ of additional leaves needed to make $N$ tree-based, and the minimum difference $\eta^\ast(N)$ between the number of vertices of $N$ and the number of vertices of a subtree of $N$ that shares the root and leaf set with $N$. Hayamizu (2021) has established a canonical decomposition of almost-binary phylogenetic networks of $N$, called the maximal zig-zag trail decomposition, which has many implications including a linear time algorithm for computing $\delta^\ast(N)$. The Maximum Covering Subtree Problem (MCSP) is the problem of computing $\eta^\ast(N)$, and Davidov et al. (2022) showed that this can be solved in polynomial time (in cubic time when $N$ is binary) by an algorithm for the minimum cost flow problem. In this paper, under the assumption that $N$ is almost-binary (i.e. each internal vertex has in-degree and out-degree at most two), we show that $\delta^\ast(N)\leq \eta^\ast (N)$ holds, which is tight, and give a characterisation of such phylogenetic networks $N$ that satisfy $\delta^\ast(N)=\eta^\ast(N)$. Our approach uses the canonical decomposition of $N$ and focuses on how the maximal W-fences (i.e. the forbidden subgraphs of tree-based networks) are connected to maximal M-fences in the network $N$. Our results introduce a new class of phylogenetic networks for which MCSP can be solved in linear time, which can be seen as a generalisation of tree-based networks.
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Networking：IFIP International Conferences on Networking。
Explanation：國際網(wang)絡會議。
Publisher：IFIP。
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For several decades the dominant techniques for integer linear programming have been branching and cutting planes. Recently, several authors have developed core point methods for solving symmetric integer linear programs (ILPs). An integer point is called a core point if its orbit polytope is lattice-free. It has been shown that for symmetric ILPs, optimizing over the set of core points gives the same answer as considering the entire space. Existing core point techniques rely on the number of core points (or equivalence classes) being finite, which requires special symmetry groups. In this paper we develop some new methods for solving symmetric ILPs (based on outer approximations of core points) that do not depend on finiteness but are more efficient if the group has large disjoint cycles in its set of generators.
We consider the problem of query-efficient global max-cut on a weighted undirected graph in the value oracle model examined by [RSW18]. This model arises as a natural special case of submodular function maximization: on query $S \subseteq V$, the oracle returns the total weight of the cut between $S$ and $V \backslash S$. For most constants $c \in (0,1]$, we nail down the query complexity of achieving a $c$-approximation, for both deterministic and randomized algorithms (up to logarithmic factors). Analogously to general submodular function maximization in the same model, we observe a phase transition at $c = 1/2$: we design a deterministic algorithm for global $c$-approximate max-cut in $O(\log n)$ queries for any $c < 1/2$, and show that any randomized algorithm requires $\tilde{\Omega}(n)$ queries to find a $c$-approximate max-cut for any $c > 1/2$. Additionally, we show that any deterministic algorithm requires $\Omega(n^2)$ queries to find an exact max-cut (enough to learn the entire graph), and develop a $\tilde{O}(n)$-query randomized $c$-approximation for any $c < 1$. Our approach provides two technical contributions that may be of independent interest. One is a query-efficient sparsifier for undirected weighted graphs (prior work of [RSW18] holds only for unweighted graphs). Another is an extension of the cut dimension to rule out approximation (prior work of [GPRW20] introducing the cut dimension only rules out exact solutions).
We consider a natural generalization of Vertex Cover: the Subset Vertex Cover problem, which is to decide for a graph $G=(V,E)$, a subset $T \subseteq V$ and integer $k$, if $V$ has a subset $S$ of size at most $k$, such that $S$ contains at least one end-vertex of every edge incident to a vertex of $T$. A graph is $H$-free if it does not contain $H$ as an induced subgraph. We solve two open problems from the literature by proving that Subset Vertex Cover is NP-complete on subcubic (claw,diamond)-free planar graphs and on $2$-unipolar graphs, a subclass of $2P_3$-free weakly chordal graphs. Our results show for the first time that Subset Vertex Cover is computationally harder than Vertex Cover (under P $\neq$ NP). We also prove new polynomial time results. We first give a dichotomy on graphs where $G[T]$ is $H$-free. Namely, we show that Subset Vertex Cover is polynomial-time solvable on graphs $G$, for which $G[T]$ is $H$-free, if $H = sP_1 + tP_2$ and NP-complete otherwise. Moreover, we prove that Subset Vertex Cover is polynomial-time solvable for $(sP_1 + P_2 + P_3)$-free graphs and bounded mim-width graphs. By combining our new results with known results we obtain a partial complexity classification for Subset Vertex Cover on $H$-free graphs.
