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For any natural number $d$, a graph $G$ is a (disjoint) $d$-interval graph if it is the intersection graph of (disjoint) $d$-intervals, the union of $d$ (disjoint) intervals on the real line. Two important subclasses of $d$-interval graphs are unit and balanced $d$-interval graphs (where every interval has unit length or all the intervals associated to a same vertex have the same length, respectively). A celebrated result by Roberts gives a simple characterization of unit interval graphs being exactly claw-free interval graphs. Here, we study the generalization of this characterization for $d$-interval graphs. In particular, we prove that for any $d \geq 2$, if $G$ is a $K_{1,2d+1}$-free interval graph, then $G$ is a unit $d$-interval graph. However, somehow surprisingly, under the same assumptions, $G$ is not always a \emph{disjoint} unit $d$-interval graph. This implies that the class of disjoint unit $d$-interval graphs is strictly included in the class of unit $d$-interval graphs. Finally, we study the relationships between the classes obtained under disjoint and non-disjoint $d$-intervals in the balanced case and show that the classes of disjoint balanced 2-intervals and balanced 2-intervals coincide, but this is no longer true for $d>2$.

In a digraph, a quasi-kernel is a subset of vertices that is independent and such that the shortest path from every vertex to this subset is of length at most two. The ``small quasi-kernel conjecture,'' proposed by Erd\H{o}s and Sz\'ekely in 1976, postulates that every sink-free digraph has a quasi-kernel whose size is within a fraction of the total number of vertices. The conjecture is even more precise with a $1/2$ ratio, but even with larger ratio, this property is known to hold only for few classes of graphs. The focus here is on small quasi-kernels in split graphs. This family of graphs has played a special role in the study of the conjecture since it was used to disprove a strengthening that postulated the existence of two disjoint quasi-kernels. The paper proves that every sink-free split digraph $D$ has a quasi-kernel of size at most $\frac{2}{3}|V(D)|$, and even of size at most two when the graph is an orientation of a complete split graph. It is also shown that computing a quasi-kernel of minimal size in a split digraph is W[2]-hard.

Given a flow network, the Minimum Flow Decomposition (MFD) problem is finding the smallest possible set of weighted paths whose superposition equals the flow. It is a classical, strongly NP-hard problem that is proven to be useful in RNA transcript assembly and applications outside of Bioinformatics. We improve an existing ILP (Integer Linear Programming) model by Dias et al. [RECOMB 2022] for DAGs by decreasing the solver's search space using solution safety and several other optimizations. This results in a significant speedup compared to the original ILP, of up to 55-90x on average on the hardest instances. Moreover, we show that our optimizations apply also to MFD problem variants, resulting in similar speedups, going up to 123x on the hardest instances. We also developed an ILP model of reduced dimensionality for an MFD variant in which the solution path weights are restricted to a given set. This model can find an optimal MFD solution for most instances, and overall, its accuracy significantly outperforms that of previous greedy algorithms while being up to an order of magnitude faster than our optimized ILP.

Multiple interval graphs are a well-known generalization of interval graphs introduced in the 1970s to deal with situations arising naturally in scheduling and allocation. A $d$-interval is the union of $d$ intervals on the real line, and a graph is a $d$-interval graph if it is the intersection graph of $d$-intervals. In particular, it is a unit $d$-interval graph if it admits a $d$-interval representation where every interval has unit length. Whereas it has been known for a long time that recognizing 2-interval graphs and other related classes such as 2-track interval graphs is NP-complete, the complexity of recognizing unit 2-interval graphs remains open. Here, we settle this question by proving that the recognition of unit 2-interval graphs is also NP-complete. Our proof technique uses a completely different approach from the other hardness results of recognizing related classes. Furthermore, we extend the result for unit $d$-interval graphs for any $d\geq 2$, which does not follow directly in graph recognition problems --as an example, it took almost 20 years to close the gap between $d=2$ and $d> 2$ for the recognition of $d$-track interval graphs. Our result has several implications, including that recognizing $(x, \dots, x)$ $d$-interval graphs and depth $r$ unit 2-interval graphs is NP-complete for every $x\geq 11$ and every $r\geq 4$., Comment: Accepted in ISAAC 2023

A minimum path cover (MPC) of a directed acyclic graph (DAG) $G = (V,E)$ is a minimum-size set of paths that together cover all the vertices of the DAG. Computing an MPC is a basic polynomial problem, dating back to Dilworth's and Fulkerson's results in the 1950s. Since the size $k$ of an MPC (also known as the width) can be small in practical applications, research has also studied algorithms whose running time is parameterized on $k$. We obtain a new MPC parameterized algorithm for DAGs running in time $O(k^2|V| + |E|)$. Our algorithm is the first solving the problem in parameterized linear time. Additionally, we obtain an edge sparsification algorithm preserving the width of a DAG but reducing $|E|$ to less than $2|V|$. This algorithm runs in time $O(k^2|V|)$ and requires an MPC of a DAG as input, thus its total running time is the same as the running time of our MPC algorithm., Comment: arXiv admin note: substantial text overlap with arXiv:2107.05717

