Margherita Berardi's Home Page     Research Interests: Machine Learning - Data Mining and Text Mining in Bioinformatics - Inductive Logic Programming
Margherita Berardi PhD in Computer Science Dipartimento di Informatica  Università degli Studi di Bari  Via Orabona 4  70126 Bari - Italy   phone: +39 080 5443262  fax: +39 080 5443269   email: berardi@di.uniba.it  LACAM lab.

Curriculum Vitae et Studiorum

Education

• March 2002 - She received a Laurea Degree with full marks and honors in Computer Science from the University of Bari. She discussed a thesis on "Machine learning techniques for analysis, classification and understanding of documents images". Following graduation, she kept on making research in machine learning and data mining in the Knowledge Acquisition and Machine Learning Laboratory (LACAM).
• November 2002 - She started the Ph.D. Course in Computer Science at the Department of Informatics, University of Bari, under the supervision of Prof. Malerba Donato. The topic of her thesis concerns the applications of machine learning techniques for semantic-based indexing of documents.
• March 2003 - She attended the advanced course on New Frontiers Of Information Society Technologies held in Turin (Italy).
• September 2003 - She attended the advanced course on Computational Linguistics “Statistical Methods for Natural Language Processing” held in Venice (Italy).
• June 2004 - She attended the first International School on Advanced BioMedicine and Bioinformatics held in Lipari (Italy).

Teaching and Tutoring

• Academic year 2002/2003 - Tutoring in Programming Languages.
• Academic year 2003/2004 - Tutoring in Computer Programming.
• Academic year 2003/2004 - Tutoring in Programming Languages.
• Academic year 2004/2005 - Tutoring in Computer Programming.
• Academic year 2004/2005 - Tutoring in Advanced Computer Programming Methods.
• Academic year 2005/2006 - Tutoring in Advanced Computer Programming Methods.

• Tutorial on Web Mining: (Laurea Degree in Informatics, 24/05/2003)
• Tutorial on Knowledge Discovery from Documents: (Laurea Degree in Informatics, 23/01/2006)
• Tutorial on Text Mining: (IBM Innovation Lab Bari, 14/12/2007)

Research Projects

She is currently/has been involved in the following projects:

• COLLATE "Collaboratory for Annotation, Indexing and Retrieval of Digitized Historical Archive Material" EU 5Vth Framework Programme, Key Action III (IST-1999-20882)
• IBM 1999 project on "Knowledge Management and Data Mining techniques in Bioinformatics"
• IBM Faculty Award 2005 project on "Knowledge Discovery Technologies for the development of a Gene and SNPs filtering engine"
• Ateneo-2003 project on "Methods of machine learning and data mining semantic based knowledge systems"
• Ateneo-2004 project on "Methods of multi-relational data mining for knowledge discovery in databases"
• Ateneo-2005 project on "Unstructured information management: models, methods and architectures"
• Ateneo-2006 project on "Knowledge Discovery Methods for ubiquitous computing".
• KDubiq "A Blueprint for Ubiquitous Knowledge Discovery Systems" FET Open in the 6th Framework Programme (IST-6FP-021321)
• FIRB 2003 project on "International Laboratory on Bioinformatics" ( LIBi )

Her main research activity is in the investigation of data mining and machine learning techniques to support semantic indexing of documents. She has been working for three years to the application of machine learning to intelligent document processing. In particular, she has been investigating applications on historical documents and biomedical literature. She is interested in applications of data mining techniques to bioinformatics. Currently, she is working on information extraction techniques for genomic database annotation.

Affiliations

• AI*IA (Italian Association for Artificial Intelligence),
• BITS (Bioinformatic Italian Society),
• GULP (Gruppo Ricercatori e Utenti Logic Programming).

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Publications

For more information, please do not hesitate to contact me.

