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Publicações

Publicações por Nuno Fonseca

2009

Visually Guiding and Controlling the Search While Mining Chemical Structures

Autores
Pereira, M; Costa, VS; Camacho, R; Fonseca, NA;

Publicação
DISTRIBUTED COMPUTING, ARTIFICIAL INTELLIGENCE, BIOINFORMATICS, SOFT COMPUTING, AND AMBIENT ASSISTED LIVING, PT II, PROCEEDINGS

Abstract
In this paper we present the work in progress on LogCHEM, an ILP based tool for discriminative interactive mining of chemical fragments. In particular, we describe the integration with a molecule visualisation software that allows the chemist to graphically control the search for interesting patterns in chemical fragments. Furthermore, we show how structured information, such as rings, functional groups like carboxyl, amine, methyl, ester, etc are integrated and exploited in LogCHEM.

2009

Partitional Clustering of Protein Sequences - An Inductive Logic Programming Approach

Autores
Fonseca, NA; Costa, VS; Camacho, R; Vieira, C; Vieira, J;

Publicação
DISTRIBUTED COMPUTING, ARTIFICIAL INTELLIGENCE, BIOINFORMATICS, SOFT COMPUTING, AND AMBIENT ASSISTED LIVING, PT II, PROCEEDINGS

Abstract
We present a novel approach to cluster sets of protein sequences, based on Inductive Logic Programming (ILP). Preliminary results show that; the method proposed Produces understand able descriptions/explanations of the clusters. Furthermore, it can be used as a knowledge elicitation tool to explain clusters proposed by other clustering approaches, such as standard phylogenetic programs.

2008

k-RNN: k-Relational Nearest Neighbour Algorithm

Autores
Fonseca, NA; Costa, VS; Rocha, R; Camacho, R;

Publicação
APPLIED COMPUTING 2008, VOLS 1-3

Abstract
The amount of data collected and stored in databases is growing considerably in almost all areas of human activity. In complex applications the data involves several relations and proposionalization is not a suitable approach. Multi-Relational Data Mining algorithms can analyze data from multiple relations, with no need to transform the data into a single table, but are computationally more expensive. In this paper a novel relational classification algorithm based on the k-nearest neighbour algorithm is presented and evaluated.

2007

Efficient and scalable induction of logic programs using a deductive database system

Autores
Ferreira, M; Fonseca, NA; Rocha, R; Scares, T;

Publicação
Inductive Logic Programming

Abstract
A consequence of ILP systems being implemented in Prolog or using Prolog libraries is that, usually, these systems use a Prolog internal database to store and manipulate data. However, in real-world problems, the original data is rarely in Prolog format. In fact, the data is often kept in Relational Database Management Systems (RDBMS) and then converted to a format acceptable by the ILP system. Therefore, a more interesting approach is to link the ILP system to the RDBMS and manipulate the data without converting it. This scheme has the advantage of being more scalable since the whole data does not need to be loaded into memory by the ILP system. In this paper we study several approaches of coupling ILP systems with RDBMS systems and evaluate their impact on performance. We propose to use a Deductive Database (DDB) system to transparently translate the hypotheses to relational algebra expressions. The empirical evaluation performed shows that the execution time of ILP algorithms can be effectively reduced using a DDB and that the size of the problems can be increased due to a non-memory storage of the data.

2008

ILP - Just Trie it

Autores
Camacho, R; Fonseca, NA; Rocha, R; Costa, VS;

Publicação
INDUCTIVE LOGIC PROGRAMMING

Abstract
Despite the considerable success of Inductive Logic Programming (ILP), deployed ILP systems still have efficiency problems when applied to complex problems. Several techniques have been proposed to address the efficiency issue. Such proposals include query transformations, query packs, lazy evaluation and parallel execution of ILP systems, to mention just a few. We propose a novel technique that avoids the procedure of deducing each example to evaluate each constructed clause. The technique takes advantage of the two stage procedure of Mode Directed Inverse Entailment (MDIE) systems. In the first stage of a MDIE system, where the bottom clause is constructed, we store not only the bottom clause but also valuable additional information. The information stored is sufficient to evaluate the clauses constructed in the second stage without the need for a theorem prover. We used a data structure called Trie to efficiently store all bottom clauses produced using all examples (positive and negative) as seeds. The technique was implemented and evaluated using two well known data sets from the ILP literature. The results are promising both in terms of execution time and accuracy.

2005

On applying tabling to inductive logic programming

Autores
Rocha, R; Fonseca, N; Costa, VS;

Publicação
MACHINE LEARNING: ECML 2005, PROCEEDINGS

Abstract
Inductive Logic Programming (ILP) is an established subfield of Machine Learning. Nevertheless, it is recognized that efficiency and scalability is a major obstacle to an increased usage of ILP systems in complex applications with large hypotheses spaces. In this work, we focus on improving the efficiency and scalability of ILP systems by exploring tabling mechanisms available in the underlying Logic Programming systems. Tabling is an implementation technique that improves the declarativeness and performance of Prolog systems by reusing answers to subgoals. To validate our approach, we ran the April ILP system in the YapTab Prolog tabling system using two well-known datasets. The results obtained show quite impressive gains without changing the accuracy and quality of the theories generated.

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