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Bioinformatics and Information Retrieval Data Structures Analysis and Design

Deliverables

Integration report

Integration report.

Final report of WP4

Final report of WP4, including a survey on the literature previous to this project, advances done and source code of new algorithms and data structures designed during the lifetime of the project for network analysis.

Quality management plan

Quality management plan

Benchmark and test report

Benchmark and test report.

Kick-Off Meeting documentation

Kick-Off Meeting documentation

Final report of WP6

Final dissemination report including all demonstration activities, publications, reports on workshops and summer schools, teaching material, brochures, etc., involved in this working package

Final report of WP2

Final report of WP2, including a survey on the literature previous to this project, advances done and source code of new algorithms and data structures designed during the lifetime of the project for sequence analysis.

Final report of WP3

Final report of WP3, including a survey on the literature previous to this project, advances done and source code of new algorithms and data structures designed during the lifetime of the project for compression and indexing repetitive data.

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Publications

Run Compressed Rank/Select for Large Alphabets

Author(s): Jose Fuentes-Sepulveda, Juha Karkkainen, Dmitry Kosolobov, Simon Puglisi
Published in: 2018 Data Compression Conference, 2018, Page(s) 315-324
DOI: 10.1109/dcc.2018.00040

Exploiting Computation-Friendly Graph Compression Methods for Adjacency-Matrix Multiplication

Author(s): Alexandre Francisco, Travis Gagie, Susana Ladra, Gonzalo Navarro
Published in: 2018 Data Compression Conference, 2018, Page(s) 307-314
DOI: 10.1109/dcc.2018.00039

Navigational Rule Derivation: an Algorithm to Determine the Effect of Traffic Signs on Road Networks

Author(s): Daniil Galaktionov, Miguel R. Luaces, Ángeles S. Places
Published in: Proceeding of the 20th Pacific Asia Conference on Information Systems, Issue PACIS 2016, 2016, Page(s) Paper 94

A New Method to Index and Store Spatio-Temporal Data

Author(s): Guillermo de Bernardo, Ramón Casares, Adrián Gómez-Brandón, José R. Paramá
Published in: Proceeding of the 20th Pacific Asia Conference on Information Systems, Issue PACIS 2016, 2016, Page(s) Paper 93

Two-Dimensional Block Trees

Author(s): Nieves R. Brisaboa, Travis Gagie, Adrian Gomez-Brandon, Gonzalo Navarro
Published in: 2018 Data Compression Conference, 2018, Page(s) 227-236
DOI: 10.1109/dcc.2018.00031

Compact Representations of Event Sequences

Author(s): Nieves R. Brisaboa, Guillermo de Bernardo, Gonzalo Navarro, Tirso V. Rodeiro, Diego Seco
Published in: 2018 Data Compression Conference, 2018, Page(s) 237-246
DOI: 10.1109/dcc.2018.00032

About BIRDS project (Bioinformatics and Information Retrieval Data Structures Analysis and Design)

Author(s): Guillermo de Bernardo, Susana Ladra
Published in: Proceedings of the 5th Spanish Conference on Information Retrieval - CERI '18, 2018, Page(s) 1-4
DOI: 10.1145/3230599.3230602

Non-Overlapping Indexing - Cache Obliviously

Author(s): Sahar Hooshmand, Paniz Abedin, M. Oguzhan Külekci, Sharma V. Thankachan
Published in: Annual Symposium on Combinatorial Pattern Matching (CPM 2018), 2018, Page(s) 8:1--8:9
DOI: 10.4230/lipics.cpm.2018.8

Integrating the common variability language with multilanguage annotations for web engineering

Author(s): Jose-Miguel Horcas, Alejandro Cortiñas, Lidia Fuentes, Miguel R. Luaces
Published in: Proceeedings of the 22nd International Conference on Systems and Software Product Line - SPLC '18, 2018, Page(s) 196-207
DOI: 10.1145/3233027.3233049

On the Hardness and Inapproximability of Recognizing Wheeler Graphs

Author(s): Daniel Gibney, Sharma V. Thankachan
Published in: 27th Annual European Symposium on Algorithms (ESA 2019), 2019, Page(s) 51:1--51:16
DOI: 10.4230/lipics.esa.2019.51

Parallel Optimization of Fiber Bundle Segmentation for Massive Tractography Datasets

