Bibliography

Major publications by the team in recent years

1J. Cojan, J. Lieber.

An Algorithm for Adapting Cases Represented in ALC, in: 22nd International Joint Conference on Artificial Intelligence - IJCAI 2011, Barcelone, Spain, July 2011.

http://hal.inria.fr/inria-00584103/en
2V. Dufour-Lussier, J. Lieber, E. Nauer, Y. Toussaint.

Improving case retrieval by enrichment of the domain ontology, in: 19th International Conference on Case Based Reasoning - ICCBR'2011, London, United Kingdom, 2011.

http://hal.inria.fr/inria-00617621/en
3A. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.

Spatial clustering of protein binding sites for template based protein docking, in: Bioinformatics, August 2011. [ DOI : 10.1093/bioinformatics/btr493 ]

http://hal.inria.fr/inria-00617921/en
4C. Grac, A. Braud, F. Le Ber, M. Trémolières.

Un système d'information pour le suivi et l'évaluation de la qualité des cours d'eau – Application à l'hydro-écorégion de la plaine d'Alsace, in: RSTI - Ingénierie des Systèmes d'Information, 2011, vol. 16, p. 9-30.

http://hal.archives-ouvertes.fr/hal-00601991/en/
5M. Kaytoue, S. O. Kuznetsov, A. Napoli.

Revisiting Numerical Pattern Mining with Formal Concept Analysis, in: Twenty second International Joint Conference on Artificial Intelligence - IJCAI 2011, Barcelona, Spain, 2011.

http://hal.inria.fr/inria-00584371/en
6J.-F. Mari, F. Le Ber, E.-G. Lazrak, M. Benoît, C. Eng, A. Thibessard, P. Leblond.

Using Markov Models to Mine Temporal and Spatial Data, in: New Fundamental Technologies in Data Mining, K. Funatsu, K. Hasegawa (editors), Intech, 2011, p. 561–584.

http://hal.inria.fr/inria-00566801/en
7L. Mavridis, A. Ghoorah, V. Venkatraman, D. Ritchie.

Representing and comparing protein folds and fold families using 3D shape-density representations, in: Proteins, November 2011. [ DOI : 10.1002/prot.23218 ]

http://hal.inria.fr/hal-00641815/en
8C. Raïssi, J. Pei.

Towards Bounding Sequential Patterns, in: 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD-2011, San Diego, United States, C. Apté, J. Ghosh, P. Smyth (editors), ACM, August 2011, ISBN : 978-1-4503-0813-7. [ DOI : 10.1145/2020408.2020612 ]

http://hal.inria.fr/inria-00623550/en

Publications of the year

Doctoral Dissertations and Habilitation Theses

9Y. Assess.

Conception par modélisation et criblage in solico d'inhibiteurs du récepteur c-Met, Université Henri Poincaré - Nancy I, October 2011.
10S. Benabderrahmane.

Prise en compte des connaissances du domaine dans l'analyse transcriptomique : Similarité sémantique, classification fonctionnelle et profils flous. Application au cancer colorectal., Université Henri Poincaré - Nancy I, December 2011.

http://tel.archives-ouvertes.fr/tel-00653169/en/
11J. Cojan.

Application de la théorie de la révision des connaissances au raisonnement à partir de cas, Université Henri Poincaré - Nancy I, October 2011.

http://hal.inria.fr/tel-00646841/en
12M. Kaytoue.

Traitement de données numériques par analyse formelle de concepts et structures de patrons, Université Henri Poincaré - Nancy I, April 2011.

http://hal.inria.fr/tel-00599168/en
13D. Ritchie.

Algorithmes Haute-Performance pour la Reconnaissance de Formes Moléculaires, Université Henri Poincaré - Nancy I, April 2011, Habilitation à Diriger des Recherches.

http://hal.inria.fr/tel-00587962/en
14Y. Toussaint.

Fouille de textes : des méthodes symboliques pour la construction d'ontologies et l'annotation sémantique guidée par les connaissances, Université Henri Poincaré - Nancy I, November 2011, Habilitation à diriger des recherches (HDR).

Articles in International Peer-Reviewed Journal

15A. K. R. Abadio, E. S. Kioshima, M. M. Teixeira, N. F. Martins, B. Maigret, M. S. S. Felipe.

Comparative genomics allowed the identification of drug targets against human fungal pathogens., in: BMC Genomics, January 2011, vol. 12, 75 p. [ DOI : 10.1186/1471-2164-12-75 ]

http://hal.inria.fr/inria-00610630/en
16T. Bourquard, J. Bernauer, J. Azé, A. Poupon.

A collaborative filtering approach for protein-protein docking scoring functions., in: PLoS ONE, 2011, vol. 6, n^o 4, e18541 p. [ DOI : 10.1371/journal.pone.0018541 ]

http://hal.inria.fr/inria-00625000/en
17M. Chavent, B. Lévy, M. Krone, K. Bidmon, J.-P. Nominé, T. Ertl, M. Baaden.

GPU-powered tools boost molecular visualization., in: Briefings in Bioinformatics, November 2011, vol. 12, n^o 6, p. 689-701. [ DOI : 10.1093/bib/bbq089 ]

http://hal.inria.fr/hal-00645161/en
18M. Chavent, A. Vanel, A. Tek, B. Lévy, S. Robert, B. Raffin, M. Baaden.

GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids., in: Journal of Computational Chemistry, October 2011, vol. 32, n^o 13, p. 2924-35. [ DOI : 10.1002/jcc.21861 ]

http://hal.inria.fr/hal-00645162/en
19A. Coulet, Y. Garten, M. Dumontier, R. B. Altman, M. A. Musen, N. H. Shah.

Integration and publication of heterogeneous text-mined relationships on the Semantic Web, in: Journal of Biomedical Semantics, May 2011, vol. 2, n^o S2, S10 p.

http://hal.inria.fr/hal-00585215/en
20C. Eng, A. Thibessard, M. Danielsen, T. B. Rasmussen, J.-F. Mari, P. Leblond.

In silico prediction of horizontal gene transfer in Streptococcus thermophilus, in: Archives of Microbiology, January 2011, vol. 193, n^o 4, p. 287-297. [ DOI : 10.1007/s00203-010-0671-8 ]

http://hal.inria.fr/inria-00569081/en
21S. J. Fleishman, T. A. Whitehead, E.-M. Strauch, J. E. Corn, S. Qin, H.-X. Zhou, J. C. Mitchell, O. N. A. Demerdash, M. Takeda-Shitaka, G. Terashi, I. H. Moal, X. Li, P. A. Bates, M. Zacharias, H. Park, J.-S. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Azé, S. Soner, S. K. Ovali, P. Ozbek, N. B. Tal, T. Haliloglu, H. Hwang, T. Vreven, B. G. Pierce, Z. Weng, L. Pérez-Cano, C. Pons, J. Fernández-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. H. Robert, M. Guharoy, S. Liu, Y. Huang, L. Li, D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Patapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. M. Standley, H. Nakamura, K. Kinoshita, C. M. Driggers, R. G. Hall, J. L. Morgan, V. L. Hsu, J. Zhan, Y. Yang, Y. Zhou, P. L. Kastritis, A. M. J. J. Bonvin, W. Zhang, C. J. Camacho, K. P. Kilambi, A. Sircar, J. J. Gray, M. Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodríguez, D. Kihara, P. B. Stranges, R. Jacak, B. Kuhlman, S.-Y. Huang, X. Zou, S. J. Wodak, J. Janin, D. Baker.

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology., in: Journal of Molecular Biology, September 2011. [ DOI : 10.1016/j.jmb.2011.09.031 ]

http://hal.inria.fr/inria-00637848/en
22L. Ghemtio, M. Smaïl-Tabbone, A. Djikeng, M.-D. Devignes, L. Keminse, P. Kelbert, J. Fokam, B. Maigret, O. Ouwe-Missi-Oukem-Boyer.

HIV-PDI: A Protein-Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 1. Concepts and Associated Database, in: Journal of Health & Medical Informatics, 2011, vol. 2, n^o 1, 1000104 p. [ DOI : 10.4172/2157-7420.1000104 ]

http://hal.inria.fr/hal-00642539/en
23L. Ghemtio, M. Souchet, A. Djikeng, L. Keminse, P. Kelbert, D. Ritchie, B. Maigret, O. Ouwe-Missi-Oukem-Boyer.

HIV-PDI: A Protein Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 2. Examples of Use and Proof-of-Concept, in: Journal of Health & Medical Informatics, 2011, vol. 2, n^o 1, 1000105 p. [ DOI : 10.4172/2157-7420.1000105 ]

http://hal.inria.fr/hal-00642567/en
24A. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.

Spatial clustering of protein binding sites for template based protein docking, in: Bioinformatics, August 2011. [ DOI : 10.1093/bioinformatics/btr493 ]

http://hal.inria.fr/inria-00617921/en
25C. Jonquet, P. LePendu, S. Falconer, A. Coulet, N. F. Noy, M. A. Musen, N. H. Shah.

NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources, in: Journal of Web Semantics, September 2011, vol. 9, n^o 3, p. 316-324. [ DOI : 10.1016/j.websem.2011.06.005 ]

http://hal.inria.fr/lirmm-00622155/en
26M. Kaytoue, S. O. Kuznetsov, A. Napoli, S. Duplessis.

Mining gene expression data with pattern structures in formal concept analysis, in: Information Sciences, 2011, vol. 181, n^o 10, p. 1989-2001.

http://hal.inria.fr/hal-00541100/en
27S. Martin, A. Bertaux, F. Le Ber, E. Maillard, G. Imfeld.

Seasonal Changes of Macroinvertebrate Communities in a Stormwater Wetland Collecting Pesticide Runoff From a Vineyard Catchment (Alsace, France), in: Archives of Environmental Contamination and Toxicology, 2011, 13 p. [ DOI : 10.1007/s00244-011-9687-6 ]

http://hal.inria.fr/hal-00607741/en
28L. Mavridis, A. Ghoorah, V. Venkatraman, D. Ritchie.

Representing and comparing protein folds and fold families using 3D shape-density representations, in: Proteins, November 2011. [ DOI : 10.1002/prot.23218 ]

http://hal.inria.fr/hal-00641815/en
29V. Pérez-Nueno, D. Ritchie.

