Maximum agreement and compatible supertrees

AbstractGiven a set of leaf-labelled trees with identical leaf sets, the MAST problem, respectively MCT problem, consists of finding a largest subset of leaves such that all input trees restricted to these leaves are isomorphic, respectively compatible. In this paper, we propose extensions of these problems to the context of supertree inference, where input trees have non-identical leaf sets. This situation is of particular interest in phylogenetics. The resulting problems are called SMAST and SMCT.A sufficient condition is given that identifies cases where these problems can be solved by resorting to MAST and MCT as subproblems. This condition is met, for instance, when only two input trees are considered. Then we give algorithms for SMAST and SMCT that benefit from the link with the subtree problems. These algorithms run in time linear to the time needed to solve MAST, respectively MCT, on an instance of the same or smaller size.It is shown that arbitrary instances of SMAST and SMCT can be turned in polynomial time into instances composed of trees with a bounded number of leaves.SMAST is shown to be W[2]-hard when the considered parameter is the number of input leaves that have to be removed to obtain the agreement of the input trees. A similar result holds for SMCT. Moreover, the corresponding optimization problems, that is the complements of SMAST and SMCT, cannot be approximated in polynomial time within any constant factor, unless P=NP. These results also hold when the input trees have a bounded number of leaves.The presented results apply to both collections of rooted and unrooted trees

FPGA-based smart camera mote for pervasive wireless network

International audienceSmart camera networks raise challenging issues in many fields of research, including vision processing, communication protocols, distributed algorithms or power management. The ever increasing resolution of image sensors entails huge amounts of data, far exceeding the bandwidth of current networks and thus forcing smart camera nodes to process raw data into useful information. Consequently, on-board processing has become a key issue for the expansion of such networked systems. In this context, FPGA-based platforms, supporting massive, fine grain data parallelism, offer large opportunities. Besides, the concept of a middleware, providing services for networking, data transfer, dynamic loading or hardware abstraction, has emerged as a means of harnessing the hardware and software complexity of smart camera nodes. In this paper, we prospect the development of a new kind of smart cameras, wherein FPGAs provide high performance processing and general purpose processors support middleware services. In this approach, FPGA devices can be reconfigured at run-time through the network both from explicit user request and transparent middleware decision. An embedded real-time operating system is in charge of the communication layer, and thus can autonomously decide to use a part of the FPGA as an available processing resource. The classical programmability issue, a significant obstacle when dealing with FPGAs, is addressed by resorting to a domain specific high-level programming language (CAPH) for describing operations to be implemented on FPGAs

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us

Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease

Design Productivity of a High Level Synthesis Compiler versus HDL

International audienceThe complexity of hardware systems is currently growing faster than the productivity of system designers and programmers. This phenomenon is called Design Productivity Gap and results in inflating design costs. In this paper, the notion of Design Productivity is precisely defined, as well as a metric to assess the Design Productivity of a High-Level Synthesis (HLS) method versus a manual hardware description. The proposed Design Productivity metric evaluates the trade-off between design efficiency and implementation quality. The method is generic enough to be used for comparing several HLS methods of different natures, opening opportunities for further progress in Design Productivity. To demonstrate the Design Productivity evaluation method, an HLS compiler based on the CAPH language is compared to manual VHDL writing. The causes that make VHDL lower level than CAPH are discussed. Versions of the sub-pixel interpolation filter from the MPEG HEVC standard are implemented and a design productivity gain of 2.3× in average is measured for the CAPH HLS method. It results from an average gain in design time of 4.4× and an average loss in quality of 1.9×

DreamCAM: A FPGA-based platform for smart camera networks

International audience—The main challenges in smart camera networks come from the limited capacity of network communications. Indeed, wireless protocols such as the IEEE 802.15.4 protocol target low data rate, low power consumption and low cost wireless networking in order to fit the requirements of sensor networks. Since nodes more and more often integrate image sensors, network bandwidth has become a strong limiting factor in application deployment. This means that data must be processed at the node level before being sent on the network. In this context, FPGA-based platforms, supporting massive data parallelism, offer large opportunities for on-board processing. We present in this paper our FPGA-based smart camera platform, called DreamCam, which is able to autonomously exchange processed information on an Ethernet network

Distributed FPGA-based smart camera architecture for computer vision applications

International audienceSmart camera networks (SCN) raise challenging issues in many fields of research, including vision processing, communication protocols, distributed algorithms or power management. Furthermore, application logic in SCN is not centralized but spread among network nodes meaning that each node must have to process images to extract significant features, and aggregate data to understand the surrounding environment. In this context, smart camera have first embedded general purpose processor (GPP) for image processing. Since image resolution increases, GPPs have reached their limit to maintain real-time processing constraint. More recently, FPGA-based platforms have been studied for their massive parallelism capabilities. This paper present our new FPGA-based smart camera platform supporting cooperation between nodes and run-time updatable image processing. The architecture is based on a full reconfigurable pipeline driven by a softcore

Using Underapproximations for Sparse Nonnegative Matrix Factorization

Nonnegative Matrix Factorization consists in (approximately) factorizing a nonnegative data matrix by the product of two low-rank nonnegative matrices. It has been successfully applied as a data analysis technique in numerous domains, e.g., text mining, image processing, microarray data analysis, collaborative filtering, etc. We introduce a novel approach to solve NMF problems, based on the use of an underapproximation technique, and show its effectiveness to obtain sparse solutions. This approach, based on Lagrangian relaxation, allows the resolution of NMF problems in a recursive fashion. We also prove that the underapproximation problem is NP-hard for any fixed factorization rank, using a reduction of the maximum edge biclique problem in bipartite graphs. We test two variants of our underapproximation approach on several standard image datasets and show that they provide sparse part-based representations with low reconstruction error. Our results are comparable and sometimes superior to those obtained by two standard Sparse Nonnegative Matrix Factorization techniques.Comment: Version 2 removed the section about convex reformulations, which was not central to the development of our main results; added material to the introduction; added a review of previous related work (section 2.3); completely rewritten the last part (section 4) to provide extensive numerical results supporting our claims. Accepted in J. of Pattern Recognitio

HOG-Dot: A Parallel Kernel-Based Gradient Extraction for Embedded Image Processing

International audienceIn this paper we propose HOG-Dot, a method for the direct computation of the polar image gradients coordinates from the pixels values. The proposed algorithm, to be used as the first step of the Histogram of Oriented Gradient (HOG) pipeline, approximates the exact gradient with its projection onto a versor chosen among the projection plane set. Instead of non linear computations, the HOG-Dot method exploits linear operations while introducing a bounded approximation error with respect to other HOG approaches, thus resulting a more suitable solution for embedded devices. Concerning the state of the art, it also achieves improved accuracy with the mathematical spatial gradient formulation

Shortcuts to adiabaticity for trapped ultracold gases

We study, experimentally and theoretically, the controlled transfer of harmonically trapped ultracold gases between different quantum states. In particular we experimentally demonstrate a fast decompression and displacement of both a non-interacting gas and an interacting Bose-Einstein condensate which are initially at equilibrium. The decompression parameters are engineered such that the final state is identical to that obtained after a perfectly adiabatic transformation despite the fact that the fast decompression is performed in the strongly non-adiabatic regime. During the transfer the atomic sample goes through strongly out-of-equilibrium states while the external confinement is modified until the system reaches the desired stationary state. The scheme is theoretically based on the invariants of motion and scaling equations techniques and can be generalized to decompression trajectories including an arbitrary deformation of the trap. It is also directly applicable to arbitrary initial non-equilibrium states.Comment: 36 pages, 14 figure