Author(s): Andrea Vazquez, Narciso Lopez-Lopez, Nicole Labra, Miguel Figueroa, Cyril Poupon, Jean-Francois Mangin, Cecilia Hernandez, Pamela Guevara
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), 2019, Page(s) 178-181
DOI: 10.1109/isbi.2019.8759208

Simulating the DNA Overlap Graph in Succinct Space

Author(s): Diego Díaz-Domínguez, Travis Gagie, Gonzalo Navarro
Published in: 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019), 2019, Page(s) 26:1--26:20
DOI: 10.4230/lipics.cpm.2019.26

A Compact Representation of Raster Time Series

Author(s): Nataly Cruces, Diego Seco, Gilberto Guiterrez
Published in: 2019 Data Compression Conference (DCC), 2019, Page(s) 103-111
DOI: 10.1109/dcc.2019.00018

Dv2v: A Dynamic Variable-to-Variable Compressor

Author(s): Nieves R. Brisaboa, Antonio Farina, Adrian Gomez-Brandon, Gonzalo Navarro, Tirso V. Rodeiro
Published in: 2019 Data Compression Conference (DCC), 2019, Page(s) 83-92
DOI: 10.1109/dcc.2019.00016

Tunneling on Wheeler Graphs

Author(s): Jarno Alanko, Travis Gagie, Gonzalo Navarro, Louisa Seelbach Benkner
Published in: 2019 Data Compression Conference (DCC), 2019, Page(s) 122-131
DOI: 10.1109/dcc.2019.00020

Improved Compressed String Dictionaries

Author(s): Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernardo, Gonzalo Navarro
Published in: Proceedings of the 28th ACM International Conference on Information and Knowledge Management - CIKM '19, 2019, Page(s) 29-38
DOI: 10.1145/3357384.3357972

Order-Preserving Pattern Matching Indeterminate Strings

Author(s): Rui Henriques, Alexandre P. Francisco, Luís M. S. Russo, Hideo Bannai
Published in: Annual Symposium on Combinatorial Pattern Matching (CPM 2018), Issue 2:1--2:15, 2018
DOI: 10.4230/lipics.cpm.2018.2

Cortical surface parcellation based on intra-subject white matter fiber clustering

Author(s): Narciso Lopez-Lopez, Andrea Vazquez, Cyril Poupon, Jean-Francois Mangin, Pamela Guevara
Published in: 2019 IEEE CHILEAN Conference on Electrical, Electronics Engineering, Information and Communication Technologies (CHILECON), 2019, Page(s) 1-6
DOI: 10.1109/chilecon47746.2019.8988066

Bitvectors with runs and the successor/predecessor problem

Author(s): Adrián Gómez-Brandón
Published in: 2020 Data Compression Conference, 2020

Revisiting compact RDF stores based on k2-trees

Author(s): Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernardo, Antonio Fariña
Published in: 2020 Data Compression Conference, 2020

On dynamic succinct graph representations

Author(s): Miguel E. Coimbra, Alexandre P. Francisco, Luís M. S. Russo, Guillermo de Bernardo, Susana Ladra, Gonzalo Navarro
Published in: 2020 Data Compression Conference, 2020

Semantrix: A Compressed Semantic Matrix

Author(s): Nieves R. Brisaboa, Antonio Fariña, Gonzalo Navarro, Tirso V. Rodeiro
Published in: 2020 Data Compression Conference, 2020

Approximating Optimal Bidirectional Macro Schemes

Author(s): Luís M. S. Russo, Ana D. Correia, Gonzalo Navarro, Alexandre P. Francisco
Published in: 2020 Data Compression Conference, 2020

Pivot Selection for Median String Problem

Author(s): Pedro Mirabal, Jose Abreu, Oscar Pedreira
Published in: 2019 38th International Conference of the Chilean Computer Science Society (SCCC), 2019, Page(s) 1-5
DOI: 10.1109/sccc49216.2019.8966441

Efficient Compression and Indexing of Trajectories

Author(s): Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá
Published in: Procs. of 24th International Symposium on String Processing and Information Retrieval, Issue SPIRE 2017, 2017, Page(s) 103-115
DOI: 10.1007/978-3-319-67428-5_10

Fast and Compact Planar Embeddings

Author(s): Leo Ferres, José Fuentes, Travis Gagie, Meng He, Gonzalo Navarro
Published in: Algorithms and Data Structures Symposium, Issue WADS 2017, 2017, Page(s) 385-396
DOI: 10.1007/978-3-319-62127-2_33