Identifying and characterizing promiscuous targets: Implications for virtual screening, in: Expert Opinion on Drug Discovery, November 2011. [ DOI : 10.1517/17460441.2011.632406 ]

http://hal.inria.fr/hal-00641835/en
30V. Pérez-Nueno, D. Ritchie.

Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening, in: Journal of Chemical Information and Modeling, May 2011, vol. 51, n^o 6, p. 1233-1248. [ DOI : 10.1021/ci100492r ]

http://hal.inria.fr/inria-00617922/en

Articles in National Peer-Reviewed Journal

31C. Grac, A. Braud, F. Le Ber, M. Trémolières.

Un système d'information pour le suivi et l'évaluation de la qualité des cours d'eau – Application à l'hydro-écorégion de la plaine d'Alsace, in: RSTI - Ingénierie des Systèmes d'Information, 2011, vol. 16, p. 9-30.

http://hal.inria.fr/hal-00601991/en
32F. Le Ber, S. Nogry, C. Brassac, M. Benoît.

Capitalisation d'expériences pour la mise en place d'observatoires de pratiques agricoles, in: Revue internationale de Géomatique, 2011, vol. 21, p. 99–118.

http://hal.inria.fr/hal-00576238/en

International Conferences with Proceedings

33P. Agarwal, M. Kaytoue, S. Kuznetsov, A. Napoli, G. Polaillon.

Symbolic Galois Lattices with Pattern Structures, in: Thirteenth International Conference on Rough Sets, Fuzzy Sets and Granular Computing - RSFDGrC-2011, Moscou, Russian Federation, S. O. Kuznetsov, D. Slezak, D. H. Hepting, B. G. Mirkin (editors), Lecture Notes in Computer Science, Springer-Verlag, 2011, vol. 6743, p. 191-198. [ DOI : 10.1007/978-3-642-21881-1_31 ]

http://hal.inria.fr/hal-00631473/en
34Z. Assaghir, M. Kaytoue, W. Meira, J. Villerd.

Extracting Decision Trees from Interval Pattern Concept Lattices, in: The Eighth International Conference on Concept Lattices and their Applications - CLA 2011, Nancy, France, A. Napoli, V. Vychodil (editors), INRIA Nancy Grand Est - LORIA, 2011.

http://hal.inria.fr/hal-00640938/en
35Z. Assaghir, A. Napoli, M. Kaytoue, D. Dubois, H. Prade.

Numerical information fusion: Lattice of answers with supporting arguments, in: 23rd IEEE International Conference on Tools with Artificial Intelligence - ICTAI 2011, Boca-Raton, United States, October 2011, p. 621-628.

http://hal.inria.fr/hal-00646484/en
36Z. Azmeh, M. Huchard, A. Napoli, M. Rouane-Hacene, P. Valtchev.

Querying Relational Concept Lattices, in: CLA'11: The 8th International Conference on Concept Lattices and their Applications, France, 2011, p. 377-392.

http://hal.inria.fr/lirmm-00646409/en
37J. Azé, T. Bourquard, S. Hamel, A. Poupon, D. Ritchie.

Using Kendall-Tau Meta-Bagging to Improve Protein-Protein Docking Predictions, in: PRIB 2011, DELFT, Netherlands, M. Loog, L. Wessels, M. J. Reinders, D. de Ridder (editors), 2011, p. 284-295.

http://hal.inria.fr/inria-00628038/en
38S. Benabderrahmane, M.-D. Devignes, M. Smaïl-Tabbone, A. Napoli, O. Poch.

Ontology-based functional classification of genes: evaluation with reference sets and overlap analysis, in: The second workshop on Integrative Data in Systems Biology held in conjunction with the IEEE BIBM 2011 conference, Atlanta, United States, Z. Zhao (editor), IEEE Computer Society, 2011.

http://hal.inria.fr/hal-00644438/en
39A. Braud, C. Nica, C. Grac, F. Le Ber.

A lattice-based query system for assessing the quality of hydro-ecosystems, in: CLA 2011, Nancy, France, A. Napoli, V. Vychodil (editors), INRIA NGE et LORIA, 2011, p. 265-277.

http://hal.inria.fr/hal-00640048/en
40E. Bresso, S. Benabderrahmane, M. Smaïl-Tabbone, G. Marchetti, A. S. Karaboga, M. Souchet, A. Napoli, M.-D. Devignes.

Use of domain knowledge for dimension reduction: application to mining of drug side effects, in: International Conference on Knowledge Discovery and Information Retrieval - KDIR 2011, Paris, France, A. Fred (editor), INSTICC, SciTePress Digital Library, 2011, 8 p.

http://hal.inria.fr/hal-00642520/en
41V. Codocedo, C. Taramasco, H. Astudillo.

Cheating to achieve Formal Concept Analysis over a large formal context, in: The Eighth International Conference on Concept Lattices and their Applications - CLA 2011, Nancy, France, A. Napoli, V. Vychodil (editors), INRIA Nancy Grand Est - LORIA, 2011, p. 349–362.
42J. Cojan, V. Dufour-Lussier, E. Gaillard, J. Lieber, E. Nauer, Y. Toussaint.

Knowledge extraction for improving case retrieval and recipe adaptation, in: Computer Cooking Contest Workshop, London, United Kingdom, September 2011.

http://hal.inria.fr/hal-00646717/en
43J. Cojan, J. Lieber.

