On space efficiency of algorithms working on structural decompositions of graphs

Dynamic programming on path and tree decompositions of graphs is a technique that is ubiquitous in the field of parameterized and exponential-time algorithms. However, one of its drawbacks is that the space usage is exponential in the decomposition's width. Following the work of Allender et al. [Theory of Computing, '14], we investigate whether this space complexity explosion is unavoidable. Using the idea of reparameterization of Cai and Juedes [J. Comput. Syst. Sci., '03], we prove that the question is closely related to a conjecture that the Longest Common Subsequence problem parameterized by the number of input strings does not admit an algorithm that simultaneously uses XP time and FPT space. Moreover, we complete the complexity landscape sketched for pathwidth and treewidth by Allender et al. by considering the parameter tree-depth. We prove that computations on tree-depth decompositions correspond to a model of non-deterministic machines that work in polynomial time and logarithmic space, with access to an auxiliary stack of maximum height equal to the decomposition's depth. Together with the results of Allender et al., this describes a hierarchy of complexity classes for polynomial-time non-deterministic machines with different restrictions on the access to working space, which mirrors the classic relations between treewidth, pathwidth, and tree-depth.Comment: An extended abstract appeared in the proceedings of STACS'16. The new version is augmented with a space-efficient algorithm for Dominating Set using the Chinese remainder theore

Log-space Algorithms for Paths and Matchings in k-trees

Reachability and shortest path problems are NL-complete for general graphs. They are known to be in L for graphs of tree-width 2 [JT07]. However, for graphs of tree-width larger than 2, no bound better than NL is known. In this paper, we improve these bounds for k-trees, where k is a constant. In particular, the main results of our paper are log-space algorithms for reachability in directed k-trees, and for computation of shortest and longest paths in directed acyclic k-trees. Besides the path problems mentioned above, we also consider the problem of deciding whether a k-tree has a perfect macthing (decision version), and if so, finding a perfect match- ing (search version), and prove that these two problems are L-complete. These problems are known to be in P and in RNC for general graphs, and in SPL for planar bipartite graphs [DKR08]. Our results settle the complexity of these problems for the class of k-trees. The results are also applicable for bounded tree-width graphs, when a tree-decomposition is given as input. The technique central to our algorithms is a careful implementation of divide-and-conquer approach in log-space, along with some ideas from [JT07] and [LMR07].Comment: Accepted in STACS 201

Measuring and Understanding Throughput of Network Topologies

High throughput is of particular interest in data center and HPC networks. Although myriad network topologies have been proposed, a broad head-to-head comparison across topologies and across traffic patterns is absent, and the right way to compare worst-case throughput performance is a subtle problem. In this paper, we develop a framework to benchmark the throughput of network topologies, using a two-pronged approach. First, we study performance on a variety of synthetic and experimentally-measured traffic matrices (TMs). Second, we show how to measure worst-case throughput by generating a near-worst-case TM for any given topology. We apply the framework to study the performance of these TMs in a wide range of network topologies, revealing insights into the performance of topologies with scaling, robustness of performance across TMs, and the effect of scattered workload placement. Our evaluation code is freely available

An Efficient Dynamic Programming Algorithm for the Generalized LCS Problem with Multiple Substring Exclusion Constrains

In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of total length $r$, the problem is to find a common subsequence $Z$ of $X$ and $Y$ excluding each of constrain string in $P$ as a substring and the length of $Z$ is maximized. The problem was declared to be NP-hard\cite{1}, but we finally found that this is not true. A new dynamic programming solution for this problem is presented in this paper. The correctness of the new algorithm is proved. The time complexity of our algorithm is $O(nmr)$.Comment: arXiv admin note: substantial text overlap with arXiv:1301.718

Optimal Computation of Avoided Words

The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the standard deviation of $w$, denoted by $std(w)$, effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word $w$ of length $k>2$ is a $\rho$-avoided word in $x$ if $std(w) \leq \rho$, for a given threshold $\rho < 0$. Notice that such a word may be completely absent from $x$. Hence computing all such words na\"{\i}vely can be a very time-consuming procedure, in particular for large $k$. In this article, we propose an $O(n)$-time and $O(n)$-space algorithm to compute all $\rho$-avoided words of length $k$ in a given sequence $x$ of length $n$ over a fixed-sized alphabet. We also present a time-optimal $O(\sigma n)$-time and $O(\sigma n)$-space algorithm to compute all $\rho$-avoided words (of any length) in a sequence of length $n$ over an alphabet of size $\sigma$. Furthermore, we provide a tight asymptotic upper bound for the number of $\rho$-avoided words and the expected length of the longest one. We make available an open-source implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency of our implementation

The complexity of resolving conflicts on MAC

We consider the fundamental problem of multiple stations competing to transmit on a multiple access channel (MAC). We are given $n$ stations out of which at most $d$ are active and intend to transmit a message to other stations using MAC. All stations are assumed to be synchronized according to a time clock. If $l$ stations node transmit in the same round, then the MAC provides the feedback whether $l=0$, $l=2$ (collision occurred) or $l=1$. When $l=1$, then a single station is indeed able to successfully transmit a message, which is received by all other nodes. For the above problem the active stations have to schedule their transmissions so that they can singly, transmit their messages on MAC, based only on the feedback received from the MAC in previous round. For the above problem it was shown in [Greenberg, Winograd, {\em A Lower bound on the Time Needed in the Worst Case to Resolve Conflicts Deterministically in Multiple Access Channels}, Journal of ACM 1985] that every deterministic adaptive algorithm should take $\Omega(d (\lg n)/(\lg d))$ rounds in the worst case. The fastest known deterministic adaptive algorithm requires $O(d \lg n)$ rounds. The gap between the upper and lower bound is $O(\lg d)$ round. It is substantial for most values of $d$: When $d =$ constant and $d \in O(n^{\epsilon})$ (for any constant $\epsilon \leq 1$, the lower bound is respectively $O(\lg n)$ and O(n), which is trivial in both cases. Nevertheless, the above lower bound is interesting indeed when $d \in$ poly($\lg n$). In this work, we present a novel counting argument to prove a tight lower bound of $\Omega(d \lg n)$ rounds for all deterministic, adaptive algorithms, closing this long standing open question.}Comment: Xerox internal report 27th July; 7 page

EERTREE: An Efficient Data Structure for Processing Palindromes in Strings

We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using this structure, we present simple and efficient solutions for a number of problems involving palindromes.Comment: 21 pages, 2 figures. Accepted to IWOCA 201