OpenRaiser/Intern-Atlas huggingface dataset:
Cloud Infrastructure Provenance Collection and Management to Reproduce Scientific Workflow Execution
Venue: arXiv cs.DC 2018
Year: 2018

The emergence of Cloud computing provides a new computing paradigm for scientific workflow execution. It provides dynamic, on-demand and scalable resources that enable the processing of complex workflow-based experiments. With the ever growing size of the experimental data and increasingly complex processing workflows, the need for reproducibility has also become essential. Provenance has been thought of a mechanism to verify a workflow and to provide workflow reproducibility. One of the obstacles in reproducing an experiment execution is the lack of information about the execution infrastructure in the collected provenance. This information becomes critical in the context of Cloud in which resources are provisioned on-demand and by specifying resource configurations. Therefore, a mechanism is required that enables capturing of infrastructure information along with the provenance of workflows executing on the Cloud to facilitate the re-creation of execution environment on the Cloud. This paper presents a framework, ReCAP, along with the proposed mapping approaches that aid in capturing the Cloud-aware provenance information and help in re-provisioning the execution resource on the Cloud with similar configurations. Experimental evaluation has shown the impact of different resource configurations on the workflow execution performance, therefore justifies the need for collecting such provenance information in the context of Cloud. The evaluation has also demonstrated that the proposed mapping approaches can capture Cloud information in various Cloud usage scenarios without causing performance overhead and can also enable the re-provisioning of resources on Cloud. Experiments were conducted using workflows from different scientific domains such as astronomy and neuroscience to demonstrate the applicability of this research for different workflows.
Newton: Gravitating Towards the Physical Limits of Crossbar Acceleration
Venue: arXiv cs.LG 2018
Year: 2018

Many recent works have designed accelerators for Convolutional Neural Networks (CNNs). While digital accelerators have relied on near data processing, analog accelerators have further reduced data movement by performing in-situ computation. Recent works take advantage of highly parallel analog in-situ computation in memristor crossbars to accelerate the many vector-matrix multiplication operations in CNNs. However, these in-situ accelerators have two significant short-comings that we address in this work. First, the ADCs account for a large fraction of chip power and area. Second, these accelerators adopt a homogeneous design where every resource is provisioned for the worst case. By addressing both problems, the new architecture, Newton, moves closer to achieving optimal energy-per-neuron for crossbar accelerators. We introduce multiple new techniques that apply at different levels of the tile hierarchy. Two of the techniques leverage heterogeneity: one adapts ADC precision based on the requirements of every sub-computation (with zero impact on accuracy), and the other designs tiles customized for convolutions or classifiers. Two other techniques rely on divide-and-conquer numeric algorithms to reduce computations and ADC pressure. Finally, we place constraints on how a workload is mapped to tiles, thus helping reduce resource provisioning in tiles. For a wide range of CNN dataflows and structures, Newton achieves a 77% decrease in power, 51% improvement in energy efficiency, and 2.2x higher throughput/area, relative to the state-of-the-art ISAAC accelerator.
PyGOM - A Python Package for Simplifying Modelling with Systems of Ordinary Differential Equations
Venue: arXiv cs.MS 2018
Year: 2018

Ordinary Differential Equations (ODE) are used throughout science where the capture of rates of change in states is sought. While both pieces of commercial and open software exist to study such systems, their efficient and accurate usage frequently requires deep understanding of mathematics and programming. The package we present here, PyGOM, seeks to remove these obstacles for models based on ODE systems. We provide a simple interface for the construction of such systems backed by a comprehensive and easy to use tool--box. This tool--box implements functions to easily perform common operations for ODE systems such as solving, parameter estimation, and stochastic simulation. The package source is freely available and organized in a way that permits easy extension. With both the algebraic and numeric calculations performed automatically (but still accessible), the end user is freed to focus on model development.
Techniques for Shared Resource Management in Systems with Throughput Processors
Venue: arXiv cs.AR 2018
Year: 2018

