Hidden Markov models for the stimulus-response relationships of multistate neural systems

Given recent experimental results suggesting that neural circuits may evolve through multiple firing states, we develop a framework for estimating state-dependent neural response properties from spike train data. We modify the traditional hidden Markov model (HMM) framework to incorporate stimulus-driven, non-Poisson point-process observations. For maximal flexibility, we allow external, time-varying stimuli and the neurons' own spike histories to drive both the spiking behavior in each state and the transitioning behavior between states. We employ an appropriately modified expectation-maximization algorithm to estimate the model parameters. The expectation step is solved by the standard forward-backward algorithm for HMMs. The maximization step reduces to a set of separable concave optimization problems if the model is restricted slightly. We first test our algorithm on simulated data and are able to fully recover the parameters used to generate the data and accurately recapitulate the sequence of hidden states. We then apply our algorithm to a recently published data set in which the observed neuronal ensembles displayed multistate behavior and show that inclusion of spike history information significantly improves the fit of the model. Additionally, we show that a simple reformulation of the state space of the underlying Markov chain allows us to implement a hybrid half-multistate, half-histogram model that may be more appropriate for capturing the complexity of certain data sets than either a simple HMM or a simple peristimulus time histogram model alone.     

Accelerating scientific computations with mixed precision algorithms

On modern architectures, the performance of 32-bit operations is often at least twice as fast as the performance of 64-bit operations. By using a combination of 32-bit and 64-bit floating point arithmetic, the performance of many dense and sparse linear algebra algorithms can be significantly enhanced while maintaining the 64-bit accuracy of the resulting solution. The approach presented here can apply not only to conventional processors but also to other technologies such as Field Programmable Gate Arrays (FPGA), Graphical Processing Units (GPU), and the STI Cell BE processor. Results on modern processor architectures and the STI Cell BE are presented.

Program summary

Program title: ITER-REFCatalogue identifier: AECO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECO_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 7211No. of bytes in distributed program, including test data, etc.: 41 862Distribution format: tar.gzProgramming language: FORTRAN 77Computer: desktop, serverOperating system: Unix/LinuxRAM: 512 MbytesClassification: 4.8External routines: BLAS (optional)Nature of problem: On modern architectures, the performance of 32-bit operations is often at least twice as fast as the performance of 64-bit operations. By using a combination of 32-bit and 64-bit floating point arithmetic, the performance of many dense and sparse linear algebra algorithms can be significantly enhanced while maintaining the 64-bit accuracy of the resulting solution.Solution method: Mixed precision algorithms stem from the observation that, in many cases, a single precision solution of a problem can be refined to the point where double precision accuracy is achieved. A common approach to the solution of linear systems, either dense or sparse, is to perform the LU factorization of the coefficient matrix using Gaussian elimination. First, the coefficient matrix A is factored into the product of a lower triangular matrix L and an upper triangular matrix U. Partial row pivoting is in general used to improve numerical stability resulting in a factorization PA=LU, where P is a permutation matrix. The solution for the system is achieved by first solving Ly=Pb (forward substitution) and then solving Ux=y (backward substitution). Due to round-off errors, the computed solution, x, carries a numerical error magnified by the condition number of the coefficient matrix A. In order to improve the computed solution, an iterative process can be applied, which produces a correction to the computed solution at each iteration, which then yields the method that is commonly known as the iterative refinement algorithm. Provided that the system is not too ill-conditioned, the algorithm produces a solution correct to the working precision.Running time: seconds/minutes     

Pattern analysis of dermoscopic images based on Markov random fields

In this paper a method for detecting different patterns in dermoscopic images is presented. In order to diagnose a possible skin cancer, physicians assess the lesion based on different rules. While the most famous one is the ABCD rule (asymmetry, border, colour, diameter), the new tendency in dermatology is to classify the lesion performing a pattern analysis. Due to the colour textured appearance of these patterns, this paper presents a novel method based on Markov random field (MRF) extended for colour images that classifies images representing different dermatologic patterns. First, each image plane in L^*a^*b^* colour space is modelled as a MRF following a finite symmetric conditional model (FSCM). Coupling of colour components is taken into account by supposing that features of the MRF in the three colour planes follow a multivariate Normal distribution. Performance is analysed in different colour spaces. The best classification rate is 86% on average.     

Convolutional Sparse Coding for High Dynamic Range Imaging

Current HDR acquisition techniques are based on either (i) fusing multibracketed, low dynamic range (LDR) images, (ii) modifying existing hardware and capturing different exposures simultaneously with multiple sensors, or (iii) reconstructing a single image with spatially‐varying pixel exposures. In this paper, we propose a novel algorithm to recover high‐quality HDRI images from a single, coded exposure. The proposed reconstruction method builds on recently‐introduced ideas of convolutional sparse coding (CSC); this paper demonstrates how to make CSC practical for HDR imaging. We demonstrate that the proposed algorithm achieves higher‐quality reconstructions than alternative methods, we evaluate optical coding schemes, analyze algorithmic parameters, and build a prototype coded HDR camera that demonstrates the utility of convolutional sparse HDRI coding with a custom hardware platform.     

