A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Probabilistic Shaping for Finite Blocklengths: Distribution Matching and Sphere Shaping

In this paper, we provide for the first time a systematic comparison of distribution matching (DM) and sphere shaping (SpSh) algorithms for short blocklength probabilistic amplitude shaping. For asymptotically large blocklengths, constant composition distribution matching (CCDM) is known to generate the target capacity-achieving distribution. As the blocklength decreases, however, the resulting rate loss diminishes the efficiency of CCDM. We claim that for such short blocklengths and over the additive white Gaussian channel (AWGN), the objective of shaping should be reformulated as obtaining the most energy-efficient signal space for a given rate (rather than matching distributions). In light of this interpretation, multiset-partition DM (MPDM), enumerative sphere shaping (ESS) and shell mapping (SM), are reviewed as energy-efficient shaping techniques. Numerical results show that MPDM and SpSh have smaller rate losses than CCDM. SpSh--whose sole objective is to maximize the energy efficiency--is shown to have the minimum rate loss amongst all. We provide simulation results of the end-to-end decoding performance showing that up to 1 dB improvement in power efficiency over uniform signaling can be obtained with MPDM and SpSh at blocklengths around 200. Finally, we present a discussion on the complexity of these algorithms from the perspective of latency, storage and computations.Comment: 18 pages, 10 figure

Dataplane Specialization for High-performance OpenFlow Software Switching

OpenFlow is an amazingly expressive dataplane program- ming language, but this expressiveness comes at a severe performance price as switches must do excessive packet clas- sification in the fast path. The prevalent OpenFlow software switch architecture is therefore built on flow caching, but this imposes intricate limitations on the workloads that can be supported efficiently and may even open the door to mali- cious cache overflow attacks. In this paper we argue that in- stead of enforcing the same universal flow cache semantics to all OpenFlow applications and optimize for the common case, a switch should rather automatically specialize its dat- aplane piecemeal with respect to the configured workload. We introduce ES WITCH , a novel switch architecture that uses on-the-fly template-based code generation to compile any OpenFlow pipeline into efficient machine code, which can then be readily used as fast path. We present a proof- of-concept prototype and we demonstrate on illustrative use cases that ES WITCH yields a simpler architecture, superior packet processing speed, improved latency and CPU scala- bility, and predictable performance. Our prototype can eas- ily scale beyond 100 Gbps on a single Intel blade even with complex OpenFlow pipelines

Entropy-based parametric estimation of spike train statistics

We consider the evolution of a network of neurons, focusing on the asymptotic behavior of spikes dynamics instead of membrane potential dynamics. The spike response is not sought as a deterministic response in this context, but as a conditional probability : "Reading out the code" consists of inferring such a probability. This probability is computed from empirical raster plots, by using the framework of thermodynamic formalism in ergodic theory. This gives us a parametric statistical model where the probability has the form of a Gibbs distribution. In this respect, this approach generalizes the seminal and profound work of Schneidman and collaborators. A minimal presentation of the formalism is reviewed here, while a general algorithmic estimation method is proposed yielding fast convergent implementations. It is also made explicit how several spike observables (entropy, rate, synchronizations, correlations) are given in closed-form from the parametric estimation. This paradigm does not only allow us to estimate the spike statistics, given a design choice, but also to compare different models, thus answering comparative questions about the neural code such as : "are correlations (or time synchrony or a given set of spike patterns, ..) significant with respect to rate coding only ?" A numerical validation of the method is proposed and the perspectives regarding spike-train code analysis are also discussed.Comment: 37 pages, 8 figures, submitte

Gunrock: GPU Graph Analytics

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs, have presented two significant challenges to developing a programmable high-performance graph library. "Gunrock", our graph-processing system designed specifically for the GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on operations on a vertex or edge frontier. Gunrock achieves a balance between performance and expressiveness by coupling high performance GPU computing primitives and optimization strategies with a high-level programming model that allows programmers to quickly develop new graph primitives with small code size and minimal GPU programming knowledge. We characterize the performance of various optimization strategies and evaluate Gunrock's overall performance on different GPU architectures on a wide range of graph primitives that span from traversal-based algorithms and ranking algorithms, to triangle counting and bipartite-graph-based algorithms. The results show that on a single GPU, Gunrock has on average at least an order of magnitude speedup over Boost and PowerGraph, comparable performance to the fastest GPU hardwired primitives and CPU shared-memory graph libraries such as Ligra and Galois, and better performance than any other GPU high-level graph library.Comment: 52 pages, invited paper to ACM Transactions on Parallel Computing (TOPC), an extended version of PPoPP'16 paper "Gunrock: A High-Performance Graph Processing Library on the GPU

A Light-Weight Forwarding Plane for Content-Centric Networks

We present CCN-DART, a more efficient forwarding approach for content-centric networking (CCN) than named data networking (NDN) that substitutes Pending Interest Tables (PIT) with Data Answer Routing Tables (DART) and uses a novel approach to eliminate forwarding loops. The forwarding state required at each router using CCN-DART consists of segments of the routes between consumers and content providers that traverse a content router, rather than the Interests that the router forwards towards content providers. Accordingly, the size of a DART is proportional to the number of routes used by Interests traversing a router, rather than the number of Interests traversing a router. We show that CCN-DART avoids forwarding loops by comparing distances to name prefixes reported by neighbors, even when routing loops exist. Results of simulation experiments comparing CCN-DART with NDN using the ndnSIM simulation tool show that CCN-DART incurs 10 to 20 times less storage overhead