pinecone/core-2020-05-10-deduplication huggingface dataset:
Duality relations for the ASEP conditioned on a low current

We consider the asymmetric simple exclusion process (ASEP) on a finite
lattice with periodic boundary conditions, conditioned to carry an atypically
low current. For an infinite discrete set of currents, parametrized by the
driving strength $s_K$, $K \geq 1$, we prove duality relations which arise from
the quantum algebra $U_q[\mathfrak{gl}(2)]$ symmetry of the generator of the
process with reflecting boundary conditions. Using these duality relations we
prove on microscopic level a travelling-wave property of the conditioned
process for a family of shock-antishock measures for $N>K$ particles: If the
initial measure is a member of this family with $K$ microscopic shocks at
positions $(x_1,\dots,x_K)$, then the measure at any time $t>0$ of the process
with driving strength $s_K$ is a convex combination of such measures with
shocks at positions $(y_1,\dots,y_K)$. which can be expressed in terms of
$K$-particle transition probabilities of the conditioned ASEP with driving
strength $s_N$.Comment: 26 page
Performance analysis of a parallel, multi-node pipeline for DNA sequencing

Post-sequencing DNA analysis typically consists of read mapping followed by variant calling and is very time-consuming, even on a multi-core machine. Recently, we proposed Halvade, a parallel, multi-node implementation of a DNA sequencing pipeline according to the GATK Best Practices recommendations. The MapReduce programming model is used to distribute the workload among different workers. In this paper, we study the impact of different hardware configurations on the performance of Halvade. Benchmarks indicate that especially the lack of good multithreading capabilities in the existing tools (BWA, SAMtools, Picard, GATK) cause suboptimal scaling behavior. We demonstrate that it is possible to circumvent this bottleneck by using multiprocessing on high-memory machines rather than using multithreading. Using a 15-node cluster with 360 CPU cores in total, this results in a runtime of 1 h 31 min. Compared to a single-threaded runtime of similar to 12 days, this corresponds to an overall parallel efficiency of 53%
Parallelising the Computation of Minimal Absent Words

International audienceAn absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their computation also provides a fast alternative for measuring approximation in sequence comparison. There exists an O(n)-time and O(n)-space algorithm for computing all minimal absent words on a fixed-sized alphabet based on the construction of suffix array (Barton et al., 2014). An implementation of this algorithm was also provided by the authors and is currently the fastest available. In this article, we present a new O(n)-time and O(n)-space algorithm for computing all minimal absent words; it has the desirable property that, given the indexing data structure at hand, the computation of minimal absent words can be executed in parallel. Experimental results show that a mul-tiprocessing implementation of this algorithm can accelerate the overall computation by more than a factor of two compared to state-of-the-art approaches. By excluding the indexing data structure construction time, we show that the implementation achieves near-optimal speed-ups
Conflict Solution According to "Aggressiveness" of Agents in
  Floor-Field-Based Model

This contribution introduces an element of "aggressiveness" into the
Floor-Field based model with adaptive time-span. The aggressiveness is
understood as an ability to win conflicts and push through the crowd. From
experiments it is observed that this ability is not directly correlated with
the desired velocity in the free flow regime. The influence of the
aggressiveness is studied by means of the dependence of the travel time on the
occupancy of a room. A simulation study shows that the conflict solution based
on the aggressiveness parameter can mimic the observations from the experiment.Comment: Submitted to LNCS (Springer), In proceedings of 11th international
  conference on Parallel Processing and Applied Mathematic
The Internet of Things : promise of a better connected world

The progressive adoption of Internet-enabled devices and technologies may yield significant social and economic benefits for countries, organisations and individuals able to leverage the enhanced communication, integration, and data synthesis capabilities lauded for these developments. This chapter considers the varieties of application that are emerging and discusses the likely merits and demerits of such progress. Although the technological advances seem to be inevitable, the economic and social benefits are less assured. In particular, issues of availability, security, and privacy raise prospective concerns that may curtail the ultimate gains from the Internet of Things
What is the 'minimum inhibitory concentration' (MIC) of pexiganan acting
  on Escherichia coli? - A cautionary case study

