Encontrados 15 documentos, a visualizar página 1 de 2
Predicting the secondary structure of proteins using Machine Learning algorithms
Rui Camacho; Rita Ferreira; Natacha Rosa; Vânia Guimarães; Nuno A. Fonseca; Vítor Santos Costa; Miguel de Sousa; Alexandre MagalhãesThe functions of proteins in living organisms are related to their 3-D structure, which is known to be ultimately determined by their linear sequence of amino acids that together form these macromolecules. It is, therefore, of great importance to be able to understand and predict how the protein 3Dstructure arises from a particular linear sequence of amino acids. In this paper we report the application of Machi...
A Relational Learning approach to Structure-Activity Relationships in Drug Desi...
Rui Camacho; Max Pereira; Vítor Santos Costa; Nuno Foseca; Carlos Adriano; Carlos Simões; Rui BritoIt has been recognized that the development of new therapeutic drugs is a complex and expensive process. A large number of factors affect the activity in vivo of putative candidate molecules and the propensity for causing adverse and toxic effects is recognized as one of the major hurdles behind the current "target-rich, lead-poor" scenario. Structure-Activity Relationship (SAR) studies, using relational Machin...
Portability of Prolog programs: theory and case-studies
Jan Wielemaker; Vitor Santos Costa(Non-)portability of Prolog programs is widely considered as an important factor in the lack of acceptance of the language. Since 1995, the core of the language is covered by the ISO standard 13211-1. Since 2007, YAP and SWI-Prolog have established a basic compatibility framework. This article describes and evaluates this framework. The aim of the framework is running the same code on both systems rather than m...
Partitional Clustering of Protein Sequences - An Inductive Logic Programming Ap...
Nuno A. Fonseca; Vítor Santos Costa; Rui Camacho; Cristina Vieira; Jorge VieiraWe present a novel approach to cluster sets of protein sequences, based on Inductive Logic Programming (ILP). Preliminary results show that the method proposed produces understandable 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.
Visually Guiding and Controlling the search while Mining Chemical Structures
Max Pereira; Vítor Santos Costa; Rui Camacho; Nuno A. FonsecaIn this paper we present the work in progress on LogCHEM, an ILP based tool for discriminative interactive mining of chemical frag- ments. In particular, we describe the integration with a molecule visual- isation 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 lik...
Improving the Efficiency of ILP Systems
Nuno A. Fonseca; Vítor Santos Costa; Ricardo Rocha; Rui Camacho; Fernando SilvaInductive Logic Programming (ILP) is a sub-field of Machine Learning that provides an excellent framework for Multi-Relational Data Mining applications. The advantages of ILP have been successfully demonstrated in complex and relevant industrial and scientific problems. However, to produce valuable models, ILP systems often require long running times and large amounts of memory. In this article we address funda...
LogCHEM: Interactive Discriminative Mining of Chemical Structure
Vítor Santos Costa; Nuno A Fonseca; Rui CamachoOne of the most well known successes of Inductive Logic Programming (ILP) is on Structure-Activity Relationship (SAR) problems. In such problems, ILP has proved several times to be capable of constructing expert comprehensible models that help to explain the activity of chemical compounds based on their structure and properties. However, despite its successes on SAR problems, ILP has severe scalability problems...
K-RNN: k-Relational Neareast Neighbour Algorithm
Nuno A Fonseca; Vítor Santos Costa; Rui CamachoThe 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 ...
Induction as a search procedure
Stasinos Konstantopoulos; Rui Camacho; Nuno A. Foseca; Vítor Santos CostaThis chapter introduces Inductive Logic Programming (ILP) from the perspective of search algorithms in Computer Science. It first briefly considers the Version Spaces approach to induction, and then focuses on Inductive Logic Programming: from its formal definition and main techniques and strategies, to priors used to restrict the search space and optimized sequential, parallel, and stochastic algorithms. The a...
Compile the hypothesis space: do it once, use it often
Nuno A. Fonseca; Rui Camacho; Ricardo Rocha; Vítor Santos CostaInductive Logic Programming (ILP) is a powerful and well-developed abstraction for multi-relational data mining techniques. Despite the considerable success of ILP, deployed ILP systems still have efficiency problems when applied to complex problems. In this paper we propose a novel technique that avoids the procedure of deducing each example to evaluate each constructed clause. The technique is based on the Mo...
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