The paper: Protein Structure Prediction on GPU: a Declarative Approach in a Multi-agent Framework, by F. Campeotto, A. Dovier, and E. Pontelli is accepted in ICPP conference (IEEE) http://icpp2013.ens-lyon.fr/ Lyon (FR), October 2013.
This paper provides a novel perspective in the Protein Structure Prediction (PSP) problem. The PSP problem focuses on determining putative 3D structures of a protein starting from its primary sequence. The proposed approach relies on a multi-agents approach, where concurrent agents explore the folding of different parts of a protein. The strength of the approach lies in the agents’ ability to apply different types of knowledge (expressed in the form of declarative constraints to prune the local space of folding alternatives. The paper demonstrates the suitability of a GPU approach to implement such multi-agent infrastructure, with significant improvements in speed and quality of solutions w.r.t. other methods (e.g., based on fragments assembly approaches).
Autonomous agents coordination: Action languages meet CLP(FD) and Linda
The paper presents a knowledge representation formalism, in the form of a high-level Action Description Language (ADL) for multi-agent systems, where autonomous agents reason and act in a shared environment. Agents are autonomously pursuing individual goals, but are capable of interacting through a shared knowledge repository. In their interactions through shared portions of the world, the agents deal with problems of synchronization and concurrency; the action language allows the description of strategies to ensure a consistent global execution of the agents’ autonomously derived plans. A distributed planning problem is formalized by providing the declarative specifications of the portion of the problem pertaining to a single agent. Each of these specifications is executable by a stand-alone CLP-based planner. The coordination among agents exploits a Linda infrastructure. The proposal is validated in a prototype implementation developed in SICStus Prolog.
Official Entry in the Journal
Free Version on CORR
The relevance of CLP Lab in the Italian community of Logic Programming GULP has been witnessed by the election results
- Agostino Dovier has been elected as president of the association.
- Andrea Formisano, Enrico Pontelli, and Alessandro Dal Palù have been elected as members of the Executive Committee (Consiglio Direttivo).
Alessandro dal Palù presented the paper “A Filtering Technique for Fragment Assembly-based Proteins Loop Modeling with Constraints” at the 18-th International Conference on Principles and Practice of Constraint Programming in Québec City, Canada.
Alessandro Dal Palù presenting the paper
CLP lab contributed to the Association for Constraint Programming by sharing the expertise on Constraints and Biology in the summer school in Wrocław (Poland).
This is the web site of the school, this is our material, and this is a report on that school.
We are proud to announce that the CLP DIMI lab team composed by Alessandro Dal Palù, Agostino Dovier, and Enrico Pontelli won the 19th Prolog Programming Contest organized by the Association for Logic Programming in Budapest in September 6, 2012.
A report on the contest can be found here