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.

There has been increased interest in devising learning techniques that combine unlabeled data with labeled data - i.e. semi-supervised learning. However, to the best of our knowledge, no study has been performed across various techniques and different types and amounts of labeled and unlabeled data. Moreover, most of the published work on semi-supervised learning techniques assumes that the labeled and unlabeled data come from the same distribution. It is possible for the labeling process to be associated with a selection bias such that the distributions of data points in the labeled and unlabeled sets are different. Not correcting for such bias can result in biased function approximation with potentially poor performance. In this paper, we present an empirical study of various semi-supervised learning techniques on a variety of datasets. We attempt to answer various questions such as the effect of independence or relevance amongst features, the effect of the size of the labeled and unlabeled sets and the effect of noise. We also investigate the impact of sample-selection bias on the semi -supervised learning techniques under study and implement a bivariate probit technique particularly designed to correct for such bias.

Formal treatment of collaborative multi-agent systems has been lagging behind the rapid progress in sequential decision making by individual agents. Recent work in the area of decentralized Markov Decision Processes (MDPs) has contributed to closing this gap, but the computational complexity of these models remains a serious obstacle. To overcome this complexity barrier, we identify a specific class of decentralized MDPs in which the agents' transitions are independent. The class consists of independent collaborating agents that are tied together through a structured global reward function that depends on all of their histories of states and actions. We present a novel algorithm for solving this class of problems and examine its properties, both as an optimal algorithm and as an anytime algorithm. To the best of our knowledge, this is the first algorithm to optimally solve a non-trivial subclass of decentralized MDPs. It lays the foundation for further work in this area on both exact and approximate algorithms.

We introduce a stochastic graph-based method for computing relative importance of textual units for Natural Language Processing. We test the technique on the problem of Text Summarization (TS). Extractive TS relies on the concept of sentence salience to identify the most important sentences in a document or set of documents. Salience is typically defined in terms of the presence of particular important words or in terms of similarity to a centroid pseudo-sentence. We consider a new approach, LexRank, for computing sentence importance based on the concept of eigenvector centrality in a graph representation of sentences. In this model, a connectivity matrix based on intra-sentence cosine similarity is used as the adjacency matrix of the graph representation of sentences. Our system, based on LexRank ranked in first place in more than one task in the recent DUC 2004 evaluation. In this paper we present a detailed analysis of our approach and apply it to a larger data set including data from earlier DUC evaluations. We discuss several methods to compute centrality using the similarity graph. The results show that degree-based methods (including LexRank) outperform both centroid-based methods and other systems participating in DUC in most of the cases. Furthermore, the LexRank with threshold method outperforms the other degree-based techniques including continuous LexRank. We also show that our approach is quite insensitive to the noise in the data that may result from an imperfect topical clustering of documents.

Multiagent learning is a necessary yet challenging problem as multiagent systems become more prevalent and environments become more dynamic. Much of the groundbreaking work in this area draws on notable results from game theory, in particular, the concept of Nash equilibria. Learners that directly learn an equilibrium obviously rely on their existence. Learners that instead seek to play optimally with respect to the other players also depend upon equilibria since equilibria are fixed points for learning. From another perspective, agents with limitations are real and common. These may be undesired physical limitations as well as self-imposed rational limitations, such as abstraction and approximation techniques, used to make learning tractable. This article explores the interactions of these two important concepts: equilibria and limitations in learning. We introduce the question of whether equilibria continue to exist when agents have limitations. We look at the general effects limitations can have on agent behavior, and define a natural extension of equilibria that accounts for these limitations. Using this formalization, we make three major contributions: (i) a counterexample for the general existence of equilibria with limitations, (ii) sufficient conditions on limitations that preserve their existence, (iii) three general classes of games and limitations that satisfy these conditions. We then present empirical results from a specific multiagent learning algorithm applied to a specific instance of limited agents. These results demonstrate that learning with limitations is feasible, when the conditions outlined by our theoretical analysis hold.