The continued growth of the computational capability of throughput processors has made throughput processors the platform of choice for a wide variety of high performance computing applications. Graphics Processing Units (GPUs) are a prime example of throughput processors that can deliver high performance for applications ranging from typical graphics applications to general-purpose data parallel (GPGPU) applications. However, this success has been accompanied by new performance bottlenecks throughout the memory hierarchy of GPU-based systems. We identify and eliminate performance bottlenecks caused by major sources of interference throughout the memory hierarchy. We introduce changes to the memory hierarchy for systems with GPUs that allow the memory hierarchy to be aware of both CPU and GPU applications' characteristics. We introduce mechanisms to dynamically analyze different applications' characteristics and propose four major changes throughout the memory hierarchy. We propose changes to the cache management and memory scheduling mechanisms to mitigate intra-application interference in GPGPU applications. We propose changes to the memory controller design and its scheduling policy to mitigate inter-application interference in heterogeneous CPU-GPU systems. We redesign the MMU and the memory hierarchy in GPUs to be aware of ddress-translation data in order to mitigate the inter-address-space interference. We introduce a hardware-software cooperative technique that modifies the memory allocation policy to enable large page support in order to further reduce the inter-address-space interference at the shared Translation Lookaside Buffer (TLB). Our evaluations show that the GPU-aware cache and memory management techniques proposed in this dissertation are effective at mitigating the interference caused by GPUs on current and future GPU-based systems.
Synthesis of Logical Clifford Operators via Symplectic Geometry
Venue: arXiv cs.IT 2018
Year: 2018

Quantum error-correcting codes can be used to protect qubits involved in quantum computation. This requires that logical operators acting on protected qubits be translated to physical operators (circuits) acting on physical quantum states. We propose a mathematical framework for synthesizing physical circuits that implement logical Clifford operators for stabilizer codes. Circuit synthesis is enabled by representing the desired physical Clifford operator in $\mathbb{C}^{N \times N}$ as a partial $2m \times 2m$ binary symplectic matrix, where $N = 2^m$. We state and prove two theorems that use symplectic transvections to efficiently enumerate all symplectic matrices that satisfy a system of linear equations. As an important corollary of these results, we prove that for an $[\![ m,m-k ]\!]$ stabilizer code every logical Clifford operator has $2^{k(k+1)/2}$ symplectic solutions. The desired physical circuits are then obtained by decomposing each solution as a product of elementary symplectic matrices. Our assembly of the possible physical realizations enables optimization over them with respect to a suitable metric. Furthermore, we show that any circuit that normalizes the stabilizer of the code can be transformed into a circuit that centralizes the stabilizer, while realizing the same logical operation. Our method of circuit synthesis can be applied to any stabilizer code, and this paper provides a proof of concept synthesis of universal Clifford gates for the $[\![ 6,4,2 ]\!]$ CSS code. We conclude with a classical coding-theoretic perspective for constructing logical Pauli operators for CSS codes. Since our circuit synthesis algorithm builds on the logical Pauli operators for the code, this paper provides a complete framework for constructing all logical Clifford operators for CSS codes. Programs implementing our algorithms can be found at https://github.com/nrenga/symplectic-arxiv18a
Experimental Molecular Communication Testbed Based on Magnetic Nanoparticles in Duct Flow
Venue: arXiv cs.ET 2018
Year: 2018

Simple and easy to implement testbeds are needed to further advance molecular communication research. To this end, this paper presents an in-vessel molecular communication testbed using magnetic nanoparticles dispersed in an aqueous suspension as they are also used for drug targeting in biotechnology. The transmitter is realized by an electronic pump for injection via a Y-connector. A second pump provides a background flow for signal propagation. For signal reception, we employ a susceptometer, an electronic device including a coil, where the magnetic particles move through and generate an electrical signal. We present experimental results for the transmission of a binary sequence and the system response following a single injection. For this flow-driven particle transport, we propose a simple parameterized mathematical model for evaluating the system response.
Specifying and Analyzing Virtual Network Services Using Queuing Petri Nets
Venue: arXiv cs.NI 2018
Year: 2018

