Publications – Bioinformatics and Information Retrieval Data Structures Analysis and Design

Publications:

Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernarno, Gonzalo Navarro, Óscar Pedreira. Extending general compact querieable representations to GIS applications. Information Sciences 506, pp. 196-216 (2020). DOI: 10.1016/j.ins.2019.08.007. Joint work UDC-UCHILE
Carlos Quijada-Fuentes, Miguel R. Penabad, Susana Ladra, Gilberto Gutiérrez. Compressed Data Structures for Binary Relations in Practice. IEEE Access 8, pp. 25949-25963 (2020). DOI: 10.1109/ACCESS.2020.2970983. Work UDC
Fernando Silva-Coira, José R. Paramá, Susana Ladra, Juan R. López, Gilberto Gutiérrez. Efficient processing of raster and vector data. PLoS ONE 15(1): e0226943 (2020). Work UDC.
Leo Ferres, José Fuentes-Sepúlveda, Travis Gagie, Meng He, Gonzalo Navarro. Fast and Compact Planar Embeddings. To appear in Computational Geometry Theory and Applications (2020). Work UCHILE.
Luís M. S. Russo, Ana D. Correia, Gonzalo Navarro, Alexandre P. Francisco. Approximating Optimal Bidirectional Macro Schemes. To appear in Procs. of the 30th Data Compression Conference (DCC) (2020). Joint work INESCID-UCHILE
Miguel E. Coimbra, Alexandre P. Francisco, Luís M. S. Russo, Guillermo de Bernardo, Susana Ladra, Gonzalo Navarro. On dynamic succinct graph representations. To appear in Procs. of the 30th Data Compression Conference (DCC) (2020). Joint work UDC-INESCID-ENX-UCHILE
Nieves R. Brisaboa, Antonio Fariña, Gonzalo Navarro, Tirso V. Rodeiro. Semantrix: a compressed semantic matrix. To appear in Procs. of the 30th Data Compression Conference (DCC) (2020). Joint work UDC-UCHILE
Adrián Gómez-Brandón. Bitvectors with runs and the successor/predecessor problem. To appear in Procs. of the 30th Data Compression Conference (DCC) (2020). Work UDC
Manuel Caceres, Simon J. Puglisi, Bella Zhukova. Fast Indexes for Gapped Pattern Matching. Procs. of 46th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM) (2020). Joint work UH-UCHILE
Pedro Mirabal, José Abreu, Diego Seco. Assessing the best edit in perturbation-based iterative refinement algorithms to compute the median string. Pattern Recognition Letters 120, 104-111 (2019). DOI: 10.1016/j.patrec.2019.02.004. Work UDEC.
José Fuentes-Sepúlveda, Susana Ladra. Energy consumption in compact integer vectors: A study case. IEEE Access 7, pp. 155625-155636 (2019). DOI: 10.1109/ACCESS.2019.2949655. Joint work UDC-UCHILE
Sandra Álvarez-García, Borja Freire, Susana Ladra, Óscar Pedreira. Compact and Efficient Representation of General Graph Databases. Knowledge and Information Systems 60(3), pp 1479–1510 (2019). DOI: 10.1007/s10115-018-1275-x. Joint work UDC-ENX
Nieves R. Brisaboa, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá. GraCT: A Grammar-based Compressed Index for Trajectory Data. Information Sciences 483, pp. 106-135 (2019). DOI: 10.1016/j.ins.2019.01.035. Joint work UDC-UCHILE
Antonio Fariña, Miguel A. Martínez-Prieto, Francisco Claude, Gonzalo Navarro, Juan J. Lastra-Díaz, Nicola Prezza, Diego Seco. On the reproducibility of experiments of indexing repetitive document collections. Information Systems 83, pp. 181-194 (2019). DOI: 10.1016/j.is.2019.03.007. Joint work UDC-UCHILE-UDEC
Luís M. S. Russo. A study on splay trees. Theoretical Computer Science 776(12), pp. 1-18 (2019). DOI: 10.1016/j.tcs.2018.12.020. Work INESC-ID
Daniel Inostroz, Cecilia Hernández, Diego Seco, Gonzalo Navarro, Alvaro Olivera-Nappa. Cell cycle and protein complex dynamics in discovering signaling pathways. Journal of Bioinformatics and Computational Biology 17(3), 21 pages (2019). DOI: 10.1142/S0219720019500112. Joint work UCHILE-UDEC
Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernardo, Gonzalo Navarro. Improved Compressed String Dictionaries. Procs. of 28th ACM International Conference on Information and Knowledge Management (CIKM), pp. 29-38 (2019). DOI: 10.1145/3357384.3357972. Joint work UDC-UCHILE
Nieves R. Brisaboa, Antonio Fariña, Adrián Gómez-Brandón, Gonzalo Navarro, Tirso V. Rodeiro. Dv2v: A Dynamic Variable-to-Variable Compressor. Procs. of Data Compression Conference (DCC), pp. 83-92 (2019). DOI: 10.1109/DCC.2019.00016. Joint work UDC-UCHILE
Nataly Cruces, Diego Seco, Gilberto Gutiérrez. A Compact Representation of Raster Time Series. Procs. of Data Compression Conference (DCC), pp. 103-111 (2019). DOI: 10.1109/DCC.2019.00018. Work UDEC
Jarno Alanko, Travis Gagie, Gonzalo Navarro, Louisa Seelbach Benkner. Tunneling on Wheeler Graphs. Procs. of Data Compression Conference (DCC), pp. 122-131 (2019). DOI: 10.1109/dcc.2019.00020. Joint work UH-UCHILE
Andrea Vázquez, Narciso López-López, Nicole Labra, Miguel Figueroa, Cyril Poupon, Jean-François Mangin, Cecilia Hernández, Pamela Guevara. Parallel Optimization of Fiber Bundle Segmentation for Massive Tractography Datasets. Procs. of the 16th International Symposium on Biomedical Imaging (ISBI), pp. 178-181 (2019). DOI: 10.1109/ISBI.2019.8759208. Work UDC-UDEC.
