Automatic visualization and control of arbitrary numerical simulations

Authors’ preprint version as submitted to ECCOMAS Congress 2016, Minisymposium 505 - Interactive Simulations in Computational Engineering. Abstract: Visualization of numerical simulation data has become a cornerstone for many industries and research areas today. There exists a large amount of software support, which is usually tied to specific problem domains or simulation platforms. However, numerical simulations have commonalities in the building blocks of their descriptions (e. g., dimensionality, range constraints, sample frequency). Instead of encoding these descriptions and their meaning into software architecures we propose to base their interpretation and evaluation on a data-centric model. This approach draws much inspiration from work of the IEEE Simulation Interoperability Standards Group as currently applied in distributed (military) training and simulation scenarios and seeks to extend those ideas. By using an extensible self-describing protocol format, simulation users as well as simulation-code providers would be able to express the meaning of their data even if no access to the underlying source code was available or if new and unforseen use cases emerge. A protocol definition will allow simulation-domain experts to describe constraints that can be used for automatically creating appropriate visualizations of simulation data and control interfaces. Potentially, this will enable leveraging innovations on both the simulation and visualization side of the problem continuum. We envision the design and development of algorithms and software tools for the automatic visualization of complex data from numerical simulations executed on a wide variety of platforms (e. g., remote HPC systems, local many-core or GPU-based systems). We also envisage using this automatically gathered information to control (or steer) the simulation while it is running, as well as providing the ability for fine-tuning representational aspects of the visualizations produced

Automatic visualization and control of arbitrary numerical simulations

Authors’ preprint version as submitted to ECCOMAS Congress 2016, Minisymposium 505 - Interactive Simulations in Computational Engineering. Abstract: Visualization of numerical simulation data has become a cornerstone for many industries and research areas today. There exists a large amount of software support, which is usually tied to specific problem domains or simulation platforms. However, numerical simulations have commonalities in the building blocks of their descriptions (e. g., dimensionality, range constraints, sample frequency). Instead of encoding these descriptions and their meaning into software architecures we propose to base their interpretation and evaluation on a data-centric model. This approach draws much inspiration from work of the IEEE Simulation Interoperability Standards Group as currently applied in distributed (military) training and simulation scenarios and seeks to extend those ideas. By using an extensible self-describing protocol format, simulation users as well as simulation-code providers would be able to express the meaning of their data even if no access to the underlying source code was available or if new and unforseen use cases emerge. A protocol definition will allow simulation-domain experts to describe constraints that can be used for automatically creating appropriate visualizations of simulation data and control interfaces. Potentially, this will enable leveraging innovations on both the simulation and visualization side of the problem continuum. We envision the design and development of algorithms and software tools for the automatic visualization of complex data from numerical simulations executed on a wide variety of platforms (e. g., remote HPC systems, local many-core or GPU-based systems). We also envisage using this automatically gathered information to control (or steer) the simulation while it is running, as well as providing the ability for fine-tuning representational aspects of the visualizations produced

Deliverable JRA1.1: Evaluation of current network control and management planes for multi-domain network infrastructure

This deliverable includes a compilation and evaluation of available control and management architectures and protocols applicable to a multilayer infrastructure in a multi-domain Virtual Network environment.The scope of this deliverable is mainly focused on the virtualisation of the resources within a network and at processing nodes. The virtualization of the FEDERICA infrastructure allows the provisioning of its available resources to users by means of FEDERICA slices. A slice is seen by the user as a real physical network under his/her domain, however it maps to a logical partition (a virtual instance) of the physical FEDERICA resources. A slice is built to exhibit to the highest degree all the principles applicable to a physical network (isolation, reproducibility, manageability, ...). Currently, there are no standard definitions available for network virtualization or its associated architectures. Therefore, this deliverable proposes the Virtual Network layer architecture and evaluates a set of Management- and Control Planes that can be used for the partitioning and virtualization of the FEDERICA network resources. This evaluation has been performed taking into account an initial set of FEDERICA requirements; a possible extension of the selected tools will be evaluated in future deliverables. The studies described in this deliverable define the virtual architecture of the FEDERICA infrastructure. During this activity, the need has been recognised to establish a new set of basic definitions (taxonomy) for the building blocks that compose the so-called slice, i.e. the virtual network instantiation (which is virtual with regard to the abstracted view made of the building blocks of the FEDERICA infrastructure) and its architectural plane representation. These definitions will be established as a common nomenclature for the FEDERICA project. Other important aspects when defining a new architecture are the user requirements. It is crucial that the resulting architecture fits the demands that users may have. Since this deliverable has been produced at the same time as the contact process with users, made by the project activities related to the Use Case definitions, JRA1 has proposed a set of basic Use Cases to be considered as starting point for its internal studies. When researchers want to experiment with their developments, they need not only network resources on their slices, but also a slice of the processing resources. These processing slice resources are understood as virtual machine instances that users can use to make them behave as software routers or end nodes, on which to download the software protocols or applications they have produced and want to assess in a realistic environment. Hence, this deliverable also studies the APIs of several virtual machine management software products in order to identify which best suits FEDERICA’s needs.Postprint (published version

