Evaluating ASP and Commercial Solvers on the CSPLib

This paper deals with four solvers for combinatorial problems: the commercial state-of-the-art solver ILOG oplstudio, and the research answer set programming (ASP) systems dlv, smodels and cmodels. The first goal of this research is to evaluate the relative performance of such systems when used in a purely declarative way, using a reproducible and extensible experimental methodology. In particular, we consider a third-party problem library, i.e., the CSPLib, and uniform rules for modelling and instance selection. The second goal is to analyze the marginal effects of popular reformulation techniques on the various solving technologies. In particular, we consider structural symmetry breaking, the adoption of global constraints, and the addition of auxiliary predicates. Finally, we evaluate, on a subset of the problems, the impact of numbers and arithmetic constraints on the different solving technologies. Results show that there is not a single solver winning on all problems, and that reformulation is almost always beneficial: symmetry-breaking may be a good choice, but its complexity has to be carefully chosen, by taking into account also the particular solver used. Global constraints often, but not always, help opl, and the addition of auxiliary predicates is usually worth, especially when dealing with ASP solvers. Moreover, interesting synergies among the various modelling techniques exist.     

An efficient deconvolution algorithm for estimating oxygen consumption during muscle activities

The reconstruction of an unknown input function from noisy measurements in a biological system is an ill-posed inverse problem. Any computational algorithm for its solution must use some kind of regularization technique to neutralize the disastrous effects of amplified noise components on the computed solution. In this paper, following a hierarchical Bayesian statistical inversion approach, we seek estimates for the input function and regularization parameter (hyperparameter) that maximize the posterior probability density function. We solve the maximization problem simultaneously for all unknowns, hyperparameter included, by a suitably chosen quasi-Newton method. The optimization approach is compared to the sampling-based Bayesian approach. We demonstrate the efficiency and robustness of the deconvolution algorithm by applying it to reconstructing the time courses of mitochondrial oxygen consumption during muscle state transitions (e.g., from resting state to contraction and recovery), from the simulated noisy output of oxygen concentration dynamics on the muscle surface. The model of oxygen transport and metabolism in skeletal muscle assumes an in vitro cylindrical structure of the muscle in which the oxygen from the surrounding oxygenated solution diffuses into the muscle and is then consumed by the muscle mitochondria. The algorithm can be applied to other deconvolution problems by suitably replacing the forward model of the system.     

The multimod application framework: a rapid application development tool for computer aided medicine

This paper describes a new application framework (OpenMAF) for rapid development of multimodal applications in computer-aided medicine. MAF applications are multimodal in data, in representation, and in interaction. The framework supports almost any type of biomedical data, including DICOM datasets, motion-capture recordings, or data from computer simulations (e.g. finite element modeling). The interactive visualization approach (multimodal display) helps the user interpret complex datasets, providing multiple representations of the same data. In addition, the framework allows multimodal interaction by supporting the simultaneous use of different input-output devices like 3D trackers, stereoscopic displays, haptics hardware and speech recognition/synthesis systems. The Framework has been designed to run smoothly even on limited power computers, but it can take advantage of all hardware capabilities. The Framework is based on a collection of portable libraries and it can be compiled on any platform that supports OpenGL, including Windows, MacOS X and any flavor of Unix/linux.     

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.     

Subacute proteome changes following traumatic injury of the developing brain: Implications for a dysregulation of neuronal migration and neurite arborization

Traumatic brain injury (TBI) is a major cause of morbidity and mortality among children and adolescents. To gain insight into developmental events influenced by TBI, we analyzed subacute mouse brain proteome changes in a percussion head trauma model at P7 ipsi- and contralateral to the site of injury. The comparison of brain proteomes of trauma mice and controls revealed reproducible changes in the intensity of 28 proteins (30 protein spots) in response to trauma. The changes detected suggest that TBI leads to apoptosis, inflammation, and oxidative stress. These changes were consistent with our results of histological and biochemical evaluation of the brains which revealed widespread apoptotic neurodegeneration, microglia activation, and increased levels of protein carbonyls. Furthermore, we detected changes in proteins involved in neuronal migration as well as axonal and dendritic growth and guidance, suggesting interference of trauma with these developmental events.     