Diego Díaz-Domínguez, Travis Gagie, Gonzalo Navarro. Simulating the DNA String Graph in Succinct Space. Procs. of 30th Annual Symposium on Combinatorial Pattern Matching (CPM), pp. 26:1-26:20 (2019). DOI: 10.4230/LIPIcs.CPM.2019.26. Work UCHILE
Diego Díaz-Domínguez. An Index for Sequencing Reads Based on the Colored de Bruijn Graph. Procs. of 26th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11811, pp. 304-321 (2019). DOI: 10.1007/978-3-030-32686-9_22. Work UCHILE
Diego Arroyuelo, Guillermo de Bernardo, Travis Gagie, Gonzalo Navarro. Faster Dynamic Compressed d-ary Relation. Procs. of 26th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11811, pp. 419-433 (2019). DOI: 110.1007/978-3-030-32686-9_30. Joint work UDC-UCHILE
Susana Ladra, Miguel R. Luaces, José R. Paramá, Fernando Silva-Coira. Space- and Time-Efficient Storage of LiDAR Point Clouds. Procs. of 26th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11811, pp. 513-527 (2019). DOI: 10.1007/978-3-030-32686-9_36. Work UDC
José Fuentes-Sepúlveda, Gonzalo Navarro, Diego Seco. Implementing the Topological Model Succinctly. Procs. of 26th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11811, pp. 499-512 (2019). DOI: 10.1007/978-3-030-32686-9_35. Work UCHILE-UDEC
Daniel Gibney, Sharma V. Thankachan On the Hardness and Inapproximability of Recognizing Wheeler Graphs. Procs. of the 27th Annual European Symposium on Algorithms Euroa (ESA), article no. 51 (2019). DOI: 10.4230/LIPIcs.ESA.2019.51. Work generated during networking and research activities.
Narciso López-López, Andrea Vázquez, Cyril Poupon, Jean-François Mangin, Pamela Guevara. Cortical surface parcellation based on intra-subject white matter fiber clustering. Proceedings of the 2019 IEEE CHILEAN Conference on Electrical, Electronics Engineering, Information and Communication Technologies (CHILECON) (2019). DOI: 10.1109/CHILECON47746.2019.8988066. Work UDC-UDEC
Suilen H. Alvarado. Design of Mutation Operators for Testing Geographic Information Systems. Proceedings of the 2nd XoveTIC Conference (XoveTIC 2019). Proceedings 2019, 21(1), 43. DOI: 10.3390/proceedings2019021043. Work UDEC-UDC
Nieves R. Brisaboa, Antonio Fariña, Daniil Galaktionov, M. Andrea Rodríguez. A Compact Representation for Trips over Networks built on self-indexes. Information Systems 578, pp. 1-22 (2018). DOI: 10.1016/j.is.2018.06.010. Joint work UDC-ENX-UDEC
Nieves R. Brisaboa, Diego Caro, Antonio Fariña, M. Andrea Rodríguez. Using Compressed Suffix-Arrays for a Compact Representation of Temporal-Graphs. Information Sciences 465, pp. 459-483 (2018). DOI: 10.1016/j.ins.2018.07.023. Joint work UDC-UDEC
Luís M. S. Russo, Andreia Sofia Teixeira, Alexandre P. Francisco. Linking and Cutting Spanning Trees. Algorithms 11(4), 53 (2018). DOI: 10.3390/a11040053. Work INESC-ID
Nieves R. Brisaboa, Antonio Fariña, Daniil Galaktionov, Tirso V. Rodeiro, M. Andrea Rodríguez. New structures to solve aggregated queries for trips over public transportation networks. Procs. of 25th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11147, pp. 85-101 (2018). DOI: 10.1007/978-3-030-00479-8_8. Joint work UDC-ENX-UDEC
Nieves R. Brisaboa, Adrián Gómez-Brandón, Miguel A. Martínez-Prieto, José R. Paramá. 3DGraCT: A Grammar based Compressed representation of 3D Trajectories. Procs. of 25th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11147, pp. 102-106 (2018). DOI: 10.1007/978-3-030-00479-8_9. Work UDC
