Arlindo L. Oliveira

Alexandre P. Francisco, Ricardo A. Baeza-Yates, Arlindo L. Oliveira: Mining query log graphs towards a query folksonomy. Concurrency and Computation: Practice and Experience 24(17): 2179-2192 (2012)

Alexandra M. Carvalho, Arlindo L. Oliveira: GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge. Algorithms for Molecular Biology 6: 13 (2011)

Ana Graça, João Marques-Silva, Inês Lynce, Arlindo L. Oliveira: Haplotype inference with pseudo-Boolean optimization. Annals OR 184(1): 137-162 (2011)

Joana P. Gonçalves, Alexandre P. Francisco, Nuno P. Mira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira, Sara C. Madeira: TFRank: network-based prioritization of regulatory associations underlying transcriptional responses. Bioinformatics 27(22): 3149-3157 (2011)

Francisco Fernandes, Paulo G. S. da Fonseca, Luís M. S. Russo, Arlindo L. Oliveira, Ana T. Freitas: Efficient alignment of pyrosequencing reads for re-sequencing applications. BMC Bioinformatics 12: 163 (2011)

Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira: Quantitative Modeling of the Saccharomyces cerevisiae Flr1 regulatory Network Using an S-System Formalism. J. Bioinformatics and Computational Biology 9(5): 613-630 (2011)

Alexandra M. Carvalho, Teemu Roos, Arlindo L. Oliveira, Petri Myllymäki: Discriminative Learning of Bayesian Networks via Factorized Conditional Log-Likelihood. Journal of Machine Learning Research 12: 2181-2210 (2011)

Dário Abdulrehman, Pedro T. Monteiro, Miguel C. Teixeira, Nuno P. Mira, Artur B. Lourenço, Sandra Costa dos Santos, Tânia Rodrigues Cabrito, Alexandre P. Francisco, Sara C. Madeira, Ricardo Santos Aires, Arlindo L. Oliveira, Isabel Sá-Correia, Ana T. Freitas: YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Research 39(Database-Issue): 136-140 (2011)

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira: Fully compressed suffix trees. ACM Transactions on Algorithms 7(4): 53 (2011)

Artur J. Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo: Sliding Window Update Using Suffix Arrays. DCC 2011: 456

Dulce Calçada, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira: Quantitative Modeling the Saccharomyces cerevisiae FLR1 Regulatory Network Using an S-System Formalism. HISB 2011: 69-75

Ana Graça, Inês Lynce, João Marques-Silva, Arlindo L. Oliveira: Haplotype Inference by Pure Parsimony: A Survey. Journal of Computational Biology 17(8): 969-992 (2010)

Sara C. Madeira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira: Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm. IEEE/ACM Trans. Comput. Biology Bioinform. 7(1): 153-165 (2010)

Ana Graça, Inês Lynce, João Marques-Silva, Arlindo L. Oliveira: Efficient and Accurate Haplotype Inference by Combining Parsimony and Pedigree Information. ANB 2010: 38-56

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira: Parallel and Distributed Compressed Indexes. CPM 2010: 348-360

Orlando Anunciação, Bruno C. Gomes, Susana Vinga, Jorge Gaspar, Arlindo L. Oliveira, José Rueff: A Data Mining Approach for the Detection of High-Risk Breast Cancer Groups. IWPACBB 2010: 43-51

Paulo Trezentos, Inês Lynce, Arlindo L. Oliveira: Apt-pbo: solving the software dependency problem using pseudo-boolean optimization. ASE 2010: 427-436

Alexandre P. Francisco, Ricardo A. Baeza-Yates, Arlindo L. Oliveira: Mining Large Query Induced Graphs towards a Hierarchical Query Folksonomy. SPIRE 2010: 237-242

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira, Pedro Morales: Approximate String Matching with Compressed Indexes. Algorithms 2(3): 1105-1136 (2009)

Sara C. Madeira, Arlindo L. Oliveira: A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series. Algorithms for Molecular Biology 4 (2009)

Miguel M. F. Bugalho, Arlindo L. Oliveira: Constant Time Clash Detection in protein Folding. J. Bioinformatics and Computational Biology 7(1): 55-74 (2009)

Artur J. Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo: On the Use of Suffix Arrays for Memory-Efficient Lempel-Ziv Data Compression. DCC 2009: 444

Sara C. Madeira, Arlindo L. Oliveira: Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis. IWANN (2) 2009: 1013-1019

Artur J. Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo: On the Use of Suffix Arrays for Memory-Efficient Lempel-Ziv Data Compression. CoRR abs/0903.4251 (2009)

