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Background. The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set $L$ is known to be solvable in linear time. Existing approaches refine one input tree using information of the others and then test whether the results are isomorphic. Results. A linear-time algorithm, LinCR, for constructing the common refinement $T$ of $k$ input trees with a common leaf set is proposed that explicitly computes the parent function of $T$ in a bottom-up approach. Conclusion. LinCR is simpler to implement than other asymptotically optimal algorithms for the problem and outperforms the alternatives in empirical comparisons. Availability. An implementation of LinCR in Python is freely available at //github.com/david-schaller/tralda.

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Multi-criteria decision-making often requires finding a small representative subset from the database. A recently proposed method is the regret minimization set (RMS) query. RMS returns a fixed size subset S of dataset D that minimizes the regret ratio of S (the difference between the score of top1 in S and the score of top-1 in D, for any possible utility function). Existing work showed that the regret-ratio is not able to accurately quantify the regret level of a user. Further, relative to the regret-ratio, users do understand the notion of rank. Consequently, it considered the problem of finding a minimal set S with at most k rank-regret (the minimal rank of tuples of S in the sorted list of D). Corresponding to RMS, we focus on the dual version of the above problem, defined as the rank-regret minimization (RRM) problem, which seeks to find a fixed size set S that minimizes the maximum rank-regret for all possible utility functions. Further, we generalize RRM and propose the restricted rank-regret minimization (RRRM) problem to minimize the rank-regret of S for functions in a restricted space. The solution for RRRM usually has a lower regret level and can better serve the specific preferences of some users. In 2D space, we design a dynamic programming algorithm 2DRRM to find the optimal solution for RRM. In HD space, we propose an algorithm HDRRM for RRM that bounds the output size and introduces a double approximation guarantee for rank-regret. Both 2DRRM and HDRRM can be generalized to the RRRM problem. Extensive experiments are performed on the synthetic and real datasets to verify the efficiency and effectiveness of our algorithms.

It is well-known that an algorithm exists which approximates the NP-complete problem of Set Cover within a factor of ln(n), and it was recently proven that this approximation ratio is optimal unless P = NP. This optimality result is the product of many advances in characterizations of NP, in terms of interactive proof systems and probabilistically checkable proofs (PCP), and improvements to the analyses thereof. However, as a result, it is difficult to extract the development of Set Cover approximation bounds from the greater scope of proof system analysis. This paper attempts to present a chronological progression of results on lower-bounding the approximation ratio of Set Cover. We analyze a series of proofs of progressively better bounds and unify the results under similar terminologies and frameworks to provide an accurate comparison of proof techniques and their results. We also treat many preliminary results as black-boxes to better focus our analysis on the core reductions to Set Cover instances. The result is alternative versions of several hardness proofs, beginning with initial inapproximability results and culminating in a version of the proof that ln(n) is a tight lower bound.

An influential 1990 paper of Hochbaum and Shanthikumar made it common wisdom that "convex separable optimization is not much harder than linear optimization" [JACM 1990]. We exhibit two fundamental classes of mixed integer (linear) programs that run counter this intuition. Namely those whose constraint matrices have small coefficients and small primal or dual treedepth: While linear optimization is easy [Brand, Kouteck\'y, Ordyniak, AAAI 2021], we prove that separable convex optimization IS much harder. Moreover, in the pure integer and mixed integer linear cases, these two classes have the same parameterized complexity. We show that they yet behave quite differently in the separable convex mixed integer case. Our approach employs the mixed Graver basis introduced by Hemmecke [Math. Prog. 2003]. We give the first non-trivial lower and upper bounds on the norm of mixed Graver basis elements. In previous works involving the integer Graver basis, such upper bounds have consistently resulted in efficient algorithms for integer programming. Curiously, this does not happen in our case. In fact, we even rule out such an algorithm.

The concept of Nash equilibrium enlightens the structure of rational behavior in multi-agent settings. However, the concept is as helpful as one may compute it efficiently. We introduce the Cut-and-Play, an algorithm to compute Nash equilibria for non-cooperative simultaneous games where each player's objective is linear in their variables and bilinear in the other players' variables. Using the rich theory of integer programming, we alternate between constructing (i.) increasingly tighter outer approximations of the convex hull of each player's feasible set -- by using branching and cutting plane methods -- and (ii.) increasingly better inner approximations of these hulls -- by finding extreme points and rays of the convex hulls. In particular, we prove the correctness of our algorithm when these convex hulls are polyhedra. Our algorithm allows us to leverage the mixed integer programming technology to compute equilibria for a large class of games. Further, we integrate existing cutting plane families inside the algorithm, significantly speeding up equilibria computation. We showcase a set of extensive computational results for Integer Programming Games and simultaneous games among bilevel leaders. In both cases, our framework outperforms the state-of-the-art in computing time and solution quality.

Finding minimum dominating set and maximum independent set for graphs in the classical online setup are notorious due to their disastrous $\Omega(n)$ lower bound of the competitive ratio that even holds for interval graphs, where $n$ is the number of vertices. In this paper, inspired by Newton number, first, we introduce the independent kissing number $\zeta$ of a graph. We prove that the well known online greedy algorithm for dominating set achieves optimal competitive ratio $\zeta$ for any graph. We show that the same greedy algorithm achieves optimal competitive ratio $\zeta$ for online maximum independent set of a class of graphs with independent kissing number $\zeta$. For minimum connected dominating set problem, we prove that online greedy algorithm achieves an asymptotic competitive ratio of $2(\zeta-1)$, whereas for a family of translated convex objects the lower bound is $\frac{2\zeta-1}{3}$. Finally, we study the value of $\zeta$ for some specific families of geometric objects: fixed and arbitrary oriented unit hyper-cubes in $I\!\!R^d$, congruent balls in $I\!\!R^3$, fixed oriented unit triangles, fixed and arbitrary oriented regular polygons in $I\!\!R^2$. For each of these families, we also present lower bounds of the minimum connected dominating set problem.