The profitable tour problem (PTP) is a well-known NP-hard routing problem searching for a tour visiting a subset of customers while maximizing profit as the difference between total revenue collected and traveling costs. PTP is known to be solvable in polynomial time when special structures of the underlying graph are considered. However, the computational complexity of the corresponding probabilistic generalizations is still an open issue in many cases. In this paper, we analyze the probabilistic PTP where customers are located on a tree and need, with a known probability, for a service provision at a predefined prize. The problem objective is to select a priori a subset of customers with whom to commit the service so to maximize the expected profit. We provide a polynomial time algorithm computing the optimal solution in $O(n^2)$, where $n$ is the number of nodes in the tree.

In a strongly connected graph $G = (V,E)$, a cut arc (also called strong bridge) is an arc $e \in E$ whose removal makes the graph no longer strongly connected. Equivalently, there exist $u,v \in V$, such that all $u$-$v$ walks contain $e$. Cut arcs are a fundamental graph-theoretic notion, with countless applications, especially in reachability problems. In this paper we initiate the study of cut paths, as a generalisation of cut arcs, which we naturally define as those paths $P$ for which there exist $u,v \in V$, such that all $u$-$v$ walks contain $P$ as subwalk. We first prove various properties of cut paths and define their remainder structures, which we use to present a simple $O(m)$-time verification algorithm for a cut path ($|V| = n$, $|E| = m$). Secondly, we apply cut paths and their remainder structures to improve several reachability problems from bioinformatics. A walk is called safe if it is a subwalk of every node-covering closed walk of a strongly connected graph. Multi-safety is defined analogously, by considering node-covering sets of closed walks instead. We show that cut paths provide simple $O(m)$-time algorithms verifying if a walk is safe or multi-safe. For multi-safety, we present the first linear time algorithm, while for safety, we present a simple algorithm where the state-of-the-art employed complex data structures. Finally we show that the simultaneous computation of remainder structures of all subwalks of a cut path can be performed in linear time. These properties yield an $O(mn)$ algorithm outputting all maximal multi-safe walks, improving over the state-of-the-art algorithm running in time $O(m^2+n^3)$. The results of this paper only scratch the surface in the study of cut paths, and we believe a rich structure of a graph can be revealed, considering the perspective of a path, instead of just an arc.

Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow/circulation $X$ on a directed graph $G$ into weighted source-to-sink paths whose superposition equals $X$. We show that, for acyclic graphs, considering the \emph{width} of the graph (the minimum number of paths needed to cover all of its edges) yields advances in our understanding of its approximability. For the version of the problem that uses only non-negative weights, we identify and characterise a new class of \emph{width-stable} graphs, for which a popular heuristic is a \gwsimple-approximation ($|X|$ being the total flow of $X$), and strengthen its worst-case approximation ratio from $\Omega(\sqrt{m})$ to $\Omega(m / \log m)$ for sparse graphs, where $m$ is the number of edges in the graph. We also study a new problem on graphs with cycles, Minimum Cost Circulation Decomposition (MCCD), and show that it generalises MFD through a simple reduction. For the version allowing also negative weights, we give a $(\lceil \log \Vert X \Vert \rceil +1)$-approximation ($\Vert X \Vert$ being the maximum absolute value of $X$ on any edge) using a power-of-two approach, combined with parity fixing arguments and a decomposition of unitary circulations ($\Vert X \Vert \leq 1$), using a generalised notion of width for this problem. Finally, we disprove a conjecture about the linear independence of minimum (non-negative) flow decompositions posed by Kloster et al. [ALENEX 2018], but show that its useful implication (polynomial-time assignments of weights to a given set of paths to decompose a flow) holds for the negative version., Comment: A preliminary version was submitted to ESA 2022

Among the most important variants of the traveling salesman problem (TSP) are those relaxing the constraint that every locus should necessarily get visited, rather taking into account a revenue (prize) for visiting customers. In the Profitable Tour Problem (PTP), we seek for a tour visiting a subset of customers while maximizing net gain (profit) as difference between total revenue collected from visited customers and incurred traveling costs. The metric TSP can be modeled as a PTP with large revenues. As such, PTP is well-known to be NP-hard and also APX-hardness follows. Nevertheless, PTP is solvable in polynomial time on particular graph structures like lines, trees and circles. Following recent emphasis on robust optimization, and motivated by current flourishing of retail delivery services, we study the Probabilistic Profitable Tour Problem (PPTP), the generalization of PTP where customers will show up with a known probability, in their respective loci,only after the tour has been planned. Here, the selection of customers has to be made a priori, before knowing if a customer will actually submit his request or will not. While the tour has to be designed without this knowledge, revenues will only be collected from customers who will require the service. The objective is to maximize the expected net gain obtained by visiting only the customers that show up. We provide a polynomial time algorithm computing and characterizing the space of optimal solutions for the special case of the PPTP where customers are distributed on a line.

