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There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf labels X but with distinct topologies. This leads naturally to the goal of quantifying the difference between two such trees T_1 and T_2. Here we introduce the problem of computing a 'maximum relaxed agreement forest' (MRAF) and use this as a proxy for the dissimilarity of T_1 and T_2, which in this article we assume to be unrooted binary phylogenetic trees. MRAF asks for a partition of the leaf labels X into a minimum number of blocks S_1, S_2, ... S_k such that for each i, the subtrees induced in T_1 and T_2 by S_i are isomorphic up to suppression of degree-2 nodes and taking the labels X into account. Unlike the earlier introduced maximum agreement forest (MAF) model, the subtrees induced by the S_i are allowed to overlap. We prove that it is NP-hard to compute MRAF, by reducing from the problem of partitioning a permutation into a minimum number of monotonic subsequences (PIMS). Furthermore, we show that MRAF has a polynomial time O(log n)-approximation algorithm where n=|X| and permits exact algorithms with single-exponential running time. When at least one of the two input trees has a caterpillar topology, we prove that testing whether a MRAF has size at most k can be answered in polynomial time when k is fixed. We also note that on two caterpillars the approximability of MRAF is related to that of PIMS. Finally, we establish a number of bounds on MRAF, compare its behaviour to MAF both in theory and in an experimental setting and discuss a number of open problems., Comment: 14 pages plus appendix

Let $G$ be an undirected graph. We say that $G$ contains a ladder of length $k$ if the $2 \times (k+1)$ grid graph is an induced subgraph of $G$ that is only connected to the rest of $G$ via its four cornerpoints. We prove that if all the ladders contained in $G$ are reduced to length 4, the treewidth remains unchanged (and that this bound is tight). Our result indicates that, when computing the treewidth of a graph, long ladders can simply be reduced, and that minimal forbidden minors for bounded treewidth graphs cannot contain long ladders. Our result also settles an open problem from algorithmic phylogenetics: the common chain reduction rule, used to simplify the comparison of two evolutionary trees, is treewidth-preserving in the display graph of the two trees., Comment: Compared to the earlier arXiv/WG version we have added analytical (as opposed to empirical) tightness bounds, and an extended discussion. See also Authors note 2 at the end of the introduction about earlier work in this area by Marchand et al

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary phylogenetic trees. This problem is better-known in the literature as the maximum agreement forest problem, where the goal is to partition the two trees into a minimum number of common, non-overlapping subtrees. We have implemented two well-known reduction rules, the subtree and chain reduction, and five more recent, theoretically stronger reduction rules, and compare the reduction achieved with and without the stronger rules. We find that the new rules yield smaller reduced instances and thus have clear practical added value. In many cases they also cause the TBR distance to decrease in a controlled fashion. Next, we compare the achieved reduction to the known worst-case theoretical bounds of 15k-9 and 11k-9 respectively, on the number of leaves of the two reduced trees, where k is the TBR distance, observing in both cases a far larger reduction in practice. As a by-product of our experimental framework we obtain a number of new insights into the actual computation of TBR distance. We find, for example, that very strong lower bounds on TBR distance can be obtained efficiently by randomly sampling certain carefully constructed partitions of the leaf labels, and identify instances which seem particularly challenging to solve exactly. The reduction rules have been implemented within our new solver Tubro which combines kernelization with an Integer Linear Programming (ILP) approach. Tubro also incorporates a number of additional features, such as a cluster reduction and a practical upper-bounding heuristic, and it can leverage combinatorial insights emerging from the proofs of correctness of the reduction rules to simplify the ILP., Comment: Updated version. New figures and analysis. Accepted for journal publication

The Cloud infrastructure offers to end users a broad set of heterogenous computational resources using the pay-as-you-go model. These virtualized resources can be provisioned using different pricing models like the unreliable model where resources are provided at a fraction of the cost but with no guarantee for an uninterrupted processing. However, the enormous gamut of opportunities comes with a great caveat as resource management and scheduling decisions are increasingly complicated. Moreover, the presented uncertainty in optimally selecting resources has also a negatively impact on the quality of solutions delivered by scheduling algorithms. In this paper, we present a dynamic scheduling algorithm (i.e., the Uncertainty-Driven Scheduling - UDS algorithm) for the management of scientific workflows in Cloud. Our model minimizes both the makespan and the monetary cost by dynamically selecting reliable or unreliable virtualized resources. For covering the uncertainty in decision making, we adopt a Fuzzy Logic Controller (FLC) to derive the pricing model of the resources that will host every task. We evaluate the performance of the proposed algorithm using real workflow applications being tested under the assumption of different probabilities regarding the revocation of unreliable resources. Numerical results depict the performance of the proposed approach and a comparative assessment reveals the position of the paper in the relevant literature.