An Algorithm for Adapting Cases Represented in ALC, in: 22nd International Joint Conference on Artificial Intelligence - IJCAI 2011, Barcelone, Spain, July 2011.

http://hal.inria.fr/inria-00584103/en
44V. Dufour-Lussier, B. Guillaume, G. Perrier.

Parsing Coordination Extragrammatically, in: 5th Language & Technology Conference - LTC'11, Poznan, Poland, 2011.

http://hal.inria.fr/hal-00639929/en
45V. Dufour-Lussier, J. Lieber, E. Nauer, Y. Toussaint.

Improving case retrieval by enrichment of the domain ontology, in: 19th International Conference on Case Based Reasoning - ICCBR'2011, London, United Kingdom, 2011.

http://hal.inria.fr/inria-00617621/en
46E. Egho, N. Jay, C. Raïssi, A. Napoli.

A FCA-based analysis of sequential care trajectories, in: The Eighth International Conference on Concept Lattices and their Applications - CLA 2011, Nancy, France, A. Napoli, V. Vychodil (editors), INRIA Nancy Grand Est - LORIA, October 2011.

http://hal.inria.fr/hal-00641649/en
47E. Gaillard, J. Lieber, E. Nauer.

Adaptation knowledge discovery for cooking using closed itemset extraction, in: The Eighth International Conference on Concept Lattices and their Applications - CLA 2011, Nancy, France, October 2011.

http://hal.inria.fr/hal-00646732/en
48M. Kaytoue, S. O. Kuznetsov, J. Macko, W. Meira, A. Napoli.

Mining Biclusters of Similar Values with Triadic Concept Analysis, in: The Eighth International Conference on Concept Lattices and their Applications - CLA 2011, Nancy, France, A. Napoli, V. Vychodil (editors), INRIA Nancy Grand Est - LORIA, 2011.

http://hal.inria.fr/hal-00640873/en
49M. Kaytoue, S. O. Kuznetsov, A. Napoli.

Biclustering Numerical Data in Formal Concept Analysis, in: 9th International Conference on Formal Concept Analysis - ICFCA 2011, Nicosia, Cyprus, P. Valtchev, R. Jäschke (editors), Lecture Notes in Computer Science, Springer, 2011, vol. 6628, p. 135-150. [ DOI : 10.1007/978-3-642-20514-9 ]

http://hal.inria.fr/inria-00600203/en
50M. Kaytoue, S. O. Kuznetsov, A. Napoli.

Revisiting Numerical Pattern Mining with Formal Concept Analysis, in: Twenty second International Joint Conference on Artificial Intelligence - IJCAI 2011, Barcelona, Spain, 2011.

http://hal.inria.fr/inria-00584371/en
51B. Lamiroy, D. Lopresti, H. Korth, J. Heflin.

How Carefully Designed Open Resource Sharing Can Help and Expand Document Analysis Research, in: Document Recognition and Retrieval XVIII - DRR 2011, San Francisco, United States, G. Agam, C. Viard-Gaudin (editors), SPIE, January 2011, vol. 7874, ISBN : 9780819484116. [ DOI : 10.1117/12.876483 ]

http://hal.inria.fr/inria-00537035/en
52D. Lopresti, B. Lamiroy.

Document Analysis Research in the Year 2021, in: Twenty-fourth International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems (IEA/AIE 2011), Syracuse, NY, United States, Lecture Notes in Computer Science, Springer, July 2011.

http://hal.inria.fr/inria-00570000/en
53C. Raïssi, J. Pei.

Towards Bounding Sequential Patterns, in: 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD-2011, San Diego, United States, C. Apté, J. Ghosh, P. Smyth (editors), ACM, August 2011, ISBN : 978-1-4503-0813-7. [ DOI : 10.1145/2020408.2020612 ]

http://hal.inria.fr/inria-00623550/en
54L. Shi, Y. Toussaint, A. Napoli, A. Blansché.

Mining for Reengineering: an Application to Semantic Wikis using Formal and Relational Concept Analysis, in: The Semanic Web: Research and Applications - 8th Extended Semantic Web Conference, ESWC 2011, Heraklion, Crete, Greece, G. Antoniou, M. Grobelnik, E. Simperl, B. Parsia, D. Plexousakis, J. Pan, P. De Leenhee (editors), Lecture Notes in Computer Science, Springer, 2011, vol. 6644, p. 421–435.

http://hal.inria.fr/hal-00646450/en
55A. Soulet, C. Raïssi, M. Plantevit, B. Crémilleux.

Mining Dominant Patterns in the Sky, in: The 11th IEEE International Conference on Data Mining - ICDM 2011, Vancouver, B.C, Canada, IEEE, December 2011.

http://hal.inria.fr/inria-00623566/en
56L. Szathmary, P. Valtchev, A. Napoli, R. Godin, A. Boc, V. Makarenkov.

Fast Mining of Iceberg Lattices: A Modular Approach Using Generators, in: The Eighth International Conference on Concept Lattices and their Applications - CLA 2011, Nancy, France, A. Napoli, V. Vychodil (editors), INRIA Nancy Grand Est - LORIA, October 2011.

http://hal.inria.fr/hal-00640898/en
57M. Xue, P. Karras, C. Raïssi, H. K. Pung.

