7,331 research outputs found
Approximate Computing Survey, Part I: Terminology and Software & Hardware Approximation Techniques
The rapid growth of demanding applications in domains applying multimedia
processing and machine learning has marked a new era for edge and cloud
computing. These applications involve massive data and compute-intensive tasks,
and thus, typical computing paradigms in embedded systems and data centers are
stressed to meet the worldwide demand for high performance. Concurrently, the
landscape of the semiconductor field in the last 15 years has constituted power
as a first-class design concern. As a result, the community of computing
systems is forced to find alternative design approaches to facilitate
high-performance and/or power-efficient computing. Among the examined
solutions, Approximate Computing has attracted an ever-increasing interest,
with research works applying approximations across the entire traditional
computing stack, i.e., at software, hardware, and architectural levels. Over
the last decade, there is a plethora of approximation techniques in software
(programs, frameworks, compilers, runtimes, languages), hardware (circuits,
accelerators), and architectures (processors, memories). The current article is
Part I of our comprehensive survey on Approximate Computing, and it reviews its
motivation, terminology and principles, as well it classifies and presents the
technical details of the state-of-the-art software and hardware approximation
techniques.Comment: Under Review at ACM Computing Survey
Beam scanning by liquid-crystal biasing in a modified SIW structure
A fixed-frequency beam-scanning 1D antenna based on Liquid Crystals (LCs) is designed for application in 2D scanning with lateral alignment. The 2D array environment imposes full decoupling of adjacent 1D antennas, which often conflicts with the LC requirement of DC biasing: the proposed design accommodates both. The LC medium is placed inside a Substrate Integrated Waveguide (SIW) modified to work as a Groove Gap Waveguide, with radiating slots etched on the upper broad wall, that radiates as a Leaky-Wave Antenna (LWA). This allows effective application of the DC bias voltage needed for tuning the LCs. At the same time, the RF field remains laterally confined, enabling the possibility to lay several antennas in parallel and achieve 2D beam scanning. The design is validated by simulation employing the actual properties of a commercial LC medium
Using machine learning to predict pathogenicity of genomic variants throughout the human genome
Geschätzt mehr als 6.000 Erkrankungen werden durch Veränderungen im Genom verursacht. Ursachen gibt es viele: Eine genomische Variante kann die Translation eines Proteins stoppen, die Genregulation stören oder das Spleißen der mRNA in eine andere Isoform begünstigen. All diese Prozesse müssen überprüft werden, um die zum beschriebenen Phänotyp passende Variante zu ermitteln. Eine Automatisierung dieses Prozesses sind Varianteneffektmodelle. Mittels maschinellem Lernen und Annotationen aus verschiedenen Quellen bewerten diese Modelle genomische Varianten hinsichtlich ihrer Pathogenität.
Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier präsentiere ich ein allgemeines Workflow dieses Prozesses. Dieses ermöglicht es den Prozess zu konfigurieren, Modellmerkmale zu bearbeiten, und verschiedene Annotationen zu testen. Der Workflow umfasst außerdem die Optimierung von Hyperparametern, Validierung und letztlich die Anwendung des Modells durch genomweites Berechnen von Varianten-Scores.
Der Workflow wird in der Entwicklung von Combined Annotation Dependent Depletion (CADD), einem Varianteneffektmodell zur genomweiten Bewertung von SNVs und InDels, verwendet. Durch Etablierung des ersten Varianteneffektmodells für das humane Referenzgenome GRCh38 demonstriere ich die gewonnenen Möglichkeiten Annotationen aufzugreifen und neue Modelle zu trainieren. Außerdem zeige ich, wie Deep-Learning-Scores als Feature in einem CADD-Modell die Vorhersage von RNA-Spleißing verbessern. Außerdem werden Varianteneffektmodelle aufgrund eines neuen, auf Allelhäufigkeit basierten, Trainingsdatensatz entwickelt.
