Compatibility of unrooted phylogenetic trees is FPT

A collection of _T1,_T2,…,_Tk$T_1,T_2,\dots ,T_k$ of unrooted, leaf labelled (phylogenetic) trees, all with different leaf sets, is said to be compatible   if there exists a tree T$T$ such that each tree _Ti$T_i$ can be obtained from T$T$ by deleting leaves and contracting edges. Determining compatibility is NP-hard, and the fastest algorithm to date has worst case complexity of around Ω(n^k)$\mathrm{\Omega }(n^k)$ time, n$n$ being the number of leaves. Here, we present an O(nf(k))$\mathrm{O}(\mathit{nf}(k))$ algorithm, proving that compatibility of unrooted phylogenetic trees is fixed parameter tractable   (FPT) with respect to the number k$k$ of trees.     

Adaptive timeliness of consensus in presence of crash and timing faults

The Δ$\mathrm{\Delta }$-timed uniform consensus is a stronger variant of the traditional consensus and it satisfies the following additional property: every correct process terminates its execution within a constant time Δ$\mathrm{\Delta }$ (Δ$\mathrm{\Delta }$-timeliness), and no two processes decide differently (uniformity). In this paper, we consider the Δ$\mathrm{\Delta }$-timed uniform consensus problem in presence of _fc$f_{\mathrm{c}}$ crash processes and _ft$f_{\mathrm{t}}$ timing-faulty processes, and propose a Δ$\mathrm{\Delta }$-timed uniform consensus algorithm. The proposed algorithm is adaptive in the following sense: it solves the Δ$\mathrm{\Delta }$-timed uniform consensus when at least _ft+1$f_{\mathrm{t}}+1$ correct processes exist in the system. If the system has less than _ft+1$f_{\mathrm{t}}+1$ correct processes, the algorithm cannot solve the Δ$\mathrm{\Delta }$-timed uniform consensus. However, as long as _ft+1$f_{\mathrm{t}}+1$ processes are non-crashed, the algorithm solves (non-timed) uniform consensus. We also investigate the maximum number of faulty processes that can be tolerated. We show that any Δ$\mathrm{\Delta }$-timed uniform consensus algorithm tolerating up to _ft$f_{\mathrm{t}}$ timing-faulty processes requires that the system has at least _ft+1$f_{\mathrm{t}}+1$ correct processes. This impossibility result implies that the proposed algorithm attains the maximum resilience about the number of faulty processes. We also show that any Δ$\mathrm{\Delta }$-timed uniform consensus algorithm tolerating up to _ft$f_{\mathrm{t}}$ timing-faulty processes cannot solve the (non-timed) uniform consensus when the system has less than _ft+1$f_{\mathrm{t}}+1$ non-crashed processes. This impossibility result implies that our algorithm attains the maximum adaptiveness.     

A palindromization map for the free group

We define a self-map Pal:_F2→_F2$Pal:F_2\to F_2$ of the free group on two generators a,b$a,b$, using automorphisms of _F2$F_2$ that form a group isomorphic to the braid group _B3$B_3$. The map Pal$Pal$ restricts to de Luca’s right iterated palindromic closure on the submonoid generated by a,b$a,b$. We show that Pal$Pal$ is continuous for the profinite topology on _F2$F_2$; it is the unique continuous extension of de Luca’s right iterated palindromic closure to _F2$F_2$. The values of Pal$Pal$ are palindromes and coincide with the elements g∈_F2$g\in F_2$ such that abg$abg$ and bag$bag$ are conjugate.     

Large independent sets in random regular graphs

We present algorithmic lower bounds on the size _sd$s_d$ of the largest independent sets of vertices in random d$d$-regular graphs, for each fixed d≥3$d\ge 3$. For instance, for d=3$d=3$ we prove that, for graphs on n$n$ vertices, _sd≥0.43475n$s_d\ge 0.43475n$ with probability approaching one as n$n$ tends to infinity.     

Complexity of question/answer games

Question/Answer games (Q/A games for short) are a generalization of the Rényi–Ulam game and they are a model for information extraction in parallel. A Q/A game, G=(D,s,(_q1,…,_qk))$G=(D,s,(q_1,\dots ,q_k))$, is played on a directed acyclic graph, D=(V,E)$D=(V,E)$, with a distinguished start vertex s$s$. In the i$i$th round, Paul selects a set, _Qi⊆V$Q_i\subseteq V$, of at most _qi$q_i$ non-terminal vertices. Carole responds by choosing an outgoing edge from each vertex in _Qi$Q_i$. At the end of k$k$ rounds, Paul wins if Carole’s answers define a unique path from the root to one of the terminal vertices in D$D$.     

