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75
Partially Supervised Classification of Text Documents
, 2002
"... We investigate the following problem: Given a set of documents of a particular topic or class # , and a large set # of mixed documents that contains documents from class # and other types of documents, identify the documents from class # in # . The key feature of this problem is that there is n ..."
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Cited by 96 (20 self)
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We investigate the following problem: Given a set of documents of a particular topic or class # , and a large set # of mixed documents that contains documents from class # and other types of documents, identify the documents from class # in # . The key feature of this problem is that there is no labeled non # document, which makes traditional machine learning techniques inapplicable, as they all need labeled documents of both classes. We call this problem partially supervised classification. In this paper, we show that this problem can be posed as a constrained optimization problem and that under appropriate conditions, solutions to the constrained optimization problem will give good solutions to the partially supervised classification problem. We present a novel technique to solve the problem and demonstrate the effectiveness of the technique through extensive experimentation.
Building Text Classifiers using Positive and Unlabeled Examples
 In Proc. of the ICDM’03
, 2003
"... This paper studies the problem of building text classifiers using positive and unlabeled examples. The key feature of this problem is that there is no negative example for learning. Recently, a few techniques for solving this problem were proposed in the literature. These techniques are based on the ..."
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Cited by 67 (11 self)
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This paper studies the problem of building text classifiers using positive and unlabeled examples. The key feature of this problem is that there is no negative example for learning. Recently, a few techniques for solving this problem were proposed in the literature. These techniques are based on the same idea, which builds a classifier in two steps. Each existing technique uses a different method for each step. In this paper, we first introduce some new methods for the two steps, and perform a comprehensive evaluation of all possible combinations of methods of the two steps. We then propose a more principled approach to solving the problem based on a biased formulation of SVM, and show experimentally that it is more accurate than the existing techniques. 1.
Learning to classify text using positive and unlabeled data
 In: Proceedings of the 19th international joint conference on artificial intelligence
, 2003
"... In traditional text classification, a classifier is built using labeled training documents of every class. This paper studies a different problem. Given a set P of documents of a particular class (called positive class) and a set U of unlabeled documents that contains documents from class P and also ..."
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Cited by 59 (12 self)
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In traditional text classification, a classifier is built using labeled training documents of every class. This paper studies a different problem. Given a set P of documents of a particular class (called positive class) and a set U of unlabeled documents that contains documents from class P and also other types of documents (called negative class documents), we want to build a classifier to classify the documents in U into documents from P and documents not from P. The key feature of this problem is that there is no labeled negative document, which makes traditional text classification techniques inapplicable. In this paper, we propose an effective technique to solve the problem. It combines the Rocchio method and the SVM technique for classifier building. Experimental results show that the new method outperforms existing methods significantly. 1
Pharmacophore Discovery using the Inductive Logic Programming System Progol
 Machine Learning
, 1998
"... This paper is a case study of a machine aided knowledge discovery process within the general area of drug design. More specifically, the paper describes a sequence of experiments in which an Inductive Logic Programming(ILP) system is used for pharmacophore discovery. Within drug design, a pharmacoph ..."
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Cited by 55 (16 self)
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This paper is a case study of a machine aided knowledge discovery process within the general area of drug design. More specifically, the paper describes a sequence of experiments in which an Inductive Logic Programming(ILP) system is used for pharmacophore discovery. Within drug design, a pharmacophore is a description of the substructure of a ligand (a small molecule) which is responsible for medicinal activity. This medicinal activity is produced by interaction between the ligand and a binding site on a target protein. ILP was chosen by the domain expert (first author) at Pfizer since active molecules are most naturally described, in relational terms, as requiring a substructure (pharmacophore) with various 3D relations which hold among the atoms involved. The results described in this paper build on previous investigations into prediction of mutagenicity using ILP with a 2D (bond connectivity only) representation of molecules. The case study supports general lessons for knowledge discovery, as well as more specific lessons for pharmacophorediscovery, the use of ILP for 3D problems, and for the particular medicinal activity of ACE inhibition, a treatment for hypertension.
Learning with Positive and Unlabeled Examples Using Weighted Logistic Regression
 Proceedings of the Twentieth International Conference on Machine Learning (ICML
, 2003
"... The problem of learning with positive and unlabeled examples arises frequently in retrieval applications. ..."
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Cited by 38 (7 self)
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The problem of learning with positive and unlabeled examples arises frequently in retrieval applications.
Loglinear Models for FirstOrder Probabilistic Reasoning
 In Proceedings of the Fifteenth Conference on Uncertainty in Artificial Intelligence
, 1999
"... Recent work on loglinear models in probabilistic constraint logic programming is applied to firstorder probabilistic reasoning. Probabilities are defined directly on the proofs of atomic formulae, and by marginalisation on the atomic formulae themselves. We use Stochastic Logic Programs (SLPs) com ..."