Diese Ergebnisse zeigen, dass der entwickelte Workflow eine skalierbare und flexible Möglichkeit ist, um Varianteneffektmodelle zu entwickeln. Alle entstandenen Scores sind unter cadd.gs.washington.edu und cadd.bihealth.org frei verfügbar.More than 6,000 diseases are estimated to be caused by genomic variants. This can happen in many possible ways: a variant may stop the translation of a protein, interfere with gene regulation, or alter splicing of the transcribed mRNA into an unwanted isoform. It is necessary to investigate all of these processes in order to evaluate which variant may be causal for the deleterious phenotype. A great help in this regard are variant effect scores. Implemented as machine learning classifiers, they integrate annotations from different resources to rank genomic variants in terms of pathogenicity.
Developing a variant effect score requires multiple steps: annotation of the training data, feature selection, model training, benchmarking, and finally deployment for the model's application. Here, I present a generalized workflow of this process. It makes it simple to configure how information is converted into model features, enabling the rapid exploration of different annotations. The workflow further implements hyperparameter optimization, model validation and ultimately deployment of a selected model via genome-wide scoring of genomic variants.
The workflow is applied to train Combined Annotation Dependent Depletion (CADD), a variant effect model that is scoring SNVs and InDels genome-wide. I show that the workflow can be quickly adapted to novel annotations by porting CADD to the genome reference GRCh38. Further, I demonstrate the integration of deep-neural network scores as features into a new CADD model, improving the annotation of RNA splicing events. Finally, I apply the workflow to train multiple variant effect models from training data that is based on variants selected by allele frequency.
In conclusion, the developed workflow presents a flexible and scalable method to train variant effect scores. All software and developed scores are freely available from cadd.gs.washington.edu and cadd.bihealth.org
Machine Learning Meets Mental Training -- A Proof of Concept Applied to Memory Sports
This work aims to combine these two fields together by presenting a practical
implementation of machine learning to the particular form of mental training
that is the art of memory, taken in its competitive version called "Memory
Sports". Such a fusion, on the one hand, strives to raise awareness about both
realms, while on the other it seeks to encourage research in this mixed field
as a way to, ultimately, drive forward the development of this seemingly
underestimated sport.Comment: 75 pages, 47 figures, 2 tables, 26 code excerpt
Architecture and Advanced Electronics Pathways Toward Highly Adaptive Energy- Efficient Computing
With the explosion of the number of compute nodes, the bottleneck of future computing systems lies in the network architecture connecting the nodes. Addressing the bottleneck requires replacing current backplane-based network topologies. We propose to revolutionize computing electronics by realizing embedded optical waveguides for onboard networking and wireless chip-to-chip links at 200-GHz carrier frequency connecting neighboring boards in a rack. The control of novel rate-adaptive optical and mm-wave transceivers needs tight interlinking with the system software for runtime resource management
Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria
Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases
Inductive biases in deep learning models for weather prediction
Deep learning has recently gained immense popularity in the Earth sciences as
it enables us to formulate purely data-driven models of complex Earth system
processes. Deep learning-based weather prediction (DLWP) models have made
significant progress in the last few years, achieving forecast skills
comparable to established numerical weather prediction (NWP) models with
comparatively lesser computational costs. In order to train accurate, reliable,
and tractable DLWP models with several millions of parameters, the model design
needs to incorporate suitable inductive biases that encode structural
assumptions about the data and modelled processes. When chosen appropriately,
these biases enable faster learning and better generalisation to unseen data.
Although inductive biases play a crucial role in successful DLWP models, they
are often not stated explicitly and how they contribute to model performance
remains unclear. Here, we review and analyse the inductive biases of six
state-of-the-art DLWP models, involving a deeper look at five key design
elements: input data, forecasting objective, loss components, layered design of
the deep learning architectures, and optimisation methods. We show how the
design choices made in each of the five design elements relate to structural
assumptions. Given recent developments in the broader DL community, we
anticipate that the future of DLWP will likely see a wider use of foundation
models -- large models pre-trained on big databases with self-supervised
learning -- combined with explicit physics-informed inductive biases that allow
the models to provide competitive forecasts even at the more challenging
subseasonal-to-seasonal scales
LASSO – an observatorium for the dynamic selection, analysis and comparison of software
Mining software repositories at the scale of 'big code' (i.e., big data) is a challenging activity. As well as finding a suitable software corpus and making it programmatically accessible through an index or database, researchers and practitioners have to establish an efficient analysis infrastructure and precisely define the metrics and data extraction approaches to be applied. Moreover, for analysis results to be generalisable, these tasks have to be applied at a large enough scale to have statistical significance, and if they are to be repeatable, the artefacts need to be carefully maintained and curated over time. Today, however, a lot of this work is still performed by human beings on a case-by-case basis, with the level of effort involved often having a significant negative impact on the generalisability and repeatability of studies, and thus on their overall scientific value.
