9748208
CAGER: classification analysis of gene expression regulation using multiple information sources
BackgroundMany classification approaches have been applied to analyzing transcriptional regulation of gene expressions. These methods build models that can explain a gene's expression level from the regulatory elements (features) on its promoter sequence. Different types of features, such as experimentally verified binding motifs, motifs discovered by computer programs, or transcription factor binding data measured with Chromatin Immunoprecipitation (ChIP) assays, have been used towards this goal. Each type of features has been shown successful in modeling gene transcriptional regulation under certain conditions. However, no comparison has been made to evaluate the relative merit of these features. Furthermore, most publicly available classification tools were not designed specifically for modeling transcriptional regulation, and do not allow the user to combine different types of features.ResultsIn this study, we use a specific classification method, decision trees, to model transcriptional regulation in yeast with features based on predefined motifs, automatically identified motifs, ChlP-chip data, or their combinations. We compare the accuracies and stability of these models, and analyze their capabilities in identifying functionally related genes. Furthermore, we design and implement a user-friendly web server called CAGER (Classification Analysis of Gene Expression Regulation) that integrates several software components for automated analysis of transcriptional regulation using decision trees. Finally, we use CAGER to study the transcriptional regulation of Arabidopsis genes in response to abscisic acid, and report some interesting new results.ConclusionModels built with ChlP-chip data suffer from low accuracies when the condition under which gene expressions are measured is significantly different from the condition under which the ChIP experiment is conducted. Models built with automatically identified motifs can sometimes discover new features, but their modeling accuracies may have been over-estimated in previous studies. Furthermore, models built with automatically identified motifs are not stable with respect to noises. A combination of ChlP-chip data and predefined motifs can substantially improve modeling accuracies, and is effective in identifying true regulons. The CAGER web server, which is freely available at http://cic.cs.wustl.edu/CAGER/, allows the user to select combinations of different feature types for building decision trees, and interact with the models graphically. We believe that it will be a useful tool to facilitate the discovery of gene transcriptional regulatory networks.
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.
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.
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.
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.
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.
16468092
Group rekeying for filtering false data in sensor networks: a predistribution and local collaboration-based approach
When a sensor network is deployed in hostile environments, the adversary may compromise some sensor nodes, and use the compromised nodes to inject false sensing reports or modify the reports sent by other nodes. In order to defend against the attacks with low cost, researchers have proposed symmetric group key-based en-route filtering schemes, such as SEF [F. Ye et al., March 2004] and I-LHAP [S. Zhu et al., 2004]. However, if the adversary has compromised a large number of nodes, many group keys can be captured, and the filtering schemes may become ineffective or even useless. To deal with node compromise, the compromised nodes should be identified and the innocent nodes should update their group keys. Some existing intruder identification schemes can be used to identify the compromised nodes, but most existing group rekeying schemes are not suitable for sensor networks since they have large overhead and are not scalable. To address the problem, we propose a family of predistribution and local collaboration-based group rekeying (PCGR) schemes. These schemes are designed based on the ideas that future group keys can be preloaded to the sensor nodes before deployment, and neighbors can collaborate to protect and appropriately use the preloaded keys. Extensive analyses and simulations are conducted to evaluate the proposed schemes, and the results show that the proposed schemes can achieve a good level of security, outperform most previous group rekeying schemes, and significantly improve the effectiveness of filtering false data.
16097405
A Biodiversity Semantic Associative Annotation Tool
MorphBank, an on-line museum quality collection of biological images, is an NSF funded project designed to facilitate the on-line collaboration of biologists from around the world [3]. This paper presents a methodology for the creation of an annotation tool for on-line collaboration and sharing of heterogeneous data through a common medium. The annotation tool combines the advantages of highly organized relational database, extensible XML schemas, Life Science Identifiers, and accepted industry ontologies using DataGrid technologies to facilitate collection and sharing information on biological specimens. Schematized annotation provides biologists with a flexible framework to perform annotations using their own data models. Structured XML documents enable structure-based semantic retrieval to improve the query accuracy. Retrieval performance can also be improved by combining the relational database and
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.
28687598
Some Basic Data Structures and Algorithms for Chemical Generic Programming
Here, we report a template library used for molecular operation, the Molecular Handling Template Library (MHTL). The library includes some generic data structures and generic algorithms, and the two parts are associated with each other by two concepts: Properties and Molecule. The concept Properties describes the interface to access objects' properties, and the concept Molecule describes the minimum requirement for a molecular class. Data structures include seven models of Properties, each using a different method to access properties, and two models of molecular classes. Algorithms include molecular file manipulation subroutines, SMARTS language interpreter and matcher functions, and molecular OpenGL rendering functions.
9644406
Moving vehicles segmentation based on Bayesian framework for Gaussian motion model
Accurate moving vehicles segmentation is an interesting yet difficult problem in intelligent transportation system. Robust segmentation is obstructed by some problems: the interferential moving objects in dynamic scenes, the vibration of cameras and the change of lighting conditions are all examples. In this paper, we propose Gaussian motion model for moving vehicles segmentation in the dynamic scenes. By investigating the distinction between the motion vectors of the dynamic background and those of the moving vehicles, we find the fact that the motion vectors of the moving vehicles cluster in a small region while those of the dynamic background are dispersive. Gaussian motion model is then proposed to model the motion of the moving vehicles and that of the dynamic background. Bayesian framework is utilized to classify the motion in the scenes to improve the robustness of the model and EM algorithm is used to estimate the parameters of the model. Experimental results on typical scenes, such as waving trees, camera vibration, snowfall and fog, show that the proposed model can segment the moving vehicles correctly in the complex scenes. Quantitative evaluations demonstrate that the proposed method outperform the existing methods.