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

Web Data Extraction, Applications and Techniques: A Survey

Web Data Extraction is an important problem that has been studied by means of different scientific tools and in a broad range of applications. Many approaches to extracting data from the Web have been designed to solve specific problems and operate in ad-hoc domains. Other approaches, instead, heavily reuse techniques and algorithms developed in the field of Information Extraction. This survey aims at providing a structured and comprehensive overview of the literature in the field of Web Data Extraction. We provided a simple classification framework in which existing Web Data Extraction applications are grouped into two main classes, namely applications at the Enterprise level and at the Social Web level. At the Enterprise level, Web Data Extraction techniques emerge as a key tool to perform data analysis in Business and Competitive Intelligence systems as well as for business process re-engineering. At the Social Web level, Web Data Extraction techniques allow to gather a large amount of structured data continuously generated and disseminated by Web 2.0, Social Media and Online Social Network users and this offers unprecedented opportunities to analyze human behavior at a very large scale. We discuss also the potential of cross-fertilization, i.e., on the possibility of re-using Web Data Extraction techniques originally designed to work in a given domain, in other domains.Comment: Knowledge-based System

Multi modal multi-semantic image retrieval

PhDThe rapid growth in the volume of visual information, e.g. image, and video can overwhelm users’ ability to find and access the specific visual information of interest to them. In recent years, ontology knowledge-based (KB) image information retrieval techniques have been adopted into in order to attempt to extract knowledge from these images, enhancing the retrieval performance. A KB framework is presented to promote semi-automatic annotation and semantic image retrieval using multimodal cues (visual features and text captions). In addition, a hierarchical structure for the KB allows metadata to be shared that supports multi-semantics (polysemy) for concepts. The framework builds up an effective knowledge base pertaining to a domain specific image collection, e.g. sports, and is able to disambiguate and assign high level semantics to ‘unannotated’ images. Local feature analysis of visual content, namely using Scale Invariant Feature Transform (SIFT) descriptors, have been deployed in the ‘Bag of Visual Words’ model (BVW) as an effective method to represent visual content information and to enhance its classification and retrieval. Local features are more useful than global features, e.g. colour, shape or texture, as they are invariant to image scale, orientation and camera angle. An innovative approach is proposed for the representation, annotation and retrieval of visual content using a hybrid technique based upon the use of an unstructured visual word and upon a (structured) hierarchical ontology KB model. The structural model facilitates the disambiguation of unstructured visual words and a more effective classification of visual content, compared to a vector space model, through exploiting local conceptual structures and their relationships. The key contributions of this framework in using local features for image representation include: first, a method to generate visual words using the semantic local adaptive clustering (SLAC) algorithm which takes term weight and spatial locations of keypoints into account. Consequently, the semantic information is preserved. Second a technique is used to detect the domain specific ‘non-informative visual words’ which are ineffective at representing the content of visual data and degrade its categorisation ability. Third, a method to combine an ontology model with xi a visual word model to resolve synonym (visual heterogeneity) and polysemy problems, is proposed. The experimental results show that this approach can discover semantically meaningful visual content descriptions and recognise specific events, e.g., sports events, depicted in images efficiently. Since discovering the semantics of an image is an extremely challenging problem, one promising approach to enhance visual content interpretation is to use any associated textual information that accompanies an image, as a cue to predict the meaning of an image, by transforming this textual information into a structured annotation for an image e.g. using XML, RDF, OWL or MPEG-7. Although, text and image are distinct types of information representation and modality, there are some strong, invariant, implicit, connections between images and any accompanying text information. Semantic analysis of image captions can be used by image retrieval systems to retrieve selected images more precisely. To do this, a Natural Language Processing (NLP) is exploited firstly in order to extract concepts from image captions. Next, an ontology-based knowledge model is deployed in order to resolve natural language ambiguities. To deal with the accompanying text information, two methods to extract knowledge from textual information have been proposed. First, metadata can be extracted automatically from text captions and restructured with respect to a semantic model. Second, the use of LSI in relation to a domain-specific ontology-based knowledge model enables the combined framework to tolerate ambiguities and variations (incompleteness) of metadata. The use of the ontology-based knowledge model allows the system to find indirectly relevant concepts in image captions and thus leverage these to represent the semantics of images at a higher level. Experimental results show that the proposed framework significantly enhances image retrieval and leads to narrowing of the semantic gap between lower level machinederived and higher level human-understandable conceptualisation

Automatic extraction of knowledge from web documents

A large amount of digital information available is written as text documents in the form of web pages, reports, papers, emails, etc. Extracting the knowledge of interest from such documents from multiple sources in a timely fashion is therefore crucial. This paper provides an update on the Artequakt system which uses natural language tools to automatically extract knowledge about artists from multiple documents based on a predefined ontology. The ontology represents the type and form of knowledge to extract. This knowledge is then used to generate tailored biographies. The information extraction process of Artequakt is detailed and evaluated in this paper