Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Limits of Preprocessing

We present a first theoretical analysis of the power of polynomial-time preprocessing for important combinatorial problems from various areas in AI. We consider problems from Constraint Satisfaction, Global Constraints, Satisfiability, Nonmonotonic and Bayesian Reasoning. We show that, subject to a complexity theoretic assumption, none of the considered problems can be reduced by polynomial-time preprocessing to a problem kernel whose size is polynomial in a structural problem parameter of the input, such as induced width or backdoor size. Our results provide a firm theoretical boundary for the performance of polynomial-time preprocessing algorithms for the considered problems.Comment: This is a slightly longer version of a paper that appeared in the proceedings of AAAI 201

The PLC: a logical development

Programmable Logic Controllers (PLCs) have been used to control industrial processes and equipment for over 40 years, having their first commercially recognised application in 1969. Since then there have been enormous changes in the design and application of PLCs, yet developments were evolutionary rather than radical. The flexibility of the PLC does not confine it to industrial use and it has been used for disparate non-industrial control applications . This article reviews the history, development and industrial applications of the PLC

Online Independent Set Beyond the Worst-Case: Secretaries, Prophets, and Periods

We investigate online algorithms for maximum (weight) independent set on graph classes with bounded inductive independence number like, e.g., interval and disk graphs with applications to, e.g., task scheduling and spectrum allocation. In the online setting, it is assumed that nodes of an unknown graph arrive one by one over time. An online algorithm has to decide whether an arriving node should be included into the independent set. Unfortunately, this natural and practically relevant online problem cannot be studied in a meaningful way within a classical competitive analysis as the competitive ratio on worst-case input sequences is lower bounded by $\Omega(n)$. As a worst-case analysis is pointless, we study online independent set in a stochastic analysis. Instead of focussing on a particular stochastic input model, we present a generic sampling approach that enables us to devise online algorithms achieving performance guarantees for a variety of input models. In particular, our analysis covers stochastic input models like the secretary model, in which an adversarial graph is presented in random order, and the prophet-inequality model, in which a randomly generated graph is presented in adversarial order. Our sampling approach bridges thus between stochastic input models of quite different nature. In addition, we show that our approach can be applied to a practically motivated admission control setting. Our sampling approach yields an online algorithm for maximum independent set with competitive ratio $O(\rho^2)$ with respect to all of the mentioned stochastic input models. for graph classes with inductive independence number $\rho$. The approach can be extended towards maximum-weight independent set by losing only a factor of $O(\log n)$ in the competitive ratio with $n$ denoting the (expected) number of nodes

Online Influence Maximization under Independent Cascade Model with Semi-Bandit Feedback

We study the online influence maximization problem in social networks under the independent cascade model. Specifically, we aim to learn the set of "best influencers" in a social network online while repeatedly interacting with it. We address the challenges of (i) combinatorial action space, since the number of feasible influencer sets grows exponentially with the maximum number of influencers, and (ii) limited feedback, since only the influenced portion of the network is observed. Under a stochastic semi-bandit feedback, we propose and analyze IMLinUCB, a computationally efficient UCB-based algorithm. Our bounds on the cumulative regret are polynomial in all quantities of interest, achieve near-optimal dependence on the number of interactions and reflect the topology of the network and the activation probabilities of its edges, thereby giving insights on the problem complexity. To the best of our knowledge, these are the first such results. Our experiments show that in several representative graph topologies, the regret of IMLinUCB scales as suggested by our upper bounds. IMLinUCB permits linear generalization and thus is both statistically and computationally suitable for large-scale problems. Our experiments also show that IMLinUCB with linear generalization can lead to low regret in real-world online influence maximization.Comment: Compared with the previous version, this version has fixed a mistake. This version is also consistent with the NIPS camera-ready versio