Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits of exact algorithms further. Since MSA can be cast as a classical path finding problem, it is attracting a growing number of AI researchers interested in heuristic search algorithms as a challenge with actual practical relevance. In this paper, we first review two previous, complementary lines of research. Based on Hirschberg's algorithm, Dynamic Programming needs O(kN^(k-1)) space to store both the search frontier and the nodes needed to reconstruct the solution path, for k sequences of length N. Best first search, on the other hand, has the advantage of bounding the search space that has to be explored using a heuristic. However, it is necessary to maintain all explored nodes up to the final solution in order to prevent the search from re-expanding them at higher cost. Earlier approaches to reduce the Closed list are either incompatible with pruning methods for the Open list, or must retain at least the boundary of the Closed list. In this article, we present an algorithm that attempts at combining the respective advantages; like A* it uses a heuristic for pruning the search space, but reduces both the maximum Open and Closed size to O(kN^(k-1)), as in Dynamic Programming. The underlying idea is to conduct a series of searches with successively increasing upper bounds, but using the DP ordering as the key for the Open priority queue. With a suitable choice of thresholds, in practice, a running time below four times that of A* can be expected. In our experiments we show that our algorithm outperforms one of the currently most successful algorithms for optimal multiple sequence alignments, Partial Expansion A*, both in time and memory. Moreover, we apply a refined heuristic based on optimal alignments not only of pairs of sequences, but of larger subsets. This idea is not new; however, to make it practically relevant we show that it is equally important to bound the heuristic computation appropriately, or the overhead can obliterate any possible gain. Furthermore, we discuss a number of improvements in time and space efficiency with regard to practical implementations. Our algorithm, used in conjunction with higher-dimensional heuristics, is able to calculate for the first time the optimal alignment for almost all of the problems in Reference 1 of the benchmark database BAliBASE.

Variable elimination is a general technique for constraint processing. It is often discarded because of its high space complexity. However, it can be extremely useful when combined with other techniques. In this paper we study the applicability of variable elimination to the challenging problem of finding still-lifes. We illustrate several alternatives: variable elimination as a stand-alone algorithm, interleaved with search, and as a source of good quality lower bounds. We show that these techniques are the best known option both theoretically and empirically. In our experiments we have been able to solve the n 20 instance, which is far beyond reach with alternative approaches.

This is the third of three papers describing ZAP, a satisfiability engine that substantially generalizes existing tools while retaining the performance characteristics of modern high-performance solvers. The fundamental idea underlying ZAP is that many problems passed to such engines contain rich internal structure that is obscured by the Boolean representation used; our goal has been to define a representation in which this structure is apparent and can be exploited to improve computational performance. The first paper surveyed existing work that (knowingly or not) exploited problem structure to improve the performance of satisfiability engines, and the second paper showed that this structure could be understood in terms of groups of permutations acting on individual clauses in any particular Boolean theory. We conclude the series by discussing the techniques needed to implement our ideas, and by reporting on their performance on a variety of problem instances.

Many current large-scale multiagent team implementations can be characterized as following the ``belief-desire-intention'' (BDI) paradigm, with explicit representation of team plans. Despite their promise, current BDI team approaches lack tools for quantitative performance analysis under uncertainty. Distributed partially observable Markov decision problems (POMDPs) are well suited for such analysis, but the complexity of finding optimal policies in such models is highly intractable. The key contribution of this article is a hybrid BDI-POMDP approach, where BDI team plans are exploited to improve POMDP tractability and POMDP analysis improves BDI team plan performance. Concretely, we focus on role allocation, a fundamental problem in BDI teams: which agents to allocate to the different roles in the team. The article provides three key contributions. First, we describe a role allocation technique that takes into account future uncertainties in the domain; prior work in multiagent role allocation has failed to address such uncertainties. To that end, we introduce RMTDP (Role-based Markov Team Decision Problem), a new distributed POMDP model for analysis of role allocations. Our technique gains in tractability by significantly curtailing RMTDP policy search; in particular, BDI team plans provide incomplete RMTDP policies, and the RMTDP policy search fills the gaps in such incomplete policies by searching for the best role allocation. Our second key contribution is a novel decomposition technique to further improve RMTDP policy search efficiency. Even though limited to searching role allocations, there are still combinatorially many role allocations, and evaluating each in RMTDP to identify the best is extremely difficult. Our decomposition technique exploits the structure in the BDI team plans to significantly prune the search space of role allocations. Our third key contribution is a significantly faster policy evaluation algorithm suited for our BDI-POMDP hybrid approach. Finally, we also present experimental results from two domains: mission rehearsal simulation and RoboCupRescue disaster rescue simulation.

