A list of parameterized problems in bioinformatics

In this report we present a list of problems that originated in bionformatics. Our aim is to collect information on such problems that have been analyzed from the point of view of Parameterized Complexity. For every problem we give its definition and biological motivation together with known complexity results.Postprint (published version

An Examination of Railroad Capacity and its Implications for Rail-Highway Intermodal Transportation

After many years of decline in market share, railroads are now experiencing an increasing demand for their services. Service intensive intermodal transportation seems to be an especially promising market area. Since the historic decline in traffic has been accompanied by a reduction in network infrastructure, however, the railroads\u27 ability to handle sizable traffic increases, at least in the short term, is in question. Since rail transportation is critical to the domestic economy of the nation, and is increasingly important in international logistics channels, shortfalls in railroad capacity are not desirable. The published literature on railroad capacity is relatively sparse, especially in comparison to the highway mode. Much of what is available pertains to individual network components such as lines or terminals. Evaluation of system capacity, considering the interactive effects of traffic flowing through a network of lines and terminals, has received less attention. A tool specifically designed for evaluating freight railroad system capacity issues could be a useful addition to the rail analyst\u27s toolbox. The research conducted in this study resulted in the formulation and application of RAILNET, a multicomrnodity, multicarrier network model for predicting equilibrium flows within a railroad network. Designed for strategic planning with a short term horizon, the model assumes fixed external demand. The predicted flows meet the conditions for Wardropian system equilibrium. At completion, the solution algorithm predicts the expected delay per train on each link, allowing the analyst to identify areas of congestion. Following completion of the model, it was applied to a case study examining the railroad network in the southeastern U.S. The public use version of the Interstate Commerce Commission\u27s Commodity Waybill Sample (CWS) provided flow data. The dissertation describes the procedure used to develop the case study and presents some results. The case points to major deficiencies in the CWS data which resulted in substantially less traffic in the network than is actually present. In general, given this limitation, the model behaved well and results appear reasonable, although not necessarily reflective of actual network conditions

On the Combination of Game-Theoretic Learning and Multi Model Adaptive Filters

This paper casts coordination of a team of robots within the framework of game theoretic learning algorithms. In particular a novel variant of fictitious play is proposed, by considering multi-model adaptive filters as a method to estimate other players’ strategies. The proposed algorithm can be used as a coordination mechanism between players when they should take decisions under uncertainty. Each player chooses an action after taking into account the actions of the other players and also the uncertainty. Uncertainty can occur either in terms of noisy observations or various types of other players. In addition, in contrast to other game-theoretic and heuristic algorithms for distributed optimisation, it is not necessary to find the optimal parameters a priori. Various parameter values can be used initially as inputs to different models. Therefore, the resulting decisions will be aggregate results of all the parameter values. Simulations are used to test the performance of the proposed methodology against other game-theoretic learning algorithms.</p

Security Analysis: A Critical Thinking Approach

Security Analysis: A Critical-Thinking Approach is for anyone desiring to learn techniques for generating the best answers to complex questions and best solutions to complex problems. It furnishes current and future analysts in national security, homeland security, law enforcement, and corporate security an alternative, comprehensive process for conducting both intelligence analysis and policy analysis. The target audience is upper-division undergraduate students and new graduate students, along with entry-level practitioner trainees. The book centers on a Security Analysis Critical-Thinking Framework that synthesizes critical-thinking and existing analytic techniques. Ample examples are provided to assist readers in comprehending the material. Newly created material includes techniques for analyzing beliefs and political cultures. The book also functions as an introduction to Foreign Policy and Security Studies.https://encompass.eku.edu/ekuopen/1005/thumbnail.jp

Machine Learning Solutions for Transportation Networks

This thesis brings a collection of novel models and methods that result from a new look at practical problems in transportation through the prism of newly available sensor data. There are four main contributions: First, we design a generative probabilistic graphical model to describe multivariate continuous densities such as observed traffic patterns. The model implements a multivariate normal distribution with covariance constrained in a natural way, using a number of parameters that is only linear (as opposed to quadratic) in the dimensionality of the data. This means that learning these models requires less data. The primary use for such a model is to support inferences, for instance, of data missing due to sensor malfunctions. Second, we build a model of traffic flow inspired by macroscopic flow models. Unlike traditional such models, our model deals with uncertainty of measurement and unobservability of certain important quantities and incorporates on-the-fly observations more easily. Because the model does not admit efficient exact inference, we develop a particle filter. The model delivers better medium- and long- term predictions than general-purpose time series models. Moreover, having a predictive distribution of traffic state enables the application of powerful decision-making machinery to the traffic domain. Third, two new optimization algorithms for the common task of vehicle routing are designed, using the traffic flow model as their probabilistic underpinning. Their benefits include suitability to highly volatile environments and the fact that optimization criteria other than the classical minimal expected time are easily incorporated. Finally, we present a new method for detecting accidents and other adverse events. Data collected from highways enables us to bring supervised learning approaches to incident detection. We show that a support vector machine learner can outperform manually calibrated solutions. A major hurdle to performance of supervised learners is the quality of data which contains systematic biases varying from site to site. We build a dynamic Bayesian network framework that learns and rectifies these biases, leading to improved supervised detector performance with little need for manually tagged data. The realignment method applies generally to virtually all forms of labeled sequential data

