Community standards for open cell migration data

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration

The 1990 progress report and future plans

This document describes the progress and plans of the Artificial Intelligence Research Branch (RIA) at ARC in 1990. Activities span a range from basic scientific research to engineering development and to fielded NASA applications, particularly those applications that are enabled by basic research carried out at RIA. Work is conducted in-house and through collaborative partners in academia and industry. Our major focus is on a limited number of research themes with a dual commitment to technical excellence and proven applicability to NASA short, medium, and long-term problems. RIA acts as the Agency's lead organization for research aspects of artificial intelligence, working closely with a second research laboratory at JPL and AI applications groups at all NASA centers

Ontology-driven conceptual modeling: A'systematic literature mapping and review

All rights reserved. Ontology-driven conceptual modeling (ODCM) is still a relatively new research domain in the field of information systems and there is still much discussion on how the research in ODCM should be performed and what the focus of this research should be. Therefore, this article aims to critically survey the existing literature in order to assess the kind of research that has been performed over the years, analyze the nature of the research contributions and establish its current state of the art by positioning, evaluating and interpreting relevant research to date that is related to ODCM. To understand and identify any gaps and research opportunities, our literature study is composed of both a systematic mapping study and a systematic review study. The mapping study aims at structuring and classifying the area that is being investigated in order to give a general overview of the research that has been performed in the field. A review study on the other hand is a more thorough and rigorous inquiry and provides recommendations based on the strength of the found evidence. Our results indicate that there are several research gaps that should be addressed and we further composed several research opportunities that are possible areas for future research

Open TURNS: An industrial software for uncertainty quantification in simulation

The needs to assess robust performances for complex systems and to answer tighter regulatory processes (security, safety, environmental control, and health impacts, etc.) have led to the emergence of a new industrial simulation challenge: to take uncertainties into account when dealing with complex numerical simulation frameworks. Therefore, a generic methodology has emerged from the joint effort of several industrial companies and academic institutions. EDF R&D, Airbus Group and Phimeca Engineering started a collaboration at the beginning of 2005, joined by IMACS in 2014, for the development of an Open Source software platform dedicated to uncertainty propagation by probabilistic methods, named OpenTURNS for Open source Treatment of Uncertainty, Risk 'N Statistics. OpenTURNS addresses the specific industrial challenges attached to uncertainties, which are transparency, genericity, modularity and multi-accessibility. This paper focuses on OpenTURNS and presents its main features: openTURNS is an open source software under the LGPL license, that presents itself as a C++ library and a Python TUI, and which works under Linux and Windows environment. All the methodological tools are described in the different sections of this paper: uncertainty quantification, uncertainty propagation, sensitivity analysis and metamodeling. A section also explains the generic wrappers way to link openTURNS to any external code. The paper illustrates as much as possible the methodological tools on an educational example that simulates the height of a river and compares it to the height of a dyke that protects industrial facilities. At last, it gives an overview of the main developments planned for the next few years

Algorithm Selection Framework for Cyber Attack Detection

The number of cyber threats against both wired and wireless computer systems and other components of the Internet of Things continues to increase annually. In this work, an algorithm selection framework is employed on the NSL-KDD data set and a novel paradigm of machine learning taxonomy is presented. The framework uses a combination of user input and meta-features to select the best algorithm to detect cyber attacks on a network. Performance is compared between a rule-of-thumb strategy and a meta-learning strategy. The framework removes the conjecture of the common trial-and-error algorithm selection method. The framework recommends five algorithms from the taxonomy. Both strategies recommend a high-performing algorithm, though not the best performing. The work demonstrates the close connectedness between algorithm selection and the taxonomy for which it is premised.Comment: 6 pages, 7 figures, 1 table, accepted to WiseML '2

The consistency of empirical comparisons of regression and analogy-based software project cost prediction

OBJECTIVE - to determine the consistency within and between results in empirical studies of software engineering cost estimation. We focus on regression and analogy techniques as these are commonly used. METHOD – we conducted an exhaustive search using predefined inclusion and exclusion criteria and identified 67 journal papers and 104 conference papers. From this sample we identified 11 journal papers and 9 conference papers that used both methods. RESULTS – our analysis found that about 25% of studies were internally inconclusive. We also found that there is approximately equal evidence in favour of, and against analogy-based methods. CONCLUSIONS – we confirm the lack of consistency in the findings and argue that this inconsistent pattern from 20 different studies comparing regression and analogy is somewhat disturbing. It suggests that we need to ask more detailed questions than just: “What is the best prediction system?

Plant Metabolomics Applications in the Brassicaceae: Added Value for Science and Industry

Crops from the family Brassicaceae represent a diverse and very interesting group of plants. In addition, their close relationship with the model plant, Arabidopsis thaliana, makes combined research on these species both scientifically valuable and of considerable commercial importance. In the post-genomics era, much effort is being placed on expanding our capacity to use advanced technologies such as proteomics and metabolomics, to broaden our knowledge of the molecular organization of plants and how genetic differences are translated into phenotypic ones. Metabolomics in particular is gaining much attention mainly due both to the comprehensiveness of the technology and also the potentially close relationship between biochemical composition (including human health-related phytochemicals) and phenotype. In this short review, a brief introduction to the main metabolomics technologies is given taking examples from research on the Brassicaceae for illustratio

Designing algorithms to aid discovery by chemical robots

Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery

Polynomial-Chaos-based Kriging

Computer simulation has become the standard tool in many engineering fields for designing and optimizing systems, as well as for assessing their reliability. To cope with demanding analysis such as optimization and reliability, surrogate models (a.k.a meta-models) have been increasingly investigated in the last decade. Polynomial Chaos Expansions (PCE) and Kriging are two popular non-intrusive meta-modelling techniques. PCE surrogates the computational model with a series of orthonormal polynomials in the input variables where polynomials are chosen in coherency with the probability distributions of those input variables. On the other hand, Kriging assumes that the computer model behaves as a realization of a Gaussian random process whose parameters are estimated from the available computer runs, i.e. input vectors and response values. These two techniques have been developed more or less in parallel so far with little interaction between the researchers in the two fields. In this paper, PC-Kriging is derived as a new non-intrusive meta-modeling approach combining PCE and Kriging. A sparse set of orthonormal polynomials (PCE) approximates the global behavior of the computational model whereas Kriging manages the local variability of the model output. An adaptive algorithm similar to the least angle regression algorithm determines the optimal sparse set of polynomials. PC-Kriging is validated on various benchmark analytical functions which are easy to sample for reference results. From the numerical investigations it is concluded that PC-Kriging performs better than or at least as good as the two distinct meta-modeling techniques. A larger gain in accuracy is obtained when the experimental design has a limited size, which is an asset when dealing with demanding computational models

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.11Ysciescopu