Utility-Driven Anonymization in Data Publishing, in: 20th ACM Conference on Information and Knowledge Management - CIKM 2011, Glasgow, United Kingdom, ACM, October 2011, This is a "to appear" publication.

http://hal.inria.fr/inria-00623578/en
58M. Xue, P. Papadimitriou, C. Raïssi, P. Kalnis, H. K. Pung.

Distributed Privacy Preserving Data Collection, in: 16th International Conference on Database Systems for Advanced Applications - DASFAA 2011, Hong Kong, China, J. X. Yu, M. H. Kim, R. Unland (editors), Lecture Notes in Computer Science, springer, 2011, vol. 6587, p. 93-107. [ DOI : 10.1007/978-3-642-20149-3_9 ]

http://hal.inria.fr/inria-00610951/en

National Conferences with Proceeding

59S. Benabderrahmane, M.-D. Devignes, M. Smaïl-Tabbone, O. Poch, A. Napoli, W. Raffelsberger, D. Guenot, N. Hoan, E. Guerin.

Benchmarking a new semantic similarity measure using fuzzy clustering and reference sets: Application to cancer expression data, in: 11ème Conférence Internationale Francophone sur l'Extraction et la Gestion des Connaissances - EGC 2011, Brest, France, January 2011.

http://hal.inria.fr/inria-00617692/en
60T. Bourquard, J. Azé, A. Poupon, D. Ritchie.

Protein-protein docking based on shape complementarity and Voronoi fingerprint, in: Journées Ouvertes Biologie Informatique Mathématiques, Paris, France, E. Barillot, C. Froidevaux, Eduardo PC. Rocha (editors), Institut Pasteur, July 2011, p. 9-16.

http://hal.inria.fr/inria-00613186/en
61J. Cojan, J. Lieber.

Adaptation par révision et adaptation différentielle : comparaison de deux approches de l'adaptation, in: 19ème atelier Français de Raisonnement à Partir de Cas - Rapc2011, Chambéry, France, Fadi Badra and Amélie Cordier, May 2011.

http://hal.inria.fr/inria-00595400/en
62S. Da Silva, C. Lavigne, F. Le Ber.

Analyse de la structure des haies dans les vergers pour la définition de paysages mieux adaptés contre les bioagresseurs, in: SAGEO 2011 - International Conference on Spatial Analysis and GEOmatics Conférence internationale de Géomatique et d'Analyse Spatiale Au sein de la 25e Conférence Internationale de Cartographie, Paris, France, 2011, p. 1-4.

http://hal.inria.fr/hal-00615301/en
63V. Dufour-Lussier, F. Le Ber, J. Lieber.

Quels formalismes temporels pour représenter des connaissances extraites de textes de recettes de cuisine ?, in: Représentation et raisonnement sur le temps et l'espace, Chambéry, France, S. Laborie, F. Le Ber (editors), May 2011.

http://hal.inria.fr/inria-00634735/en
64M. Kaytoue, S. O. Kuznetsov, A. Napoli.

Revisiting Numerical Pattern Mining with Formal Concept Analysis, in: Journées Nationales de l'Intelligence Artificielle Fondamentale, Lyon, France, 2011.

http://hal.inria.fr/inria-00600222/en
65M. Kaytoue, S. Kuznetsov, A. Napoli, G. Polaillon.

Symbolic Data Analysis and Formal Concept Analysis, in: XVIIIeme Rencontres de la Société Francophone de Classification - SFC 2011, Orléans, France, R. Emilion, G. Cleuziou (editors), MAPMO - LIFO Orléans, 2011.

http://hal.inria.fr/hal-00646457/en
66T. Meilender, N. Jay, J. Lieber, F. Palomares.

Les moteurs de wikis sémantiques : un état de l'art, in: Extraction et gestion des connaissances (EGC'2011), Brest, France, 2011, p. 575-580.

http://hal.inria.fr/hal-00573821/en
67T. Meilender, N. Jay, J. Lieber, F. Palomares.

Édition sémantique d'arbres de décision pour l'oncologie avec KcatoS, in: 1ère édition du Symposium sur l'Ingénierie de l'Information Médicale - SIIM 2011, Toulouse, France, June 2011.

http://hal.inria.fr/hal-00646843/en
68M. Plantevit, C. Raïssi, B. Crémilleux.

Motifs séquentiels $δ$ -libres, in: Extraction et gestion des connaissances (EGC'2011), Brest, France, Hermann-Éditions, January 2011.

http://hal.inria.fr/hal-00653579/en
69V. Venkatraman, D. Ritchie.

Predicting Multicomponent Protein Assemblies Using an Ant Colony Approach, in: International Conference on Swarm Intelligence, Cergy, France, June 2011.

http://hal.inria.fr/inria-00619204/en

Conferences without Proceedings

70E.-G. Lazrak, N. Schaller, J.-F. Mari.

Extraction de connaissances agronomiques par fouille des voisinages entre occupations du sol, in: Atelier en marge d'EGC 2011, Brest, France, January 2011.

http://hal.inria.fr/inria-00560098/en

Scientific Books (or Scientific Book chapters)

71A. Coulet, M. Smaïl-Tabbone, A. Napoli, M.-D. Devignes.