Ana Cerdeira-Pena, Guillermo de Bernardo, Antonio Fariña, José R. Paramá, Fernando Silva-Coira. Towards a compact representation of temporal raster. Procs. of 25th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11147, pp. 117-130 (2018). DOI: 10.1007/978-3-030-00479-8_10. Joint work UDC-ENX
Rodrigo Rivera, M. Andrea Rodríguez, Diego Seco. Faster and Smaller Two-Level Index for Network-Based Trajectories. Procs. of 25th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 11147, pp. 348-362 (2018). DOI: 10.1007/978-3-030-00479-8_28. Work UDEC
Alejandro Cortiñas, Miguel R. Luaces, Tirso V. Rodeiro. A Case Study on Visualizing Large Spatial Datasets in a Web-Based Map Viewer. Procs. of 18th International Conference on Web Engineering (IGWE), LNCS 10845, pp. 296-303 (2018). DOI: 10.1007/978-3-319-91662-0_23. Work UDC.
Jose-Miguel Horcas, Alejandro Cortiñas, Lidia Fuentes, Miguel R. Luaces. Integrating the Common Variability Language with Multilanguage Annotations for Web Engineering. Procs. of the 22nd International Systems and Software Product Line Conferences (SPLC), pp. 196-207 (2018). DOI: 10.1145/3233027.3233049.
Sahar Hooshmand, Paniz Abedin, M. Oğuzhan Külekci, Sharma V. Thankachan. Non-Overlapping Indexing – Cache Obliviously. Procs. of 29th Annual Symposium on Combinatorial Pattern Matching (CPM), pp. 8:1-8:9 (2018). DOI: 10.4230/LIPIcs.CPM.2018.8. Work generated during networking and research activities.
Rui Henriques, Alexandre P. Francisco, Luís M. S. Russo, Hideo Bannai. Order-Preserving Pattern Matching Indeterminate Strings. Procs. of the 29th Annual Symposium on Combinatorial Pattern Matching (CPM), pp. 2:1-2:15 (2018). DOI: 10.4230/LIPIcs.CPM.2018.2. Work INESC-ID-KU.
José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi. Run Compressed Rank/Select for Large Alphabets. Procs. of Data Compression Conference (DCC), pp. 315-324 (2018). DOI: 10.1109/DCC.2018.00040. Joint work UH-UCHILE.
Nieves R. Brisaboa, Guillermo de Bernardo, Gonzalo Navarro, Tirso V. Rodeiro, Diego Seco. Compact Representations of Event Sequences. Procs. of Data Compression Conference (DCC), pp. 237-246 (2018). DOI: 10.1109/DCC.2018.00032. Joint work UDC-UCHILE-UDEC.
Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro. Two-Dimensional Block Trees. Procs. of Data Compression Conference (DCC). pp. 227-236 (2018). DOI: 10.1109/DCC.2018.00031. Joint work UDC-UCHILE.
Alexandre P Francisco, Travis Gagie, Susana Ladra, Gonzalo Navarro. Exploiting Computation-Friendly Graph Compression Methods. Procs. of Data Compression Conference (DCC), pp. 307-314 (2018). DOI: 10.1109/DCC.2018.00039. Joint work UDC-INESCID-UCHILE.
Guillermo de Bernardo, Susana Ladra About BIRDS project (Bioinformatics and Information Retrieval Data Structures Analysis and Design). Procs. 5th Spanish Conference on Information Retrieval (CERI), art:2 (2018). DOI: 10.1145/3230599.3230602. Joint work UDC-ENX
Alexandre Francisco, Travis Gagie, Dominik Kempa, Leena Salmela, Sophie Sverdlov, Jarkko Toivonen, Esko Ukkonen. An Experiment in Learning the Language of Sequence Motifs: Sequence Logos vs. Finite-State Machines. bioRxiv (2017). DOI: 10.1101/143024. Joint work INESCID-UH.
Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá. Efficient Compression and Indexing of Trajectories. Procs. of 24th International Symposium on String Processing and Information Retrieval (SPIRE) 2017. DOI: 10.1007/978-3-319-67428-5_10. Joint work UDC-UCHILE.
