12824361
Data Mining Methods for Modeling Gene Expression Regulation and Their Applications
This paper demonstrates machine learning and data mining methods that can be developed and applied to analyzing large quantities of genomic information and gene expression data for characterizing and modeling gene expression regulation. In particular, there will be a discussion on some of the methods that have been developed for modeling gene expression regulation underlying abiotic stress (e.g., drought, low temperature and salinity) tolerance, for identifying gene responsive to particular environmental stress conditions, and for characterizing the functions of microRNA genes for stress regulation in model plant Arabidopsis thaliana.
205692410
Average-case analysis of best-first search in two representative directed acyclic graphs
Many problems that arise in the real world have search spaces that are graphs rather than trees. Understanding the properties of search algorithms and analyzing their performance have been major objectives of research in AI. But most published work on the analysis of search algorithms has been focused on tree search, and comparatively little has been reported on graph search. One of the major obstacles in analyzing average-case complexity of graph search is that no single graph can serve as a suitable representative of graph search problems. In this paper we propose one possible approach to analyzing graph search. We take two problem domains for which the search graphs are directed acyclic graphs of similar structure, and determine the average case performance of the best-first search algorithm A* on these graphs. The first domain relates to one-machine job sequencing problems in which a set of jobs must be sequenced on a machine in such a way that a penalty function is minimized. The second domain concerns the Traveling Salesman Problem. Our mathematical formulation extends a technique that has been used previously for analyzing tree search. We demonstrate the existence of a gap in computational cost between two classes of problem instances. One class has exponential complexity and the other has polynomial complexity. For the job sequencing domain we provide supporting experimental evidence showing that problems exhibit a huge difference in computational cost under different conditions. For the Traveling Salesman Problem, our theoretical results reflect on the long-standing debate on the expected complexity of branch-and-bound algorithms for solving the problem, indicating that the complexity can be polynomial or exponential, depending on the accuracy of the heuristic function used.
2426741
An analysis and application of distributed constraint satisfaction and optimization algorithms in sensor networks
This research is motivated by a distributed scheduling problem in distributed sensor networks, in which computational resources are scarce. To cope with limited computational resources and restricted real-time requirement, it is imperative to apply distributed algorithms that have low overhead on resource requirement and high anytime performance. In this paper, We study distributed stochastic algorithm (DSA) and distributed breakout algorithm (DBA), two distributed algorithms developed earlier for distributed constraint satisfaction problems. We experimentally investigate their properties and compare their performance using our distributed scheduling problem as a benchmark. We first formulate the scheduling problem as a distributed multi-coloring problem. We then experimentally show that the solution quality and communication cost of DSA exhibit phase-transition or threshold behavior, in that the performance degenerates abruptly and dramatically when the degree of parallel executions of distributed agents increases beyond some critical value. The results show that when controlled properly, DSA is superior to DBA, having better or competitive solution quality and significantly smaller communication cost than DBA. Therefore, DSA is the algorithm of choice for our distributed scan scheduling problem.
3517573
A template-based and pattern-driven approach to situation awareness and assessment in virtual humans
Situation awareness and assessment are fundamental components of rational virtual humans. They are central parts of models of virtual humans and critical elements of efficient reasoning and planning systems. In this paper, we describe our efforts of developing the capability of situation awareness in autonomous, synthetic virtual pilots in a military domain. After briefly describing the motivations of this research, we present an agent architecture that integrates perception, reasoning with situation awareness, and actions. We describe a representation of situations, methods for situation assessment, and applications of situation awareness in information collection, and creating focused attention. The quantitative measure from our experiment shows that by using focused attention based on the ability of situation awareness, the perceptional load of virtual pilots is significantly reduced, reducing pilots’ response time by more than 50 percent.
10379128
Searching for backbones and fat: a limit-crossing approach with applications
Backbone variables are the elements that are common to all optimal solutions of a problem instance. We call variables that are absent from every optimal solution <i>fat</i> variables. Identification of backbone and fat variables is a valuable asset when attempting to solve complex problems. In this paper, we demonstrate a method for identifying backbones and fat. Our method is based on an intuitive concept, which we refer to as <i>limit crossing</i>. Limit crossing occurs when we force the lower bound of a graph problem to exceed the upper bound by applying the lower-bound function to a constrained version of the graph. A desirable feature of this procedure is that it uses approximation functions to derive exact information about optimal solutions. In this paper, we prove the validity of the limit-crossing concept as well as other related properties. Then we exploit limit crossing and devise a pre-processing tool for discovering backbone and fat arcs for various instances of the Asymmetric Traveling Salesman Problem (ATSP). Our experimental results demonstrate the power of the limit-crossing method. We compare our pre-processor with the Carpaneto, Dell'Amico, and Toth pre-processor for several different classes of ATSP instances and reveal dramatic performance improvements.