Integrated Data Management for a Fleet of Search‐and‐rescue Robots

Search‐and‐rescue operations have recently been confronted with the introduction of robotic tools that assist the human search‐and‐rescue workers in their dangerous but life‐saving job of searching for human survivors after major catastrophes. However, the world of search and rescue is highly reliant on strict procedures for the transfer of messages, alarms, data, and command and control over the deployed assets. The introduction of robotic tools into this world causes an important structural change in this procedural toolchain. Moreover, the introduction of search‐and‐rescue robots acting as data gatherers could potentially lead to an information overload toward the human search‐and‐rescue workers, if the data acquired by these robotic tools are not managed in an intelligent way. With that in mind, we present in this paper an integrated data combination and data management architecture that is able to accommodate real‐time data gathered by a fleet of robotic vehicles on a crisis site, and we present and publish these data in a way that is easy to understand by end‐users. In the scope of this paper, a fleet of unmanned ground and aerial search‐and‐rescue vehicles is considered, developed within the scope of the European ICARUS project. As a first step toward the integrated data‐management methodology, the different robotic systems require an interoperable framework in order to pass data from one to another and toward the unified command and control station. As a second step, a data fusion methodology will be presented, combining the data acquired by the different heterogenic robotic systems. The computation needed for this process is done in a novel mobile data center and then (as a third step) published in a software as a service (SaaS) model. The SaaS model helps in providing access to robotic data over ubiquitous Ethernet connections. As a final step, we show how the presented data‐management architecture allows for reusing recorded exercises with real robots and rescue teams for training purposes and teaching search‐and‐rescue personnel how to handle the different robotic tools. The system was validated in two experiments. First, in the controlled environment of a military testing base, a fleet of unmanned ground and aerial vehicles was deployed in an earthquake‐response scenario. The data gathered by the different interoperable robotic systems were combined by a novel mobile data center and presented to the end‐user public. Second, an unmanned aerial system was deployed on an actual mission with an international relief team to help with the relief operations after major flooding in Bosnia in the spring of 2014. Due to the nature of the event (floods), no ground vehicles were deployed here, but all data acquired by the aerial system (mainly three‐dimensional maps) were stored in the ICARUS data center, where they were securely published for authorized personnel all over the world. This mission (which is, to our knowledge, the first recorded deployment of an unmanned aerial system by an official governmental international search‐and‐rescue team in another country) proved also the concept of the procedural integration of the ICARUS data management system into the existing procedural toolchain of the search and rescue workers, and this in an international context (deployment from Belgium to Bosnia). The feedback received from the search‐and‐rescue personnel on both validation exercises was highly positive, proving that the ICARUS data management system can efficiently increase the situational awareness of the search‐and‐rescue personnel.     

Minimize the Maximum Duty in Multi-interface Networks

We consider devices equipped with multiple wired or wireless interfaces. By switching of various interfaces, each device might establish several connections. A connection is established when the devices at its endpoints share at least one active interface. Each interface is assumed to require an activation cost. In this paper, we consider two basic networking problems in the field of multi-interface networks. The first one, known as the Coverage problem, requires to establish the connections defined by a network. The second one, known as Connectivity problem, requires to guarantee a connecting path between any pair of nodes of a network. Both are subject to the constraint of keeping as low as possible the maximum cost set of active interfaces at each single node. We study the problems of minimizing the maximum cost set of active interfaces among the nodes of the network in order to cover all the edges in the first case, or to ensure connectivity in the second case. We prove that the Coverage problem is NP-hard for any fixed Δ≥5 and k≥16, with Δ being the maximum degree, and k being the number of different interfaces among the network. We also show that, unless P=NP, the problem cannot be approximated within a factor of ηln?Δ, for a certain constant η. We then provide a general approximation algorithm which guarantees a factor of O((1+b)ln?Δ), with b being a parameter depending on the topology of the input graph. Interestingly, b can be bounded by a constant for many graph classes. Other approximation and exact algorithms for special cases are presented. Concerning the Connectivity problem, we prove that it is NP-hard for any fixed Δ≥3 and k≥10. Also for this problem, the inapproximability result holds, that is, unless P=NP, the problem cannot be approximated within a factor of ηln?Δ, for a certain constant η. We then provide approximation and exact algorithms for the general problem and for special cases, respectively.     

Classification of human brain tumours from MRS data using Discrete Wavelet Transform and Bayesian Neural Networks

The diagnosis of brain tumours is an extremely sensitive and complex clinical task that must rely upon information gathered through non-invasive techniques. One such technique is Magnetic Resonance Spectroscopy. In this task, radiology experts are likely to benefit from the support of computer-based systems built around robust classification processes. In this paper, a Discrete Wavelet Transform procedure was applied to the pre-processing of spectra corresponding to several brain tumour pathologies. This procedure does not alleviate the high dimensionality of the data by itself. For this reason, dimensionality reduction was subsequently implemented using Moving Window with Variance Analysis for feature selection or Principal Component Analysis for feature extraction. The combined method yielded very encouraging results in terms of diagnostic discriminatory binary classification using Bayesian Neural Networks. In most cases, the classification accuracy improved on previously reported results.     

Cytoskeleton Elements Contribute to Prion Peptide-Induced Endothelial Barrier Breakdown in a Blood–Brain Barrier In Vitro System

The mechanisms involved in the interaction of PrP 106-126, a peptide corresponding to the prion protein amyloidogenic region, with the blood–brain barrier (BBB) were studied. PrP 106-126 treatment that was previously shown to impair BBB function, reduced cAMP levels in cultured brain endothelial cells, increased nitric oxide (NO) levels, and changed the activation mode of the small GTPases Rac1 (inactivation) and RhoA (activation). The latter are well established regulators of endothelial barrier properties that act via cytoskeletal elements. Indeed, liquid chromatography-mass spectrometry (LC-MS)-based proteomic profiling study revealed extensive changes in expression of cytoskeleton-related proteins. These results shed light on the nature of the interaction between the prion peptide PrP 106-126 and the BBB and emphasize the importance of the cytoskeleton in endothelium response to prion- induced stress.