We use the k-core decomposition to develop algorithms for the analysis of large scale complex networks. This decomposition, based on a recursive pruning of the least connected vertices, allows to disentangle the hierarchical structure of networks by progressively focusing on their central cores. By using this strategy we develop a general visualization algorithm that can be used to compare the structural properties of various networks and highlight their hierarchical structure. The low computational complexity of the algorithm, O(n e), where n is the size of the network, and e is the number of edges, makes it suitable for the visualization of very large sparse networks. We show how the proposed visualization tool allows to find specific structural fingerprints of networks.

We propose a model by which dopamine (DA) and norepinepherine (NE) combine to alternate behavior between relatively exploratory and exploitative modes. The model is developed for a target detection task for which there is extant single neuron recording data available from locus coeruleus (LC) NE neurons. An exploration-exploitation tradeoff is elicited by regularly switching which of the two stimuli are rewarded. DA functions within the model to change synaptic weights according to a reinforcement learning algorithm. Exploration is mediated by the state of LC firing, with higher tonic and lower phasic activity producing greater response variability. The opposite state of LC function, with lower baseline firing rate and greater phasic responses, favors exploitative behavior. Changes in LC firing mode result from combined measures of response conflict and reward rate, where response conflict is monitored using models of anterior cingulate cortex (ACC). Increased long-term response conflict and decreased reward rate, which occurs following reward contingency switch, favors the higher tonic state of LC function and NE release.

Diffusion Tensor Magnetic Resonance Imaging (DT-MRI) is a non invasive method for brain neuronal fibers delineation. Here we show a modification for DT-MRI that allows delineation of neuronal fibers which are infiltrated by edema. We use the Muliple Tensor Variational (MTV) framework which replaces the diffusion model of DT-MRI with a multiple component model and fits it to the signal attenuation with a variational regularization mechanism. In order to reduce free water contamination we estimate the free water compartment volume fraction in each voxel, remove it, and then calculate the anisotropy of the remaining compartment. The variational framework was applied on data collected with conventional clinical parameters, containing only six diffusion directions. By using the variational framework we were able to overcome the highly ill posed fitting. The results show that we were able to find fibers that were not found by DT-MRI.

Given a redundant dictionary of basis vectors (or atoms), our goal is to find maximally sparse representations of signals. Previously, we have argued that a sparse Bayesian learning (SBL) framework is particularly well-suited for this task, showing that it has far fewer local minima than other Bayesian-inspired strategies. In this paper, we provide further evidence for this claim by proving a restricted equivalence condition, based on the distribution of the nonzero generating model weights, whereby the SBL solution will equal the maximally sparse representation. We also prove that if these nonzero weights are drawn from an approximate Jeffreys prior, then with probability approaching one, our equivalence condition is satisfied. Finally, we motivate the worst-case scenario for SBL and demonstrate that it is still better than the most widely used sparse representation algorithms.

We propose a model by which dopamine (DA) and norepinepherine (NE) combine to alternate behavior between relatively exploratory and exploitative modes. The model is developed for a target detection task for which there is extant single neuron recording data available from locus coeruleus (LC) NE neurons. An exploration-exploitation tradeoff is elicited by regularly switching which of the two stimuli are rewarded. DA functions within the model to change synaptic weights according to a reinforcement learning algorithm. Exploration is mediated by the state of LC firing, with higher tonic and lower phasic activity producing greater response variability. The opposite state of LC function, with lower baseline firing rate and greater phasic responses, favors exploitative behavior. Changes in LC firing mode result from combined measures of response conflict and reward rate, where response conflict is monitored using models of anterior cingulate cortex (ACC). Increased long-term response conflict and decreased reward rate, which occurs following reward contingency switch, favors the higher tonic state of LC function and NE release.