A minimum path cover (MPC) of a directed acyclic graph (DAG) $G = (V,E)$ is a minimum-size set of paths that together cover all the vertices of the DAG. Computing an MPC is a basic polynomial problem, dating back to Dilworth's and Fulkerson's results in the 1950s. Since the size $k$ of an MPC (also known as the width) can be small in practical applications, research has also studied algorithms whose complexity is parameterized on $k$. We obtain two new MPC parameterized algorithms for DAGs running in time $O(k^2|V|\log{|V|} + |E|)$ and $O(k^3|V| + |E|)$. We also obtain a parallel algorithm running in $O(k^2|V| + |E|)$ parallel steps and using $O(\log{|V|})$ processors (in the PRAM model). Our latter two algorithms are the first solving the problem in parameterized linear time. Finally, we present an algorithm running in time $O(k^2|V|)$ for transforming any MPC to another MPC using less than $2|V|$ distinct edges, which we prove to be asymptotically tight. As such, we also obtain edge sparsification algorithms preserving the width of the DAG with the same running time as our MPC algorithms. At the core of all our algorithms we interleave the usage of three techniques: transitive sparsification, shrinking of a path cover, and the splicing of a set of paths along a given path.

In a digraph, a quasi-kernel is a subset of vertices that is independent and such that every vertex can reach some vertex in that set via a directed path of length at most two. Whereas Chv\'atal and Lov\'asz proved in 1974 that every digraph has a quasi-kernel, very little is known so far about the complexity of finding small quasi-kernels. In 1976 Erd\H{o}s and Sz\'ekely conjectured that every sink-free digraph $D = (V, A)$ has a quasi-kernel of size at most $|V|/2$. Obviously, if $D$ has two disjoint quasi-kernels then it has a quasi-kernel of size at most $|V|/2$, and in 2001 Gutin, Koh, Tay and Yeo conjectured that every sink-free digraph has two disjoint quasi-kernels. Yet, they constructed in 2004 a counterexample, thereby disproving this stronger conjecture. We shall show that, not only sink-free digraphs occasionally fail to contain two disjoint quasi-kernels, but it is computationally hard to distinguish those that do from those that do not. We also prove that the problem of computing a small quasi-kernel is polynomial time solvable for orientations of trees but is computationally hard in most other cases (and in particular for restricted acyclic digraphs).

Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of an arc-covering walk of the graph. Since assembly graphs admit many solutions, the goal is to find what is definitely present in all solutions, or what is safe. Most practical assemblers are based on heuristics having at their core unitigs, namely paths whose internal nodes have unit in-degree and out-degree, and which are clearly safe. The long-standing open problem of finding all the safe parts of the solutions was recently solved [RECOMB 2016] yielding a 60% increase in contig length. This safe and complete genome assembly algorithm was followed by other works improving the time bounds, as well as extending the results for different notions of assembly solution. But it remained open whether one can be complete also for models of genome assembly of practical applicability. In this paper we present a universal framework for obtaining safe and complete algorithms which unify the previous results, while also allowing for easy generalisations to assembly problems including many practical aspects. This is based on a novel graph structure, called the hydrostructure of a walk, which highlights the reachability properties of the graph from the perspective of the walk. The hydrostructure allows for simple characterisations of the existing safe walks, and of their new practical versions. Almost all of our characterisations are directly adaptable to optimal verification algorithms, and simple enumeration algorithms. Most of these algorithms are also improved to optimality using an incremental computation procedure and a previous optimal algorithm of a specific model.

The width $k$ of a directed acyclic graph (DAG) $G = (V, E)$ equals the largest number of pairwise non-reachable vertices. Computing the width dates back to Dilworth's and Fulkerson's results in the 1950s, and is doable in quadratic time in the worst case. Since $k$ can be small in practical applications, research has also studied algorithms whose complexity is parameterized on $k$. Despite these efforts, it is still open whether there exists a linear-time $O(f(k)(|V| + |E|))$ parameterized algorithm computing the width. We answer this question affirmatively by presenting an $O(k^24^k|V| + k2^k|E|)$ time algorithm, based on a new notion of frontier antichains. As we process the vertices in a topological order, all frontier antichains can be maintained with the help of several combinatorial properties, paying only $f(k)$ along the way. The fact that the width can be computed by a single $f(k)$-sweep of the DAG is a new surprising insight into this classical problem. Our algorithm also allows deciding whether the DAG has width at most $w$ in time $O(f(\min(w,k))(|V|+|E|))$.