For optimal placement and orchestration of network services, it is crucial that their structure and semantics are specified clearly and comprehensively and are available to an orchestrator. Existing specification approaches are either ambiguous or miss important aspects regarding the behavior of virtual network functions (VNFs) forming a service. We propose to formally and unambiguously specify the behavior of these functions and services using Queuing Petri Nets (QPNs). QPNs are an established method that allows to express queuing, synchronization, stochastically distributed processing delays, and changing traffic volume and characteristics at each VNF. With QPNs, multiple VNFs can be connected to complete network services in any structure, even specifying bidirectional network services containing loops. We propose a tool-based workflow that supports the specification of network services and the automatic generation of corresponding simulation code to enable an in-depth analysis of their behavior and performance. In a case study, we show how developers can benefit from analysis insights, e.g., to anticipate the impact of different service configurations. We also discuss how management and orchestration systems can benefit from our clear and comprehensive specification approach and its extensive analysis possibilities, leading to better placement of VNFs and improved Quality of Service.
Factorised spatial representation learning: application in semi-supervised myocardial segmentation
Venue: arXiv cs.CV 2018
Year: 2018

The success and generalisation of deep learning algorithms heavily depend on learning good feature representations. In medical imaging this entails representing anatomical information, as well as properties related to the specific imaging setting. Anatomical information is required to perform further analysis, whereas imaging information is key to disentangle scanner variability and potential artefacts. The ability to factorise these would allow for training algorithms only on the relevant information according to the task. To date, such factorisation has not been attempted. In this paper, we propose a methodology of latent space factorisation relying on the cycle-consistency principle. As an example application, we consider cardiac MR segmentation, where we separate information related to the myocardium from other features related to imaging and surrounding substructures. We demonstrate the proposed method's utility in a semi-supervised setting: we use very few labelled images together with many unlabelled images to train a myocardium segmentation neural network. Specifically, we achieve comparable performance to fully supervised networks using a fraction of labelled images in experiments on ACDC and a dataset from Edinburgh Imaging Facility QMRI. Code will be made available at https://github.com/agis85/spatial_factorisation.
Controlling Decoding for More Abstractive Summaries with Copy-Based Networks
Venue: arXiv cs.CL 2018
Year: 2018

Attention-based neural abstractive summarization systems equipped with copy mechanisms have shown promising results. Despite this success, it has been noticed that such a system generates a summary by mostly, if not entirely, copying over phrases, sentences, and sometimes multiple consecutive sentences from an input paragraph, effectively performing extractive summarization. In this paper, we verify this behavior using the latest neural abstractive summarization system - a pointer-generator network. We propose a simple baseline method that allows us to control the amount of copying without retraining. Experiments indicate that the method provides a strong baseline for abstractive systems looking to obtain high ROUGE scores while minimizing overlap with the source article, substantially reducing the n-gram overlap with the original article while keeping within 2 points of the original model's ROUGE score.
Time-Domain Multi-Beam Selection and Its Performance Improvement for mmWave Systems
Venue: arXiv cs.IT 2018
Year: 2018

Multi-beam selection is one of the crucial technologies in hybrid beamforming systems for frequency-selective fading channels. Addressing the problem in the frequency domain facilitates the procedure of acquiring observations for analog beam selection. However, it is difficult to improve the quality of the contaminated observations at low SNR. To this end, this paper uses an idea that the significant observations are sparse in the time domain to further enhance the quality of signals as well as the beam selection performance. By exploiting properties of channel impulse responses and circular convolutions in the time domain, we can reduce the size of a Toeplitz matrix in deconvolution to generate periodic true values of coupling coefficients plus random noise signals. An arithmetic mean of these signals yields refined observations with minor noise effects and provides more accurate sparse multipath delay information. As a result, only the refined observations associated with the estimated multipath delay indices have to be taken into account for the analog beam selection problem.
VGAN-Based Image Representation Learning for Privacy-Preserving Facial Expression Recognition
Venue: arXiv cs.CV 2018
Year: 2018