Path planning for robotic truss assembly

A new Potential Fields approach to the robotic path planning problem is proposed and implemented. Our approach, which is based on one originally proposed by Munger, computes an incremental joint vector based upon attraction to a goal and repulsion from obstacles. By repetitively adding and computing these 'steps', it is hoped (but not guaranteed) that the robot will reach its goal. An attractive force exerted by the goal is found by solving for the the minimum norm solution to the linear Jacobian equation. A repulsive force between obstacles and the robot's links is used to avoid collisions. Its magnitude is inversely proportional to the distance. Together, these forces make the goal the global minimum potential point, but local minima can stop the robot from ever reaching that point. Our approach improves on a basic, potential field paradigm developed by Munger by using an active, adaptive field - what we will call a 'flexible' potential field. Active fields are stronger when objects move towards one another and weaker when they move apart. An adaptive field's strength is individually tailored to be just strong enough to avoid any collision. In addition to the local planner, a global planning algorithm helps the planner to avoid local field minima by providing subgoals. These subgoals are based on the obstacles which caused the local planner to fail. A best-first search algorithm A* is used for graph search

Incentive-driven QoS in peer-to-peer overlays

A well known problem in peer-to-peer overlays is that no single entity has control over the software, hardware and configuration of peers. Thus, each peer can selfishly adapt its behaviour to maximise its benefit from the overlay. This thesis is concerned with the modelling and design of incentive mechanisms for QoS-overlays: resource allocation protocols that provide strategic peers with participation incentives, while at the same time optimising the performance of the peer-to-peer distribution overlay. The contributions of this thesis are as follows. First, we present PledgeRoute, a novel contribution accounting system that can be used, along with a set of reciprocity policies, as an incentive mechanism to encourage peers to contribute resources even when users are not actively consuming overlay services. This mechanism uses a decentralised credit network, is resilient to sybil attacks, and allows peers to achieve time and space deferred contribution reciprocity. Then, we present a novel, QoS-aware resource allocation model based on Vickrey auctions that uses PledgeRoute as a substrate. It acts as an incentive mechanism by providing efficient overlay construction, while at the same time allocating increasing service quality to those peers that contribute more to the network. The model is then applied to lagsensitive chunk swarming, and some of its properties are explored for different peer delay distributions. When considering QoS overlays deployed over the best-effort Internet, the quality received by a client cannot be adjudicated completely to either its serving peer or the intervening network between them. By drawing parallels between this situation and well-known hidden action situations in microeconomics, we propose a novel scheme to ensure adherence to advertised QoS levels. We then apply it to delay-sensitive chunk distribution overlays and present the optimal contract payments required, along with a method for QoS contract enforcement through reciprocative strategies. We also present a probabilistic model for application-layer delay as a function of the prevailing network conditions. Finally, we address the incentives of managed overlays, and the prediction of their behaviour. We propose two novel models of multihoming managed overlay incentives in which overlays can freely allocate their traffic flows between different ISPs. One is obtained by optimising an overlay utility function with desired properties, while the other is designed for data-driven least-squares fitting of the cross elasticity of demand. This last model is then used to solve for ISP profit maximisation

The PAK-U.S. alliance in the fight against terrorism: a cost-benefit analysis

The cost-benefit equation of the Pak-U.S. alliance, in the fight against terrorism, reflects a direct correlation between the fluctuating patterns of U.S. assistance and their direct and indirect implications for Pakistan. While the U.S. strives to achieve a better return on its investment through military-oriented support, Pakistan seeks to adopt an approach that suits both the U.S. and its own domestic and regional interests. This research traces the trend of Pak-U.S. relations, highlights the impact of the fluctuating U.S. aid in shaping perceptions, and provides a game theoretical analysis on the issue. Besides highlighting measures to achieve cost effectiveness through micro alliances, decentralization, accountability, and transparency in fund management, the study supports development of entrepreneurial culture and micro-alliances in Pakistan. More importantly, it provides an in-depth analysis of the military and population-centric approaches and their associated costs and benefits for the two countries. The research concludes by suggesting a more population-centric U.S. approach towards Pakistan to achieve a better return on investment besides laying foundation for a long-term strategic alliance. It suggests future research on the prospects and methodology of achieving a long-term partnership between the two nations.http://archive.org/details/thepakuslliancei1094510631Pakistan Air Force autho

Fourth Conference on Artificial Intelligence for Space Applications

Proceedings of a conference held in Huntsville, Alabama, on November 15-16, 1988. The Fourth Conference on Artificial Intelligence for Space Applications brings together diverse technical and scientific work in order to help those who employ AI methods in space applications to identify common goals and to address issues of general interest in the AI community. Topics include the following: space applications of expert systems in fault diagnostics, in telemetry monitoring and data collection, in design and systems integration; and in planning and scheduling; knowledge representation, capture, verification, and management; robotics and vision; adaptive learning; and automatic programming