Given a directed graph $G$ and a pair of nodes $s$ and $t$, an \emph{$s$-$t$ bridge} of $G$ is an edge whose removal breaks all $s$-$t$ paths of $G$ (and thus appears in all $s$-$t$ paths). Computing all $s$-$t$ bridges of $G$ is a basic graph problem, solvable in linear time. In this paper, we consider a natural generalisation of this problem, with the notion of "safety" from bioinformatics. We say that a walk $W$ is \emph{safe} with respect to a set $\mathcal{W}$ of $s$-$t$ walks, if $W$ is a subwalk of all walks in $\mathcal{W}$. We start by considering the maximal safe walks when $\mathcal{W}$ consists of: all $s$-$t$ paths, all $s$-$t$ trails, or all $s$-$t$ walks of $G$. We show that the first two problems are immediate linear-time generalisations of finding all $s$-$t$ bridges, while the third problem is more involved. In particular, we show that there exists a compact representation computable in linear time, that allows outputting all maximal safe walks in time linear in their length. We further generalise these problems, by assuming that safety is defined only with respect to a subset of \emph{visible} edges. Here we prove a dichotomy between the $s$-$t$ paths and $s$-$t$ trails cases, and the $s$-$t$ walks case: the former two are NP-hard, while the latter is solvable with the same complexity as when all edges are visible. We also show that the same complexity results hold for the analogous generalisations of \emph{$s$-$t$ articulation points} (nodes appearing in all $s$-$t$ paths). We thus obtain the best possible results for natural "safety"-generalisations of these two fundamental graph problems. Moreover, our algorithms are simple and do not employ any complex data structures, making them ideal for use in practice.

Given a directed graph $G$ and a pair of nodes $s$ and $t$, an $s$-$t$ bridge of $G$ is an edge whose removal breaks all $s$-$t$ paths of $G$. Similarly, an $s$-$t$ articulation point of $G$ is a node whose removal breaks all $s$-$t$ paths of $G$. Computing the sequence of all $s$-$t$ bridges of $G$ (as well as the $s$-$t$ articulation points) is a basic graph problem, solvable in linear time using the classical min-cut algorithm. When dealing with cuts of unit size ($s$-$t$ bridges) this algorithm can be simplified to a single graph traversal from $s$ to $t$ avoiding an arbitrary $s$-$t$ path, which is interrupted at the $s$-$t$ bridges. Further, the corresponding proof is also simplified making it independent of the theory of network flows., Comment: 5 pages, 5 figures

Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from practical issues (size and errors of real data), and from the fact that problem formulations inherently admit multiple solutions. Given these, at their core, most state-of-the-art assemblers are based on finding non-branching paths (unitigs) in an assembly graph. If one defines a genome assembly solution as a closed arc-covering walk of the graph, then unitigs appear in all solutions, being thus safe partial solutions. All all such safe walks were recently characterized as omnitigs, leading to the first safe and complete genome assembly algorithm. Even if omnitig finding was improved to quadratic time, it remained open whether the crucial linear-time feature of finding unitigs can be attained with omnitigs. We describe a surprising $O(m)$-time algorithm to identify all maximal omnitigs of a graph with $n$ nodes and $m$ arcs, notwithstanding the existence of families of graphs with $\Theta(mn)$ total maximal omnitig size. This is based on the discovery of a family of walks (macrotigs) with the property that all the non-trivial omnitigs are univocal extensions of subwalks of a macrotig, with two consequences: (1) A linear-time output-sensitive algorithm enumerating all maximal omnitigs. (2) A compact $O(m)$ representation of all maximal omnitigs, which allows, e.g., for $O(m)$-time computation of various statistics on them. Our results close a long-standing theoretical question inspired by practical genome assemblers, originating with the use of unitigs in 1995. We envision our results to be at the core of a reverse transfer from theory to practical and complete genome assembly programs, as has been the case for other key Bioinformatics problems.

The Burrows-Wheeler-Transform (BWT) is a reversible string transformation which plays a central role in text compression and is fundamental in many modern bioinformatics applications. The BWT is a permutation of the characters, which is in general better compressible and allows to answer several different query types more efficiently than the original string. It is easy to see that not every string is a BWT image, and exact characterizations of BWT images are known. We investigate a related combinatorial question. In many applications, a sentinel character dollar is added to mark the end of the string, and thus the BWT of a string ending with dollar contains exactly one dollar-character. Given a string w, we ask in which positions, if any, the dollar-character can be inserted to turn w into the BWT image of a word ending with dollar. We show that this depends only on the standard permutation of w and present a O(n log n)-time algorithm for identifying all such positions, improving on the naive quadratic time algorithm. We also give a combinatorial characterization of such positions and develop bounds on their number and value. This is an extended version of [Giuliani et al. ICTCS 2019]., Comment: This is the journal version of paper at ICTCS 2019 (20th Italian Conference on Theoretical Computer Science, 9-11 Sept. 2019, Como, Italy). Journal version appeared in TCS 2021

