A Bidirectional Collaboration Framework for Bio-Model Development

High-level graph data structures have gained favour in representing biologicalknowledge in a computationally executable form, but the information containedtherein must remain accessible to all users no matter their background. Bidirectionalgraph transformations may be used to synchronise and maintain the consistencyof these graph data structures as they evolve through the process of creatingand refining a bio-model knowledge base. We outline a bidirectional collaborationframework by which users with vastly differing backgrounds may contribute to thedevelopment and evolution of such a knowledge base, and examine a simple example to illustrate its merits. We also identify avenues for further research necessary to refine the framework. No prior biological knowledge is assumed

Bringing the OpenMI to LIFE Progress Report No. 4 - 31st March 2008 – 30th September 2008

The Water Framework Directive demands an integrated approach to water management. This requires the ability to predict how catchment processes will behave and interact in response to the activities of water managers and others. In most contexts, it is not feasible to build a single predictive model that adequately represents all the processes; therefore a means of linking models of individual processes is required. This is met by the FP5 HarmonIT project’s Open Modelling Interface and Environment (the OpenMI). The purpose of this project is to transform the OpenMI from a research output to a sustainable operational Standard. It will build the capacity to use the OpenMI and will demonstrate it under operational conditions. It will also develop, test and demonstrate the future support organisation for the OpenMI. Finally, information about the OpenMI will be disseminated to users

A novel monitoring system for fall detection in older people

Indexación: Scopus.This work was supported in part by CORFO - CENS 16CTTS-66390 through the National Center on Health Information Systems, in part by the National Commission for Scientific and Technological Research (CONICYT) through the Program STIC-AMSUD 17STIC-03: ‘‘MONITORing for ehealth," FONDEF ID16I10449 ‘‘Sistema inteligente para la gestión y análisis de la dotación de camas en la red asistencial del sector público’’, and in part by MEC80170097 ‘‘Red de colaboración científica entre universidades nacionales e internacionales para la estructuración del doctorado y magister en informática médica en la Universidad de Valparaíso’’. The work of V. H. C. De Albuquerque was supported by the Brazilian National Council for Research and Development (CNPq), under Grant 304315/2017-6.Each year, more than 30% of people over 65 years-old suffer some fall. Unfortunately, this can generate physical and psychological damage, especially if they live alone and they are unable to get help. In this field, several studies have been performed aiming to alert potential falls of the older people by using different types of sensors and algorithms. In this paper, we present a novel non-invasive monitoring system for fall detection in older people who live alone. Our proposal is using very-low-resolution thermal sensors for classifying a fall and then alerting to the care staff. Also, we analyze the performance of three recurrent neural networks for fall detections: Long short-term memory (LSTM), gated recurrent unit, and Bi-LSTM. As many learning algorithms, we have performed a training phase using different test subjects. After several tests, we can observe that the Bi-LSTM approach overcome the others techniques reaching a 93% of accuracy in fall detection. We believe that the bidirectional way of the Bi-LSTM algorithm gives excellent results because the use of their data is influenced by prior and new information, which compares to LSTM and GRU. Information obtained using this system did not compromise the user's privacy, which constitutes an additional advantage of this alternative. © 2013 IEEE.https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=842305

Samples and data accessibility in research biobanks. An explorative survey

Biobanks, which contain human biological samples and/or data, provide a crucial contribution to the progress of biomedical research. However, the effective and efficient use of biobank resources depends on their accessibility. In fact, making bio-resources promptly accessible to everybody may increase the benefits for society. Furthermore, optimizing their use and ensuring their quality will promote scientific creativity and, in general, contribute to the progress of bio-medical research. Although this has become a rather common belief, several laboratories are still secretive and continue to withhold samples and data. In this study, we conducted a questionnairebased survey in order to investigate sample and data accessibility in research biobanks operating all over the world. The survey involved a total of 46 biobanks. Most of them gave permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seemed not to be common practice. The analysis of the guidelines regarding the accessibility to resources of the biobanks that responded to the survey highlights three issues: (i) the request for applicants to explain what they would like to do with the resources requested; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) the request of co-authorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sample and data sharing stored in biobanks. As a second step of this study, we investigated the reasons behind the high diversity of requirements to access biobank resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where the biobanks operate

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Gravity-Inspired Graph Autoencoders for Directed Link Prediction

Graph autoencoders (AE) and variational autoencoders (VAE) recently emerged as powerful node embedding methods. In particular, graph AE and VAE were successfully leveraged to tackle the challenging link prediction problem, aiming at figuring out whether some pairs of nodes from a graph are connected by unobserved edges. However, these models focus on undirected graphs and therefore ignore the potential direction of the link, which is limiting for numerous real-life applications. In this paper, we extend the graph AE and VAE frameworks to address link prediction in directed graphs. We present a new gravity-inspired decoder scheme that can effectively reconstruct directed graphs from a node embedding. We empirically evaluate our method on three different directed link prediction tasks, for which standard graph AE and VAE perform poorly. We achieve competitive results on three real-world graphs, outperforming several popular baselines.Comment: ACM International Conference on Information and Knowledge Management (CIKM 2019

Fame for sale: efficient detection of fake Twitter followers

$\textit{Fake followers}$ are those Twitter accounts specifically created to inflate the number of followers of a target account. Fake followers are dangerous for the social platform and beyond, since they may alter concepts like popularity and influence in the Twittersphere - hence impacting on economy, politics, and society. In this paper, we contribute along different dimensions. First, we review some of the most relevant existing features and rules (proposed by Academia and Media) for anomalous Twitter accounts detection. Second, we create a baseline dataset of verified human and fake follower accounts. Such baseline dataset is publicly available to the scientific community. Then, we exploit the baseline dataset to train a set of machine-learning classifiers built over the reviewed rules and features. Our results show that most of the rules proposed by Media provide unsatisfactory performance in revealing fake followers, while features proposed in the past by Academia for spam detection provide good results. Building on the most promising features, we revise the classifiers both in terms of reduction of overfitting and cost for gathering the data needed to compute the features. The final result is a novel $\textit{Class A}$ classifier, general enough to thwart overfitting, lightweight thanks to the usage of the less costly features, and still able to correctly classify more than 95% of the accounts of the original training set. We ultimately perform an information fusion-based sensitivity analysis, to assess the global sensitivity of each of the features employed by the classifier. The findings reported in this paper, other than being supported by a thorough experimental methodology and interesting on their own, also pave the way for further investigation on the novel issue of fake Twitter followers