10248617
Towards flexible teamwork in persistent teams
Teamwork is a critical capability in multi-agent environments. Many such environments mandate that the agents and agent-teams mast be persistent i.e., exist over long periods of time. Agents in such persistent teams are bound together by their long-term common interests and goals. This paper focuses on flexible teamwork in such persistent teams. Unfortunately, while previous work has investigated flexible teamwork, persistent teams remain unexplored. For flexible teamwork, one promising approach that has emerged is model-based, i.e., providing agents with general models of teamwork that explicitly specify their commitments in teamwork. Such models enable agents to autonomously reason about coordination. Unfortunately, for persistent teams, such models may lead to coordination and communication actions that while locally optimal, are highly problematic for the team's long-term goals. We present a decision-theoretic technique to enable persistent teams to overcome such limitations of the model-based approach. In particular, agents reason about expected team utilities of future team states that are projected to result from actions recommended by the teamwork model, as well as lower-cost (or higher-cost) variations on these actions. To accommodate real-time constraints, this reasoning is done in an any-time fashion. Implemented examples from an analytic search tree and some real-world domains are presented.
5425522
Temporal Interpolation of Spatially Dynamic Object
During the past decade there has been increasing research into the temporal component of geographic information systems (GIS). Most of the research has focused on the treatment of discrete changes in spatial objects, for example in cadastral parcels. However less attention has been paid to the treatment of continuous change which occurs primarily in dynamic objects found in the natural environment, for example in seasonal coastal changes. In order to represent these objects appropriately in a GIS, which by their inherent structure tend to treat the real-world in a discrete manner, temporal interpolation techniques are required. The aim of this paper is to discuss the techniques available for handling the temporal interpolation of spatially dynamic objects, with particular emphasis on changes to their geometric properties. The paper also proposes a range of interpolation methods for three key variants of geometric change.
1539580
Exploring Remote Object Coherence in XMLWeb Services
Object-level coherence in distributed applications and systems has been studied extensively. Object coherence in platform-specific and tightly-coupled systems is achieved with binary serialization protocols to ensure data structures and object graphs are safely transmitted, manipulated, and stored. On the opposite side of the spectrum are platform-neutral Web services that embrace XML as a serialization protocol for building loosely coupled systems. The advantages of XML to connect heterogeneous systems are plenty, but rendering programming-language specific data structures and object graphs in text form incurs a performance hit and presents challenges for systems that require object coherence. Achieving the latter goal poses difficulties by a phenomenon that is sometimes referred to as the "impedance mismatch" between programming language data types and XML schema types. This paper examines the problem, debunks the O/X-mismatch controversy, and presents a mix of static/dynamic algorithms for accurate XML serialization. Experimental results show that the implementation in C/C++ is efficient and competitive to binary protocols. Application of the approach to other programming languages, such as Java, is also discussed
11150901
Web-log Mining for Quantitative Temporal-Event Prediction
The web log data embed much of web users’ browsing behavior. From the web logs, one can discover patterns that predict the users’ future requests based on their current behavior. These web data are very complex due to their large size and sequential nature. In the past, researchers have proposed different methods to predict what pages will be visited next based on their present visit patterns. In this paper, we extend this work to discover patterns that can predict when these web page accesses will occur. Our method is based on a novel extension of association rule classification method. We extend the traditional association rules by including the temporal information explicitly in each rule, and reason about the confidence of each prediction in terms of its temporal region. We compare two different methods for temporal event prediction, demonstrate the effectiveness of our methods empirically on realistic web logs, and explore the tradeoff between prediction accuracy and data mining time for our models.
17966983
Flexible Workflow Driven Job Shop Manufacturing Execution and Automation Based on Multi Agent System
Manufacturing automation with adoptability to the changing environment is a competitive advantage for shop floors. This paper presents a flexible workflow enacted job shop manufacturing execution and automation system. The manufacturing process sequence of each part is modeled as an abstract workflow and each manufacturing job resulting in a batch of the part items is recognized as corresponding workflow instance. The production schedule is generated to establish executable workflow instances to be enacted by the workflow engine and executed by the resources in the shop floor. Agent technology is applied to construct the system to take the advantage of distributed system architecture, reactivity, adaptability and cooperation. The proposed system can help to achieve production efficiency without huge investment on industrial automation system. The system architecture and implementation methods are discussed with demonstration and the performance of manufacturing shop floor is enhanced after the application.
12047559
Binary analysis and optimization-based normalization of gene expression data
MOTIVATION
Most approaches to gene expression analysis use real-valued expression data, produced by high-throughput screening technologies, such as microarrays. Often, some measure of similarity must be computed in order to extract meaningful information from the observed data. The choice of this similarity measure frequently has a profound effect on the results of the analysis, yet no standards exist to guide the researcher.


RESULTS
To address this issue, we propose to analyse gene expression data entirely in the binary domain. The natural measure of similarity becomes the Hamming distance and reflects the notion of similarity used by biologists. We also develop a novel data-dependent optimization-based method, based on Genetic Algorithms (GAs), for normalizing gene expression data. This is a necessary step before quantizing gene expression data into the binary domain and generally, for comparing data between different arrays. We then present an algorithm for binarizing gene expression data and illustrate the use of the above methods on two different sets of data. Using Multidimensional Scaling, we show that a reasonable degree of separation between different tumor types in each data set can be achieved by working solely in the binary domain. The binary approach offers several advantages, such as noise resilience and computational efficiency, making it a viable approach to extracting meaningful biological information from gene expression data.