In 2005 Kumar studied the Restricted Disjunctive Temporal Problem (RDTP), a restricted but very expressive class of disjunctive temporal problems (DTPs). It was shown that that RDTPs are solvable in deterministic strongly-polynomial time by reducing them to the Connected Row-Convex (CRC) constraints problem; plus, Kumar devised a randomized algorithm whose expected running time is less than that of the deterministic one. Instead, the most general form of DTPs allows for multi-variable disjunctions of many interval constraints and it is NP-complete. This work offers a deeper comprehension on the tractability of RDTPs, leading to an elementary deterministic strongly-polynomial time algorithm for them, significantly improving the asymptotic running times of both the deterministic and randomized algorithms of Kumar. The result is obtained by reducing RDTPs to the Single-Source Shortest-Paths (SSSP) and the 2-SAT problem (jointly), instead of reducing to CRCs. In passing, we obtain a faster (quadratic-time) algorithm for RDTPs having only Type-1 and Type-2 constraints (and no Type-3 constraint). As a second main contribution, we study the tractability frontier of solving RDTPs by considering Hyper Temporal Networks (\HTNs), a strict generalization of \STNs grounded on hypergraphs: on one side, we prove that solving temporal problems having only Type-2 constraints and either only multi-tail or only multi-head hyperarc constraints lies in both NP and co-NP and it admits deterministic pseudo-polynomial time algorithms; on the other side, solving problems with Type-3 constraints and either only multi-tail or only multi-head hyperarc constraints turns strongly NP-complete.

Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurovi\'c et al. (IEEE TCBB, to appear) introduced the minimum conflict-free row split (MCRS) problem: split each row of a given binary matrix into a bitwise OR of a set of rows so that the resulting matrix corresponds to a perfect phylogeny and has the minimum possible number of rows among all matrices with this property. Hajirasouliha and Raphael also proposed the study of a similar problem, in which the task is to minimize the number of distinct rows of the resulting matrix. Hujdurovi\'c et al. proved that both problems are NP-hard, gave a related characterization of transitively orientable graphs, and proposed a polynomial-time heuristic algorithm for the MCRS problem based on coloring cocomparability graphs. We give new, more transparent formulations of the two problems, showing that the problems are equivalent to two optimization problems on branchings in a derived directed acyclic graph. Building on these formulations, we obtain new results on the two problems, including: (i) a strengthening of the heuristic by Hujdurovi\'c et al. via a new min-max result in digraphs generalizing Dilworth's theorem, which may be of independent interest, (ii) APX-hardness results for both problems, (iii) approximation algorithms, and (iv) exponential-time algorithms solving the two problems to optimality faster than the na\"ive brute-force approach. Our work relates to several well studied notions in combinatorial optimization: chain partitions in partially ordered sets, laminar hypergraphs, and (classical and weighted) colorings of graphs., Comment: 29 pages, 10 figures, extended abstract appeared in Proceedings of WG 2017, full paper accepted for publication in ACM Transactions on Algorithms

Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence analysis. In this paper, we show that the computational complexity will change for natural extensions of alignments to pan-genome representations and to diploid genomes. More broadly, our approach can also be seen as a minimal extension of sequence alignment to labelled directed acyclic graphs (labeled DAGs). Namely, we show that finding a \emph{covering alignment} of two labeled DAGs is NP-hard even on binary alphabets. A covering alignment asks for two paths $R_1$ (red) and $G_1$ (green) in DAG $D_1$ and two paths $R_2$ (red) and $G_2$ (green) in DAG $D_2$ that cover the nodes of the graphs and maximize the sum of the global alignment scores: $\mathsf{as}(\mathsf{sp}(R_1),\mathsf{sp}(R_2))+\mathsf{as}(\mathsf{sp}(G_1),\mathsf{sp}(G_2))$, where $\mathsf{sp}(P)$ is the concatenation of labels on the path $P$. Pair-wise alignment of haplotype sequences forming a diploid chromosome can be converted to a two-path coverable labelled DAG, and then the covering alignment models the similarity of two diploids over arbitrary recombinations. We also give a reduction to the other direction, to show that such a recombination-oblivious diploid alignment is NP-hard on alphabets of size $3$.

