Laboratoire Bordelais de Recherche en Informatique

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

OBJECTIVE: Most current electroencephalography (EEG)-based brain-computer interfaces (BCIs) are based on machine learning algorithms. There is a large diversity of classifier types that are used in this field, as described in our 2007 review paper. Now, approximately ten years after this review publication, many new algorithms have been developed and tested to classify EEG signals in BCIs. The time is therefore ripe for an updated review of EEG classification algorithms for BCIs. APPROACH: We surveyed the BCI and machine learning literature from 2007 to 2017 to identify the new classification approaches that have been investigated to design BCIs. We synthesize these studies in order to present such algorithms, to report how they were used for BCIs, what were the outcomes, and to identify their pros and cons. MAIN RESULTS: We found that the recently designed classification algorithms for EEG-based BCIs can be divided into four main categories: adaptive classifiers, matrix and tensor classifiers, transfer learning and deep learning, plus a few other miscellaneous classifiers. Among these, adaptive classifiers were demonstrated to be generally superior to static ones, even with unsupervised adaptation. Transfer learning can also prove useful although the benefits of transfer learning remain unpredictable. Riemannian geometry-based methods have reached state-of-the-art performances on multiple BCI problems and deserve to be explored more thoroughly, along with tensor-based methods. Shrinkage linear discriminant analysis and random forests also appear particularly useful for small training samples settings. On the other hand, deep learning methods have not yet shown convincing improvement over state-of-the-art BCI methods. SIGNIFICANCE: This paper provides a comprehensive overview of the modern classification algorithms used in EEG-based BCIs, presents the principles of these methods and guidelines on when and how to use them. It also identifies a number of challenges to further advance EEG classification in BCI.

Abstract In the field of HPC, the current hardware trend is to design multiprocessor architectures featuring heterogeneous technologies such as specialized coprocessors (e.g. Cell/BE) or data‐parallel accelerators (e.g. GPUs). Approaching the theoretical performance of these architectures is a complex issue. Indeed, substantial efforts have already been devoted to efficiently offload parts of the computations. However, designing an execution model that unifies all computing units and associated embedded memory remains a main challenge. We therefore designed StarPU, an original runtime system providing a high‐level, unified execution model tightly coupled with an expressive data management library. The main goal of StarPU is to provide numerical kernel designers with a convenient way to generate parallel tasks over heterogeneous hardware on the one hand, and easily develop and tune powerful scheduling algorithms on the other hand. We have developed several strategies that can be selected seamlessly at run‐time, and we have analyzed their efficiency on several algorithms running simultaneously over multiple cores and a GPU. In addition to substantial improvements regarding execution times, we have obtained consistent superlinear parallelism by actually exploiting the heterogeneous nature of the machine. We eventually show that our dynamic approach competes with the highly optimized MAGMA library and overcomes the limitations of the corresponding static scheduling in a portable way. Copyright © 2010 John Wiley & Sons, Ltd.

Pervasive growth of Internet of Things (IoT) is visible across the globe. The 2016 Dyn cyberattack exposed the critical fault-lines among smart networks. Security of IoT has become a critical concern. The danger exposed by infested Internet-connected Things not only affects the security of IoT but also threatens the complete Internet eco-system which can possibly exploit the vulnerable Things (smart devices) deployed as botnets. Mirai malware compromised the video surveillance devices and paralyzed Internet via distributed denial of service attacks. In the recent past, security attack vectors have evolved bothways, in terms of complexity and diversity. Hence, to identify and prevent or detect novel attacks, it is important to analyze techniques in IoT context. This survey classifies the IoT security threats and challenges for IoT networks by evaluating existing defense techniques. Our main focus is on network intrusion detection systems (NIDSs); hence, this paper reviews existing NIDS implementation tools and datasets as well as free and open-source network sniffing software. Then, it surveys, analyzes, and compares state-of-the-art NIDS proposals in the IoT context in terms of architecture, detection methodologies, validation strategies, treated threats, and algorithm deployments. The review deals with both traditional and machine learning (ML) NIDS techniques and discusses future directions. In this survey, our focus is on IoT NIDS deployed via ML since learning algorithms have a good success rate in security and privacy. The survey provides a comprehensive review of NIDSs deploying different aspects of learning techniques for IoT, unlike other top surveys targeting the traditional systems. We believe that, this paper will be useful for academia and industry research, first, to identify IoT threats and challenges, second, to implement their own NIDS and finally to propose new smart techniques in IoT context considering IoT limitations. Moreover, the survey will enable security individuals differentiate IoT NIDS from traditional ones.