Ontology-based knowledge discovery in pharmacogenomics., in: Software Tools and Algorithms for Biological Systems, H. R. Arabnia, Q.-N. Tran (editors), Advances in Experimental Medicine and Biology, Springer, 2011, vol. 696, p. 357-66. [ DOI : 10.1007/978-1-4419-7046-6_36 ]

http://hal.inria.fr/inria-00585072/en
72M. Kaytoue, S. Duplessis, A. Napoli.

Toward the Discovery of Itemsets with Significant Variations in Gene Expression Matrices, in: Classification and Multivariate Analysis for Complex Data Structures, B. Fichet, D. Piccolo, R. Verde, M. Vichi (editors), Studies in Classification, Data Analysis, and Knowledge Organization, Springer Berlin Heidelberg, 2011, p. 463–471. [ DOI : 10.1007/978-3-642-13312-1_49 ]

http://hal.inria.fr/inria-00600233/en
73J.-F. Mari, F. Le Ber, E.-G. Lazrak, M. Benoît, C. Eng, A. Thibessard, P. Leblond.

Using Markov Models to Mine Temporal and Spatial Data, in: New Fundamental Technologies in Data Mining, K. Funatsu, K. Hasegawa (editors), Intech, 2011, p. 561–584.

http://hal.inria.fr/inria-00566801/en

Books or Proceedings Editing

74A. Napoli, V. Vychodil (editors)

The Eighth International Conference on Concept Lattices and their Applications - CLA 2011, INRIA Nancy Grand Est - LORIA, 2011.

Other Publications

75M. Huchard, A. Napoli, M. Rouane-Hacene, P. Valtchev.

A gentle introduction to Relational Concept Analysis, Tutorial ICFCA 2011, May 2011.

http://hal.inria.fr/lirmm-00616275/en

References in notes

76F. Baader, D. Calvanese, D. McGuinness, D. Nardi, P. Patel-Schneider (editors)

The Description Logic Handbook, Cambridge University Press, Cambridge, UK, 2003.
77P. Buitelaar, P. Cimiano, B. Magnini (editors)

Ontology Learning from Text: Methods, Evaluation and Applications, Frontiers in Artificial Intelligence and Applications, IOS Press, Amsterdam, 2005.
78P. Hitzler, M. Krötsch, S. Rudolph (editors)

Foundations of Semantic Web Technologies, CRC Press, Boca raton (FL), 2009.
79S. Staab, R. Studer (editors)

Handbook on Ontologies (Second Edition), Springer, Berlin, 2009.
80F. Badra, A. Cordier, J. Lieber.

Opportunistic Adaptation Knowledge Discovery, in: 8th International Conference on Case-Based Reasoning - ICCBR 2009, Seattle, United States, L. McGinty, D. C. Wilson (editors), Lecture Notes in Computer Science, Springer, July 2009, vol. 5650, p. 60-74, The original publication is available at www.springerlink.com. [ DOI : 10.1007/978-3-642-02998-1_6 ]

http://hal.inria.fr/inria-00437693/en
81M. Barbut, B. Monjardet.

Ordre et classification – Algèbre et combinatoire (2 tomes), Hachette, Paris, 1970.
82S. Benabderrahmane, M. Smaïl-Tabbone, O. Poch, A. Napoli, M.-D. Devignes.

IntelliGO: a new vector-based semantic similarity measure including annotation origin, in: BMC Bioinformatics, December 2010, vol. 11, n^o 1, 588 p. [ DOI : 10.1186/1471-2105-11-588 ]

http://www.biomedcentral.com/1471-2105/11/588/abstract, http://hal.inria.fr/inria-00543910/en
83R. Bendaoud, A. Napoli, Y. Toussaint.

A proposal for an Interactive Ontology Design Process based on Formal Concept Analysis, in: Formal Ontology in Information Systems – Proceedings of the Fifth International Conference (FOIS 2008), Amsterdam, C. Eschenbach, M. Grüninger (editors), Frontiers in Artificial Intelligence and Applications, IOS Press, 2008, p. 311–323.
84R. Bendaoud, A. Napoli, Y. Toussaint.

Formal Concept Analysis: A unified framework for building and refining ontologies, in: Knowledge Engineering: Practice and Patterns - Proceedings of the 16th International Conference EKAW, A. Gangemi, J. Euzenat (editors), Lecture Notes in Computer Science 5268, 2008, p. 156–171.
85R. Bendaoud, Y. Toussaint, A. Napoli.

PACTOLE: A methodology and a system for semi-automatically enriching an ontology from a collection of texts, in: Proceedings of the 16th International Conference on Conceptual Structures, ICCS 2008, Toulouse, France, P. Eklund, O. Haemmerlé (editors), Lecture Notes in Computer Science 5113, 2008, p. 203–216.
86H. M. Berman, T. Battistuz, T. N. Bhat, W. F. Bluhm, P. E. Bourne, K. Burkhardt, L. Iype, S. Jain, P. Fagan, J. Marvin, D. Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, J. D. Westbrook, C. Zardecki.

The Protein Data Bank, in: Acta Crystallographica Section D-Biological Crystallography, 2002, vol. 58, p. 899–907.
87A. Carrieri, V. Pérez-Nueno, A. Fano, C. Pistone, D. Ritchie, J. Teixidó.