We measured the minimum inhibitory concentration (MIC) of the antimicrobial
peptide pexiganan acting on Escherichia coli, and report an intrinsic
variability in such measurements. These results led to a detailed study of the
effect of pexiganan on the growth curve of E. coli, using a plate reader and
manual plating (i.e. time-kill curves). The measured growth curves, together
with single-cell observations and peptide depletion assays, suggested that
addition of a sub-MIC concentration of pexiganan to a population of this
bacterium killed a fraction of the cells, reducing peptide activity during the
process, while leaving the remaining cells unaffected. This pharmacodynamic
hypothesis suggests a considerable inoculum effect, which we quantified. Our
results cast doubt on the use of the MIC as 'a measure of the concentration
needed for peptide action' and show how 'coarse-grained' studies at the
population level give vital information for the correct planning and
interpretation of MIC measurements.Comment: 17 pages, 5 figure
Optimization of modular wiring harnesses by means of regression models for temperature prediction of wire bundles

Automotive wiring harnesses have become heavier and more complex due to their increasing number of electrical components. It is now desired to reduce their mass of copper. For this purpose, experimentation can be partially replaced by simulation, but it is still impossible to exhaustively simulate all of the combinations of modular wiring harness. This proposed approach consists of carrying out simulations using the FEM method and using their results to create regression models. Polynomial formulae can give the same information as simulations within a clearly reduced time and satisfying accuracy. An optimization algorithm introduced in this study will use them to assign new cable cross-sections of harnesses considering their currents and the ambient temperature.Postprint (author's final draft
Parallelization Strategy for Elementary Morphological Operators on Graphs

International audienceThis article focuses on the graph-based mathematical morphology operators presented in [J. Cousty et al, Morphological ltering on graphs, CVIU 2013]. These operators depend on a size parameter that species the number of iterations of elementary dilations/erosions. Thus, the associated running times increase with the size parameter. In this article, we present distance maps that allow us to recover (by thresh-olding) all considered dilations and erosions. The algorithms based on distance maps allow the operators to be computed with a single linear-time iteration, without any dependence to the size parameter. Then, we investigate a parallelization strategy to compute these distance maps. The idea is to build iteratively the successive level-sets of the distance maps, each level set being traversed in parallel. Under some reasonable assumptions about the graph and sets to be dilated, our parallel algorithm runs in O(n/p + K log 2 p) where n, p, and K are the size of the graph, the number of available processors, and the number of distinct level-sets of the distance map, respectively
Bijective rigid motions of the 2D Cartesian grid

International audienceRigid motions are fundamental operations in image processing. While they are bijective and isometric in R^2, they lose these properties when digitized in Z^2. To investigate these defects, we first extend a combinatorial model of the local behavior of rigid motions on Z^2, initially proposed by Nouvel and Rémila for rotations on Z^2. This allows us to study bijective rigid motions on Z^2, and to propose two algorithms for verifying whether a given rigid motion restricted to a given finite subset of Z^2 is bijective
Representation of Imprecise Digital Objects

International audienceIn this paper, we investigate a new framework to handle noisy digital objects. We consider digital closed simple 4-connected curves that are the result of an imperfect digital conversion (scan, picture, etc), and call digital imprecise contours such curves for which an imprecision value is known at each point. This imprecision value stands for the radius of a ball around each point, such that the result of a perfect digitization lies in the union of all the balls. In the first part, we show how to define an imprecise digital object from such an imprecise digital contour. To do so, we define three classes of pixels : inside, outside and uncertain pixels. In the second part of the paper, we build on this definition for a volumetric analysis (as opposed to contour analysis) of imprecise digital objects. From so-called toleranced balls, a filtration of objects, called λ-objects is defined. We show how to define a set of sites to encode this filtration of objects
General Formula for Event-Based Stabilization of Nonlinear Systems with Delays in the State

International audienceIn this chapter, a universal formula is proposed for event-based stabilization of nonlinear systems affine in the control and with delays in the state. The feedback is derived from the seminal law proposed by E. Sontag (1989) and then extended to event-based control of affine nonlinear undelayed systems. Under the assumption of the existence of a control Lyapunov-Krasovskii functional (CLKF), the proposal enables smooth (except at the origin) asymptotic stabilization while ensuring that the sampling intervals do not contract to zero. Global asymptotic stability is obtained under the small control property assumption. Moreover, the control can be proved to be smooth anywhere under certain conditions. Simulation results highlight the ability of the proposed formula. The particular linear case is also discussed
Automated Analysis of Asynchronously Communicating Systems

International audienceAnalyzing systems communicating asynchronously via reliable FIFO buffers is an undecidable problem. A typical approach is to check whether the system is bounded, and if not, the corresponding state space can be made finite by limiting the presence of communication cycles in behavioral models or by fixing the buffer size. In this paper, our focus is on systems that are likely to be unbounded and therefore result in infinite systems. We do not want to restrict the system by imposing any arbitrary bound. We introduce a notion of stability and prove thatonce the system is stable for a specific buffer bound, it remains stable whatever larger bounds are chosen for buffers. This enables one to check certain properties on the system for that bound and to ensure that the system will preserve them whatever larger bounds are used for buffers. We also prove that computing this bound is undecidable but we show how we succeed in computing these bounds for many examples using heuristics and equivalence checking
On-the-Fly Model Checking for Extended Action-Based Probabilistic Operators

