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22
Clp(bn): Constraint logic programming for probabilistic knowledge
 In Proceedings of the 19th Conference on Uncertainty in Artificial Intelligence (UAI03
, 2003
"... Abstract. In Datalog, missing values are represented by Skolem constants. More generally, in logic programming missing values, or existentially quantified variables, are represented by terms built from Skolem functors. The CLP(BN) language represents the joint probability distribution over missing v ..."
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Cited by 49 (6 self)
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Abstract. In Datalog, missing values are represented by Skolem constants. More generally, in logic programming missing values, or existentially quantified variables, are represented by terms built from Skolem functors. The CLP(BN) language represents the joint probability distribution over missing values in a database or logic program by using constraints to represent Skolem functions. Algorithms from inductive logic programming (ILP) can be used with only minor modification to learn CLP(BN) programs. An implementation of CLP(BN) is publicly available as part of YAP Prolog at
Discriminative Structure and Parameter Learning for Markov Logic Networks
"... Markov logic networks (MLNs) are an expressive representation for statistical relational learning that generalizes both firstorder logic and graphical models. Existing methods for learning the logical structure of an MLN are not discriminative; however, many relational learning problems involve spe ..."
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Cited by 36 (5 self)
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Markov logic networks (MLNs) are an expressive representation for statistical relational learning that generalizes both firstorder logic and graphical models. Existing methods for learning the logical structure of an MLN are not discriminative; however, many relational learning problems involve specific target predicates that must be inferred from given background information. We found that existing MLN methods perform very poorly on several such ILP benchmark problems, and we present improved discriminative methods for learning MLN clauses and weights that outperform existing MLN and traditional ILP methods. 1.
Deep transfer via secondorder markov logic
 In Proceedings of the AAAI Workshop on Transfer Learning For Complex Tasks
, 2008
"... Standard inductive learning requires that training and test instances come from the same distribution. Transfer learning seeks to remove this restriction. In shallow transfer, test instances are from the same domain, but have a different distribution. In deep transfer, test instances are from a diff ..."
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Cited by 23 (3 self)
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Standard inductive learning requires that training and test instances come from the same distribution. Transfer learning seeks to remove this restriction. In shallow transfer, test instances are from the same domain, but have a different distribution. In deep transfer, test instances are from a different domain entirely (i.e., described by different predicates). Humans routinely perform deep transfer, but few learning systems, if any, are capable of it. In this paper we propose an approach based on a form of secondorder Markov logic. Our algorithm discovers structural regularities in the source domain in the form of Markov logic formulas with predicate variables, and instantiates these formulas with predicates from the target domain. Using this approach, we have successfully transferred learned knowledge among molecular biology, social network and Web domains. The discovered patterns include broadly useful properties of predicates, like symmetry and transitivity, and relations among predicates, such as various forms of homophily. 1.
Structure learning of Markov logic networks through iterated local search
 Proc. ECAI’08
, 2008
"... Many realworld applications of AI require both probability and firstorder logic to deal with uncertainty and structural complexity. Logical AI has focused mainly on handling complexity, and statistical AI on handling uncertainty. Markov Logic Networks (MLNs) are a powerful representation that comb ..."
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Cited by 17 (2 self)
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Many realworld applications of AI require both probability and firstorder logic to deal with uncertainty and structural complexity. Logical AI has focused mainly on handling complexity, and statistical AI on handling uncertainty. Markov Logic Networks (MLNs) are a powerful representation that combine Markov Networks (MNs) and firstorder logic by attaching weights to firstorder formulas and viewing these as templates for features of MNs. Stateoftheart structure learning algorithms of MLNs maximize the likelihood of a relational database by performing a greedy search in the space of candidates. This can lead to suboptimal results because of the incapability of these approaches to escape local optima. Moreover, due to the combinatorially explosive space of potential candidates these methods are computationally prohibitive. We propose a novel algorithm for learning MLNs structure, based on the Iterated Local Search (ILS) metaheuristic that explores the space of structures through a biased sampling of the set of local optima. The algorithm focuses the search not on the full space of solutions but on a smaller subspace defined by the solutions that are locally optimal for the optimization engine. We show through experiments in two realworld domains that the proposed approach improves accuracy and learning time over the existing stateoftheart algorithms. 1
Change of representation for statistical relational learning
 Proc. IJCAI’07
, 2007
"... Statistical relational learning (SRL) algorithms learn statistical models from relational data, such as that stored in a relational database. We previously introduced view learning for SRL, in which the view of a relational database can be automatically modified, yielding more accurate statistical m ..."
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Cited by 15 (4 self)
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Statistical relational learning (SRL) algorithms learn statistical models from relational data, such as that stored in a relational database. We previously introduced view learning for SRL, in which the view of a relational database can be automatically modified, yielding more accurate statistical models. The present paper presents SAYUVISTA, an algorithm which advances beyond the initial view learning approach in three ways. First, it learns views that introduce new relational tables, rather than merely new fields for an existing table of the database. Second, new tables or new fields are not limited to being approximations to some target concept; instead, the new approach performs a type of predicate invention. The new approach avoids the classical problem with predicate invention, of learning many useless predicates, by keeping only new fields or tables (i.e., new predicates) that immediately improve the performance of the statistical model. Third, retained fields or tables can then be used in the definitions of further new fields or tables. We evaluate the new view learning approach on three relational classification tasks. 1
Gleaner: Creating Ensembles of Firstorder Clauses to Improve RecallPrecision Curves
 Machine Learning
, 2006
"... Abstract. Many domains in the field of Inductive Logic Programming (ILP) involve highly unbalanced data. A common way to measure performance in these domains is to use precision and recall instead of simply using accuracy. The goal of our research is to find new approaches within ILP particularly su ..."