Minimum cost source location problem with local 3-vertex-connectivity requirements

Let G=(V,E)$G=(V,E)$ be a simple undirected graph with a set V$V$ of vertices and a set E$E$ of edges. Each vertex v∈V$v\in V$ has a demand d(v)∈_Z+$d\left(v\right)\in Z_{+}$ and a cost c(v)∈_R+$c\left(v\right)\in R_{+}$, where _Z+$Z_{+}$ and _R+$R_{+}$ denote the set of nonnegative integers and the set of nonnegative reals, respectively. The source location problem with vertex-connectivity requirements in a given graph G$G$ requires finding a set S$S$ of vertices minimizing _∑v∈Sc(v)${\sum }_{v\in S}c\left(v\right)$ such that there are at least d(v)$d\left(v\right)$ pairwise vertex-disjoint paths from S$S$ to v$v$ for each vertex v∈V−S$v\in V-S$. It is known that if there exists a vertex v∈V$v\in V$ with d(v)≥4$d\left(v\right)\ge 4$, then the problem is NP-hard even in the case where every vertex has a uniform cost. In this paper, we show that the problem can be solved in O(|V|⁴log²|V|)$O\left({\left|V\right|}^4{log}^2\left|V\right|\right)$ time if d(v)≤3$d\left(v\right)\le 3$ holds for each vertex v∈V$v\in V$.     

Degree-constrained decompositions of graphs: Bounded treewidth and planarity

We study the problem of decomposing the vertex set V$V$ of a graph into two nonempty parts _V1,_V2$V_1,V_2$ which induce subgraphs where each vertex v∈_V1$v\in V_1$ has degree at least a(v)$a(v)$ inside _V1$V_1$ and each v∈_V2$v\in V_2$ has degree at least b(v)$b(v)$ inside _V2$V_2$. We give a polynomial-time algorithm for graphs with bounded treewidth which decides if a graph admits a decomposition, and gives such a decomposition if it exists. This result and its variants are then applied to designing polynomial-time approximation schemes for planar graphs where a decomposition does not necessarily exist but the local degree conditions should be met for as many vertices as possible.     

Divergence bounded computable real numbers

A real x$x$ is called h$h$-bounded computable  , for some function h:N→N$h:\mathbb{N}\to \mathbb{N}$, if there is a computable sequence (_xs)$(x_s)$ of rational numbers which converges to x$x$ such that, for any n∈N$n\in \mathbb{N}$, at most h(n)$h(n)$ non-overlapping pairs of its members are separated by a distance larger than 2^-n$2^{-n}$. In this paper we discuss properties of h$h$-bounded computable reals for various functions h$h$. We will show a simple sufficient condition for a class of functions h$h$ such that the corresponding h$h$-bounded computable reals form an algebraic field. A hierarchy theorem for h$h$-bounded computable reals is also shown. Besides we compare semi-computability and weak computability with the h$h$-bounded computability for special functions h$h$.     

Performance tradeoffs in structured peer to peer streaming

We consider the following basic question: a source node wishes to stream an ordered sequence of packets to a collection of receivers, which are in K$K$ clusters. A node may send a packet to another node in its own cluster in one time step and to a node in a different cluster in _Tc$T_c$ time steps (_Tc>1)$(T_c>1)$. Each cluster has two special nodes. We assume that the source and the special nodes in each cluster have a higher capacity and thus can send multiple packets at each step, while all other nodes can both send and receive a packet at each step. We construct two (intra-cluster) data communication schemes, one based on multi-trees (using a collection of d$d$-ary interior-disjoint trees) and the other based on hypercubes. The multi-tree scheme sustains streaming within a cluster with O(dlogN)$O(dlogN)$ maximum playback delay and O(dlogN)$O(dlogN)$ size buffers, while communicating with O(d)$O\left(d\right)$ neighbors, where N$N$ is the maximum size of any cluster. We also show that this protocol is optimal when d=2$d=2$ or 3. The hypercube scheme sustains streaming within a cluster, with O(log²(N))$O\left({log}^2\left(N\right)\right)$ maximum playback delay and O(1)$O\left(1\right)$ size buffers, while communicating with O(log(N))$O(log\left(N\right))$ neighbors, for arbitrary N$N$. In addition, we extend our multi-tree scheme to work when receivers depart and arrive over time. We also evaluate our dynamic schemes using simulations.     