An alternating graph is a directed graph whose vertex set is partitioned into two classes, existential and universal. This forms the basic arena for a plethora of infinite duration two-player games where Player~$\square$ and~$\ocircle$ alternate in a turn-based sliding of a pebble along the arcs they control. We study alternating strongly-connectedness as a generalization of strongly-connectedness in directed graphs, aiming at providing a linear time decomposition and a sound structural graph characterization. For this a refined notion of alternating reachability is introduced: Player~$\square$ attempts to reach vertices without leaving a prescribed subset of the vertices, while Player~$\ocircle$ works against. This is named \emph{safe alternating reachability}. It is shown that every arena uniquely decomposes into safe alternating strongly-connected components where Player~$\square$ can visit each vertex within a given component infinitely often, without having to ever leave out the component itself. Our main result is a linear time algorithm for computing this alternating graph decomposition. Both the underlying graph structures and the algorithm generalize the classical decomposition of a directed graph into strongly-connected components. The algorithm builds on a linear time generalization of the depth-first search on alternation, taking inspiration from Tarjan 1972 machinery. Our theory has direct applications in solving well-known infinite duration pebble games faster. Dinneen and Khoussainov showed in 1999 that deciding a given Update Game costs $O(mn)$ time, where $n$ is the number of vertices and $m$ is that of arcs. We solve the task in $\Theta(m+n)$ linear~time. The complexity of Explicit McNaughton-M\"uller Games also improves from cubic to quadratic.

This study strengthens the links between Mean Payoff Games (\MPG{s}) and Energy Games (EG{s}). Firstly, we offer a faster $O(|V|^2|E|W)$ pseudo-polynomial time and $\Theta(|V|+|E|)$ space deterministic algorithm for solving the Value Problem and Optimal Strategy Synthesis in \MPG{s}. This improves the best previously known estimates on the pseudo-polynomial time complexity to: \[ O(|E|\log |V|) + \Theta\Big(\sum_{v\in V}\texttt{deg}_{\Gamma}(v)\cdot\ell_{\Gamma}(v)\Big) = O(|V|^2|E|W), \] where $\ell_{\Gamma}(v)$ counts the number of times that a certain energy-lifting operator $\delta(\cdot, v)$ is applied to any $v\in V$, along a certain sequence of Value-Iterations on reweighted \EG{s}; and $\texttt{deg}_{\Gamma}(v)$ is the degree of $v$. This improves significantly over a previously known pseudo-polynomial time estimate, i.e. $\Theta\big(|V|^2|E|W + \sum_{v\in V}\texttt{deg}_{\Gamma}(v)\cdot\ell_{\Gamma}(v)\big)$ \citep{CR15, CR16}, as the pseudo-polynomiality is now confined to depend solely on $\ell_\Gamma$. Secondly, we further explore on the relationship between Optimal Positional Strategies (OPSs) in \MPG{s} and Small Energy-Progress Measures (SEPMs) in reweighted \EG{s}. It is observed that the space of all OPSs, $\texttt{opt}_{\Gamma}\Sigma^M_0$, admits a unique complete decomposition in terms of extremal-SEPM{s} in reweighted EG{s}. This points out what we called the "Energy-Lattice $\mathcal{X}^*_{\Gamma}$ associated to $\texttt{opt}_{\Gamma}\Sigma^M_0$". Finally, it is offered a pseudo-polynomial total-time recursive procedure for enumerating (w/o repetitions) all the elements of $\mathcal{X}^*_{\Gamma}$, and for computing the corresponding partitioning of $\texttt{opt}_{\Gamma}\Sigma^M_0$.

Even after the proposal of various solution algorithms, the precise computational complexity of checking whether a Conditional Temporal Network is Dynamically Controllable had still remained widely open. This issue gets settled in this paper which provides constructions, algorithms, and bridging lemmas and arguments to formally prove that: (1) the problem is PSPACE-hard, and (2) the problem lies in PSPACE., Comment: Accepted to TIME2016

CSTNs is a constraint-based graph-formalism for conditional temporal planning. In order to address the DC-Checking problem, in [Comin and Rizzi, TIME 2015] we introduced epsilon-DC (a refined, more realistic, notion of DC), and provided an algorithmic solution to it. The epsilon-DC notion is interesting per se, and the epsilon-DC-Checking algorithm in [Comin and Rizzi, TIME 2015] rests on the assumption that the reaction-time satisfies epsilon > 0; leaving unsolved the question of what happens when epsilon = 0. In this work, we introduce and study pi-DC, a sound notion of DC with an instantaneous reaction-time (i.e. one in which the planner can react to any observation at the same instant of time in which the observation is made). Firstly, we demonstrate by a counter-example that pi-DC is not equivalent to 0-DC, and that 0-DC is actually inadequate for modeling DC with an instantaneous reaction-time. This shows that the main results obtained in our previous work do not apply directly, as they were formulated, to the case of epsilon=0. Motivated by this observation, as a second contribution, our previous tools are extended in order to handle pi-DC, and the notion of ps-tree is introduced, also pointing out a relationship between pi-DC and HyTN-Consistency. Thirdly, a simple reduction from pi-DC-Checking to DC-Checking is identified. This allows us to design and to analyze the first sound-and-complete pi-DC-Checking procedure. Remarkably, the time complexity of the proposed algorithm remains (pseudo) singly-exponential in the number of propositional letters. Finally, it is observed that the technique can be leveraged to actually reduce from pi-DC to 1-DC, this allows us to further improve the exponents in the time complexity of pi-DC-Checking., Comment: 23rd International Symposium on Temporal Representation and Reasoning (TIME2016)

