Logic-based approaches in Bioinformatics Workshop

Satellite workshop of the AI*IA 2009: International Conference of the Italian Association for Artificial Intelligence

12 December 2009, Reggio Emilia (Italy)


The Bio-Logical: Logic-based Approaches in Bioinformatics Workshop will take place in Reggio Emilia (Italy) on December 12, 2009, following the AI*IA 2009 International Conference (9-11 December 2009)

The conference and all the workshops will be hosted in the new building of the Department of Social, Cognitive and Quantitative Sciences and of the Faculty of Communication and Economics, located in the centre of Reggio Emilia Address: via Allegri 9, I 42100 Reggio Emilia


Bioinformatics is a truly interdisciplinary field at the boundary between biology and computer science. It encompasses every aspect of computational biology, from DNA sequence analysis to protein structure analysis and prediction. The goal is to aid biologists in gathering and processing genomic data to study protein function and protein interactions. Most of the tools routinely used in bioinformatics have been developed by scientists with a background in biological sciences. Some prominent examples are tools for comparing sequences. However, the vast amount of biological data available and the demand for increasingly complex cations for their analysis offer vast opportunities for the systematic application of a wide range of techniques from computer science, including those based on computational logics.

This workshop aims at collecting contributes, and at bringing together scientists and practitioners, whose research interests lie across the areas of Logics (along various possible representation formalisms, inference strategies and approaches) and Bioinformatics. The former is a broad branch of Artificial Intelligence in general, and includes many sub-areas of interest. The latter is a discipline that is gaining more and more interest nowadays and that can take great advantage from the application of Artificial Intelligence techniques, because of the high domain complexity and the scarce explicit domain knowledge available. The mixture of both turns out to be particularly interesting, because of the peculiarity of Logic approaches to be able to express and manipulate relations among objects. Indeed, such a characteristic might play a crucial role in the biological domain. Hence, the twofold attempt of the workshop: stimulating application of Logic approaches in Bioinformatics, and searching for new challenges posed by Bioinformatics that can be successfully tackled by Logic-based approaches. Contributes are welcome concerning any aspect involved in such disciplines: problems, methodologies, techniques, systems and applications.

The workshop should be of interest, in addition to researchers working in the Logic-oriented branch of Artificial Intelligence in order to propose their solutions, also for those who are interested more specifically in the biological domain, that can take the chance to discover a branch of Artificial Intelligence less known to the wide audience but that can turn out to be important for the solution of their problems. Moreover, the meeting could also be a chance to bring together researchers that work in the Bioinformatics application domain using approaches that fall into different areas of Artificial Intelligence, with the aim of identifying possibilities of cooperation and synergies between the respective areas of interest.


Topics of interest include, but are not limited to:
  • logic programming
  • multi-strategic inference: induction, abduction, abstraction, deduction
  • representation and reasoning
  • constraint logic programming
  • fuzzy logic
  • description logics
  • (probabilistic) logic based learning
Applications include, but are not limited to:
  • genome annotation
  • protein sequence annotation
  • protein structure comparison
  • reconstruction and analysis biochemical pathways
  • structural analysis and protein structure prediction
  • drug design
  • information extraction from biological literature
  • integration of biological information sources
  • inferring cell regulation
  • determining protein function and metabolic pathways


Papers not exceeding 10 pages, written in English and complying with the LNCS Springer-Verlag format (http://www.springer.com/computer/lncs?SGWID=0-164-7-72376-0) should be submitted electronically. Submissions are due in PDF format and can be performed with EasyChair at

Accepted papers will be published on the official CD-Rom of the AI*IA2009 International conference with regular ISBN number.


  • Paper submission: October 4, 2009
  • Camera-ready of accepted papers: November 11, 2009
  • Workshop day: December 12, 2009


Attendance to the conference and to the workshops IS limited to members of AI*IA. Participants are kindly requested to register before the conference, although on-site registration will also be offered.