We consider the randomized communication complexity of the distributed $\ell_p$-regression problem in the coordinator model, for $p\in (0,2]$. In this problem, there is a coordinator and $s$ servers. The $i$-th server receives $A^i\in\{-M, -M+1, \ldots, M\}^{n\times d}$ and $b^i\in\{-M, -M+1, \ldots, M\}^n$ and the coordinator would like to find a $(1+\epsilon)$-approximate solution to $\min_{x\in\mathbb{R}^n} \|(\sum_i A^i)x - (\sum_i b^i)\|_p$. Here $M \leq \mathrm{poly}(nd)$ for convenience. This model, where the data is additively shared across servers, is commonly referred to as the arbitrary partition model. We obtain significantly improved bounds for this problem. For $p = 2$, i.e., least squares regression, we give the first optimal bound of $\tilde{\Theta}(sd^2 + sd/\epsilon)$ bits. For $p \in (1,2)$,we obtain an $\tilde{O}(sd^2/\epsilon + sd/\mathrm{poly}(\epsilon))$ upper bound. Notably, for $d$ sufficiently large, our leading order term only depends linearly on $1/\epsilon$ rather than quadratically. We also show communication lower bounds of $\Omega(sd^2 + sd/\epsilon^2)$ for $p\in (0,1]$ and $\Omega(sd^2 + sd/\epsilon)$ for $p\in (1,2]$. Our bounds considerably improve previous bounds due to (Woodruff et al. COLT, 2013) and (Vempala et al., SODA, 2020).
Motivated by the planarization of 2-layered straight-line drawings, we consider the problem of modifying a graph such that the resulting graph has pathwidth at most 1. The problem Pathwidth-One Vertex Explosion (POVE) asks whether such a graph can be obtained using at most $k$ vertex explosions, where a vertex explosion replaces a vertex $v$ by deg$(v)$ degree-1 vertices, each incident to exactly one edge that was originally incident to $v$. For POVE, we give an FPT algorithm with running time $O(4^k \cdot m)$ and an $O(k^2)$ kernel, thereby improving over the $O(k^6)$-kernel by Ahmed et al. [GD 22] in a more general setting. Similarly, a vertex split replaces a vertex $v$ by two distinct vertices $v_1$ and $v_2$ and distributes the edges originally incident to $v$ arbitrarily to $v_1$ and $v_2$. Analogously to POVE, we define the problem variant Pathwidth-One Vertex Splitting (POVS) that uses the split operation instead of vertex explosions. Here we obtain a linear kernel and an algorithm with running time $O((6k+12)^k \cdot m)$. This answers an open question by Ahmed et al. [GD22]. Finally, we consider the problem $\Pi$ Vertex Splitting ($\Pi$-VS), which generalizes the problem POVS and asks whether a given graph can be turned into a graph of a specific graph class $\Pi$ using at most $k$ vertex splits. For graph classes $\Pi$ that can be tested in monadic second-order graph logic (MSO$_2$), we show that the problem $\Pi$-VS can be expressed as an MSO$_2$ formula, resulting in an FPT algorithm for $\Pi$-VS parameterized by $k$ if $\Pi$ additionally has bounded treewidth. We obtain the same result for the problem variant using vertex explosions.
Social distance games have been extensively studied as a coalition formation model where the utilities of agents in each coalition were captured using a utility function u that took into account distances in a given social network. In this paper, we consider a non-normalized score-based definition of social distance games where the utility function u_v depends on a generic scoring vector v, which may be customized to match the specifics of each individual application scenario. As our main technical contribution, we establish the tractability of computing a welfare-maximizing partitioning of the agents into coalitions on tree-like networks, for every score-based function u_v. We provide more efficient algorithms when dealing with specific choices of u_v or simpler networks, and also extend all of these results to computing coalitions that are Nash stable or individually rational. We view these results as a further strong indication of the usefulness of the proposed score-based utility function: even on very simple networks, the problem of computing a welfare-maximizing partitioning into coalitions remains open for the originally considered canonical function u.