We consider the rooted prize-collecting walks (PCW) problem, wherein we seek a collection $C$ of rooted walks having minimum prize-collecting cost, which is the (total cost of walks in $C$) + (total node-reward of nodes not visited by any walk in $C$). This problem arises naturally as the Lagrangian relaxation of both orienteering, where we seek a length-bounded walk of maximum reward, and the $\ell$-stroll problem, where we seek a minimum-length walk covering at least $\ell$ nodes. Our main contribution is to devise a simple, combinatorial algorithm for the PCW problem in directed graphs that returns a rooted tree whose prize-collecting cost is at most the optimum value of the prize-collecting walks problem. We utilize our algorithm to develop combinatorial approximation algorithms for two fundamental vehicle-routing problems (VRPs): (1) orienteering; and (2) $k$-minimum-latency problem ($k$-MLP), wherein we seek to cover all nodes using $k$ paths starting at a prescribed root node, so as to minimize the sum of the node visiting times. Our combinatorial algorithm allows us to sidestep the part where we solve a preflow-based LP in the LP-rounding algorithms of Friggstand and Swamy (2017) for orienteering, and in the state-of-the-art $7.183$-approximation algorithm for $k$-MP in Post and Swamy (2015). Consequently, we obtain combinatorial implementations of these algorithms with substantially improved running times compared with the current-best approximation factors. We report computational results for our resulting (combinatorial implementations of) orienteering algorithms, which show that the algorithms perform quite well in practice, both in terms of the quality of the solution they return, as also the upper bound they yield on the orienteering optimum (which is obtained by leveraging the workings of our PCW algorithm).

Given an $n$-vertex planar embedded digraph $G$ with non-negative edge weights and a face $f$ of $G$, Klein presented a data structure with $O(n\log n)$ space and preprocessing time which can answer any query $(u,v)$ for the shortest path distance in $G$ from $u$ to $v$ or from $v$ to $u$ in $O(\log n)$ time, provided $u$ is on $f$. This data structure is a key tool in a number of state-of-the-art algorithms and data structures for planar graphs. Klein's data structure relies on dynamic trees and the persistence technique as well as a highly non-trivial interaction between primal shortest path trees and their duals. The construction of our data structure follows a completely different and in our opinion very simple divide-and-conquer approach that solely relies on Single-Source Shortest Path computations and contractions in the primal graph. Our space and preprocessing time bound is $O(n\log |f|)$ and query time is $O(\log |f|)$ which is an improvement over Klein's data structure when $f$ has small size.

Hierarchical Clustering has been studied and used extensively as a method for analysis of data. More recently, Dasgupta [2016] defined a precise objective function. Given a set of $n$ data points with a weight function $w_{i,j}$ for each two items $i$ and $j$ denoting their similarity/dis-similarity, the goal is to build a recursive (tree like) partitioning of the data points (items) into successively smaller clusters. He defined a cost function for a tree $T$ to be $Cost(T) = \sum_{i,j \in [n]} \big(w_{i,j} \times |T_{i,j}| \big)$ where $T_{i,j}$ is the subtree rooted at the least common ancestor of $i$ and $j$ and presented the first approximation algorithm for such clustering. Then Moseley and Wang [2017] considered the dual of Dasgupta's objective function for similarity-based weights and showed that both random partitioning and average linkage have approximation ratio $1/3$ which has been improved in a series of works to $0.585$ [Alon et al. 2020]. Later Cohen-Addad et al. [2019] considered the same objective function as Dasgupta's but for dissimilarity-based metrics, called $Rev(T)$. It is shown that both random partitioning and average linkage have ratio $2/3$ which has been only slightly improved to $0.667078$ [Charikar et al. SODA2020]. Our first main result is to consider $Rev(T)$ and present a more delicate algorithm and careful analysis that achieves approximation $0.71604$. We also introduce a new objective function for dissimilarity-based clustering. For any tree $T$, let $H_{i,j}$ be the number of $i$ and $j$'s common ancestors. Intuitively, items that are similar are expected to remain within the same cluster as deep as possible. So, for dissimilarity-based metrics, we suggest the cost of each tree $T$, which we want to minimize, to be $Cost_H(T) = \sum_{i,j \in [n]} \big(w_{i,j} \times H_{i,j} \big)$. We present a $1.3977$-approximation for this objective.

This paper considers the basic problem of scheduling jobs online with preemption to maximize the number of jobs completed by their deadline on $m$ identical machines. The main result is an $O(1)$ competitive deterministic algorithm for any number of machines $m >1$.

We present new greedy and beam search heuristic methods to find small-size $k$-dominating sets in graphs. The methods are inspired by a new problem formulation which explicitly highlights a certain structure of the problem. An empirical evaluation of the new methods is done with respect to two existing methods, using instances of graphs corresponding to street networks. The k-domination problem with respect to this class of graphs can be used to model real-world facility location problem scenarios. For the classic minimum dominating set ($1$-domination) problem, all except one methods perform similarly, which is due to their equivalence in this particular case. However, for the k-domination problem with k>1, the new methods outperform the benchmark methods, and the performance gain is more significant for larger values of k.

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