Biological Profiling of Anti-HIV Agents and Insight into CCR5 Antagonist Binding Using in silico Techniques, in: ChemMedChem, 2009, vol. 4, p. 1153–1163.

http://dx.doi.org/10.1002/cmdc.200900101
88P. Cimiano, A. Hotho, S. Staab.

Learning Concept Hierarchies from Text Corpora using Formal Concept Analysis, in: Journal of Artificial Intelligence Research, 2005, vol. 24, p. 305–339.
89R. D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J. E. Pollington, O. L. Gavin, P. Gunasekaran, G. Ceric, K. Forslund, L. Holm, E. L. L. Sonnhammer, S. R. Eddy, A. Bateman.

The Pfam protein families database, in: Nucleic Acids Research, 2010, vol. 38, p. D211–D222.
90B. Ganter, S. O. Kuznetsov.

Pattern Structures and Their Projections, in: Conceptual Structures: Broadening the Base, Proceedings of the 9th International Conference on Conceptual Structures, ICCS 2001, Stanford, CA, H. Delugach, G. Stumme (editors), Lecture Notes in Computer Science 2120, Springer, 2001, p. 129–142.
91B. Ganter, R. Wille.

Formal Concept Analysis, Springer, Berlin, 1999.
92Y. Garten.

Text mining the scientific literature to identify pharmacogenomic interactions, Stanford University, USA, Dec 2010.
93I. Guyon, A. Elisseeff.

An Introduction to Variable and Feature Selection, in: Journal of Machine Learning Research, 2003, vol. 3, n^o 7-8, p. 1157–1182.
94H. Hwang, T. Vreven, J. Janin, Z. Weng.

Protein-protein docking benchmark version 4.0., in: Proteins: Structure Function and Bioinformatics, 2010, vol. 78, n^o 15, p. 3111–3114.
95M. Kaytoue, F. Marcuola, A. Napoli, L. Szathmary, J. Villerd.

The Coron System, in: 8th International Conference on Formal Concept Analsis (ICFCA) - Supplementary Proceedings, L. Boumedjout, P. Valtchev, L. Kwuida, B. Sertkaya (editors), 2010, p. 55–58.
96E.-G. Lazrak, M. Benoît, J.-F. Mari.

Time-Space Dependencies in Land-Use Successions at Agricultural Landscape Scales, in: International Conference on Integrative Landscape Modelling, Montpellier France, UMR LISAH, 02 2010.

http://hal.inria.fr/inria-00482890/en/
97J. Lieber, M. d'Aquin, F. Badra, A. Napoli.

Modeling adaptation of breast cancer treatment decision protocols in the KASIMIR project, in: Applied Intelligence, 2008, vol. 28, n^o 3, p. 261–274.
98J. Lieber, A. Napoli, L. Szathmary, Y. Toussaint.

First Elements on Knowledge Discovery guided by Domain Knowledge (KDDK), in: Concept Lattices and Their Applications (CLA 06), S. B. Yahia, E. M. Nguifo, R. Belohlavek (editors), Lecture Notes in Artificial Intelligence 4923, Springer, Berlin, 2008, p. 22–41.
99G. Macindoe, L. Mavridis, V. Venkatraman, M.-D. Devignes, D. Ritchie.

HexServer: an FFT-based protein docking server powered by graphics processors, in: Nucleic Acids Research, May 2010, vol. 38, p. W445-W449. [ DOI : 10.1093/nar/gkq311 ]

http://hal.inria.fr/inria-00522712/en
100J.-F. Mari, J.-P. Haton, A. Kriouile.

Automatic Word Recognition Based on Second-Order Hidden Markov Models, in: IEEE Transactions on Speech and Audio Processing, 1997, vol. 5, p. 22 – 25.
101J.-F. Mari, F. Le Ber.

Temporal and Spatial Data Mining with Second-Order Hidden Models, in: Soft Computing, 2006, vol. 10, n^o 5, p. 406–414.
102L. Mavridis, D. Ritchie.

3D-blast: 3D protein structure alignment, comparison, and classification using spherical polar Fourier correlations, in: Pacific Symposium on Biocomputing 2010, United States Hawaii, World Scientific Publishing, January 2010, p. 281–292. [ DOI : 10.1142/9789814295291_0030 ]

http://hal.inria.fr/inria-00434263/en
103L. Mavridis, V. Venkatraman, D. Ritchie, H. Morikawa, R. Andonov, A. Cornu, N. Malod-Dognin, J. Nicolas, M. Temerinac-Ott, M. Reisert, H. Burkhardt, A. Axenopoulos, P. Daras.

SHREC'10 Track: Protein Models, in: Eurographics Workshop on 3D Object Retrieval - 3DOR 2010, Sweden Norrköping, 2010.

http://hal.inria.fr/inria-00536680/en
104R. Mosca, C. Pons, J. Fernandez-Recio, P. Aloy.

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments, in: PLoS Computational Biology, 2009, vol. 5, n^o 8, e1000490 p.
105A. Napoli.

A smooth introduction to symbolic methods for knowledge discovery, in: Handbook of Categorization in Cognitive Science, H. Cohen, C. Lefebvre (editors), Elsevier, Amsterdam, 2005, p. 913–933.
106C. A. Orengo, A. D. Michine, S. Jones, D. T. Jones, M. B. Swindells, J. M. Thornton.