Artur J. Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo: Time and Memory Efficient Lempel-Ziv Compression Using Suffix Arrays. CoRR abs/0912.5449 (2009)

André L. Martins, Helena Sofia Pinto, Arlindo L. Oliveira: Using Grammatical Inference Techniques to Learn Ontologies that Describe the Structure of Domain Instances. Applied Artificial Intelligence 22(1&2): 139-167 (2008)

Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira: An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. BMC Bioinformatics 9 (2008)

Luís M. S. Russo, Arlindo L. Oliveira: A compressed self-index using a Ziv-Lempel dictionary. Inf. Retr. 11(4): 359-388 (2008)

Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas: YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research 36(Database-Issue): 132-136 (2008)

Ana Graça, João Marques-Silva, Inês Lynce, Arlindo L. Oliveira: Efficient Haplotype Inference with Combined CP and OR Techniques. CPAIOR 2008: 308-312

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira: Dynamic Fully-Compressed Suffix Trees. CPM 2008: 191-203

Xiaoshu Wang, Jonas S. Almeida, Arlindo L. Oliveira: Ontology Design Principles and Normalization Techniques in the Web. DILS 2008: 28-43

Inês Lynce, Ana Graça, João Marques-Silva, Arlindo L. Oliveira: Haplotype Inference with Boolean Constraint Solving: An Overview. ICTAI (1) 2008: 92-100

Alexandre P. Francisco, Arlindo L. Oliveira, Ana T. Freitas: Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph. ISBRA 2008: 220-231

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira: Fully-Compressed Suffix Trees. LATIN 2008: 362-373

Artur J. Ferreira, Arlindo L. Oliveira, Mário A. T. Figueiredo: Suffix Arrays - A Competitive Choice for Fast Lempel-Ziv Compressions. SIGMAP 2008: 5-12

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira: Indexed Hierarchical Approximate String Matching. SPIRE 2008: 144-154

Alexandre P. Francisco, Ricardo A. Baeza-Yates, Arlindo L. Oliveira: Clique Analysis of Query Log Graphs. SPIRE 2008: 188-199

Miguel M. F. Bugalho, Arlindo L. Oliveira: An Evaluation of the Impact of Side Chain Positioning on the Accuracy of Discrete Models of Protein Structures. BSB 2008: 23-34

Luís M. S. Russo, Arlindo L. Oliveira: Efficient generation of super condensed neighborhoods. J. Discrete Algorithms 5(3): 501-513 (2007)

Ana Graça, João Marques-Silva, Inês Lynce, Arlindo L. Oliveira: Efficient Haplotype Inference with Pseudo-boolean Optimization. AB 2007: 125-139

Sara C. Madeira, Arlindo L. Oliveira: An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression Data. APBC 2007: 67-80

Alexandra M. Carvalho, Arlindo L. Oliveira, Marie-France Sagot: Efficient Learning of Bayesian Network Classifiers. Australian Conference on Artificial Intelligence 2007: 16-25

João Marques-Silva, Inês Lynce, Ana Graça, Arlindo L. Oliveira: Efficient and Tight Upper Bounds for Haplotype Inference by Pure Parsimony Using Delayed Haplotype Selection. EPIA Workshops 2007: 621-632

Alexandra M. Carvalho, Arlindo L. Oliveira: Learning bayesian networks consistent with the optimal branching. ICMLA 2007: 369-374

Ana Cardoso-Cachopo, Arlindo L. Oliveira: Semi-supervised single-label text categorization using centroid-based classifiers. SAC 2007: 844-851

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira: Approximate String Matching with Lempel-Ziv Compressed Indexes. SPIRE 2007: 264-275

Nuno D. Mendes, Ana C. Casimiro, Pedro M. Santos, Isabel Sá-Correia, Arlindo L. Oliveira, Ana T. Freitas: MUSA: a parameter free algorithm for the identification of biologically significant motifs. Bioinformatics 22(24): 2996-3002 (2006)

Miguel C. Teixeira, Pedro T. Monteiro, Pooja Jain, Sandra Tenreiro, Alexandra R. Fernandes, Nuno P. Mira, Marta Alenquer, Ana T. Freitas, Arlindo L. Oliveira, Isabel Sá-Correia: The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research 34(Database-Issue): 446-451 (2006)

Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot: An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences. IEEE/ACM Trans. Comput. Biology Bioinform. 3(2): 126-140 (2006)

José M. Fernandes, Marcelino B. Santos, Arlindo L. Oliveira, João Paulo Teixeira: Probabilistic Testability Analysis and DFT Methods at RTL. DDECS 2006: 216-217

