Overview
Using Machine Learning to Design and Interpret Gene-Expression Microarrays
Molla, Michael, Waddell, Michael, Page, David, Shavlik, Jude
Gene-expression microarrays, commonly called gene chips, make it possible to simultaneously measure the rate at which a cell or tissue is expressing -- translating into a protein -- each of its thousands of genes. One can use these comprehensive snapshots of biological activity to infer regulatory pathways in cells; identify novel targets for drug design; and improve the diagnosis, prognosis, and treatment planning for those suffering from disease. However, the amount of data this new technology produces is more than one can manually analyze. Hence, the need for automated analysis of microarray data offers an opportunity for machine learning to have a significant impact on biology and medicine. This article describes microarray technology, the data it produces, and the types of machine learning tasks that naturally arise with these data. It also reviews some of the recent prominent applications of machine learning to gene-chip data, points to related tasks where machine learning might have a further impact on biology and medicine, and describes additional types of interesting data that recent advances in biotechnology allow biomedical researchers to collect.
Generalizing Boolean Satisfiability I: Background and Survey of Existing Work
Dixon, H. E., Ginsberg, M. L., Parkes, A. J.
This is the first of three planned papers describing ZAP, a satisfiability engine that substantially generalizes existing tools while retaining the performance characteristics of modern high-performance solvers. The fundamental idea underlying ZAP is that many problems passed to such engines contain rich internal structure that is obscured by the Boolean representation used; our goal is to define a representation in which this structure is apparent and can easily be exploited to improve computational performance. This paper is a survey of the work underlying ZAP, and discusses previous attempts to improve the performance of the Davis-Putnam-Logemann-Loveland algorithm by exploiting the structure of the problem being solved. We examine existing ideas including extensions of the Boolean language to allow cardinality constraints, pseudo-Boolean representations, symmetry, and a limited form of quantification. While this paper is intended as a survey, our research results are contained in the two subsequent articles, with the theoretical structure of ZAP described in the second paper in this series, and ZAP's implementation described in the third.
Adaptive Nonlinear System Identification with Echo State Networks
Echo state networks (ESN) are a novel approach to recurrent neural network training. An ESN consists of a large, fixed, recurrent "reservoir" network, from which the desired output is obtained by training suitable output connection weights. Determination of optimal output weights becomes a linear, uniquely solvable task of MSE minimization. This article reviews the basic ideas and describes an online adaptation scheme based on the RLS algorithm known from adaptive linear systems. As an example, a 10th order NARMA system is adaptively identified.
Adaptive Nonlinear System Identification with Echo State Networks
Echo state networks (ESN) are a novel approach to recurrent neural network training. An ESN consists of a large, fixed, recurrent "reservoir" network, from which the desired output is obtained by training suitable output connection weights. Determination of optimal output weights becomes a linear, uniquely solvable task of MSE minimization. This article reviews the basic ideas and describes an online adaptation scheme based on the RLS algorithm known from adaptive linear systems. As an example, a 10th order NARMA system is adaptively identified.
Adaptive Nonlinear System Identification with Echo State Networks
Echo state networks (ESN) are a novel approach to recurrent neural networktraining. An ESN consists of a large, fixed, recurrent "reservoir" network, from which the desired output is obtained by training suitable output connection weights. Determination of optimal outputweights becomes a linear, uniquely solvable task of MSE minimization. This article reviews the basic ideas and describes anonline adaptation scheme based on the RLS algorithm known from adaptive linear systems. As an example, a 10th order NARMAsystem is adaptively identified.
PDDL2.1: An Extension to PDDL for Expressing Temporal Planning Domains
In recent years research in the planning community has moved increasingly toward s application of planners to realistic problems involving both time and many typ es of resources. For example, interest in planning demonstrated by the space res earch community has inspired work in observation scheduling, planetary rover ex ploration and spacecraft control domains. Other temporal and resource-intensive domains including logistics planning, plant control and manufacturing have also helped to focus the community on the modelling and reasoning issues that must be confronted to make planning technology meet the challenges of application. The International Planning Competitions have acted as an important motivating fo rce behind the progress that has been made in planning since 1998. The third com petition (held in 2002) set the planning community the challenge of handling tim e and numeric resources. This necessitated the development of a modelling langua ge capable of expressing temporal and numeric properties of planning domains. In this paper we describe the language, PDDL2.1, that was used in the competition. We describe the syntax of the language, its formal semantics and the validation of concurrent plans. We observe that PDDL2.1 has considerable modelling power --- exceeding the capabilities of current planning technology --- and presents a number of important challenges to the research community.
The 3rd International Planning Competition: Results and Analysis
This paper reports the outcome of the third in the series of biennial international planning competitions, held in association with the International Conference on AI Planning and Scheduling (AIPS) in 2002. In addition to describing the domains, the planners and the objectives of the competition, the paper includes analysis of the results. The results are analysed from several perspectives, in order to address the questions of comparative performance between planners, comparative difficulty of domains, the degree of agreement between planners about the relative difficulty of individual problem instances and the question of how well planners scale relative to one another over increasingly difficult problems. The paper addresses these questions through statistical analysis of the raw results of the competition, in order to determine which results can be considered to be adequately supported by the data. The paper concludes with a discussion of some challenges for the future of the competition series.
A Framework for the Development of Personalized, Distributed Web-Based Configuration Systems
Ardissono, Liliana, Felfernig, Alexander, Friedrich, Gerhard, Goy, Anna, Jannach, Dietmar, Petrone, Giovanna, Schafer, Ralph, Zanker, Markus
For the last two decades, configuration systems relying on AI techniques have successfully been applied in industrial environments. These systems support the configuration of complex products and services in shorter time with fewer errors and, therefore, reduce the costs of a mass-customization business model. The European Union-funded project entitled CUSTOMER-ADAPTIVE WEB INTERFACE FOR THE CONFIGURATION OF PRODUCTS AND SERVICES WITH MULTIPLE SUPPLIERS (CAWICOMS) aims at the next generation of web-based configuration applications that cope with two challenges of today's open, networked economy: (1) the support for heterogeneous user groups in an open-market environment and (2) the integration of configurable subproducts provided by specialized suppliers. This article describes the CAWICOMS WORKBENCH for the development of configuration services, offering personalized user interaction as well as distributed configuration of products and services in a supply chain.
The Process Specification Language (PSL) Theory and Applications
Gruninger, Michael, Menzel, Christopher
The PROCESS SPECIFICATION language (PSL) has been designed to facilitate correct and complete exchange of process information among manufacturing systems, such as scheduling, process modeling, process planning, production planning, simulation, project management, work flow, and business-process reengineering. We give an overview of the theories within the PSL ontology, discuss some of the design principles for the ontology, and finish with examples of process specifications that are based on the ontology.