We introduce a novel method for 3D object detection and pose estimation from color images only. We first use segmentation to detect the objects of interest in 2D even in presence of partial occlusions and cluttered background. By contrast with recent patch-based methods, we rely on a “holistic” approach: We apply to the detected objects a Convolutional Neural Network (CNN) trained to predict their 3D poses in the form of 2D projections of the corners of their 3D bounding boxes. This, however, is not sufficient for handling objects from the recent T-LESS dataset: These objects exhibit an axis of rotational symmetry, and the similarity of two images of such an object under two different poses makes training the CNN challenging. We solve this problem by restricting the range of poses used for training, and by introducing a classifier to identify the range of a pose at run-time before estimating it. We also use an optional additional step that refines the predicted poses. We improve the state-of-the-art on the LINEMOD dataset from 73.7% [2] to 89.3% of correctly registered RGB frames. We are also the first to report results on the Occlusion dataset [1] using color images only. We obtain 54% of frames passing the Pose 6D criterion on average on several sequences of the T-LESS dataset, compared to the 67% of the state-of-the-art [10] on the same sequences which uses both color and depth. The full approach is also scalable, as a single network can be trained for multiple objects simultaneously.

The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results.

At the heart of software evolution is a sequence of edit actions, called an edit script, made to a source code file. Since software systems are stored version by version, the edit script has to be computed from these versions, which is known as a complex task. Existing approaches usually compute edit scripts at the text granularity with only add line and delete line actions. However, inferring syntactic changes from such an edit script is hard. Since moving code is a frequent action performed when editing code, it should also be taken into account. In this paper, we tackle these issues by introducing an algorithm computing edit scripts at the abstract syntax tree granularity including move actions. Our objective is to compute edit scripts that are short and close to the original developer intent. Our algorithm is implemented in a freely-available and extensible tool that has been intensively validated.

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

Large scale distributed systems such as Grids are difficult to study from theoretical models and simulators only. Most Grids deployed at large scale are production platforms that are inappropriate research tools because of their limited reconfiguration, control and monitoring capabilities. In this paper, we present Grid'5000, a 5000 CPU nation-wide infrastructure for research in Grid computing. Grid'5000 is designed to provide a scientific tool for computer scientists similar to the large-scale instruments used by physicists, astronomers, and biologists. We describe the motivations, design considerations, architecture, control, and monitoring infrastructure of this experimental platform. We present configuration examples and performance results for the reconfiguration subsystem.

Diffusion Weighted Images (DWI) normally shows a low Signal to Noise Ratio (SNR) due to the presence of noise from the measurement process that complicates and biases the estimation of quantitative diffusion parameters. In this paper, a new denoising methodology is proposed that takes into consideration the multicomponent nature of multi-directional DWI datasets such as those employed in diffusion imaging. This new filter reduces random noise in multicomponent DWI by locally shrinking less significant Principal Components using an overcomplete approach. The proposed method is compared with state-of-the-art methods using synthetic and real clinical MR images, showing improved performance in terms of denoising quality and estimation of diffusion parameters.

Abstract: A new BRDF model is presented which can be viewed as an kind of intermediary model between empirism and theory. Main results of physics are observed (energy conservation, reciprocity rule, microfacet theory) and numerous phenomena involved in light reflection are accounted for, in a physically plausible way (incoherent and coherent reflection, spectrum modifications, anisotropy, self‐shadowing, multiple surface and subsurface reflection, differences between homogeneous and heterogeneous materials). The model has been especially intended for computer graphics applications and therefore includes two main features: simplicity (a small number of intuitively understandable parameters controls the model) and efficiency (the formulation provides adequation to Monte‐Carlo rendering techniques and/or hardware implementations).

Neurofeedback has begun to attract the attention and scrutiny of the scientific and medical mainstream. Here, neurofeedback researchers present a consensus-derived checklist that aims to improve the reporting and experimental design standards in the field.

The increasing numbers of cores, shared caches and memory nodes within machines introduces a complex hardware topology. High-performance computing applications now have to carefully adapt their placement and behavior according to the underlying hierarchy of hardware resources and their software affinities. We introduce the Hardware Locality (hwloc) software which gathers hardware information about processors, caches, memory nodes and more, and exposes it to applications and runtime systems in a abstracted and portable hierarchical manner. hwloc may significantly help performance by having runtime systems place their tasks or adapt their communication strategies depending on hardware affinities. We show that hwloc can already be used by popular high-performance OpenMP or MPI software. Indeed, scheduling OpenMP threads according to their affinities or placing MPI processes according to their communication patterns shows interesting performance improvement thanks to hwloc. An optimized MPI communication strategy may also be dynamically chosen according to the location of the communicating processes in the machine and its hardware characteristics.