Large amounts of geospatial data have been made available recently on the linked open data cloud and the portals of many national cartographic agencies (e.g., OpenStreetMap data, administrative geographies of various countries, or land cover/land use data sets). These datasets use various geospatial vocabularies and can be queried using SPARQL or its OGC-standardized extension GeoSPARQL. In this paper, we go beyond these approaches to offer a question-answering engine for natural language questions on top of linked geospatial data sources. Our system has been implemented as re-usable components of the Frankenstein question answering architecture. We give a detailed description of the system's architecture, its underlying algorithms, and its evaluation using a set of 201 natural language questions. The set of questions is offered to the research community as a gold standard dataset for the comparative evaluation of future geospatial question answering engines., Comment: 27 pages, 2 figures

Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a function of many common dissimilarity measures between phylogenetic trees and this has been leveraged in fixed parameter tractability results. Here we further elucidate the properties of display graphs and their interaction with treewidth. We show that it is NP-hard to recognize display graphs, but that display graphs of bounded treewidth can be recognized in linear time. Next we show that if a phylogenetic network displays (i.e. topologically embeds) a phylogenetic tree, the treewidth of their display graph is bounded by a function of the treewidth of the original network (and also by various other parameters). In fact, using a bramble argument we show that this treewidth bound is sharp up to an additive term of 1. We leverage this bound to give an FPT algorithm, parameterized by treewidth, for determining whether a network displays a tree, which is an intensively-studied problem in the field. We conclude with a discussion on the future use of display graphs and treewidth in phylogenetics.

We study the integrality gap of the natural linear programming relaxation for the \textit{Bounded Color Matching} (BCM) problem. We provide several families of instances and establish lower bounds on their integrality gaps and we study how the Sherali-Adams "lift-and-project" technique behaves on these instances. We complement these results by showing that if we exclude certain simple sub-structures from our input graphs, then the integrality gap of the natural linear formulation strictly improves. To prove this, we adapt for our purposes the results of F\"{u}redi [\emph{Combinatorica}, 1(2):155-162, 1981]. We further leverage this to show upper bounds on the performance of the Sherali-Adams hierarchy when applied to the natural LP relaxation of the BCM problem., Comment: 25 pages, 3 Figures

In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display graph is bounded if the trees are in some formal sense topologically similar. Here we further expand upon this relationship. We analyse a number of reduction rules which are commonly used in the phylogenetics literature to obtain fixed parameter tractable algorithms. In some cases (the \emph{subtree} reduction) the reduction rules behave similarly with respect to treewidth, while others (the \emph{cluster} reduction) behave very differently, and the behaviour of the \emph{chain reduction} is particularly intriguing because of its link with graph separators and forbidden minors. We also show that the gap between treewidth and Tree Bisection and Reconnect (TBR) distance can be infinitely large, and that unlike, for example, planar graphs the treewidth of the display graph can be as much as linear in its number of vertices. On a slightly different note we show that if a display graph is formed from the fusion of a phylogenetic network and a tree, rather than from two trees, the treewidth of the display graph is bounded whenever the tree can be topologically embedded ("displayed") within the network. This opens the door to the formulation of the display problem in Monadic Second Order Logic (MSOL). A number of other auxiliary results are given. We conclude with a discussion and list a number of open problems., Comment: 29 pages, 12 figures

Weighted counting problems are a natural generalization of counting problems where a weight is associated with every computational path of polynomial-time non-deterministic Turing machines and the goal is to compute the sum of the weights of all paths (instead of just computing the number of accepting paths). Useful closure properties and plenty of applications make weighted counting problems interesting. The general definition of these problems captures even undecidable problems, but it turns out that obtaining an exponentially small additive approximation is just as hard as solving conventional counting problems. In many cases such an approximation is sufficient and working with weighted counting problems tends to be very convenient. We present a structured view on weighted counting by defining classes that depend on the range of the function that assigns weights to paths and by showing the relationships between these different classes. These classes constitute generalizations of the usual counting problems. Weighted counting allows us to easily cast a number of famous results of computational complexity in its terms, especially regarding counting and quantum computation. Moreover, these classes are flexible enough and capture the complexity of various problems in fields such as probabilistic graphical models and stochastic combinatorial optimization. Using the weighted counting terminology and our results, we are able to simplify and answer some open questions in those fields., Comment: 32 pages

