We present a novel approach to pseudo-feedback-based ad hoc retrieval that uses language models induced from both documents and clusters. First, we treat the pseudo-feedback documents produced in response to the original query as a set of pseudo-queries that themselves can serve as input to the retrieval process. Observing that the documents returned in response to the pseudo-queries can then act as pseudo-queries for subsequent rounds, we arrive at a formulation of pseudo-query-based retrieval as an iterative process. Experiments show that several concrete instantiations of this idea, when applied in conjunction with techniques designed to heighten precision, yield performance results rivaling those of a number of previously-proposed algorithms, including the standard language-modeling approach. The use of cluster-based language models is a key contributing factor to our algorithms' success.

Inspired by the PageRank and HITS (hubs and authorities) algorithms for Web search, we propose a structural re-ranking approach to ad hoc information retrieval: we reorder the documents in an initially retrieved set by exploiting asymmetric relationships between them. Specifically, we consider generation links, which indicate that the language model induced from one document assigns high probability to the text of another; in doing so, we take care to prevent bias against long documents. We study a number of re-ranking criteria based on measures of centrality in the graphs formed by generation links, and show that integrating centrality into standard language-model-based retrieval is quite effective at improving precision at top ranks.

We present a technique for the automated verification of abstract models of multithreaded programs providing fresh name generation, name mobility, and unbounded control. As high level specification language we adopt here an extension of communication finite-state machines with local variables ranging over an infinite name domain, called TDL programs. Communication machines have been proved very effective for representing communication protocols as well as for representing abstractions of multithreaded software. The verification method that we propose is based on the encoding of TDL programs into a low level language based on multiset rewriting and constraints that can be viewed as an extension of Petri Nets. By means of this encoding, the symbolic verification procedure developed for the low level language in our previous work can now be applied to TDL programs. Furthermore, the encoding allows us to isolate a decidable class of verification problems for TDL programs that still provide fresh name generation, name mobility, and unbounded control. Our syntactic restrictions are in fact defined on the internal structure of threads: In order to obtain a complete and terminating method, threads are only allowed to have at most one local variable (ranging over an infinite domain of names).

In this paper, a mathematical schema theory is developed. This theory has three roots: brain theory schemas, grid automata, and block-shemas. In Section 2 of this paper, elements of the theory of grid automata necessary for the mathematical schema theory are presented. In Section 3, elements of brain theory necessary for the mathematical schema theory are presented. In Section 4, other types of schemas are considered. In Section 5, the mathematical schema theory is developed. The achieved level of schema representation allows one to model by mathematical tools virtually any type of schemas considered before, including schemas in neurophisiology, psychology, computer science, Internet technology, databases, logic, and mathematics.

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.

We establish a relationship between the online mistake-bound model of learning and resource-bounded dimension. This connection is combined with the Winnow algorithm to obtain new results about the density of hard sets under adaptive reductions. This improves previous work of Fu (1995) and Lutz and Zhao (2000), and solves one of Lutz and Mayordomo's "Twelve Problems in Resource-Bounded Measure" (1999).

Artificial life models, swarm intelligent and evolutionary computation algorithms are usually built on fixed size populations. Some studies indicate however that varying the population size can increase the adaptability of these systems and their capability to react to changing environments. In this paper we present an extended model of an artificial ant colony system designed to evolve on digital image habitats. We will show that the present swarm can adapt the size of the population according to the type of image on which it is evolving and reacting faster to changing images, thus converging more rapidly to the new desired regions, regulating the number of his image foraging agents. Finally, we will show evidences that the model can be associated with the Mathematical Morphology Watershed algorithm to improve the segmentation of digital grey-scale images. KEYWORDS: Swarm Intelligence, Perception and Image Processing, Pattern Recognition, Mathematical Morphology, Social Cognitive Maps, Social Foraging, Self-Organization, Distributed Search.

From a geometric perspective most nonlinear binary classification algorithms, including state of the art versions of Support Vector Machine (SVM) and Radial Basis Function Network (RBFN) classifiers, and are based on the idea of reconstructing indicator functions. We propose instead to use reconstruction of the signed distance function (SDF) as a basis for binary classification. We discuss properties of the signed distance function that can be exploited in classification algorithms. We develop simple versions of such classifiers and test them on several linear and nonlinear problems. On linear tests accuracy of the new algorithm exceeds that of standard SVM methods, with an average of 50% fewer misclassifications. Performance of the new methods also matches or exceeds that of standard methods on several nonlinear problems including classification of benchmark diagnostic micro-array data sets.

HIV-1 Rev is one of several clinically important proteins that are "experimentally recalcitrant," i.e., for which it has not been possible to obtain high resolution structural in formation. Identifying critic al functional residues in Rev is further complicated by the fact that Rev proteins have no significant sequence similarity to any protein with known structure, and that Rev sequences from different species have very little similarity to one another. Our comparison of predictions with experimental data on the Rev proteins from HIV-1 and EIAV demonstrates that sequence-based computational methods can identify residues in "recalcitrant" proteins that interact with other proteins or nucleic acids. When structural information is available for a protein of interest, enhanced prediction accuracy can be achieved (18, 29). Developing improved methods for predicting binding sites will contribute to our understanding of how proteins recognize their targets in cells and may significantly decrease the time needed to precisely map binding sites in the laboratory. The level of accuracy obtained using the sequence-based methods presented here suggests that they could expedite the design of experiments to explore the function of key regulatory proteins, even when no structural information is available, with obvious implications for developing new therapies for both genetic and infectious diseases. Acknowledgments This Research was supported in part by grants NIH, GM 066387 (VH, DD, & RLJ) and CA97936 (SC), by an ISU Center for Integrated Animal Genomics grant (DD, VH & RLJ), and by USDA Formula Funds (SC & DD). We thank Sijun Liu for technical assistance and Jeffrey Sander for useful comments.

The approximate nonlinear receding-horizon control law is used to treat the trajectory tracking control problem of rigid link robot manipulators. The derived nonlinear predictive law uses a quadratic performance index of the predicted tracking error and the predicted control effort. A key feature of this control law is that, for their implementation, there is no need to perform an online optimization, and asymptotic tracking of smooth reference trajectories is guaranteed. It is shown that this controller achieves the positions tracking objectives via link position measurements. The stability convergence of the output tracking error to the origin is proved. To enhance the robustness of the closed loop system with respect to payload uncertainties and viscous friction, an integral action is introduced in the loop. A nonlinear observer is used to estimate velocity. Simulation results for a two-link rigid robot are performed to validate the performance of the proposed controller. Keywords: receding-horizon control, nonlinear observer, robot manipulators, integral action, robustness.