International audienceThe quantitative analysis of concurrent systems requires expressive and user-friendly property languages combining temporal, data-handling, and quantitative aspects. In this paper, we aim at facilitating the quantitative analysis of systems modeled as PTSs (Probabilistic Transition Systems) labeled by actions containing data values and probabilities. We propose a new regular probabilistic operator that computes the probability measure of a path specified by a generalized regular formula involving arbitrary computations on data values. This operator, which subsumes the Until operators of PCTL and their action-based counterparts, can provide useful quantitative information about paths having certain (e.g., peak) cost values. We integrated the regular probabilistic operator into MCL (Model Checking Language) and we devised an associated on-the-fly model checking method, based on a combined local resolution of linear and Boolean equation systems. We implemented the method in the EVALUATOR model checker of the CADP toolbox and experimented it on realistic PTSs modeling concurrent systems
Autonomous agent behaviour modelled in PRISM -- a case study

This work was supported by the Engineering and Physical Sciences Research Council [grant number EP/N508792/1].Formal verification of agents representing robot behaviour is a growing area due to the demand that autonomous systems have to be proven safe. In this paper we present an abstract definition of autonomy which can be used to model autonomous scenarios and propose the use of small-scale simulation models representing abstract actions to infer quantitative data. To demonstrate the applicability of the approach we build and verify a model of an unmanned aerial vehicle (UAV) in an exemplary autonomous scenario, utilising this approach.Publisher PD
Superpixel quality in microscopy images: the impact of noise & denoising

Microscopy is a valuable imaging tool in various biomedical research areas. Recent developments have made high resolution acquisition possible within a relatively short time. State-of-the-art imaging equipment such as serial block-face electron microscopes acquire gigabytes of data in a matter of hours. In order to make these amounts of data manageable, a more data-efficient representation is required. A popular approach for such data efficiency are superpixels which are designed to cluster homogeneous regions without crossing object boundaries. The use of superpixels as a pre-processing step has shown significant improvements in making computationally intensive computer vision analysis algorithms more tractable on large amounts of data. However, microscopy datasets in particular can be degraded by noise and most superpixel algorithms do not take this artifact into account. In this paper, we give a quantitative and qualitative comparison of superpixels generated on original and denoised images. We show that several advanced superpixel techniques are hampered by noise artifacts and require denoising and parameter tuning as a pre-processing step. The evaluation is performed on the Berkeley segmentation dataset as well as on fluorescence and scanning electron microscopy data
An overview of quantitative magnetic resonance imaging analysis studies in the assessment of alzheimer’s disease

Medical image analysis and visualization, can contribute in quantitative and qualitative analysis of Magnetic Resonance Imaging (MRI) towards an earlier diagnosis of Alzheimer’s disease (AD). Moreover, the early detection of Mild Cognitive Impairment (MCI) has recently attracted a lot of attention. The main objective of this paper is to present a survey of recent key papers focused on the classification of MCI and AD and the prediction of conversion from MCI to AD using volume, shape and texture analysis. The most frequent anatomical features used in the assessment of AD, is the hippocampus, the cortex and the local concentration of grey matter. Shape analysis can identify the signs of early hippocampal atrophy, whereas volume analysis evaluates the structure as a whole. Shape analysis seems to be a more accurate technique both in classification of patients and in prognostic prediction. Compared to volume, shape and voxel based morphometry (VBM) techniques, texture analysis can be used to identify the microstructural changes before the larger-scale morphological characteristics which are detected by the other aforementioned techniques. We concluded that quantitative MRI measurements can be used as an in vivo surrogate for the classification of patients and furthermore, for the tracking the Alzheimer’s disease progression
Determining the optimal site for imaging the microcirculation in neonates using sidestream dark – field imaging

Sidestream dark field (SDF) spectral imaging has been used to take pictures of capillaries within the skin. The most common location to place the SDF is the mucosa area in the mouth. However, in neonates the sublingual area is not easily accessible, thus an optimal location on the skin should be found. This feasibility study aims to determine the optimal site, out of five body areas on the neonate from which to obtain image of capillary microcirculation. These preliminary results indicate that the chest wall can be considered as the optimal measurement location on the skin when using the SDF modality
Geometry and iPads in Primary Schools: Does Their Usefulness Extend Beyond Tracing an Oblong?