Fernando Silva-Coira. Compact data structures for large and complex datasets. PhD Thesis. Universidade da Coruña (2017).
Leo Ferres, José Fuentes, Travis Gagie, Meng He, Gonzalo Navarro. Fast and Compact Planar Embeddings. Procs. of Algorithms and Data Structures Symposium (WADS), LNCS 10389, pp. 385-396 (2017). DOI: 10.1007/978-3-319-62127-2_33. Work UCHILE.
Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru Tomescu. Optimal Omnitig Listing for Safe and Complete Contig Assembly. Procs. 28th Annual Symposium on Combinatorial Pattern Matching (CPM), Leibniz International Proceedings in Informatics (LIPIcs), pp. 29:1–29:12 (2017). DOI: 10.4230/LIPIcs.CPM.2017.29. Work UH.
Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén. Document Retrieval on Repetitive Collections. Information Retrieval 20, pp. 253-291 (2017). DOI: 10.1007/s10791-017-9297-7. Joint work UH-UCHILE.
Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernardo, Gonzalo Navarro. Compressed Representation of Dynamic Binary Relations with Applications. Information Systems 69, pp. 106-123 (2017). DOI: 10.1016/j.is.2017.05.003. Joint work UDC-ENX-UCHILE.
Alberto Ordóñez, Gonzalo Navarro, Nieves R. Brisaboa. Grammar Compressed Sequences with Rank/Select Support. Journal of Discrete Algorithms 43, pp. 54-71 (2017). DOI: 10.1016/j.jda.2016.10.001. Joint work UDC-UCHILE.
Sandra Alvarez-Garcia, Guillermo de Bernardo, Nieves R. Brisaboa, Gonzalo Navarro A succinct data structure for self-indexing ternary relations. Journal of Discrete Algorithms 43, pp. 38-53 (2017). DOI: 10.1016/j.jda.2016.10.002. Joint work UDC-ENX-UCHILE.
José Fuentes-Sepúlveda, Erick Elejalde, Leo Ferres, Diego Seco. Parallel construction of wavelet trees on multicore architectures. Knowledge and Information Systems, pp. 1-24 (2016). DOI: 10.1007/s10115-016-1000-6.
Antonio Fariña, Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Alberto Ordóñez. Efficient and Compact Representations of Some Non-canonical Prefix-Free Codes. Procs. of 23rd International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 9954, pp. 50-60 (2016). DOI: 10.1007/978-3-319-46049-9_5. Joint work UDC-UH-UCHILE.
Nieves R. Brisaboa, Ana Cerdeira-Pena, Narciso López-López, Gonzalo Navarro, Miguel R. Penabad, Fernando Silva-Coira. Efficient Representation of Multidimensional Data over Hierarchical Domains. Procs. of 23rd International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 9954, pp. 191-203 (2016). DOI: 10.1007/978-3-319-46049-9_19. Joint work UDC-UCHILE.
Nieves R. Brisaboa, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá. GraCT: A Grammar Based Compressed Representation of Trajectories. Procs. of 23rd International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 9954, pp. 218-230 (2016). DOI: 10.1007/978-3-319-46049-9_21. Joint work UDC-UCHILE.
Nieves R. Brisaboa, Antonio Fariña, Daniil Galaktionov, M. Andrea Rodríguez. Compact Trip Representation over Networks. Procs. of 23rd International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 9954, pp. 240-253 (2016). DOI: 10.1007/978-3-319-46049-9_23. Joint work UDC-UDEC.
Guillermo de Bernardo, Ramón Casares, Adrián Gómez-Brandón, José R. Paramá. A New Method to Index and Store Spatio-Temporal Data. Procs. of the 20th Pacific Asia Conference on Information Systems (PACIS), paper 93 (2016). Joint work UDC-ENX.
Daniil Galaktionov, Miguel R. Luaces, Ángeles S. Places. Navigational Rule Derivation: an Algorithm to Determine the Effect of Traffic Signs on Road Networks. Procs. of the 20th Pacific Asia Conference on Information Systems (PACIS), paper 94 (2016).
Nieves R. Brisaboa, Guillermo De Bernardo, Roberto Konow, Gonzalo Navarro, Diego Seco. Aggregated 2D range queries on clustered points. Information Systems 60, pp. 34-49 (2016). DOI: 10.1016/j.is.2016.03.004. Joint work UDC-ENX-UCHILE-UDEC.
Francisco Claude, Antonio Fariña, Miguel A. Martínez-Prieto, Gonzalo Navarro. Universal indexes for highly repetitive document collections. Information Systems 61, pp. 1-23 (2016). DOI: 10.1016/j.is.2016.04.002. Joint work UDC-UCHILE.