Diffusion Tensor Magnetic Resonance Imaging (DT-MRI) is a non invasive method for brain neuronal fibers delineation. Here we show a modification for DT-MRI that allows delineation of neuronal fibers which are infiltrated by edema. We use the Muliple Tensor Variational (MTV) framework which replaces the diffusion model of DT-MRI with a multiple component model and fits it to the signal attenuation with a variational regularization mechanism. In order to reduce free water contamination we estimate the free water compartment volume fraction in each voxel, remove it, and then calculate the anisotropy of the remaining compartment. The variational framework was applied on data collected with conventional clinical parameters, containing only six diffusion directions. By using the variational framework we were able to overcome the highly ill posed fitting. The results show that we were able to find fibers that were not found by DT-MRI.

We use the k-core decomposition to develop algorithms for the analysis of large scale complex networks. This decomposition, based on a recursive pruning of the least connected vertices, allows to disentangle the hierarchical structure of networks by progressively focusing on their central cores. By using this strategy we develop a general visualization algorithm that can be used to compare the structural properties of various networks and highlight their hierarchical structure. The low computational complexity of the algorithm, O(n e), where n is the size of the network, and e is the number of edges, makes it suitable for the visualization of very large sparse networks. We show how the proposed visualization tool allows to find specific structural fingerprints of networks.

Current developments in molecular electronics, motors and chemical sensors could enable constructing large numbers of devices able to sense, compute and act in micron-scale environments. Such microscopic machines, of sizes comparable to bacteria, could simultaneously monitor entire populations of cells individually in vivo. This paper reviews plausible capabilities for microscopic robots and the physical constraints due to operation in fluids at low Reynolds number, diffusion-limited sensing and thermal noise from Brownian motion. Simple distributed controls are then presented in the context of prototypical biomedical tasks, which require control decisions on millisecond time scales. The resulting behaviors illustrate trade-offs among speed, accuracy and resource use. A specific example is monitoring for patterns of chemicals in a flowing fluid released at chemically distinctive sites. Information collected from a large number of such devices allows estimating properties of cell-sized chemical sources in a macroscopic volume. The microscopic devices moving with the fluid flow in small blood vessels can detect chemicals released by tissues in response to localized injury or infection. We find the devices can readily discriminate a single cell-sized chemical source from the background chemical concentration, providing high-resolution sensing in both time and space. By contrast, such a source would be difficult to distinguish from background when diluted throughout the blood volume as obtained with a blood sample.

In this paper we present pddl+, a planning domain description language for modelling mixed discrete-continuous planning domains. We describe the syntax and modelling style of pddl+, showing that the language makes convenient the modelling of complex time-dependent effects. We provide a formal semantics for pddl+ by mapping planning instances into constructs of hybrid automata. Using the syntax of HAs as our semantic model we construct a semantic mapping to labelled transition systems to complete the formal interpretation of pddl+ planning instances. An advantage of building a mapping from pddl+ to HA theory is that it forms a bridge between the Planning and Real Time Systems research communities. One consequence is that we can expect to make use of some of the theoretical properties of HAs. For example, for a restricted class of HAs the Reachability problem (which is equivalent to Plan Existence) is decidable. pddl+ provides an alternative to the continuous durative action model of pddl2.1, adding a more flexible and robust model of time-dependent behaviour.

In this paper we propose a data intensive approach for inferring sentence-internal temporal relations. Temporal inference is relevant for practical NLP applications which either extract or synthesize temporal information (e.g., summarisation, question answering). Our method bypasses the need for manual coding by exploiting the presence of markers like ``after", which overtly signal a temporal relation. We first show that models trained on main and subordinate clauses connected with a temporal marker achieve good performance on a pseudo-disambiguation task simulating temporal inference (during testing the temporal marker is treated as unseen and the models must select the right marker from a set of possible candidates). Secondly, we assess whether the proposed approach holds promise for the semi-automatic creation of temporal annotations. Specifically, we use a model trained on noisy and approximate data (i.e., main and subordinate clauses) to predict intra-sentential relations present in TimeBank, a corpus annotated rich temporal information. Our experiments compare and contrast several probabilistic models differing in their feature space, linguistic assumptions and data requirements. We evaluate performance against gold standard corpora and also against human subjects.