The difficulty in solving optimally such problems arises when the agents lack full observability of the global state of the system when they operate. The general problem has been shown to be NEXP-complete. In this paper, we identify classes of decentralized control problems whose complexity ranges between NEXP and P. In particular, we study problems characterized by independent transitions, independent observations, and goal-oriented objective functions. Two algorithms are shown to solve optimally useful classes of goal-oriented decentralized processes in polynomial time. This paper also studies information sharing among the decision-makers, which can improve their performance. We distinguish between three ways in which agents can exchange information: indirect communication, direct communication and sharing state features that are not controlled by the agents. Our analysis shows that for every class of problems we consider, introducing direct or indirect communication does not change the worst-case complexity. The results provide a better understanding of the complexity of decentralized control problems that arise in practice and facilitate the development of planning algorithms for these problems.

Searching for and making decisions about information is becoming increasingly difficult as the amount of information and number of choices increases. Recommendation systems help users find items of interest of a particular type, such as movies or restaurants, but are still somewhat awkward to use. Our solution is to take advantage of the complementary strengths of personalized recommendation systems and dialogue systems, creating personalized aides. We present a system -- the Adaptive Place Advisor -- that treats item selection as an interactive, conversational process, with the program inquiring about item attributes and the user responding. Individual, long-term user preferences are unobtrusively obtained in the course of normal recommendation dialogues and used to direct future conversations with the same user. We present a novel user model that influences both item search and the questions asked during a conversation. We demonstrate the effectiveness of our system in significantly reducing the time and number of interactions required to find a satisfactory item, as compared to a control group of users interacting with a non-adaptive version of the system.

Information about user preferences plays a key role in automated decision making. In many domains it is desirable to assess such preferences in a qualitative rather than quantitative way. In this paper, we propose a qualitative graphical representation of preferences that reflects conditional dependence and independence of preference statements under a ceteris paribus (all else being equal) interpretation. Such a representation is often compact and arguably quite natural in many circumstances. We provide a formal semantics for this model, and describe how the structure of the network can be exploited in several inference tasks, such as determining whether one outcome dominates (is preferred to) another, ordering a set outcomes according to the preference relation, and constructing the best outcome subject to available evidence.

The 2002 Trading Agent Competition (TAC) presented a challenging market game in the domain of travel shopping. One of the pivotal issues in this domain is uncertainty about hotel prices, which have a significant influence on the relative cost of alternative trip schedules. Thus, virtually all participants employ some method for predicting hotel prices. We survey approaches employed in the tournament, finding that agents apply an interesting diversity of techniques, taking into account differing sources of evidence bearing on prices. Based on data provided by entrants on their agents' actual predictions in the TAC-02 finals and semifinals, we analyze the relative efficacy of these approaches. The results show that taking into account game-specific information about flight prices is a major distinguishing factor. Machine learning methods effectively induce the relationship between flight and hotel prices from game data, and a purely analytical approach based on competitive equilibrium analysis achieves equal accuracy with no historical data. Employing a new measure of prediction quality, we relate absolute accuracy to bottom-line performance in the game.

This paper addresses the problem of planning under uncertainty in large Markov Decision Processes (MDPs). Factored MDPs represent a complex state space using state variables and the transition model using a dynamic Bayesian network. This representation often allows an exponential reduction in the representation size of structured MDPs, but the complexity of exact solution algorithms for such MDPs can grow exponentially in the representation size. In this paper, we present two approximate solution algorithms that exploit structure in factored MDPs. Both use an approximate value function represented as a linear combination of basis functions, where each basis function involves only a small subset of the domain variables. A key contribution of this paper is that it shows how the basic operations of both algorithms can be performed efficiently in closed form, by exploiting both additive and context-specific structure in a factored MDP. A central element of our algorithms is a novel linear program decomposition technique, analogous to variable elimination in Bayesian networks, which reduces an exponentially large LP to a provably equivalent, polynomial-sized one. One algorithm uses approximate linear programming, and the second approximate dynamic programming. Our dynamic programming algorithm is novel in that it uses an approximation based on max-norm, a technique that more directly minimizes the terms that appear in error bounds for approximate MDP algorithms. We provide experimental results on problems with over 10^40 states, demonstrating a promising indication of the scalability of our approach, and compare our algorithm to an existing state-of-the-art approach, showing, in some problems, exponential gains in computation time.