• Chapters in International Volumes
  • Donato Malerba, Michelangelo Ceci, Margherita Berardi. (2008) Machine Learning for Reading Order Detection in Document Image Understanding. In S. Marinai, H. Fujisawa, (Eds.), Machine learning in Document Analysis and Recognition. Springer, Studies in Computational Intelligence, Volume 90, January 2008, pp. 45-70.
  • Donato Malerba, Margherita Berardi, Michelangelo Ceci. (2007) Discovering Spatio-Textual Association Rules in Document Images. In F. Masseglia, P. Poncelet, M.Teisseire (Eds.), Data Mining Patterns: New Methods and Applications. Idea Group, IGI Global, USA, pp. 176-197.
• International Journals
  • Oronzo Altamura, Margherita Berardi, Michelangelo Ceci, Donato Malerba, and Antonio Varlaro (2007). Using colour information to understand censorship cards of film archives, International Journal of Document Analysis and Recognition, Springer Verlag, 9, 2, 281-297.
  • Michelangelo Ceci, Margherita Berardi, and Donato Malerba (2007). Relational data mining and ILP for document image processing, Applied Artificial Intelligence, 21, 8, 317-342.
• International Collections
  • Margherita Berardi and Donato Malerba. Learning Recursive Patterns for Biomedical Information Extraction. In S. Muggleton, R. Otero, & A. Tamaddoni-Nezhad (Eds.): Inductive Logic Programming: 16th International Conference, ILP 2006, Santiago de Compostela, Spain, August 24-27, 2006, Proceedings. Springer-Verlag, LNAI 4455, 79–93, 2007.
  • Margherita Berardi, Annalisa Appice, Corrado Loglisci, and Pietro Leo. Supporting Visual Exploration of Discovered Association Rules Through Multi-Dimensional Scaling. In F. Esposito, Z. W. Ras, D. Malerba, G. Semeraro (Eds.): Foundations of Intelligent Systems, 16th International Symposium, ISMIS 2006, Bari, Italy, Springer-Verlag, LNCS 4203, 369-378, 2006.
  • Michelangelo Ceci, Margherita Berardi, and Donato Malerba. Relational Learning: Statistical approach versus logical approach in Document Image Understanding. In: S. Bandini, S. Manzoni (Eds.): AI*IA 2005: Advances in Artificial Intelligence, 9th Congress of the Italian Association for Artificial Intelligence, Milan, Italy, September 21-23, 2005, Proceedings. Springer-Verlag, LNCS 3673, 418-429, 2005.
  • Margherita Berardi, Michele Lapi, Pietro Leo, and Corrado Loglisci. Mining Generalized Association Rules on Biomedical Literature. In: M. Ali, F. Esposito (Eds.): Innovations in Applied Artificial Intelligence, 18th International Conference on Industrial and Engineering Applications of Artificial Intelligence and Expert Systems, IEA/AIE 2005, Bari, Italy, June 22-24, 2005, Proceedings. Springer-Verlag, LNCS 3533, 500-509, 2005.
  • Annalisa Appice, Margherita Berardi, Michelangelo Ceci, and Donato Malerba. Mining and filtering multi-level spatial association rules with ARES. In: M.-S. Hacid, N. V. Murray, Z. W. Ras, S. Tsumoto (Eds.): Foundations of Intelligent Systems, 15th International Symposium, ISMIS 2005, Saratoga Springs, NY, USA, May 25-28, 2005, Proceedings. Springer-Verlag, LNCS 3488, 342-353, 2005.
  • Berardi Margherita, Varlaro Antonio, and Malerba Donato. On the effect of caching in recursive theory learning. In: R. Camacho, R. D. King, A. Srinivasan (Eds.): Inductive Logic Programming, 14th International Conference, ILP 2004, Porto, Portugal, September 6-8, 2004, Proceedings. Springer-Verlag, LNCS 3194, 44-62, 2004.
  • Berardi Margherita, Lapi Michele, and Malerba Donato. An integrated approach for automatic semantic structure extraction in document images. In: S. Marinai, A. Dengel (Eds.): Document Analysis Systems VI, 6th International Workshop, DAS 2004, Florence, Italy, September 8-10, 2004, Proceedings. Springer-Verlag, LNCS 3163, 179-190, 2004.
  • Ingo Frommholz, Holger Brocks, Ulrich Thiel, Erich Neuhold, Luigi Iannone, Giovanni Semeraro, Margherita Berardi, and Michelangelo Ceci. Document-Centered Collaboration for Scholars in the Humanities - The COLLATE System. In: T. Koch, I. Sølvberg (Eds.): Research and Advanced Technology for Digital Libraries, 7th European Conference, ECDL 2003, Trondheim, Norway, August 17-22, 2003, Proceedings. Springer-Verlag, LNCS 2769, 434-445, 2003.