Reliable facial expression recognition plays a critical role in human-machine interactions. However, most of the facial expression analysis methodologies proposed to date pay little or no attention to the protection of a user's privacy. In this paper, we propose a Privacy-Preserving Representation-Learning Variational Generative Adversarial Network (PPRL-VGAN) to learn an image representation that is explicitly disentangled from the identity information. At the same time, this representation is discriminative from the standpoint of facial expression recognition and generative as it allows expression-equivalent face image synthesis. We evaluate the proposed model on two public datasets under various threat scenarios. Quantitative and qualitative results demonstrate that our approach strikes a balance between the preservation of privacy and data utility. We further demonstrate that our model can be effectively applied to other tasks such as expression morphing and image completion.
Dancing Honey bee Robot Elicits Dance-Following and Recruits Foragers
Venue: arXiv cs.RO 2018
Year: 2018

The honey bee dance communication system is one of the most popular examples of animal communication. Forager bees communicate the flight vector towards food, water, or resin sources to nestmates by performing a stereotypical motion pattern on the comb surface in the darkness of the hive. Bees that actively follow the circles of the dancer, so called dance-followers, may decode the message and fly according to the indicated vector that refers to the sun compass and their visual odometer. We investigated the dance communication system with a honeybee robot that reproduced the waggle dance pattern for a flight vector chosen by the experimenter. The dancing robot, called RoboBee, generated multiple cues contained in the biological dance pattern and elicited natural dance-following behavior in live bees. By tracking the flight trajectory of departing bees after following the dancing robot via harmonic radar we confirmed that bees used information obtained from the robotic dance to adjust their flight path. This is the first report on successful dance following and subsequent flight performance of bees recruited by a biomimetic robot.
English-Catalan Neural Machine Translation in the Biomedical Domain through the cascade approach
Venue: arXiv cs.CL 2018
Year: 2018

This paper describes the methodology followed to build a neural machine translation system in the biomedical domain for the English-Catalan language pair. This task can be considered a low-resourced task from the point of view of the domain and the language pair. To face this task, this paper reports experiments on a cascade pivot strategy through Spanish for the neural machine translation using the English-Spanish SCIELO and Spanish-Catalan El Periódico database. To test the final performance of the system, we have created a new test data set for English-Catalan in the biomedical domain which is freely available on request.
A Temporally-Aware Interpolation Network for Video Frame Inpainting
Venue: arXiv cs.CV 2018
Year: 2018

We propose the first deep learning solution to video frame inpainting, a challenging instance of the general video inpainting problem with applications in video editing, manipulation, and forensics. Our task is less ambiguous than frame interpolation and video prediction because we have access to both the temporal context and a partial glimpse of the future, allowing us to better evaluate the quality of a model's predictions objectively. We devise a pipeline composed of two modules: a bidirectional video prediction module, and a temporally-aware frame interpolation module. The prediction module makes two intermediate predictions of the missing frames, one conditioned on the preceding frames and the other conditioned on the following frames, using a shared convolutional LSTM-based encoder-decoder. The interpolation module blends the intermediate predictions to form the final result. Specifically, it utilizes time information and hidden activations from the video prediction module to resolve disagreements between the predictions. Our experiments demonstrate that our approach produces more accurate and qualitatively satisfying results than a state-of-the-art video prediction method and many strong frame inpainting baselines.
Containment of Shape Expression Schemas for RDF
Venue: arXiv cs.LO 2018
Year: 2018