Optimal Omnitig Listing for Safe and Complete Contig Assembly

Author(s): Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru Tomescu
Published in: Procs. 28th Annual Symposium on Combinatorial Pattern Matching, Issue CPM 2017, 2017, Page(s) 29:1--29:12
DOI: 10.4230/LIPIcs.CPM.2017.29

Parallel construction of wavelet trees on multicore architectures

Author(s): José Fuentes-Sepúlveda, Erick Elejalde, Leo Ferres, Diego Seco
Published in: Knowledge and Information Systems, 2016, ISSN 0219-1377
DOI: 10.1007/s10115-016-1000-6

Aggregated 2D range queries on clustered points

Author(s): Nieves R. Brisaboa, Guillermo De Bernardo, Roberto Konow, Gonzalo Navarro, Diego Seco
Published in: Information Systems, Issue 60, 2016, Page(s) 34-49, ISSN 0306-4379
DOI: 10.1016/j.is.2016.03.004

Universal indexes for highly repetitive document collections

Author(s): Francisco Claude, Antonio Fariña, Miguel A. Martínez-Prieto, Gonzalo Navarro
Published in: Information Systems, Issue 61, 2016, Page(s) 1-23, ISSN 0306-4379
DOI: 10.1016/j.is.2016.04.002

Linking and Cutting Spanning Trees

Author(s): Luís M. S.  Russo, Andreia Teixeira, Alexandre  Francisco
Published in: Algorithms, Issue 11/4, 2018, Page(s) 53, ISSN 1999-4893
DOI: 10.3390/a11040053

A compact representation for trips over networks built on self-indexes

Author(s): Nieves R. Brisaboa, Antonio Fariña, Daniil Galaktionov, M. Andrea Rodriguez
Published in: Information Systems, Issue 78, 2018, Page(s) 1-22, ISSN 0306-4379
DOI: 10.1016/j.is.2018.06.010

Using Compressed Suffix-Arrays for a compact representation of temporal-graphs

Author(s): Nieves R. Brisaboa, Diego Caro, Antonio Fariña, M. Andrea Rodriguez
Published in: Information Sciences, Issue 465, 2018, Page(s) 459-483, ISSN 0020-0255
DOI: 10.1016/j.ins.2018.07.023

Design of Mutation Operators for Testing Geographic Information Systems

Author(s): Suilen H. Alvarado
Published in: Proceedings, Issue 21/1, 2019, Page(s) 43, ISSN 2504-3900
DOI: 10.3390/proceedings2019021043

Cell cycle and protein complex dynamics in discovering signaling pathways

Author(s): Daniel Inostroza, Cecilia Hernández, Diego Seco, Gonzalo Navarro, Alvaro Olivera-Nappa
Published in: Journal of Bioinformatics and Computational Biology, Issue 17/03, 2019, Page(s) 1950011, ISSN 0219-7200
DOI: 10.1142/s0219720019500112

A study on splay trees

Author(s): Luís M.S. Russo
Published in: Theoretical Computer Science, Issue 776, 2019, Page(s) 1-18, ISSN 0304-3975
DOI: 10.1016/j.tcs.2018.12.020

On the reproducibility of experiments of indexing repetitive document collections

Author(s): Antonio Fariña, Miguel A. Martínez-Prieto, Francisco Claude, Gonzalo Navarro, Juan J. Lastra-Díaz, Nicola Prezza, Diego Seco
Published in: Information Systems, Issue 83, 2019, Page(s) 181-194, ISSN 0306-4379
DOI: 10.1016/j.is.2019.03.007

GraCT: A Grammar-based Compressed Index for Trajectory Data

Author(s): Nieves R. Brisaboa, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá
Published in: Information Sciences, Issue 483, 2019, Page(s) 106-135, ISSN 0020-0255
DOI: 10.1016/j.ins.2019.01.035

Compact and efficient representation of general graph databases

Author(s): Sandra Álvarez-García, Borja Freire, Susana Ladra, Óscar Pedreira
Published in: Knowledge and Information Systems, Issue 60/3, 2019, Page(s) 1479-1510, ISSN 0219-1377
DOI: 10.1007/s10115-018-1275-x