José M. Fernandes, Marcelino B. Santos, Arlindo L. Oliveira, João C. Teixeira: DFT and Probabilistic Testability Analysis at RTL. HLDVT 2006: 41-47

Luís M. S. Russo, Arlindo L. Oliveira: A Compressed Self-index Using a Ziv-Lempel Dictionary. SPIRE 2006: 163-180

Luís Pedro Coelho, Arlindo L. Oliveira: Dotted Suffix Trees A Structure for Approximate Text Indexing. SPIRE 2006: 329-336

Miguel M. F. Bugalho, Arlindo L. Oliveira: Inference of regular languages using state merging algorithms with search. Pattern Recognition 38(9): 1457-1467 (2005)

Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot: A highly scalable algorithm for the extraction of CIS-regulatory regions. APBC 2005: 273-282

Luís M. S. Russo, Arlindo L. Oliveira: An Efficient Algorithm for Generating Super Condensed Neighborhoods. CPM 2005: 104-115

André L. Martins, Helena Sofia Pinto, Arlindo L. Oliveira: Using a More Powerful Teacher to Reduce the Number of Queries of the L* Algorithm in Practical Applications. EPIA 2005: 325-336

Luís M. S. Russo, Arlindo L. Oliveira: Faster Generation of Super Condensed Neighbourhoods Using Finite Automata. SPIRE 2005: 246-255

Sara C. Madeira, Arlindo L. Oliveira: A Linear Time Biclustering Algorithm for Time Series Gene Expression Data. WABI 2005: 39-52

Alberto H. F. Laender, Arlindo L. Oliveira: Special issue on string processing and information retrieval. J. Discrete Algorithms 2(1): 1-2 (2004)

Sara C. Madeira, Arlindo L. Oliveira: Biclustering Algorithms for Biological Data Analysis: A Survey. IEEE/ACM Trans. Comput. Biology Bioinform. 1(1): 24-45 (2004)

José M. Fernandes, Marcelino B. Santos, Arlindo L. Oliveira, João Paulo Teixeira: A Probabilistic Method for the Computation of Testability of RTL Constructs. DATE 2004: 176-181

José Poveda, Michael Gould, Arlindo L. Oliveira: A New Quick Point Location Algorithm. ER (Workshops) 2004: 184-196

Cláudia Antunes, Arlindo L. Oliveira: Constraint Relaxations for Discovering Unknown Sequential Patterns. KDID 2004: 11-32

Alexandra M. Carvalho, Arlindo L. Oliveira, Ana T. Freitas, Marie-France Sagot: A parallel algorithm for the extraction of structured motifs. SAC 2004: 147-153

Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot: Efficient Extraction of Structured Motifs Using Box-Links. SPIRE 2004: 267-268

Arlindo L. Oliveira, Rajeev Murgai: On the problem of gate assignment under different rise and fall delays. IEEE Trans. on CAD of Integrated Circuits and Systems 22(6): 807-814 (2003)

Ana T. Freitas, Arlindo L. Oliveira: Implicit Resolution of the Chapman-Kolmogorov Equations for Sequential Circuits: An Application in Power Estimation. DATE 2003: 10764-10769

Sara C. Madeira, Arlindo L. Oliveira, Catarina S. Conceição: A Data Mining Approach to Credit Risk Evaluation and Behaviour Scoring. EPIA 2003: 184-188

Joel R. Phillips, João Afonso, Arlindo L. Oliveira, Luis Miguel Silveira: Analog Macromodeling using Kernel Methods. ICCAD 2003: 446-453

Cláudia Antunes, Arlindo L. Oliveira: Generalization of Pattern-Growth Methods for Sequential Pattern Mining with Gap Constraints. MLDM 2003: 239-251

Paulo Trezentos, Arlindo L. Oliveira: Metrics for Grid Applicability: A Distributed Elliptic Curve Platform Assessment. PPAM 2003: 864-871

Ana Cardoso-Cachopo, Arlindo L. Oliveira: An Empirical Comparison of Text Categorization Methods. SPIRE 2003: 183-196

Mario A. Nascimento, Edleno Silva de Moura, Arlindo L. Oliveira (Eds.): String Processing and Information Retrieval, 10th International Symposium, SPIRE 2003, Manaus, Brazil, October 8-10, 2003, Proceedings. Lecture Notes in Computer Science 2857, Springer 2003, isbn 3-540-20177-7

José C. Monteiro, Arlindo L. Oliveira: Implicit FSM decomposition applied to low-power design. IEEE Trans. VLSI Syst. 10(5): 560-565 (2002)