Computing the simulation preorder of a given Kripke structure (i.e., a directed graph with $n$ labeled vertices) has crucial applications in model checking of temporal logic. It amounts to solving a specific two-players reachability game, called simulation game. We offer the first conditional lower bounds for this problem, and we relate its complexity (for computation, verification, and certification) to some variants of $n\times n$ matrix multiplication. We show that any $O(n^{\alpha})$-time algorithm for simulation games, even restricting to acyclic games/structures, can be used to compute $n\times n$ boolean matrix multiplication (BMM) in $O(n^{\alpha})$ time. This is the first evidence that improving the existing $O(n^{3})$-time solutions may be difficult, without resorting to fast matrix multiplication. In the acyclic case, we match this lower bound presenting the first subcubic algorithm, based on fast BMM, and running in $n^{\omega+o(1)}$ time (where $\omega<2.376$ is the exponent of matrix multiplication). For both acyclic and cyclic structures, we point out the existence of natural and canonical $O(n^{2})$-size certificates, that can be verified in truly subcubic time. In the acyclic case, $O(n^{2})$ time is sufficient, employing standard matrix product verification. In the cyclic case, a $\max$-semi-boolean matrix multiplication (MSBMM) is used, i.e., a matrix multiplication on the semi-ring $(\max,\times)$ where one matrix contains only $0$'s and $1$'s. This MSBMM is computable (hence verifiable) in truly subcubic $n^{(3+\omega)/2+o(1)}$ time by reduction to $(\max,\min)$-multiplication. Finally, we show a reduction from MSBMM to cyclic simulation games which implies a separation between the cyclic and the acyclic cases, unless MSBMM can be verified in $n^{\omega+o(1)}$ time., Comment: Submitted. Changed in v2: This is a major rewrite of the paper. The introduction has been expanded considerably, some notation has been simplified, proofs of general results on reachability games have been moved to the appendix, more intuitive arguments for proofs have been provided, moving the formal arguments to the appendix, more references have been added

Let $S=\{K_{1,3},K_3,P_4\}$ be the set of connected graphs of size 3. We study the problem of partitioning the edge set of a graph $G$ into graphs taken from any non-empty $S'\subseteq S$. The problem is known to be NP-complete for any possible choice of $S'$ in general graphs. In this paper, we assume that the input graph is cubic, and study the computational complexity of the problem of partitioning its edge set for any choice of $S'$. We identify all polynomial and NP-complete problems in that setting, and give graph-theoretic characterisations of $S'$-decomposable cubic graphs in some cases., Comment: to appear in the proceedings of COCOON 2016

A wide range of applications, most notably in comparative genomics, involve the computation of a shortest sorting sequence of operations for a given permutation, where the set of allowed operations is fixed beforehand. Such sequences are useful for instance when reconstructing potential scenarios of evolution between species, or when trying to assess their similarity. We revisit those problems by adding a new constraint on the sequences to be computed: they must \emph{avoid} a given set of \emph{forbidden intermediates}, which correspond to species that cannot exist because the mutations that would be involved in their creation are lethal. We initiate this study by focusing on the case where the only mutations that can occur are exchanges of any two elements in the permutations, and give a polynomial time algorithm for solving that problem when the permutation to sort is an involution.

In this work we introduce the \emph{Conditional Hyper Temporal Network (CHyTN)} model, which is a natural extension and generalization of both the \CSTN and the \HTN model. Our contribution goes as follows. We show that deciding whether a given \CSTN or CHyTN is dynamically consistent is \coNP-hard. Then, we offer a proof that deciding whether a given CHyTN is dynamically consistent is \PSPACE-hard, provided that the input instances are allowed to include both multi-head and multi-tail hyperarcs. In light of this, we continue our study by focusing on CHyTNs that allow only multi-head or only multi-tail hyperarcs, and we offer the first deterministic (pseudo) singly-exponential time algorithm for the problem of checking the dynamic-consistency of such CHyTNs, also producing a dynamic execution strategy whenever the input CHyTN is dynamically consistent. Since \CSTN{s} are a special case of CHyTNs, this provides as a byproduct the first sound-and-complete (pseudo) singly-exponential time algorithm for checking dynamic-consistency in CSTNs. The proposed algorithm is based on a novel connection between CSTN{s}/CHyTN{s} and Mean Payoff Games. The presentation of the connection between \CSTN{s}/CHyTNs and \MPG{s} is mediated by the \HTN model. In order to analyze the algorithm, we introduce a refined notion of dynamic-consistency, named $\epsilon$-dynamic-consistency, and present a sharp lower bounding analysis on the critical value of the reaction time $\hat{\varepsilon}$ where a \CSTN/CHyTN transits from being, to not being, dynamically consistent. The proof technique introduced in this analysis of $\hat{\varepsilon}$ is applicable more generally when dealing with linear difference constraints which include strict inequalities., Comment: arXiv admin note: text overlap with arXiv:1505.00828