We study the problem of containment for shape expression schemas (ShEx) for RDF graphs. We identify a subclass of ShEx that has a natural graphical representation in the form of shape graphs and their semantics is captured with a tractable notion of embedding of an RDF graph in a shape graph. When applied to pairs of shape graphs, an embedding is a sufficient condition for containment, and for a practical subclass of deterministic shape graphs, it is also a necessary one, thus yielding a subclass with tractable containment. While for general shape graphs a minimal counter-example i.e., an instance proving non-containment, might be of exponential size, we show that containment is EXP-hard and in coNEXP. Finally, we show that containment for arbitrary ShEx is coNEXP-hard and in coTwoNEXP^NP.
The CTTC 5G end-to-end experimental platform: Integrating heterogeneous wireless/optical networks, distributed cloud, and IoT devices
Venue: arXiv cs.NI 2018
Year: 2018

The Internet of Things (IoT) will facilitate a wide variety of applications in different domains, such as smart cities, smart grids, industrial automation (Industry 4.0), smart driving, assistance of the elderly, and home automation. Billions of heterogeneous smart devices with different application requirements will be connected to the networks and will generate huge aggregated volumes of data that will be processed in distributed cloud infrastructures. On the other hand, there is also a general trend to deploy functions as software (SW) instances in cloud infrastructures [e.g., network function virtualization (NFV) or mobile edge computing (MEC)]. Thus, the next generation of mobile networks, the fifth-generation (5G), will need not only to develop new radio interfaces or waveforms to cope with the expected traffic growth but also to integrate heterogeneous networks from end to end (E2E) with distributed cloud resources to deliver E2E IoT and mobile services. This article presents the E2E 5G platform that is being developed by the Centre Tecnològic de Telecomunicacions de Catalunya (CTTC), the first known platform capable of reproducing such an ambitious scenario.
SOTorrent: Reconstructing and Analyzing the Evolution of Stack Overflow Posts
Venue: arXiv cs.SE 2018
Year: 2018

Stack Overflow (SO) is the most popular question-and-answer website for software developers, providing a large amount of code snippets and free-form text on a wide variety of topics. Like other software artifacts, questions and answers on SO evolve over time, for example when bugs in code snippets are fixed, code is updated to work with a more recent library version, or text surrounding a code snippet is edited for clarity. To be able to analyze how content on SO evolves, we built SOTorrent, an open dataset based on the official SO data dump. SOTorrent provides access to the version history of SO content at the level of whole posts and individual text or code blocks. It connects SO posts to other platforms by aggregating URLs from text blocks and by collecting references from GitHub files to SO posts. In this paper, we describe how we built SOTorrent, and in particular how we evaluated 134 different string similarity metrics regarding their applicability for reconstructing the version history of text and code blocks. Based on a first analysis using the dataset, we present insights into the evolution of SO posts, e.g., that post edits are usually small, happen soon after the initial creation of the post, and that code is rarely changed without also updating the surrounding text. Further, our analysis revealed a close relationship between post edits and comments. Our vision is that researchers will use SOTorrent to investigate and understand the evolution of SO posts and their relation to other platforms such as GitHub.
Ontology-Based Reasoning about the Trustworthiness of Cyber-Physical Systems
Venue: arXiv cs.CR 2018
Year: 2018

It has been challenging for the technical and regulatory communities to formulate requirements for trustworthiness of the cyber-physical systems (CPS) due to the complexity of the issues associated with their design, deployment, and operations. The US National Institute of Standards and Technology (NIST), through a public working group, has released a CPS Framework that adopts a broad and integrated view of CPS and positions trustworthiness among other aspects of CPS. This paper takes the model created by the CPS Framework and its further developments one step further, by applying ontological approaches and reasoning techniques in order to achieve greater understanding of CPS. The example analyzed in the paper demonstrates the enrichment of the original CPS model obtained through ontology and reasoning and its ability to deliver additional insights to the developers and operators of CPS.