Brain-computer interaction has already moved from assistive care to applications such as gaming. Improvements in usability, hardware, signal processing, and system integration should yield applications in other nonmedical areas.

Remorins (REMs) are proteins of unknown function specific to vascular plants. We have used imaging and biochemical approaches and in situ labeling to demonstrate that REM clusters at plasmodesmata and in approximately 70-nm membrane domains, similar to lipid rafts, in the cytosolic leaflet of the plasma membrane. From a manipulation of REM levels in transgenic tomato (Solanum lycopersicum) plants, we show that Potato virus X (PVX) movement is inversely related to REM accumulation. We show that REM can interact physically with the movement protein TRIPLE GENE BLOCK PROTEIN1 from PVX. Based on the localization of REM and its impact on virus macromolecular trafficking, we discuss the potential for lipid rafts to act as functional components in plasmodesmata and the plasma membrane.

We discuss a generalization of partitions, called overpartitions, which have proven useful in several combinatorial studies of basic hypergeometric series. After showing how a number of finite products occurring in <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="q"> <mml:semantics> <mml:mi>q</mml:mi> <mml:annotation encoding="application/x-tex">q</mml:annotation> </mml:semantics> </mml:math> </inline-formula> -series have natural interpretations in terms of overpartitions, we present an introduction to their rich structure as revealed by <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="q"> <mml:semantics> <mml:mi>q</mml:mi> <mml:annotation encoding="application/x-tex">q</mml:annotation> </mml:semantics> </mml:math> </inline-formula> -series identities.

International audience

This article proposes a surprisingly simple framework for the random generation of combinatorial configurations based on what we call Boltzmann models . The idea is to perform random generation of possibly complex structured objects by placing an appropriate measure spread over the whole of a combinatorial class – an object receives a probability essentially proportional to an exponential of its size. As demonstrated here, the resulting algorithms based on real-arithmetic operations often operate in linear time. They can be implemented easily, be analysed mathematically with great precision, and, when suitably tuned, tend to be very efficient in practice.

New high-performance computing system designs with steeply escalating processor and core counts, burgeoning heterogeneity and accelerators, and increasingly unpredictable memory access times call for one or more dramatically new programming paradigms. These new approaches must react and adapt quickly to unexpected contentions and delays, and they must provide the execution environment with sufficient intelligence and flexibility to rearrange the execution to improve resource utilization. The authors present an approach based on task parallelism that reveals the application's parallelism by expressing its algorithm as a task flow. This strategy allows the algorithm to be decoupled from the data distribution and the underlying hardware, since the algorithm is entirely expressed as flows of data. This kind of layering provides a clear separation of concerns among architecture, algorithm, and data distribution. Developers benefit from this separation because they can focus solely on the algorithmic level without the constraints involved with programming for current and future hardware trends.

While recent research on Brain-Computer Interfaces (BCI) has highlighted their potential for many applications, they remain barely used outside laboratories. The main reason is their lack of robustness. Indeed, with current BCI, mental state recognition is usually slow and often incorrect. Spontaneous BCI (i.e., mental imagery-based BCI) often rely on mutual learning efforts by the user and the machine, with BCI users learning to produce stable ElectroEncephaloGraphy (EEG) patterns (spontaneous BCI control being widely acknowledged as a skill) while the computer learns to automatically recognize these EEG patterns, using signal processing. Most research so far was focused on signal processing, mostly neglecting the human in the loop. However, how well the user masters the BCI skill is also a key element explaining BCI robustness. Indeed, if the user is not able to produce stable and distinct EEG patterns, then no signal processing algorithm would be able to recognize them. Unfortunately, despite the importance of BCI training protocols, they have been scarcely studied so far, and used mostly unchanged for years. In this paper, we advocate that current human training approaches for spontaneous BCI are most likely inappropriate. We notably study instructional design literature in order to identify the key requirements and guidelines for a successful training procedure that promotes a good and efficient skill learning. This literature study highlights that current spontaneous BCI user training procedures satisfy very few of these requirements and hence are likely to be suboptimal. We therefore identify the flaws in BCI training protocols according to instructional design principles, at several levels: in the instructions provided to the user, in the tasks he/she has to perform, and in the feedback provided. For each level, we propose new research directions that are theoretically expected to address some of these flaws and to help users learn the BCI skill more efficiently.