PZnet: Efficient 3D ConvNet Inference on Manycore CPUs

Convolutional nets have been shown to achieve state-of-the-art accuracy in many biomedical image analysis tasks. Many tasks within biomedical analysis domain involve analyzing volumetric (3D) data acquired by CT, MRI and Microscopy acquisition methods. To deploy convolutional nets in practical working systems, it is important to solve the efficient inference problem. Namely, one should be able to apply an already-trained convolutional network to many large images using limited computational resources. In this paper we present PZnet, a CPU-only engine that can be used to perform inference for a variety of 3D convolutional net architectures. PZNet outperforms MKL-based CPU implementations of PyTorch and Tensorflow by more than 3.5x for the popular U-net architecture. Moreover, for 3D convolutions with low featuremap numbers, cloud CPU inference with PZnet outperfroms cloud GPU inference in terms of cost efficiency

From Self-Interpreters to Normalization by Evaluation

We characterize normalization by evaluation as the composition of a self-interpreter with a self-reducer using a special representation scheme, in the sense of Mogensen (1992). We do so by deriving in a systematic way an untyped normalization by evaluation algorithm from a standard interpreter for the ?-calculus. The derived algorithm is not novel and indeed other published algorithms may be obtained in the same manner through appropriate adaptations to the representation scheme

maigesPack: A Computational Environment for Microarray Data Analysis

Microarray technology is still an important way to assess gene expression in molecular biology, mainly because it measures expression profiles for thousands of genes simultaneously, what makes this technology a good option for some studies focused on systems biology. One of its main problem is complexity of experimental procedure, presenting several sources of variability, hindering statistical modeling. So far, there is no standard protocol for generation and evaluation of microarray data. To mitigate the analysis process this paper presents an R package, named maigesPack, that helps with data organization. Besides that, it makes data analysis process more robust, reliable and reproducible. Also, maigesPack aggregates several data analysis procedures reported in literature, for instance: cluster analysis, differential expression, supervised classifiers, relevance networks and functional classification of gene groups or gene networks

AMaχoS—Abstract Machine for Xcerpt

Web query languages promise convenient and efficient access to Web data such as XML, RDF, or Topic Maps. Xcerpt is one such Web query language with strong emphasis on novel high-level constructs for effective and convenient query authoring, particularly tailored to versatile access to data in different Web formats such as XML or RDF. However, so far it lacks an efficient implementation to supplement the convenient language features. AMaχoS is an abstract machine implementation for Xcerpt that aims at efficiency and ease of deployment. It strictly separates compilation and execution of queries: Queries are compiled once to abstract machine code that consists in (1) a code segment with instructions for evaluating each rule and (2) a hint segment that provides the abstract machine with optimization hints derived by the query compilation. This article summarizes the motivation and principles behind AMaχoS and discusses how its current architecture realizes these principles

Algorithm Diversity for Resilient Systems

Diversity can significantly increase the resilience of systems, by reducing the prevalence of shared vulnerabilities and making vulnerabilities harder to exploit. Work on software diversity for security typically creates variants of a program using low-level code transformations. This paper is the first to study algorithm diversity for resilience. We first describe how a method based on high-level invariants and systematic incrementalization can be used to create algorithm variants. Executing multiple variants in parallel and comparing their outputs provides greater resilience than executing one variant. To prevent different parallel schedules from causing variants' behaviors to diverge, we present a synchronized execution algorithm for DistAlgo, an extension of Python for high-level, precise, executable specifications of distributed algorithms. We propose static and dynamic metrics for measuring diversity. An experimental evaluation of algorithm diversity combined with implementation-level diversity for several sequential algorithms and distributed algorithms shows the benefits of algorithm diversity

Meta-F*: Proof Automation with SMT, Tactics, and Metaprograms

We introduce Meta-F*, a tactics and metaprogramming framework for the F* program verifier. The main novelty of Meta-F* is allowing the use of tactics and metaprogramming to discharge assertions not solvable by SMT, or to just simplify them into well-behaved SMT fragments. Plus, Meta-F* can be used to generate verified code automatically. Meta-F* is implemented as an F* effect, which, given the powerful effect system of F*, heavily increases code reuse and even enables the lightweight verification of metaprograms. Metaprograms can be either interpreted, or compiled to efficient native code that can be dynamically loaded into the F* type-checker and can interoperate with interpreted code. Evaluation on realistic case studies shows that Meta-F* provides substantial gains in proof development, efficiency, and robustness.Comment: Full version of ESOP'19 pape

Reconstructing Rational Functions with FireFly\texttt{FireFly}

We present the open-source $\texttt{C++}$ library $\texttt{FireFly}$ for the reconstruction of multivariate rational functions over finite fields. We discuss the involved algorithms and their implementation. As an application, we use $\texttt{FireFly}$ in the context of integration-by-parts reductions and compare runtime and memory consumption to a fully algebraic approach with the program $\texttt{Kira}$.Comment: 46 pages, 3 figures, 6 tables; v2: matches published versio