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Publications

Publications by CRACS

2009

User Defined Indexing

Authors
Vaz, D; Costa, VS; Ferreira, M;

Publication
LOGIC PROGRAMMING

Abstract
Logic programming provides an ideal framework for tackling complex data, such as the multi-dimensional vector-based data used to represent spatial databases. Unfortunately, the usefulness of logic programming systems if often hampered by the fact that most of these systems have to rely on a single unification-based mechanism as the only way to search in the database. While unification can usually take effective advantage of hash-based indexing, it is often the case that queries over more complex and structured data, such as the vectorial terms stored in spatial databases, cannot. We propose a new extension to Prolog indexing: User Defined Indexing (UDI). In this mechanism, the programmer may add extra information to Prolog indices so that only interesting fragments of the database will be selected. UDI provides a general extension of indexing, and can be used for both instantiated and constrained variables. As a test case, we demonstrate how UDI can be combined with a constraint system to provide an elegant and efficient mechanism to generate and execute range queries and spatial queries. Experimental evaluation shows that this mechanism can achieve orders of magnitude speedups on non-trivial datasets.

2009

Visually Guiding and Controlling the Search While Mining Chemical Structures

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

Publication
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

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

Publication
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.

2009

Discovery Science, 12th International Conference, DS 2009, Porto, Portugal, October 3-5, 2009

Authors
Gama, J; Costa, VS; Jorge, AM; Brazdil, P;

Publication
Discovery Science

Abstract

2009

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

Authors
Gama, J; Costa, VS; Jorge, A; Brazdil, P;

Publication
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Abstract

2009

An Artificial Immune System for Temporal Anomaly Detection Using Cell Activation Thresholds and Clonal Size Regulation with Homeostasis

Authors
Antunes, MJ; Correia, ME;

Publication
2009 INTERNATIONAL JOINT CONFERENCE ON BIOINFORMATICS, SYSTEMS BIOLOGY AND INTELLIGENT COMPUTING, PROCEEDINGS

Abstract
This paper presents an Artificial Immune System (AIS) based on Grossman's Tunable Activation Threshold (TAT) for anomaly detection. We describe the immunological metaphor and the algorithm adopted for T-cells, emphasizing two important features: the temporal dynamic adjustment of T-cells clonal size and its associated homeostasis mechanism. We present some promising results obtained with artificially generated data sets, aiming to test the appropriateness of using TAT in dynamic changing environments, to distinguish new unseen patterns as part of what should be detected as normal or as anomalous.

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