Although research into the use of mathematics apps in classrooms is becoming more common, robust research into Geometry apps is still in its infancy. Such research is particularly necessary in the case of Geometry apps where accurate and dynamic representations are critical in enhancing mathematical learning. This chapter begins to address the lack of research in this domain and presents findings from a qualitative and quantitative analysis of 53 Geometry apps initially selected from a broader range of apps available at the iTunes App Store. These findings indicate that the majority of the 53 apps were limited in their ability to assist students in developing Geometrical conceptual understanding. While this is of concern to educators there are, however, a small number of Geometry apps which would be most useful in teaching Geometry to primary aged students.Arts, Education & Law Group, School of Education and Professional StudiesFull Tex
Exploiting structure in floating-point arithmetic

Invited paper - MACIS 2015 (Sixth International Conference on Mathematical Aspects of Computer and Information Sciences)International audienceThe analysis of algorithms in IEEE floating-point arithmetic is most often carried out via repeated applications of the so-called standard model, which bounds the relative error of each basic operation by a common epsilon depending only on the format. While this approach has been eminently useful for establishing many accuracy and stability results, it fails to capture most of the low-level features that make floating-point arithmetic so highly structured. In this paper, we survey some of those properties and how to exploit them in rounding error analysis. In particular, we review some recent improvements of several classical, Wilkinson-style error bounds from linear algebra and complex arithmetic that all rely on such structure properties
E-commerce development risk evaluation using MCDM techniques

© Springer International Publishing Switzerland 2016. Electronic commerce (EC) development takes place in a complex and dynamic environment that includes high levels of risk and uncertainty. This paper proposes a new method for assessing the risks associated with EC development using multi-criteria decision-making techniques A model based on the analytic hierarchy process (AHP) and the technique for order of preference by similarity to ideal solution (TOPSIS) is proposed to assist EC project managers and decision makers in formalizing the types of thinking that are required in assessing the current risk environment of their EC development in a more systematic manner than previously. The solution includes the use of AHP for analyzing the problem structure and determining the weights of risk factors. The TOPSIS technique helps to obtain a final ranking among projects, and the results of an evaluation show the usefulness performance of the method
A Knowledge Based System for Supporting Sustainable Industrial Management in a Clothes Manufacturing Company Based on a Data Fusion Model

In this paper we propose a knowledge based system (KBS), based on smart objects and a data fusion model to support industrial management decision making applied to a clothes manufacturing enterprise. The management processes cover factory-production levels to higher decision-making levels. Therefore, the proposed KBS contributes to solving different kind of decision problems, including factory supervision, production planning and control, productivity management, real-time monitoring, and data acquisition and processing. The web access via different middleware devices and tools at different process levels, along with the use of integrated algorithms, decision methods, and smart objects, promote an optimized use of knowledge and resources. In this paper the proposed KBS is introduced and an example of its use is illustrated with an example of a clothes manufacturing resources selection, using the embedded dynamic multi-criteria fusion model.This work was supported by FCT “Fundação para a Ciência e a Tecnologia” under the program: PEST2015-2020, reference: UID/CEC/00319/2013.info:eu-repo/semantics/publishedVersio
The university as a site of socialisation for sustainability education

This chapter reports on an innovative approach to in-service teacher education focusing on Education for Sustainable Development (ESD) aimed at faculty in a UK university. Building on the underpinning philosophies that characterise sustainability education: participation, experiential learning and authenticity, a module on ESD was designed which at first flipped and then moved beyond the classroom. An online resource was developed to house the necessary declarative content which student-teachers accessed before the class. Class time was then spent within deliberative, dialogic and ‘walkabout’ learning spaces. These included a critically informed tour of the university campus and community exploring the ‘unseen university’, following energy and waste processes, evaluating accessibility and inclusivity and considering the university as an example of an organisation in transition. They also afforded the opportunity for student-teachers to meet key sustainability individuals from procurement, estates, marketing and finances, as well as curriculum champions and of course students themselves. Discussions took place in boiler rooms, on stairwells, in coffee shops and in parks. Following an action research strategy for change leadership, student-teachers collaboratively and critically dissected these experiences and negotiated assignments which were not only informed by these experiences but that sought to address specific sustainability needs identified on our journeying through the university as a manifold learning space. At the end of the course, student-teachers used the UNECE (2012) framework for Competences in Education for Sustainable Development to assess what had been learnt and where to focus ongoing CPD. The course has proved popular in its home institution and has been showcased as an example of good practice by the European Communion through their ‘Lifelong Learning Programme’ (Mader et al. 2014)