Energy Consumption in Compact Integer Vectors: A Study Case

Author(s): Jose Fuentes-Sepulveda, Susana Ladra
Published in: IEEE Access, Issue 7, 2019, Page(s) 155625-155636, ISSN 2169-3536
DOI: 10.1109/ACCESS.2019.2949655

Assessing the best edit in perturbation-based iterative refinement algorithms to compute the median string

Author(s): P. Mirabal, J. Abreu, D. Seco
Published in: Pattern Recognition Letters, Issue 120, 2019, Page(s) 104-111, ISSN 0167-8655
DOI: 10.1016/j.patrec.2019.02.004

Efficient processing of raster and vector data

Author(s): Fernando Silva-Coira, José R. Paramá, Susana Ladra, Juan R. López, Gilberto Gutiérrez
Published in: PLOS ONE, Issue 15/1, 2020, Page(s) e0226943, ISSN 1932-6203
DOI: 10.1371/journal.pone.0226943

Document retrieval on repetitive string collections

Author(s): Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Published in: Information Retrieval Journal, Issue 20/3, 2017, Page(s) 253-291, ISSN 1386-4564
DOI: 10.1007/s10791-017-9297-7

A succinct data structure for self-indexing ternary relations

Author(s): Sandra Alvarez-Garcia, Guillermo de Bernardo, Nieves R. Brisaboa, Gonzalo Navarro
Published in: Journal of Discrete Algorithms, Issue 43, 2017, Page(s) 38-53, ISSN 1570-8667
DOI: 10.1016/j.jda.2016.10.002

Grammar compressed sequences with rank/select support

Author(s): Alberto Ordóñez, Gonzalo Navarro, Nieves R. Brisaboa
Published in: Journal of Discrete Algorithms, Issue 43, 2017, Page(s) 54-71, ISSN 1570-8667
DOI: 10.1016/j.jda.2016.10.001

Compressed representation of dynamic binary relations with applications

Author(s): Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernardo, Gonzalo Navarro
Published in: Information Systems, Issue 69, 2017, Page(s) 106-123, ISSN 0306-4379
DOI: 10.1016/j.is.2017.05.003

Compact Trip Representation over Networks

Author(s): Nieves R. Brisaboa, Antonio Fariña, Daniil Galaktionov, M. Andrea Rodríguez
Published in: String Processing and Information Retrieval, 2016, Page(s) 240-253
DOI: 10.1007/978-3-319-46049-9_23

Efficient Representation of Multidimensional Data over Hierarchical Domains

Author(s): Nieves R. Brisaboa, Ana Cerdeira-Pena, Narciso López-López, Gonzalo Navarro, Miguel R. Penabad, Fernando Silva-Coira
Published in: String Processing and Information Retrieval, 2016, Page(s) 191-203
DOI: 10.1007/978-3-319-46049-9_19

GraCT: A Grammar Based Compressed Representation of Trajectories

Author(s): Nieves R. Brisaboa, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá
Published in: String Processing and Information Retrieval, 2016, Page(s) 218-230
DOI: 10.1007/978-3-319-46049-9_21

Efficient and Compact Representations of Some Non-canonical Prefix-Free Codes

Author(s): Antonio Fariña, Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Alberto Ordóñez
Published in: String Processing and Information Retrieval, 2016, Page(s) 50-60
DOI: 10.1007/978-3-319-46049-9_5

A Case Study on Visualizing Large Spatial Datasets in a Web-Based Map Viewer

Author(s): Alejandro Cortiñas, Miguel R. Luaces, Tirso V. Rodeiro
Published in: Web Engineering, Issue 10845, 2018, Page(s) 296-303
DOI: 10.1007/978-3-319-91662-0_23

Faster and Smaller Two-Level Index for Network-Based Trajectories

Author(s): Rodrigo Rivera, M. Andrea Rodríguez, Diego Seco
Published in: String Processing and Information Retrieval - 25th International Symposium, SPIRE 2018, Lima, Peru, October 9-11, 2018, Proceedings, Issue 11147, 2018, Page(s) 348-362
DOI: 10.1007/978-3-030-00479-8_28

Towards a Compact Representation of Temporal Rasters

Author(s): Ana Cerdeira-Pena, Guillermo de Bernardo, Antonio Fariña, José Ramón Paramá, Fernando Silva-Coira
Published in: String Processing and Information Retrieval - 25th International Symposium, SPIRE 2018, Lima, Peru, October 9-11, 2018, Proceedings, Issue 11147, 2018, Page(s) 117-130
DOI: 10.1007/978-3-030-00479-8_10