  • Donato Malerba, Michelangelo Ceci, and Margherita Berardi. XML and Knowledge Technologies for Semantic-Based Indexing of Paper Documents. In: V. Marík, W. Retschitzegger, O. Stepánková (Eds.): Database and Expert Systems Applications, 14th International Conference, DEXA 2003, Prague, Czech Republic, September 1-5, 2003, Proceedings. Springer-Verlag, LNCS 2736, 256-265, 2003.
• International Conferences
  • Michelangelo Ceci, Margherita Berardi, Giuseppe A. Porcelli, and Donato Malerba. A data Mining approach to Reading Order Detection. In: Proc. of the 9th International Conference on Document Analysis and Recognition (ICDAR 2007), September 23-26, 2007, Curitiba, Brazil, IEEE Computer, 924-928, 2007.
  • Margherita Berardi, Oronzo Altamura, Michelangelo Ceci, and Donato Malerba. A color-based layout analysis to process censorship cards of film archives. Eighth International Conference on Document Analysis and Recognition (ICDAR 2005), 29 August - 1 September 2005, Seoul, Korea. IEEE Computer Society, 1110-1114, 2005.
  • Michelangelo Ceci, Margherita Berardi, and Donato Malerba. Relational Learning techniques for Document Image Understanding: Comparing Statistical and Logical approaches. Eighth International Conference on Document Analysis and Recognition (ICDAR 2005), 29 August - 1 September 2005, Seoul, Korea. IEEE Computer Society, 473-477, 2005.
  • Margherita Berardi, Michelangelo Ceci, Floriana Esposito, and Donato Malerba. Learning Logic Programs for Layout Analysis Correction. In: T. Fawcett, N. Mishra (Eds.): Machine Learning, Proceedings of the Twentieth International Conference (ICML 2003), August 21-24, 2003, Washington, DC, USA. AAAI Press, 27-34, 2003.
  • Donato Malerba, Floriana Esposito, Oronzo Altamura, Michelangelo Ceci, and Margherita Berardi. Correcting the Document Layout: A Machine Learning Approach. In: 7th International Conference on Document Analysis and Recognition (ICDAR 2003), 2-Volume Set, 3-6 August 2003, Edinburgh, Scotland, UK. IEEE Computer Society, 97-101, 2003.
• International Workshops
  • Corrado Loglisci, Saverio D'Alessandro, Margherita Berardi, and Donato Malerba: Mining non redundant generalized association rules. In Proceedings of the Statistics for Data Mining, Learning and Knowledge Extraction Conference (IASC 2007), Aveiro, Portugal, August 30 –September 1, 2007.
  • Margherita Berardi, Donato Malerba, and Marcella Attimonelli: Mining Information Extraction Models for HmtDB annotation. In: Proceedings of the Sixth IEEE International Conference on Data Mining - Workshops (ICDMW 2006), December 18, 2006, Hong Kong, IEEE Computer Society, 207-212, 2006.
  • Corrado Loglisci, Margherita Berardi: Segmentation of Evolving Complex Data and Generation of Models. In: Proceedings of the Sixth IEEE International Conference on Data Mining - Workshops (ICDMW 2006), December 18, 2006, Hong Kong, IEEE Computer Society, 269-273, 2006.
  • Margherita Berardi, Michelangelo Ceci, and Donato Malerba. A Hybrid Strategy for Knowledge Extraction from Biomedical Documents. ICDAR workshop on "Neural Networks and Learning in Document Analysis and Recognition". Seoul, Korea, August 29 - September 1, 2005.
  • Floriana Esposito, Donato Malerba, Giovanni Semeraro, Stefano Ferilli, Oronzo Altamura, Teresa Maria A.Basile, Margherita Berardi, Michelangelo Ceci, and Nicola Di Mauro. Machine Learning methods for automatically processing historical documents: from paper acquisition to XML transformation. Workshop on Document Image Analysis for Libraries (DIAL 2004), Palo Alto, CA, USA, 23-24 June 2004, IEEE Computer Society, 328-335, 2004.
  • Margherita Berardi, Michele Lapi, Pietro Leo, Donato Malerba, Caterina Marinelli, and Gaetano Scioscia. A data mining approach to PubMed query refinement. 2nd International Workshop on Biological Data Management (BIDM 2004), in conjunction with DEXA 2004, Zaragoza, Spain, September 2, 2004, IEEE Computer Society, 401-405, 2004.
  • Margherita Berardi, Michele Lapi, Pietro Leo, Donato Malerba, Caterina Marinelli, and Gaetano Scioscia. A data mining approach for disease-genes relationship discovery in biomedical literature. KDNet Symposium on Knowledge-Based Services for the Public Sector: workshop on "Knowledge-based systems and services for health care". Bonn, Germany, June 3-4, 2004.