We consider the problem of allocating a set $I$ of $m$ indivisible resources (items) to a set $P$ of $n$ customers (players) competing for the resources. Each resource $j \in I$ has a same value $v_j > 0$ for a subset of customers interested in $j$, and zero value for the remaining customers. The utility received by each customer is the sum of the values of the resources allocated to her. The goal is to find a feasible allocation of the resources to the interested customers such that for the Max-Min allocation problem (Min-Max allocation problem) the minimum of the utilities (maximum of the utilities) received by the customers is maximized (minimized). The Max-Min allocation problem is also known as the \textit{Fair Allocation problem}, or the \textit{Santa Claus problem}. The Min-Max allocation problem is the problem of Scheduling on Unrelated Parallel Machines, and is also known as the $R \, | \, | C_{\max}$ problem. In this paper, we are interested in instances of the problem that admit a Polynomial Time Approximation Scheme (PTAS). We show that an ordering property on the resources and the customers is important and paves the way for a PTAS. For the Max-Min allocation problem, we start with instances of the problem that can be viewed as a \textit{convex bipartite graph}; a bipartite graph for which there exists an ordering of the resources such that each customer is interested in (has a positive evaluation for) a set of \textit{consecutive} resources. We demonstrate a PTAS for the inclusion-free cases. This class of instances is equivalent to the class of bipartite permutation graphs. For the Min-Max allocation problem, we also obtain a PTAS for inclusion-free instances. These instances are not only of theoretical interest but also have practical applications.

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees., Comment: 28 pages, 8 Figures

Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in which the subset of species (both contemporary and extinct) that share a given state, form a connected subtree. Given an unrooted, binary phylogenetic tree T on a set of n >= 2 taxa, a closed (but fairly opaque) expression for the number of convex characters on T has been known since 1992, and this is independent of the exact topology of T. In this note we prove that this number is actually equal to the (2n-1)th Fibonacci number. Next, we define g_k(T) to be the number of convex characters on T in which each state appears on at least k taxa. We show that, somewhat curiously, g_2(T) is also independent of the topology of T, and is equal to to the (n-1)th Fibonacci number. As we demonstrate, this topological neutrality subsequently breaks down for k >= 3. However, we show that for each fixed k >= 1, g_k(T) can be computed in O(n) time and the set of characters thus counted can be efficiently listed and sampled. We use these insights to give a simple but effective exact algorithm for the NP-hard maximum parsimony distance problem that runs in time $\Theta( \phi^{n} \cdot n^2 )$, where $\phi \approx 1.618...$ is the golden ratio, and an exact algorithm which computes the tree bisection and reconnection distance (equivalently, a maximum agreement forest) in time $\Theta( \phi^{2n}\cdot \text{poly}(n))$, where $\phi^2 \approx 2.619$., Comment: added a significant number of new results to the previous version (on dynamic programming, g-spectra and so on)

Our goal in this paper is to propose a \textit{combinatorial algorithm} that beats the only such algorithm known previously, the greedy one. We study the polynomial approximation of the Maximum Vertex Cover Problem in bipartite graphs by a purely combinatorial algorithm and present a computer assisted analysis of it, that finds the worst case approximation guarantee that is bounded below by~0.821., Comment: 25 pages, 2 figures

In this work we study approximation algorithms for the \textit{Bounded Color Matching} problem (a.k.a. Restricted Matching problem) which is defined as follows: given a graph in which each edge $e$ has a color $c_e$ and a profit $p_e \in \mathbb{Q}^+$, we want to compute a maximum (cardinality or profit) matching in which no more than $w_j \in \mathbb{Z}^+$ edges of color $c_j$ are present. This kind of problems, beside the theoretical interest on its own right, emerges in multi-fiber optical networking systems, where we interpret each unique wavelength that can travel through the fiber as a color class and we would like to establish communication between pairs of systems. We study approximation and bi-criteria algorithms for this problem which are based on linear programming techniques and, in particular, on polyhedral characterizations of the natural linear formulation of the problem. In our setting, we allow violations of the bounds $w_j$ and we model our problem as a bi-criteria problem: we have two objectives to optimize namely (a) to maximize the profit (maximum matching) while (b) minimizing the violation of the color bounds. We prove how we can "beat" the integrality gap of the natural linear programming formulation of the problem by allowing only a slight violation of the color bounds. In particular, our main result is \textit{constant} approximation bounds for both criteria of the corresponding bi-criteria optimization problem.