1499660
A bi-dimensional regression tree approach to the modeling of gene expression regulation
MOTIVATION
The transcriptional regulation of a gene depends on the binding of cis-regulatory elements on its promoter to some transcription factors and the expression levels of the transcription factors. Most existing approaches to studying transcriptional regulation model these dependencies separately, i.e. either from promoters to gene expression or from the expression levels of transcription factors to the expression levels of genes. Little effort has been devoted to a single model for integrating both dependencies.


RESULTS
We propose a novel method to model gene expression using both promoter sequences and the expression levels of putative regulators. The proposed method, called bi-dimensional regression tree (BDTree), extends a multivariate regression tree approach by applying it simultaneously to both genes and conditions of an expression matrix. The method produces hypotheses about the condition-specific binding motifs and regulators for each gene. As a side-product, the method also partitions the expression matrix into small submatrices in a way similar to bi-clustering. We propose and compare several splitting functions for building the tree. When applied to two microarray datasets of the yeast Saccharomyces cerevisiae, BDTree successfully identifies most motifs and regulators that are known to regulate the biological processes underlying the datasets. Comparing with an existing algorithm, BDTree provides a higher prediction accuracy in cross-validations.
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.
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.
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.
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.
6822470
A Reinforcement Learning Approach to job-shop Scheduling
We apply reinforcement learning methods to learn domain-specific heuristics for job shop scheduling. A repair-based scheduler starts with a critical-path schedule and incrementally repairs constraint violations with the goal of finding a short conflict-free schedule. The temporal difference algorithm TD(λ) is applied to tram a neural network to learn a heuristic evaluation function over states. This evaluation function is used by a one-step lookahead search procedure to find good solutions to new scheduling problems. We evaluate this approach on synthetic problems and on problems from a NASA space shuttle pay load processing task. The evaluation function is trained on problems involving a small number of jobs and then tested on larger problems. The TD scheduler performs better than the best known existing algorithm for this task--Zwehen's iterative repair method based on simulated annealing. The results suggest that reinforcement learning can provide a new method for constructing high-performance scheduling systems.
13348734
Growing genetic regulatory networks from seed genes
MOTIVATION
A number of models have been proposed for genetic regulatory networks. In principle, a network may contain any number of genes, so long as data are available to make inferences about their relationships. Nevertheless, there are two important reasons why the size of a constructed network should be limited. Computationally and mathematically, it is more feasible to model and simulate a network with a small number of genes. In addition, it is more likely that a small set of genes maintains a specific core regulatory mechanism.


RESULTS
Subnetworks are constructed in the context of a directed graph by beginning with a seed consisting of one or more genes believed to participate in a viable subnetwork. Functionalities and regulatory relationships among seed genes may be partially known or they may simply be of interest. Given the seed, we iteratively adjoin new genes in a manner that enhances subnetwork autonomy. The algorithm is applied using both the coefficient of determination and the Boolean-function influence among genes, and it is illustrated using a glioma gene-expression dataset.


AVAILABILITY
Software for the seed-growing algorithm will be available at the website for Probabilistic Boolean Networks: http://www2.mdanderson.org/app/ilya/PBN/PBN.htm
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.
17633305
The Impact of Cache Organization in Optimizing Microprocessor Power Consumption
In the recent years, power consumption has become increasingly an important design concern as silicon area and performance in modern computer systems design. Several factors have contributed to this trend. Perhaps the most visible have been the remarkable success and growth of Personal Digital Assistants (PDA’s), Cellular phones and pagers, etc .This work is an attempt to explore the impact of feature size shrinkage and cache configuration on optimizing power consumption in modern processors. The work studies two commercially known RISC microprocessors. The StrongARM and the Alpha-21064 microprocessors. The latter is the ancestor of the former and is therefore used here as the baseline in our analysis. Our analysis has illustrated quantitatively great power saving when technology is downsized and cache is well organized
43211087
Simplify Decision Function of Reduced Support Vector Machines
Reduced Support Vector Machines (RSVM) was proposed as the alternate of standard support vector machines (SVM) in order to resolve the difficulty in the learning of nonlinear SVM for large data set problems. RSVM preselects a subset as support vectors and solves a smaller optimization problem, and it performs well with remarkable efficiency on training of SVM for large problem. All the training points of the subset will be support vectors, and more training points are selected into this subset results in high possibility to obtain RSVM with better generalization ability. So we first obtain the RSVM with more support vectors, and selects out training examples near classification hyper plane. Then only these training examples are used as training set to obtain a standard SVM with less support vector than that of RSVM. Computational results show that standard SVMs on the basis of RSVM have much less support vectors and perform equal generalization ability to that of RSVM.