Attendance to the workshops only (including participation in all the workshops, coffee-breaks and a CD-ROM with the Proceedings of all Workshops; it does not include membership to AI*IA):

  • Advance registration: 100 Euro
  • On-site registration: 200 Euro

Regular conference fee (including participation in the conference and all the workshops, a copy of the proceedings volume, the conference CD-Rom, coffee breaks for all 4 days; it does not include membership to AI*IA):

  • Early registration, before August 31, 2009: 350 Euro.
  • Late registration, since September 1, 2009: 400 Euro.
  • On-site registration: 500 Euro

Student fee (including proceedings volume and participation to the workshops, not including conference dinner): 130 Euro ** NOT AVAILABLE ON-SITE **


9:15-9:30	OPENING

9:30-10:30	INVITED TALK
	Logic-based Machine Learning for Bioinformatics
	Hendrik Blockeel

10:30-11:00	COFFEE BREAK

11:00 Constraint-based Languages to Model the Blood 
      Coagulation Cascade
	Stefano Bistarelli, Marco Bottalico, 
        Francesco Santini
11:30 Tales of Spatiality in Stochastic Concurrent 
      Constraint Programming
	Luca Bortolussi, Alberto Policriti
12:00	A Logic-based Approach to Peptide Sequencing
	Renato Bruni
12:30	Constraint-based Protein Fragment Assembly
	Alessandro Dal Palu', Agostino Dovier, 
        Federico Fogolari, Enrico Pontelli

13:00-14:00	LUNCH BREAK

14:00 First-Order Frequent Pattern Mining for 
      Analyzing Complex Phenotype Data
	Corrado Loglisci, Andrea Falcone, 
        Bachir Balech, Pietro Leo
14:30 Mining Association Rules from Sequences of 
      Spaced Motifs
	Eliana Salvemini, Michelangelo Ceci, 
        Domenica D'Elia, Marco Didonna, 
        Anna Paola Carrieri
15:00 Mining Drug Resistance Relational Features 
      with Hierarchical Multitask kFOIL
	Elisa Cilia, Niels Landwehr, Andrea Passerini
15:30 RNA Secondary Structure Prediction by 
      Mapping Zuker's Algorithm into Markov Logic
	Marco Lippi, Lukasz Popenda, Paolo Frasconi

16:00-16:30	COFFEE BREAK

         AND IMAGES
16:30 A Logic Approach to Mine Syntactic Fragments 
      of Mesh Keywords in Biomedical Literature
	Annalisa Appice
17:00 On the Perspectives of Applying Multi-Relational 
      Learning Techniques to Bio-Medical Domains
	Teresa M.A. Basile, Floriana Esposito, 
        Laura Caponetti
17:30 Non Syndromic Hereditary Hearing Loss: Gene 
      Prioritization Based on Textual Approach
	Marenglen Biba, Floriana Esposito, 
        Stefano Ferilli, Matteo Accetturo, 
        Teresa Maria Creanza, Claudia Santoro, 
        Pietro Leo

18:00-18:15	CLOSING



  • Stefano Ferilli (University of Bari)
  • Donato Malerba (University of Bari)

Local Operating Team

  • Marenglen Biba (University of Bari)
  • Nicola Di Mauro (University of Bari)
  • Corrado Loglisci (University of Bari)
  • Eliana Salvemini (University of Bari)

Program Committee

  • Giuliano Armano (University of Cagliari)
  • Marco Botta (University of Torino)
  • Renato Bruni (University of Rome "La Sapienza")
  • Alessandro Dal Palù (University of Parma)
  • Agostino Dovier (University of Udine)
  • Paolo Frasconi (University of Firenze)
  • Francesco Masulli (University of Genova)
  • Giancarlo Mauri (University of Milano-Bicocca)
  • Luigi Palopoli (University of Calabria)
  • Andrea Passerini (University of Trento)
  • Alberto Policriti (University of Udine)