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301
Probabilistic Boolean networks: a rulebased uncertainty model for gene regulatory networks
, 2002
"... Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rulebased dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selec ..."
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Cited by 391 (59 self)
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Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rulebased dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selection; and (iv ) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes.
The INQUERY Retrieval System
 In Proceedings of the Third International Conference on Database and Expert Systems Applications
"... As larger and more heterogeneous text databases become available, information retrieval research will depend on the development of powerful, efficient and flexible retrieval engines. In this paper, we describe a retrieval system (INQUERY) that is based on a probabilistic retrieval model and provides ..."
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Cited by 387 (46 self)
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As larger and more heterogeneous text databases become available, information retrieval research will depend on the development of powerful, efficient and flexible retrieval engines. In this paper, we describe a retrieval system (INQUERY) that is based on a probabilistic retrieval model and provides support for sophisticated indexing and complex query formulation. INQUERY has been used successfully with databases containing nearly 400,000 documents. 1 Introduction The increasing interest in sophisticated information retrieval (IR) techniques has led to a number of large text databases becoming available for research. The size of these databases, both in terms of the number of documents in them, and the length of the documents that are typically full text, has presented significant challenges to IR researchers who are used to experimenting with two or three thousand document abstracts. In order to carry out research with different types of text representations, retrieval models, learni...
Operations for Learning with Graphical Models
 Journal of Artificial Intelligence Research
, 1994
"... This paper is a multidisciplinary review of empirical, statistical learning from a graphical model perspective. Wellknown examples of graphical models include Bayesian networks, directed graphs representing a Markov chain, and undirected networks representing a Markov field. These graphical models ..."
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Cited by 276 (13 self)
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This paper is a multidisciplinary review of empirical, statistical learning from a graphical model perspective. Wellknown examples of graphical models include Bayesian networks, directed graphs representing a Markov chain, and undirected networks representing a Markov field. These graphical models are extended to model data analysis and empirical learning using the notation of plates. Graphical operations for simplifying and manipulating a problem are provided including decomposition, differentiation, and the manipulation of probability models from the exponential family. Two standard algorithm schemas for learning are reviewed in a graphical framework: Gibbs sampling and the expectation maximization algorithm. Using these operations and schemas, some popular algorithms can be synthesized from their graphical specification. This includes versions of linear regression, techniques for feedforward networks, and learning Gaussian and discrete Bayesian networks from data. The paper conclu...
Interactive Sketching for the Early Stages of User Interface Design
, 1995
"... Current interactive user interface construction tools are often more of a hindrance than a benefit during the early stages of user interface design. These tools take too much time to use and force designers to specify more of the design details than they wish at this early stage. Most interface desi ..."
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Cited by 266 (16 self)
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Current interactive user interface construction tools are often more of a hindrance than a benefit during the early stages of user interface design. These tools take too much time to use and force designers to specify more of the design details than they wish at this early stage. Most interface designers, especially those who have a background in graphic design, prefer to sketch early interface ideas on paper or on a whiteboard. We are developing an interactive tool called SILK that allows designers to quickly sketch an interface using an electronic pad and stylus. SILK preserves the important properties of pencil and paper: a rough drawing can be produced very quickly and the medium is very flexible. However, unlike a paper sketch, this electronic sketch is interactive and can easily be modified. In addition, our system allows designers to examine, annotate, and edit a complete history of the design. When the designer is satisfied with this early prototype, SILK can transform the sket...
A Guide to the Literature on Learning Probabilistic Networks From Data
, 1996
"... This literature review discusses different methods under the general rubric of learning Bayesian networks from data, and includes some overlapping work on more general probabilistic networks. Connections are drawn between the statistical, neural network, and uncertainty communities, and between the ..."