Cláudia Antunes, Arlindo L. Oliveira: Inference of Sequential Association Rules Guided by Context-Free Grammars. ICGI 2002: 1-13

Alberto H. F. Laender, Arlindo L. Oliveira (Eds.): String Processing and Information Retrieval, 9th International Symposium, SPIRE 2002, Lisbon, Portugal, September 11-13, 2002, Proceedings. Lecture Notes in Computer Science 2476, Springer 2002, isbn 3-540-44158-1

Arlindo L. Oliveira, João P. Marques Silva: Efficient Algorithms for the Inference of Minimum Size DFAs. Machine Learning 44(1/2): 93-119 (2001)

Arlindo L. Oliveira: Techniques for the creation of digital watermarks in sequentialcircuit designs. IEEE Trans. on CAD of Integrated Circuits and Systems 20(9): 1101-1117 (2001)

José C. Monteiro, Arlindo L. Oliveira: FSM decomposition by direct circuit manipulation applied to low power design. ASP-DAC 2000: 351-358

Arlindo L. Oliveira, Rajeev Murgai: An Exact Gate Assignment Algorithm for Tree Circuits Under Rise and Fall Delays. ICCAD 2000: 451-457

Arlindo L. Oliveira (Ed.): Grammatical Inference: Algorithms and Applications, 5th International Colloquium, ICGI 2000, Lisbon, Portugal, September 11-13, 2000, Proceedings. Lecture Notes in Computer Science 1891, Springer 2000, isbn 3-540-41011-2

Jorge M. Pena, Arlindo L. Oliveira: A new algorithm for exact reduction of incompletely specified finite state machines. IEEE Trans. on CAD of Integrated Circuits and Systems 18(11): 1619-1632 (1999)

Arlindo L. Oliveira: Robust Techniques for Watermarking Sequential Circuit Designs. DAC 1999: 837-842

Antônio Mota, Nuno Ferreira, Arlindo L. Oliveira, José C. Monteiro: Integrating Dynamic Power Management in the Design Flow. VLSI 1999: 233-244

Arlindo L. Oliveira, Luca P. Carloni, Tiziano Villa, Alberto L. Sangiovanni-Vincentelli: Exact Minimization of Binary Decision Diagrams Using Implicit Techniques. IEEE Trans. Computers 47(11): 1282-1296 (1998)

Rajeev Murgai, Masahiro Fujita, Arlindo L. Oliveira: Using Complementation and Resequencing to Minimize Transitions. DAC 1998: 694-697

José C. Monteiro, Arlindo L. Oliveira: Finite State Machine Decomposition For Low Power. DAC 1998: 758-763

Jorge M. Pena, Arlindo L. Oliveira: A new algorithm for the reduction of incompletely specified finite state machines. ICCAD 1998: 482-489

Arlindo L. Oliveira, João P. Marques Silva: Efficient Search Techniques for the Inference of Minimum Size Finite Automata. SPIRE 1998: 81-89

Vasco M. Manquinho, Paulo F. Flores, João P. Marques Silva, Arlindo L. Oliveira: Prime Implicant Computation Using Satisfiability Algorithms. ICTAI 1997: 232-239

Arlindo L. Oliveira, Alberto L. Sangiovanni-Vincentelli: Using the Minimum Description Length Principle to Infer Reduced Ordered Decision Graphs. Machine Learning 25(1): 23-50 (1996)

Arlindo L. Oliveira, Stephen Edwards: Limits of Exact Algorithms For Inference of Minimum Size Finite State Machines. ALT 1996: 59-66

Arlindo L. Oliveira, Alberto L. Sangiovanni-Vincentelli: Inferring Reduced Ordered Decision Graphs of Minimum Description Length. ICML 1995: 421-429

Arlindo L. Oliveira, Alberto L. Sangiovanni-Vincentelli: Learning Complex Boolean Functions: Algorithms and Applications. NIPS 1993: 911-918

Arlindo L. Oliveira, Alberto L. Sangiovanni-Vincentelli: Constructive Induction Using a Non-Greedy Strategy for Feature Selection. ML 1992: 355-360

Arlindo L. Oliveira, Alberto L. Sangiovanni-Vincentelli: LSAT-An Algorithm for the Synthesis of Two Level Threshold Gate Networks. ICCAD 1991: 130-133

Arlindo L. Oliveira, Alberto L. Sangiovanni-Vincentelli: Learning Concepts by Synthesizing Minimal Threshold Gate Networks. ML 1991: 193-197