A web-based e-learning system for increasing study efficiency by stimulating learner’s motivation

Due to the opportunities provided by the Internet, more and more people are taking advantage of distance learning courses and during the last few years enormous research efforts have been dedicated to the development of distance learning systems. So far, many e-learning systems are proposed and used practically. However, in these systems the e-learning completion rate is about 30%. One of the reasons is the low study desire when the learner studies the learning materials. In this research, we propose an interactive Web-based e-learning system. The purpose of our system is to increase the e-learning completion rate by stimulating learner’s motivation. The proposed system has three subsystems: the learning subsystem, learner support subsystem, and teacher support subsystem. The learning subsystem improves the learner’s study desire. The learner support subsystem supports the learner during the study, and the teacher support subsystem supports the teacher to get the learner’s study state. To evaluate the proposed system, we developed several experiments and surveys. By using new features such as: display of learner’s study history, change of interface color, encourage function, ranking function, self-determination of the study materials, and grouping of learners, the proposed system can increase the learning efficiency.

Ambient occlusion and edge cueing to enhance real time molecular visualization

The paper presents a set of combined techniques to enhance the real-time visualization of simple or complex molecules (up to order of 106 atoms) space fill mode. The proposed approach includes an innovative technique for efficient computation and storage of ambient occlusion terms, a small set of GPU accelerated procedural impostors for space-fill and ball-and-stick rendering, and novel edge-cueing techniques. As a result, the user's understanding of the three-dimensional structure under inspection is strongly increased (even for still images), while the rendering still occurs in real time.     

‘Closed Interval Process Algebra’ versus ‘Interval Process Algebra’

Summary. In this paper we extend the theory of processes with durational actions that has been proposed in [1,2] to describe and reason about the performance of systems. We associate basic actions with lower and upper time bounds, that specify their possible different durations. Depending on how the lower and upper time bounds are fixed, eager actions (those which happen as soon as they can), lazy actions (those which can wait arbitrarily long before firing) as well as patient actions (those which can be delayed for a while) can be modelled. Processes are equipped with a (soft) operational semantics which is consistent with the original one and is well-timed (observation traces are ordered with respect to time). The bisimulation-based equivalence defined on top of the new operational semantics, timed equivalence, turns out to be a congruence and, within the lazy fragment of the algebra, refines untimed equivalences. Decidability and automatic checking of timed equivalence are also stated by resorting to a finite alternative characterization which is amenable to an automatic treatment by using standard algorithms. The relationships with other timed calculi and equivalences proposed in the literature are also established. Received: 22 May 1998 / 8 November 2000     

Reasoning about reasoning in a meta-level architecture

In this paper we discuss reasoning about reasoning in a multiple agent scenario. We consider agents that are perfect reasoners, loyal, and that can take advantage of both the knowledge and ignorance of other agents. The knowledge representation formalism we use is (full) first order predicate calculus, where different agents are represented by different theories, and reasoning about reasoning is realized via a meta-level representation of knowledge and reasoning. The framework we provide is pretty general: we illustrate it by showing a machine checked solution to the three wisemen puzzle. The agents' knowledge is organized into units: the agent's own knowledge about the world and its knowledge about other agents are units containing object-level knowledge; a unit containing meta-level knowledge embodies the reasoning about reasoning and realizes the link among units. In the paper we illustrate the meta-level architecture we propose for problem solving in a multi-agent scenario; we discuss our approach in relation to the modal one and we compare it with other meta-level architectures based on logic. Finally, we look at a class of applications that can be effectively modeled by exploiting the meta-level approach to reasoning about knowledge and reasoning.     

Bridging logic and kernel machines

We propose a general framework to incorporate first-order logic (FOL) clauses, that are thought of as an abstract and partial representation of the environment, into kernel machines that learn within a semi-supervised scheme. We rely on a multi-task learning scheme where each task is associated with a unary predicate defined on the feature space, while higher level abstract representations consist of FOL clauses made of those predicates. We re-use the kernel machine mathematical apparatus to solve the problem as primal optimization of a function composed of the loss on the supervised examples, the regularization term, and a penalty term deriving from forcing real-valued constraints deriving from the predicates. Unlike for classic kernel machines, however, depending on the logic clauses, the overall function to be optimized is not convex anymore. An important contribution is to show that while tackling the optimization by classic numerical schemes is likely to be hopeless, a stage-based learning scheme, in which we start learning the supervised examples until convergence is reached, and then continue by forcing the logic clauses is a viable direction to attack the problem. Some promising experimental results are given on artificial learning tasks and on the automatic tagging of bibtex entries to emphasize the comparison with plain kernel machines.