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Cited by 35 (5 self)
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Recent work on loglinear models in probabilistic constraint logic programming is applied to firstorder probabilistic reasoning. Probabilities are defined directly on the proofs of atomic formulae, and by marginalisation on the atomic formulae themselves. We use Stochastic Logic Programs (SLPs) composed of labelled and unlabelled definite clauses to define the proof probabilities. We have a conservative extension of firstorder reasoning, so that, for example, there is a oneone mapping between logical and random variables. We show how, in this framework, Inductive Logic Programming (ILP) can be used to induce the features of a loglinear model from data. We also compare the presented framework with other approaches to firstorder probabilistic reasoning. Keywords: loglinear models, constraint logic programming, inductive logic programming 1 Introduction A framework which merges firstorder logical and probabilistic inference in a theoretically sound and applicable manner promises ma...
Theorybased causal induction
 In
, 2003
"... Inducing causal relationships from observations is a classic problem in scientific inference, statistics, and machine learning. It is also a central part of human learning, and a task that people perform remarkably well given its notorious difficulties. People can learn causal structure in various s ..."
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Cited by 33 (14 self)
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Inducing causal relationships from observations is a classic problem in scientific inference, statistics, and machine learning. It is also a central part of human learning, and a task that people perform remarkably well given its notorious difficulties. People can learn causal structure in various settings, from diverse forms of data: observations of the cooccurrence frequencies between causes and effects, interactions between physical objects, or patterns of spatial or temporal coincidence. These different modes of learning are typically thought of as distinct psychological processes and are rarely studied together, but at heart they present the same inductive challenge—identifying the unobservable mechanisms that generate observable relations between variables, objects, or events, given only sparse and limited data. We present a computationallevel analysis of this inductive problem and a framework for its solution, which allows us to model all these forms of causal learning in a common language. In this framework, causal induction is the product of domaingeneral statistical inference guided by domainspecific prior knowledge, in the form of an abstract causal theory. We identify 3 key aspects of abstract prior knowledge—the ontology of entities, properties, and relations that organizes a domain; the plausibility of specific causal relationships; and the functional form of those relationships—and show how they provide the constraints that people need to induce useful causal models from sparse data.
How Do We Evaluate Artificial Immune Systems
 Evolutionary Computation
, 2005
"... The field of Artificial Immune Systems (AIS) concerns the study and development of computationally interesting abstractions of the immune system. This survey tracks the development of AIS since its inception, and then attempts to make an assessment of its usefulness, defined in terms of ‘distinctive ..."
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Cited by 25 (0 self)
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The field of Artificial Immune Systems (AIS) concerns the study and development of computationally interesting abstractions of the immune system. This survey tracks the development of AIS since its inception, and then attempts to make an assessment of its usefulness, defined in terms of ‘distinctiveness ’ and ‘effectiveness. ’ In this paper, the standard types of AIS are examined—Negative Selection, Clonal Selection and Immune Networks—as well as a new breed of AIS, based on the immunological ‘danger theory. ’ The paper concludes that all types of AIS largely satisfy the criteria outlined for being useful, but only two types of AIS satisfy both criteria with any certainty.
A study of two sampling methods for analysing large datasets with ILP
, 1999
"... . This paper is concerned with problems that arise when submitting large quantities of data to analysis by an Inductive Logic Programming (ILP) system. Complexity arguments usually make it prohibitive to analyse such datasets in their entirety. We examine two schemes that allow an ILP system to cons ..."
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Cited by 24 (5 self)
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. This paper is concerned with problems that arise when submitting large quantities of data to analysis by an Inductive Logic Programming (ILP) system. Complexity arguments usually make it prohibitive to analyse such datasets in their entirety. We examine two schemes that allow an ILP system to construct theories by sampling from this large pool of data. The first, "subsampling", is a singlesample design in which the utility of a potential rule is evaluated on a randomly selected subsample of the data. The second, "logical windowing", is multiplesample design that tests and sequentially includes errors made by a partially correct theory. Both schemes are derived from techniques developed to enable propositional learning methods (like decision trees) to cope with large datasets. The ILP system CProgol, equipped with each of these methods, is used to construct theories for two datasets  one artificial (a chess endgame) and the other naturally occurring (a language tagging problem). I...
CProgol4.4: a tutorial introduction
 In Inductive Logic Programming and Knowledge Discovery in Databases
, 2001
"... . This chapter describes the theory and use of CProgol4.4, a stateoftheart Inductive Logic Programming (ILP) system. After explaining how to download the source code, the reader is guided through the development of Progol input les containing type denitions, mode declarations, background know ..."
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Cited by 22 (2 self)
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. This chapter describes the theory and use of CProgol4.4, a stateoftheart Inductive Logic Programming (ILP) system. After explaining how to download the source code, the reader is guided through the development of Progol input les containing type denitions, mode declarations, background knowledge, examples and integrity constraints. The theory behind the system is then described using a simple example as illustration. The main algorithms in Progol are given and methods of pruning the search space of possible hypotheses are discussed. Next the application of builtin procedures for estimating predictive accuracy and statistical signicance of Progol hypotheses is demonstrated. Lastly, the reader is shown how to use the more advanced features of CProgol4.4, including positiveonly learning and the use of metalogical predicates for pruning the search space. 1 Introduction The theory and implementation of the Inductive Logic Programming (ILP) system CProgol4.1 was rst ...