In this paper, we present a novel algorithm for the maximum a posteriori decoding (MAPD) of time-homogeneous Hidden Markov Models (HMM), improving the worst-case running time of the classical Viterbi algorithm by a logarithmic factor. In our approach, we interpret the Viterbi algorithm as a repeated computation of matrix-vector $(\max, +)$-multiplications. On time-homogeneous HMMs, this computation is online: a matrix, known in advance, has to be multiplied with several vectors revealed one at a time. Our main contribution is an algorithm solving this version of matrix-vector $(\max,+)$-multiplication in subquadratic time, by performing a polynomial preprocessing of the matrix. Employing this fast multiplication algorithm, we solve the MAPD problem in $O(mn^2/ \log n)$ time for any time-homogeneous HMM of size $n$ and observation sequence of length $m$, with an extra polynomial preprocessing cost negligible for $m > n$. To the best of our knowledge, this is the first algorithm for the MAPD problem requiring subquadratic time per observation, under the only assumption -- usually verified in practice -- that the transition probability matrix does not change with time., Comment: AAAI 2016, to appear

Given permutations $\sigma \in S_k$ and $\pi \in S_n$ with $k

Acyclic and cyclic orientations of an undirected graph have been widely studied for their importance: an orientation is acyclic if it assigns a direction to each edge so as to obtain a directed acyclic graph (DAG) with the same vertex set; it is cyclic otherwise. As far as we know, only the enumeration of acyclic orientations has been addressed in the literature. In this paper, we pose the problem of efficiently enumerating all the \emph{cyclic} orientations of an undirected connected graph with $n$ vertices and $m$ edges, observing that it cannot be solved using algorithmic techniques previously employed for enumerating acyclic orientations.We show that the problem is of independent interest from both combinatorial and algorithmic points of view, and that each cyclic orientation can be listed with $\tilde{O}(m)$ delay time. Space usage is $O(m)$ with an additional setup cost of $O(n^2)$ time before the enumeration begins, or $O(mn)$ with a setup cost of $\tilde{O}(m)$ time.

The first output-sensitive algorithm for the Maximal Clique Listing problem was given by Tsukiyama et.al. in 1977. As any algorithm falling within the Reverse Search paradigm, it performs a DFS visit of a directed tree (the RS-tree) having the objects to be listed (i.e. maximal cliques) as its nodes. In a recursive implementation, the RS-tree corresponds to the recursion tree of the algorithm. The time delay is given by the cost of generating the next child of a node, and Tsukiyama showed it is $O(mn)$. In 2004, Makino and Uno sharpened the time delay to $O(n^{\omega})$ by generating all the children of a node in one single shot performed by computing a \emph{square} fast matrix multiplication. In this paper, we further improve the asymptotics for the exploration of the same RS-tree by grouping the offsprings' computation even further. Our idea is to rely on rectangular fast matrix multiplication in order to compute all children of $n^2$ nodes in one shot. According to the current upper bounds on fast matrix multiplication, with this the time delay improves from $O(n^{2.3728639})$ to $O(n^{2.093362})$.

Conditional Simple Temporal Network (CSTN) is a constraint-based graph-formalism for conditional temporal planning. It offers a more flexible formalism than the equivalent CSTP model of Tsamardinos, Vidal and Pollack, from which it was derived mainly as a sound formalization. Three notions of consistency arise for CSTNs and CSTPs: weak, strong, and dynamic. Dynamic consistency is the most interesting notion, but it is also the most challenging and it was conjectured to be hard to assess. Tsamardinos, Vidal and Pollack gave a doubly-exponential time algorithm for deciding whether a CSTN is dynamically-consistent and to produce, in the positive case, a dynamic execution strategy of exponential size. In the present work we offer a proof that deciding whether a CSTN is dynamically-consistent is coNP-hard and provide the first singly-exponential time algorithm for this problem, also producing a dynamic execution strategy whenever the input CSTN is dynamically-consistent. The algorithm is based on a novel connection with Mean Payoff Games, a family of two-player combinatorial games on graphs well known for having applications in model-checking and formal verification. The presentation of such connection is mediated by the Hyper Temporal Network model, a tractable generalization of Simple Temporal Networks whose consistency checking is equivalent to determining Mean Payoff Games. In order to analyze the algorithm we introduce a refined notion of dynamic-consistency, named \epsilon-dynamic-consistency, and present a sharp lower bounding analysis on the critical value of the reaction time \hat{\varepsilon} where the CSTN transits from being, to not being, dynamically-consistent. The proof technique introduced in this analysis of \hat{\varepsilon} is applicable more in general when dealing with linear difference constraints which include strict inequalities.