The general purpose, 'code mining' repositories and infrastructures that have emerged in recent years represent a significant step forward because they automate many software mining tasks at an ultra-large scale and allow researchers and practitioners to focus on defining the questions they would like to explore at an abstract level. However, they are currently limited to static analysis and data extraction techniques, and thus cannot support (i.e., help automate) any studies which involve the execution of software systems. This includes experimental validations of techniques and tools that hypothesise about the behaviour (i.e., semantics) of software, or data analysis and extraction techniques that aim to measure dynamic properties of software.
In this thesis a platform called LASSO (Large-Scale Software Observatorium) is introduced that overcomes this limitation by automating the collection of dynamic (i.e., execution-based) information about software alongside static information. It features a single, ultra-large scale corpus of executable software systems created by amalgamating existing Open Source software repositories and a dedicated DSL for defining abstract selection and analysis pipelines. Its key innovations are integrated capabilities for searching for selecting software systems based on their exhibited behaviour and an 'arena' that allows their responses to software tests to be compared in a purely data-driven way. We call the platform a 'software observatorium' since it is a place where the behaviour of large numbers of software systems can be observed, analysed and compared
Generative Adversarial Network and Its Application in Aerial Vehicle Detection and Biometric Identification System
In recent years, generative adversarial networks (GANs) have shown great potential in advancing the state-of-the-art in many areas of computer vision, most notably in image synthesis and manipulation tasks. GAN is a generative model which simultaneously trains a generator and a discriminator in an adversarial manner to produce real-looking synthetic data by capturing the underlying data distribution. Due to its powerful ability to generate high-quality and visually pleasingresults, we apply it to super-resolution and image-to-image translation techniques to address vehicle detection in low-resolution aerial images and cross-spectral cross-resolution iris recognition. First, we develop a Multi-scale GAN (MsGAN) with multiple intermediate outputs, which progressively learns the details and features of the high-resolution aerial images at different scales. Then the upscaled super-resolved aerial images are fed to a You Only Look Once-version 3 (YOLO-v3) object detector and the detection loss is jointly optimized along with a super-resolution loss to emphasize target vehicles sensitive to the super-resolution process. There is another problem that remains unsolved when detection takes place at night or in a dark environment, which requires an IR detector. Training such a detector needs a lot of infrared (IR) images. To address these challenges, we develop a GAN-based joint cross-modal super-resolution framework where low-resolution (LR) IR images are translated and super-resolved to high-resolution (HR) visible (VIS) images before applying detection. This approach significantly improves the accuracy of aerial vehicle detection by leveraging the benefits of super-resolution techniques in a cross-modal domain. Second, to increase the performance and reliability of deep learning-based biometric identification systems, we focus on developing conditional GAN (cGAN) based cross-spectral cross-resolution iris recognition and offer two different frameworks. The first approach trains a cGAN to jointly translate and super-resolve LR near-infrared (NIR) iris images to HR VIS iris images to perform cross-spectral cross-resolution iris matching to the same resolution and within the same spectrum. In the second approach, we design a coupled GAN (cpGAN) architecture to project both VIS and NIR iris images into a low-dimensional embedding domain. The goal of this architecture is to ensure maximum pairwise similarity between the feature vectors from the two iris modalities of the same subject. We have also proposed a pose attention-guided coupled profile-to-frontal face recognition network to learn discriminative and pose-invariant features in an embedding subspace. To show that the feature vectors learned by this deep subspace can be used for other tasks beyond recognition, we implement a GAN architecture which is able to reconstruct a frontal face from its corresponding profile face. This capability can be used in various face analysis tasks, such as emotion detection and expression tracking, where having a frontal face image can improve accuracy and reliability. Overall, our research works have shown its efficacy by achieving new state-of-the-art results through extensive experiments on publicly available datasets reported in the literature
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