  • Antonio Varlaro, Margherita Berardi, and Donato Malerba. Learning Recursive Theories with the Separate-and-Parallel-Conquer Strategy. ECML/PKDD 04 workshop on "Advances on Inductive Rule Learning". Pisa, Italy, September 20-24, 2004.
  • Margherita Berardi, Annalisa Appice, Michelangelo Ceci, and Donato Malerba. Mining spatial data: discovery of spatial association rules with ARES. ECML/PKDD 04 workshop on "Symbolic and Spatial Data Analysis: Mining Complex Data Structures". Pisa, Italia, September 20-24, 2004.
  • Margherita Berardi, Michelangelo Ceci, and Donato Malerba. Mining spatial association rules from document layout structures. In: Proc. of the 3rd Workshop on Document Layout Interpretation and its Application (DLIA 2003), 9-13, Deutsches Forschungszentrum fur Kunstliche Intelligenz, GmbH, Germany.
  • Michelangelo Ceci, Margherita Berardi, and Donato Malerba. Mining association rules in document images. Workshop on Multimedia Discovery and Mining (MDM'03) in conjunction with ECML/PKDD 2003, September 22, 2003. Dubrovnik, Croatia.
• National Conferences
  • Corrado Loglisci, Margherita Berardi, Saverio D'Alessandro, Pietro Leo: Finding Generalized Closed Frequent Itemsets for Mining Non Redundant Association Rules. Fifteenth Italian Symposium on Advanced Database Systems (SEBD 2007). Torre Canne di Fasano (Bari), Italy, June 18-21, 2007.
  • Margherita Berardi, Vincenzo Giuliano, and Donato Malerba. Learning for Biomedical Information Extraction with ILP. Convegno italiano di Logica Computazionale (CILC 2006). Bari, Italy, June 26-27, 2006.
  • Margherita Berardi. An integrated process for Document Mining: a new perspective. Fourteenth Italian Symposium on Advanced Database Systems (SEBD 2006). Portonovo (ANCONA), June 18-21, 2006.
  • Annalisa Appice,Margherita Berardi, Michelangelo Ceci, Michele Lapi, Donato Malerba, and Antonio Turi. Mining interesting spatial association rules: two case studies. Twelfth Italian Symposium on Advanced Database Systems (SEBD 2004). S.Margherita di Pula (CAGLIARI), June 21-23, 2004.
  • Antonio Varlaro, Margherita Berardi, and Donato Malerba. Improving efficiency of recursive theory learning. Convegno italiano di Logica Computazionale (CILC 2004). Parma, Italy, June 16-17, 2004.
• Scientific Communications
  • Marcella Attimonelli, Imma Cascione, Monica Santamaria, M Accetturo, Daniela Lascaro, Margherita Berardi, Michelangelo Ceci, Corrado Loglisci, and Donato Malerba. A data mining approach to retrieve mitochondrial variability data associated to clinical phenotypes. Annual Meeting of the Bioinformatic Italian Society, BITS 2005. Milano, Marzo 17-19, 2005.
  • Margherita Berardi, Donato Malerba, Caterina Marinelli, Pietro Leo, Corrado Loglisci, and Gaetano Scioscia. A Text-Mining application able to mine association rules from biomedical texts. Annual Meeting of the Bioinformatic Italian Society, BITS 2005. Milano, Marzo 17-19, 2005.
  • Margherita Berardi, Pietro Leo, and Donato Malerba. Beyond unstructured textual data for life science. 3rd world conference on Computational Statistics & Data Analysis, CSDA 2005. Limassol, Cyprus, 28-31 October, 2005.
• Technical Reports
  • UNIBA Partner IST-1999-20882 project COLLATE “Collaboratory for Annotation, Indexing and Retrieval of Digitized Historical Archive Material”. Deliverable No 4.1: Document Processing and XML Content Manager (Part 1: Document Processing). Deliverable No 7.2: Integration of System Components. Deliverable No 10.2: Dissemination activities of the COLLATE project.
  • UNIBA Partner IBM-1999 BIC project. Deliverable 1.0: Mining the Biomedical Literature: the state of the art.


• Ph.D Thesis
  M. Berardi. Towards Semantic Indexing of documents: a data mining perspective. Ph.D. Thesis, Università degli Studi, Bari, Italy. (2006)


• "MAURIZIO PANTI" Award: she received this award for the paper entitled An integrated process for Document Mining: a new perspective presenting the results of her PhD research activities. Portonovo, Ancona, Italy. (2006)

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Software

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