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Cited by 8 (6 self)
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Abstract. Many domains in the field of Inductive Logic Programming (ILP) involve highly unbalanced data. A common way to measure performance in these domains is to use precision and recall instead of simply using accuracy. The goal of our research is to find new approaches within ILP particularly suited for large, highlyskewed domains. We propose Gleaner, a randomized search method that collects good clauses from a broad spectrum of points along the recall dimension in recallprecision curves and employs an “at least L of these K clauses ” thresholding method to combine sets of selected clauses. Our research focuses on MultiSlot Information Extraction (IE), a task that typically involves many more negative examples than positive examples. We formulate this problem into a relational domain, using two large testbeds involving the extraction of important relations from the abstracts of biomedical journal articles. We compare Gleaner to ensembles of standard theories learned by Aleph, finding that Gleaner produces comparable testset results in a fraction of the training time.
An Integrated Approach to Feature Invention and Model Construction for Drug Activity Prediction
"... We present a new machine learning approach for 3DQSAR, the task of predicting binding affinities of molecules to target proteins based on 3D structure. Our approach predicts binding affinity by using regression on substructures discovered by relational learning. We make two contributions to the sta ..."
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Cited by 4 (0 self)
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We present a new machine learning approach for 3DQSAR, the task of predicting binding affinities of molecules to target proteins based on 3D structure. Our approach predicts binding affinity by using regression on substructures discovered by relational learning. We make two contributions to the stateoftheart. First, we use multipleinstance (MI) regression, which represents a molecule as a set of 3D conformations, to model activity. Second, the relational learning component employs the “Score As You Use” (SAYU) method to select substructures for their ability to improve the regression model. This is the first application of SAYU to multipleinstance, realvalued prediction. We evaluate our approach on three tasks and demonstrate that (i) SAYU outperforms standard coverage measures when selecting features for regression, (ii) the MI representation improves accuracy over standard single featurevector encodings and (iii) combining SAYU with MI regression is more accurate for 3DQSAR than either approach by itself. 1.
D: An inductive logic programming approach to validate hexose biochemical knowledge
 In Proceedings of the 19th International Conference on ILP
"... Abstract. Hexoses are simple sugars that play a key role in many cellular pathways, and in the regulation of development and disease mechanisms. Current proteinsugar computational models are based, at least partially, on prior biochemical findings and knowledge. They incorporate different parts of ..."
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Cited by 3 (1 self)
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Abstract. Hexoses are simple sugars that play a key role in many cellular pathways, and in the regulation of development and disease mechanisms. Current proteinsugar computational models are based, at least partially, on prior biochemical findings and knowledge. They incorporate different parts of these findings in predictive blackbox models. We investigate the empirical support for biochemical findings by comparing Inductive Logic Programming (ILP) induced rules to actual biochemical results. We mine the Protein Data Bank for a representative data set of hexose binding sites, nonhexose binding sites and surface grooves. We build an ILP model of hexosebinding sites and evaluate our results against several baseline machine learning classifiers. Our method achieves an accuracy similar to that of other blackbox classifiers while providing insight into the discriminating process. In addition, it confirms wetlab findings and reveals a previously unreported TrpGlu amino acids dependency.
Transforming Graph Data for Statistical Relational Learning
"... Relational data representations have become an increasingly important topic due to the recent proliferation of network datasets (e.g., social, biological, information networks) and a corresponding increase in the application of Statistical Relational Learning (SRL) algorithms to these domains. In th ..."
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Cited by 3 (2 self)
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Relational data representations have become an increasingly important topic due to the recent proliferation of network datasets (e.g., social, biological, information networks) and a corresponding increase in the application of Statistical Relational Learning (SRL) algorithms to these domains. In this article, we examine and categorize techniques for transforming graphbased relational data to improve SRL algorithms. In particular, appropriate transformations of the nodes, links, and/or features of the data can dramatically affect the capabilities and results of SRL algorithms. We introduce an intuitive taxonomy for data representation transformations in relational domains that incorporates link transformation and node transformation as symmetric representation tasks. More specifically, the transformation tasks for both nodes and links include (i) predicting their existence, (ii) predicting their label or type, (iii) estimating their weight or importance, and (iv) systematically constructing their relevant features. We motivate our taxonomy through detailed examples and use it to survey competing approaches for each of these tasks. We also discuss general conditions for transforming links, nodes, and features. Finally, we highlight challenges that remain to be addressed. 1.
Lifted variable elimination with arbitrary constraints
, 2011
"... Lifted probabilistic inference algorithms exploit regularities in the structure of graphical models to perform inference more efficiently. More specifically, they identify groups of interchangeable variables and perform inference once for each group, as opposed to once for each variable. The groups ..."
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Cited by 3 (1 self)
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Lifted probabilistic inference algorithms exploit regularities in the structure of graphical models to perform inference more efficiently. More specifically, they identify groups of interchangeable variables and perform inference once for each group, as opposed to once for each variable. The groups are defined by means of constraints, so the flexibility of the grouping is determined by the expressivity of the constraint language. Existing approaches for exact lifted inference rely on (in)equality constraints. We show how inference methods can be generalized to work with arbitrary constraints. This allows them to capture a broader range of symmetries, leading to more opportunities for lifting. We empirically demonstrate that this improves inference efficiency with orders of magnitude, allowing exact inference in cases where until now only approximate inference was feasible. 1