3DGraCT: A Grammar-Based Compressed Representation of 3D Trajectories

Author(s): Nieves R. Brisaboa, Adrián Gómez-Brandón, Miguel A. Martínez-Prieto, José Ramón Paramá
Published in: String Processing and Information Retrieval - 25th International Symposium, SPIRE 2018, Lima, Peru, October 9-11, 2018, Proceedings, Issue 11147, 2018, Page(s) 102-116
DOI: 10.1007/978-3-030-00479-8_9

New Structures to Solve Aggregated Queries for Trips over Public Transportation Networks

Author(s): Nieves R. Brisaboa, Antonio Fariña, Daniil Galaktionov, Tirso V. Rodeiro, M. Andrea Rodríguez
Published in: String Processing and Information Retrieval - 25th International Symposium, SPIRE 2018, Lima, Peru, October 9-11, 2018, Proceedings, Issue 11147, 2018, Page(s) 88-101
DOI: 10.1007/978-3-030-00479-8_8

Faster Dynamic Compressed d-ary Relations

Author(s): Diego Arroyuelo, Guillermo de Bernardo, Travis Gagie, Gonzalo Navarro
Published in: String Processing and Information Retrieval - 26th International Symposium, SPIRE 2019, Segovia, Spain, October 7–9, 2019, Proceedings, Issue 11811, 2019, Page(s) 419-433
DOI: 10.1007/978-3-030-32686-9_30

Space- and Time-Efficient Storage of LiDAR Point Clouds

Author(s): Susana Ladra, Miguel R. Luaces, José R. Paramá, Fernando Silva-Coira
Published in: String Processing and Information Retrieval - 26th International Symposium, SPIRE 2019, Segovia, Spain, October 7–9, 2019, Proceedings, Issue 11811, 2019, Page(s) 513-527
DOI: 10.1007/978-3-030-32686-9_36

Implementing the Topological Model Succinctly

Author(s): José Fuentes-Sepúlveda, Gonzalo Navarro, Diego Seco
Published in: String Processing and Information Retrieval - 26th International Symposium, SPIRE 2019, Segovia, Spain, October 7–9, 2019, Proceedings, Issue 11811, 2019, Page(s) 499-512
DOI: 10.1007/978-3-030-32686-9_35

An Index for Sequencing Reads Based on the Colored de Bruijn Graph

Author(s): Diego Díaz-Domínguez
Published in: String Processing and Information Retrieval - 26th International Symposium, SPIRE 2019, Segovia, Spain, October 7–9, 2019, Proceedings, Issue 11811, 2019, Page(s) 304-321
DOI: 10.1007/978-3-030-32686-9_22

Fast Indexes for Gapped Pattern Matching

Author(s): Manuel Cáceres, Simon J. Puglisi, Bella Zhukova
Published in: SOFSEM 2020: Theory and Practice of Computer Science - 46th International Conference on Current Trends in Theory and Practice of Informatics, SOFSEM 2020, Limassol, Cyprus, January 20–24, 2020, Proceedings, Issue 12011, 2020, Page(s) 493-504
DOI: 10.1007/978-3-030-38919-2_40

An Experiment in Learning the Language of Sequence Motifs: Sequence Logos vs. Finite-State Machines

Author(s): Gagie, Travis; Kempa, Dominik; Salmela, Leena; Sverdlov, Sophie; Toivonen, Jarkko; Ukkonen, Esko; Francisco, Alexandre
Published in: Issue 14, 2017
DOI: 10.1101/143024

Lempel-Ziv-like Parsing in Small Space

Author(s): Valenzuela, Daniel; Kosolobov, Dmitry; Navarro, Gonzalo; Puglisi, Simon J.
Published in: 2019

Assembling Omnitigs using Hidden-Order de Bruijn Graphs

Author(s): Díaz-Domínguez, Diego; Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Navarro, Gonzalo; Puglisi, Simon J.
Published in: 2019

Compressed data structures for trajectory representation

Author(s): Daniil Galaktionov
Published in: 2020

Compact data structures for large and complex datasets

Author(s): Fernando Silva-Coira
Published in: 2017