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Cited by 204 (0 self)
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This literature review discusses different methods under the general rubric of learning Bayesian networks from data, and includes some overlapping work on more general probabilistic networks. Connections are drawn between the statistical, neural network, and uncertainty communities, and between the different methodological communities, such as Bayesian, description length, and classical statistics. Basic concepts for learning and Bayesian networks are introduced and methods are then reviewed. Methods are discussed for learning parameters of a probabilistic network, for learning the structure, and for learning hidden variables. The presentation avoids formal definitions and theorems, as these are plentiful in the literature, and instead illustrates key concepts with simplified examples. Keywords Bayesian networks, graphical models, hidden variables, learning, learning structure, probabilistic networks, knowledge discovery. I. Introduction Probabilistic networks or probabilistic gra...
Inference in belief networks: A procedural guide
 International Journal of Approximate Reasoning
, 1996
"... Belief networks are popular tools for encoding uncertainty in expert systems. These networks rely on inference algorithms to compute beliefs in the context of observed evidence. One established method for exact inference onbelief networks is the Probability Propagation in Trees of Clusters (PPTC) al ..."
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Cited by 176 (5 self)
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Belief networks are popular tools for encoding uncertainty in expert systems. These networks rely on inference algorithms to compute beliefs in the context of observed evidence. One established method for exact inference onbelief networks is the Probability Propagation in Trees of Clusters (PPTC) algorithm, as developed byLauritzen and Spiegelhalter and re ned by Jensen et al. [1, 2, 3] PPTC converts the belief network into a secondary structure, then computes probabilities by manipulating the secondary structure. In this document, we provide a selfcontained, procedural guide to understanding and implementing PPTC. We synthesize various optimizations to PPTC that are scattered throughout the literature. We articulate undocumented, \open secrets &quot; that are vital to producing a robust and e cient implementation of PPTC. We hope that this document makes probabilistic inference more accessible and a ordable to those without extensive prior exposure.
Numerical Uncertainty Management in User and Student Modeling: An Overview of Systems and Issues
, 1996
"... . A rapidly growing number of user and student modeling systems have employed numerical techniques for uncertainty management. The three major paradigms are those of Bayesian networks, the DempsterShafer theory of evidence, and fuzzy logic. In this overview, each of the first three main sections fo ..."
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Cited by 118 (10 self)
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. A rapidly growing number of user and student modeling systems have employed numerical techniques for uncertainty management. The three major paradigms are those of Bayesian networks, the DempsterShafer theory of evidence, and fuzzy logic. In this overview, each of the first three main sections focuses on one of these paradigms. It first introduces the basic concepts by showing how they can be applied to a relatively simple user modeling problem. It then surveys systems that have applied techniques from the paradigm to user or student modeling, characterizing each system within a common framework. The final main section discusses several aspects of the usability of these techniques for user and student modeling, such as their knowledge engineering requirements, their need for computational resources, and the communicability of their results. Key words: numerical uncertainty management, Bayesian networks, DempsterShafer theory, fuzzy logic, user modeling, student modeling 1. Introdu...
Control of Selective Perception Using Bayes Nets and Decision Theory
, 1993
"... A selective vision system sequentially collects evidence to support a specified hypothesis about a scene, as long as the additional evidence is worth the effort of obtaining it. Efficiency comes from processing the scene only where necessary, to the level of detail necessary, and with only the neces ..."
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Cited by 116 (2 self)
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A selective vision system sequentially collects evidence to support a specified hypothesis about a scene, as long as the additional evidence is worth the effort of obtaining it. Efficiency comes from processing the scene only where necessary, to the level of detail necessary, and with only the necessary operators. Knowledge representation and sequential decisionmaking are central issues for selective vision, which takes advantage of prior knowledge of a domain's abstract and geometrical structure and models for the expected performance and cost of visual operators. The TEA1 selective vision system uses Bayes nets for representation and benefitcost analysis for control of visual and nonvisual actions. It is the highlevel control for an active vision system, enabling purposive behavior, the use of qualitative vision modules and a pointable multiresolution sensor. TEA1 demonstrates that Bayes nets and decision theoretic techniques provide a general, reusable framework for constructi...