AAAI presented the AAAI-04 workshop program on July 25-26, 2004 in San Jose, California. This program included twelve workshops covering a wide range of topics in artificial intelligence. The titles of the workshops were as follows: (1) Adaptive Text Extraction and Mining; (2) Agent Organizations: Theory and Practice; (3) Anchoring Symbols to Sensor Data; (4) Challenges in Game AI; (5) Fielding Applications of Artificial Intelligence; (6) Forming and Maintaining Coalitions in Adaptive Multiagent Systems; (7) Intelligent Agent Architectures: Combining the Strengths of Software Engineering and Cognitive Systems; (8) Learning and Planning in Markov Processes -- Advances and Challenges; (9) Semantic Web Personalization; (10) Sensor Networks; (11) Spatial and Temporal Reasoning; and (12) Supervisory Control of Learning and Adaptive Systems.

Caesarea Edmond Benjamin de Rothschild Email: patrick.hung@uoit.ca (MDAI 2005).

Semantic integration has been a long-standing challenge for the database community. It has received steady attention over the past two decades, and has now become a prominent area of database research. In this article, we first review database applications that require semantic integration and discuss the difficulties underlying the integration process. We then describe recent progress and identify open research issues. We focus in particular on schema matching, a topic that has received much attention in the database community, but also discuss data matching (for example, tuple deduplication) and open issues beyond the match discovery context (for example, reasoning with matches, match verification and repair, and reconciling inconsistent data values). For previous surveys of database research on semantic integration, see Rahm and Bernstein (2001); Ouksel and Seth (1999); and Batini, Lenzerini, and Navathe (1986).

The Sixth International Conference on Enterprise Information Systems (ICEIS) was held in Porto, Portugal; previous venues were in Spain, France, and the United Kingdom. Since its inception in 1999, ICEIS has grown steadily, and is now one of the largest international conferences in the area of information systems. In 2004, more than 600 papers were submitted to the conference and its ten satellite workshops. One of the interesting features of this conference is the high number of invited speakers. In 2004, eighteen keynote speakers were featured at ICEIS and its workshops.

Data integration is the problem of combining data residing at different autonomous, heterogeneous sources and providing the client with a unified, reconciled global view of the data. We discuss dataintegration systems, taking the abstract viewpoint that the global view is an ontology expressed in a class-based formalism. We resort to an expressive description logic, ALCQI, that fully captures classbased representation formalisms, and we show that query answering in data integration, as well as all other relevant reasoning tasks, is decidable. However, when we have to deal with large amounts of data, the high computational complexity in the size of the data makes the use of a fullfledged expressive description logic infeasible in practice. This leads us to consider DL-Lite, a specifically tailored restriction of ALCQI that ensures tractability of query answering in data integration while keeping enough expressive power to capture the most relevant features of class-based formalisms.

We propose the use of application semantics to enhance the process of semantic reconciliation. Application semantics involves those elements of business reasoning that affect the way concepts are presented to users: their layout, and so on. In particular, we pursue in this article the notion of precedence, in which temporal constraints determine the order in which concepts are presented to the user. Existing matching algorithms use either syntactic means (such as term matching and domain matching) or model semantic means, the use of structural information that is provided by the specific data model to enhance the matching process. The novelty of our approach lies in proposing a class of matching techniques that takes advantage of ontological structures and application semantics. As an example, the use of precedence to reflect business rules has not been applied elsewhere, to the best of our knowledge. We have tested the process for a variety of web sites in domains such as car rentals and airline reservations, and we share our experiences with precedence and its limitations.