On some special solutions to periodic Benjamin-Ono equation with discrete Laplacian

We investigate a periodic version of the Benjamin-Ono (BO) equation associated with a discrete Laplacian. We find some special solutions to this equation, and calculate the values of the first two integrals of motion _I1$I_1$ and _I2$I_2$ corresponding to these solutions. It is found that there exists a strong resemblance between them and the spectra for the Macdonald q$q$-difference operators. To better understand the connection between these classical and quantum integrable systems, we consider the special degenerate case corresponding to q=0$q=0$ in more detail. Namely, we give general solutions to this degenerate periodic BO, obtain explicit formulas representing all the integrals of motions _In$I_n$ (n=1,2,…$n=1\text{,}2\text{,}\dots$), and successfully identify it with the eigenvalues of Macdonald operators in the limit q→0$q\to 0$, i.e. the limit where Macdonald polynomials tend to the Hall–Littlewood polynomials.     

Approximation algorithms for orthogonal packing problems for hypercubes

Orthogonal packing problems are natural multidimensional generalizations of the classical bin packing problem and knapsack problem and occur in many different settings. The input consists of a set I={_r1,…,_rn}$I=\{r_1,\dots ,r_n\}$ of d$d$-dimensional rectangular items _ri=(_ai,1,…,_ai,d)$r_i=(a_{i,1},\dots ,a_{i,d})$ and a space Q$Q$. The task is to pack the items in an orthogonal and non-overlapping manner without using rotations into the given space. In the strip packing setting the space Q$Q$ is given by a strip of bounded basis and unlimited height. The objective is to pack all items into a strip of minimal height. In the knapsack packing setting the given space Q$Q$ is a single, usually unit sized bin and the items have associated profits _pi$p_i$. The goal is to maximize the profit of a selection of items that can be packed into the bin.     

An approximation algorithm to the k-Steiner Forest problem

Given a graph G$G$, an integer k$k$, and a demand set D={(_s1,_t1),…,(_sl,_tl)}$D=\{(s_1,t_1),\dots ,(s_l,t_l)\}$, the k$k$-Steiner Forest problem finds a forest in graph G$G$ to connect at least k$k$ demands in D$D$ such that the cost of the forest is minimized. This problem was proposed by Hajiaghayi and Jain in SODA’06. Thereafter, using a Lagrangian relaxation technique, Segev et al. gave the first approximation algorithm to this problem in ESA’06, with performance ratio O(n^2/3logl)$O(n^{2/3}logl)$. We give a simpler and faster approximation algorithm to this problem with performance ratio O(n^2/3logk)$O(n^{2/3}logk)$ via greedy approach, improving the previously best known ratio in the literature.     

Modeling and solving the rooted distance-constrained minimum spanning tree problem

In this paper we discuss models and methods for solving the rooted distance constrained minimum spanning tree problem which is defined as follows: given a graph G=(V,E)$G=(V,E)$ with node set V={0,1,…,n}$V=\{0,1,\dots ,n\}$ and edge set E$E$, two integer weights, a cost _ce$c_e$ and a delay _we$w_e$ associated with each edge e$e$ of E$E$, and a natural (time limit) number H$H$, we wish to find a spanning tree T$T$ of the graph with minimum total cost and such that the unique path from a specified root node, node 0, to any other node has total delay not greater than H$H$. This problem generalizes the well known hop-constrained spanning tree problem and arises in the design of centralized networks with quality of service constraints and also in package shipment with service guarantee constraints. We present three theoretically equivalent modeling approaches, a column generation scheme, a Lagrangian relaxation combined with subgradient optimization procedure, both based on a path formulation of the problem, and a shortest path (compact) reformulation of the problem which views the underlying subproblem as defined in a layered extended graph. We present results for complete graph instances with up to 40 nodes. Our results indicate that the layered graph path reformulation model is still quite good when the arc weights are reasonably small. Lagrangian relaxation combined with subgradient optimization procedure appears to work much better than column generation and seems to be a quite reasonable approach to the problem for large weight, and even small weight, instances.