CATH - A Hierarchic Classification of Protein Domain Structures, in: Structure, 1997, vol. 5, n^o 8, p. 1093–1108.
107C. Pesquita, D. Faria, A. O. Falcão, P. Lord, F. M. Couto.

Semantic Similarity in Biomedical Ontologies, in: PLoS Comput Biol, 2009, vol. 5.
108M. Plantevit, A. Laurent, D. Laurent, M. Teisseire, Y. W. Choong.

Mining multidimensional and multilevel sequential patterns, in: ACM Trans. Knowl. Discov. Data, 2010, vol. 4, n^o 1, p. 1–37.

http://doi.acm.org/10.1145/1644873.1644877
109V. Pérez-Nueno, S. Pettersson, D. Ritchie, J. Borrell, J. Teixidó.

Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening, in: Journal of chemical information and modeling, Apr 2009, vol. 49, n^o 4, p. 810-823. [ DOI : 10.1021/ci800468q ]

http://hal.inria.fr/inria-00434261/en
110V. Pérez-Nueno, D. Ritchie, J. Borrell, J. Teixidó.

Clustering and Classifying Diverse HIV Entry Inhibitors Using a Novel Consensus Shape-Based Virtual Screening Approach: Further Evidence for Multiple Binding Sites within the CCR5 Extracellular Pocket, in: Journal of Chemical Information and Modeling, 2008, vol. 48, n^o 11, p. 2146–2165.
111V. Pérez-Nueno, D. Ritchie.

Applying in silico Tools to the Discovery of Novel CXCR4 Inhibitors, in: Drug Development Research, 2011, vol. 72, p. 95–111. [ DOI : 10.1002/ddr.20406 ]

http://hal.inria.fr/inria-00550645/en/
112V. Pérez-Nueno, D. Ritchie, O. Rabal, R. Pascual, J. Borrell, J. Teixidó.

Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking, in: Journal of Chemical Information and Modeling, 2008, vol. 48, n^o 3, p. 509–533.
113C. Raïssi, J. Pei, T. Kister.

Computing Closed Skycubes, in: Proceedings of the VLDB Endowment, September 2010, vol. 3, n^o 1, p. 838–847.

http://hal.inria.fr/inria-00610923/en
114D. Ritchie, G. Kemp.

Protein Docking Using Spherical Polar Fourier Correlations, in: Proteins: Structure, Function and Genetics, 2000, vol. 39, n^o 2, p. 178–194.
115D. Ritchie, V. Venkatraman.

Ultra-fast FFT protein docking on graphics processors, in: Bioinformatics, 2010, vol. 26, n^o 19, p. 2398–2405. [ DOI : 10.1093/bioinformatics/btq444 ]

http://hal.inria.fr/inria-00537988/en/
116M. Rouane-Hacene, M. Huchard, A. Napoli, P. Valtchev.

A proposal for combining Formal Concept Analysis and description Logics for mining relational data, in: Proceedings of the 5th International Conference on Formal Concept Analysis (ICFCA 2007), Clermont-Ferrand, S. O. Kuznetsov, S. Schmidt (editors), LNAI 4390, Springer, Berlin, 2007, p. 51–65.
117A. Stein, A. Ceol, P. Aloy.

3did: identification and classification of domain-based interactions of known three-dimensional structure, in: Nucleic Acids Research, 2010, vol. 39, p. D718–D723.
118L. Szathmary.

Symbolic Data Mining Methods with the Coron Platform, Université Henri Poincaré (Nancy 1), 2006.
119L. Szathmary, P. Valtchev, A. Napoli, R. Godin.

Constructing Iceberg Lattices from Frequent Closures Using Generators, in: Discovery Science, J.-F. Boulicaut, M. Berthod, T. Horváth (editors), Lecture Notes in Computer Science 5255, Springer, Berlin, 2008, p. 136–147.
120L. Szathmary, P. Valtchev, A. Napoli, R. Godin.

Efficient Vertical Mining of Frequent Closures and Generators, in: Proceedings of the 8th International Symposium on Intelligent Data Analysis (IDA-2009), Lyon, France, N. Adams, J.-F. Boulicaut, C. Robardet, A. Siebes (editors), Lecture Notes in Computer Science 5772, Springer, Berlin, 2009, p. 393–404.
121L. Szathmary, P. Valtchev, A. Napoli.

Finding Minimal Rare Itemsets and Rare Association Rules, in: Proceedings of the 4th International Conference on Knowledge Science, Engineering and Management (KSEM-2010), Belfast, Northern Ireland, UK, Y. Bi, M.-A. Williams (editors), Lecture Notes in Artificial Intelligence 6291, Springer, Berlin, 2010, p. 16–27.
122L. Szathmary, P. Valtchev, A. Napoli.

Generating Rare Association Rules Using the Minimal Rare Itemsets Family, in: International Journal of Software and Informatics, 2010, vol. 4, n^o 3, p. 219–238.
123M. d'Aquin, F. Badra, S. Lafrogne, J. Lieber, A. Napoli, L. Szathmary.

Case Base Mining for Adaptation Knowledge Acquisition, in: Proceedings of the 20th International Joint Conference on Artificial Intelligence (IJCAI'07), M. M. Veloso (editor), Morgan Kaufmann, 2007, p. 750–755.

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