We consider the classic 1-center problem: Given a set $P$ of $n$ points in a metric space find the point in $P$ that minimizes the maximum distance to the other points of $P$. We study the complexity of this problem in $d$-dimensional $\ell_p$-metrics and in edit and Ulam metrics over strings of length $d$. Our results for the 1-center problem may be classified based on $d$ as follows. $\bullet$ Small $d$: Assuming the hitting set conjecture (HSC), we show that when $d=\omega(\log n)$, no subquadratic algorithm can solve 1-center problem in any of the $\ell_p$-metrics, or in edit or Ulam metrics. $\bullet$ Large $d$: When $d=\Omega(n)$, we extend our conditional lower bound to rule out subquartic algorithms for 1-center problem in edit metric (assuming Quantified SETH). On the other hand, we give a $(1+\epsilon)$-approximation for 1-center in Ulam metric with running time $\tilde{O_{\varepsilon}}(nd+n^2\sqrt{d})$. We also strengthen some of the above lower bounds by allowing approximations or by reducing the dimension $d$, but only against a weaker class of algorithms which list all requisite solutions. Moreover, we extend one of our hardness results to rule out subquartic algorithms for the well-studied 1-median problem in the edit metric, where given a set of $n$ strings each of length $n$, the goal is to find a string in the set that minimizes the sum of the edit distances to the rest of the strings in the set.
Directed acyclic graphs (DAGs) are directed graphs in which there is no path from a vertex to itself. DAGs are an omnipresent data structure in computer science and the problem of counting the DAGs of given number of vertices and to sample them uniformly at random has been solved respectively in the 70's and the 00's. In this paper, we propose to explore a new variation of this model where DAGs are endowed with an independent ordering of the out-edges of each vertex, thus allowing to model a wide range of existing data structures. We provide efficient algorithms for sampling objects of this new class, both with or without control on the number of edges, and obtain an asymptotic equivalent of their number. We also show the applicability of our method by providing an effective algorithm for the random generation of classical labelled DAGs with a prescribed number of vertices and edges, based on a similar approach. This is the first known algorithm for sampling labelled DAGs with full control on the number of edges, and it meets a need in terms of applications, that had already been acknowledged in the literature.
We consider the problem of linearizing a pseudo-Boolean function $f : \{0,1\}^n \to \mathbb{R}$ by means of $k$ Boolean functions. Such a linearization yields an integer linear programming formulation with only $k$ auxiliary variables. This motivates the definition of the linarization complexity of $f$ as the minimum such $k$. Our theoretical contributions are the proof that random polynomials almost surely have a high linearization complexity and characterizations of its value in case we do or do not restrict the set of admissible Boolean functions. The practical relevance is shown by devising and evaluating integer linear programming models of two such linearizations for the low auto-correlation binary sequences problem. Still, many problems around this new concept remain open.
Scalarization is a general technique that can be deployed in any multiobjective setting to reduce multiple objectives into one, such as recently in RLHF for training reward models that align human preferences. Yet some have dismissed this classical approach because linear scalarizations are known to miss concave regions of the Pareto frontier. To that end, we aim to find simple non-linear scalarizations that can explore a diverse set of $k$ objectives on the Pareto frontier, as measured by the dominated hypervolume. We show that hypervolume scalarizations with uniformly random weights are surprisingly optimal for provably minimizing the hypervolume regret, achieving an optimal sublinear regret bound of $O(T^{-1/k})$, with matching lower bounds that preclude any algorithm from doing better asymptotically. As a theoretical case study, we consider the multiobjective stochastic linear bandits problem and demonstrate that by exploiting the sublinear regret bounds of the hypervolume scalarizations, we can derive a novel non-Euclidean analysis that produces improved hypervolume regret bounds of $\tilde{O}( d T^{-1/2} + T^{-1/k})$. We support our theory with strong empirical performance of using simple hypervolume scalarizations that consistently outperforms both the linear and Chebyshev scalarizations, as well as standard multiobjective algorithms in bayesian optimization, such as EHVI.
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