62,468 research outputs found

    Integrating and Ranking Uncertain Scientific Data

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    Mediator-based data integration systems resolve exploratory queries by joining data elements across sources. In the presence of uncertainties, such multiple expansions can quickly lead to spurious connections and incorrect results. The BioRank project investigates formalisms for modeling uncertainty during scientific data integration and for ranking uncertain query results. Our motivating application is protein function prediction. In this paper we show that: (i) explicit modeling of uncertainties as probabilities increases our ability to predict less-known or previously unknown functions (though it does not improve predicting the well-known). This suggests that probabilistic uncertainty models offer utility for scientific knowledge discovery; (ii) small perturbations in the input probabilities tend to produce only minor changes in the quality of our result rankings. This suggests that our methods are robust against slight variations in the way uncertainties are transformed into probabilities; and (iii) several techniques allow us to evaluate our probabilistic rankings efficiently. This suggests that probabilistic query evaluation is not as hard for real-world problems as theory indicates

    The Shortest Path to Happiness: Recommending Beautiful, Quiet, and Happy Routes in the City

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    When providing directions to a place, web and mobile mapping services are all able to suggest the shortest route. The goal of this work is to automatically suggest routes that are not only short but also emotionally pleasant. To quantify the extent to which urban locations are pleasant, we use data from a crowd-sourcing platform that shows two street scenes in London (out of hundreds), and a user votes on which one looks more beautiful, quiet, and happy. We consider votes from more than 3.3K individuals and translate them into quantitative measures of location perceptions. We arrange those locations into a graph upon which we learn pleasant routes. Based on a quantitative validation, we find that, compared to the shortest routes, the recommended ones add just a few extra walking minutes and are indeed perceived to be more beautiful, quiet, and happy. To test the generality of our approach, we consider Flickr metadata of more than 3.7M pictures in London and 1.3M in Boston, compute proxies for the crowdsourced beauty dimension (the one for which we have collected the most votes), and evaluate those proxies with 30 participants in London and 54 in Boston. These participants have not only rated our recommendations but have also carefully motivated their choices, providing insights for future work.Comment: 11 pages, 7 figures, Proceedings of ACM Hypertext 201

    Structured Psychosocial Stress and Therapeutic Intervention: Toward a Realistic Biological Medicine

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    Using generalized 'language of thought' arguments appropriate to interacting cognitive modules, we explore how disease states can interact with medical treatment, including, but not limited to, drug therapy. The feedback between treatment and response creates a kind of idiotypic 'hall of mirrors' generating a pattern of 'efficacy', 'treatment failure', and 'adverse reactions' which will, from a Rate Distortion perspective, embody a distorted image of externally-imposed structured psychosocial stress. This analysis, unlike current pharmacogenetics, does not either reify 'race' or blame the victim by using genetic structure to place the locus-of-control within a group or individual. Rather, it suggests that a comparatively simple series of questions to identify longitudinal and cross-sectional stressors may provide more effective guidance for specification of individual therapy than complicated genotyping strategies of dubious meaning. These latter are likely to be both very expensive and utterly blind to the impact of structured psychosocial stress -- a euphemism for various forms of racism and ethnic cleansing -- which, we contend, is often a principal determinant of treatment outcome at both individual and community levels of organization. We propose, to effectively address 'health disparities' between populations, and in contrast to current biomedical ideology based on a simplistic genetic determinism, a richer program of biological medicine reflecting Lewontin's 'triple helix' of genes, environment, and development, a program more in concert with the realities of a basic human biology marked by hypersociality unusual in vertibrates. Aggressive social, economic, and other policies of affirmative action to redress the persisting burdens of history would be an integral component of any such project

    Research and Education in Computational Science and Engineering

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    Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

    MPA network design based on graph network theory and emergent properties of larval dispersal

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    Despite the recognised effectiveness of networks of Marine Protected Areas (MPAs) as a biodiversity conservation instrument, nowadays MPA network design frequently disregards the importance of connectivity patterns. In the case of sedentary marine populations, connectivity stems not only from the stochastic nature of the physical environment that affects early-life stages dispersal, but also from the spawning stock attributes that affect the reproductive output (e.g., passive eggs and larvae) and its survivorship. Early-life stages are virtually impossible to track in the ocean. Therefore, numerical ocean current simulations coupled to egg and larval Lagrangian transport models remain the most common approach for the assessment of marine larval connectivity. Inferred larval connectivity may be different depending on the type of connectivity considered; consequently, the prioritisation of sites for marine populations' conservation might also differ. Here, we introduce a framework for evaluating and designing MPA networks based on the identification of connectivity hotspots using graph theoretic analysis. We use as a case of study a network of open-access areas and MPAs, off Mallorca Island (Spain), and test its effectiveness for the protection of the painted comber Serranus scriba. Outputs from network analysis are used to: (1) identify critical areas for improving overall larval connectivity; (2) assess the impact of species' biological parameters in network connectivity; and (3) explore alternative MPA configurations to improve average network connectivity. Results demonstrate the potential of graph theory to identify non-trivial egg/larval dispersal patterns and emerging collective properties of the MPA network which are relevant for increasing protection efficiency.Comment: 8 figures, 3 tables, 1 Supplementary material (including 4 table; 3 figures and supplementary methods

    Information access tasks and evaluation for personal lifelogs

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    Emerging personal lifelog (PL) collections contain permanent digital records of information associated with individuals’ daily lives. This can include materials such as emails received and sent, web content and other documents with which they have interacted, photographs, videos and music experienced passively or created, logs of phone calls and text messages, and also personal and contextual data such as location (e.g. via GPS sensors), persons and objects present (e.g. via Bluetooth) and physiological state (e.g. via biometric sensors). PLs can be collected by individuals over very extended periods, potentially running to many years. Such archives have many potential applications including helping individuals recover partial forgotten information, sharing experiences with friends or family, telling the story of one’s life, clinical applications for the memory impaired, and fundamental psychological investigations of memory. The Centre for Digital Video Processing (CDVP) at Dublin City University is currently engaged in the collection and exploration of applications of large PLs. We are collecting rich archives of daily life including textual and visual materials, and contextual context data. An important part of this work is to consider how the effectiveness of our ideas can be measured in terms of metrics and experimental design. While these studies have considerable similarity with traditional evaluation activities in areas such as information retrieval and summarization, the characteristics of PLs mean that new challenges and questions emerge. We are currently exploring the issues through a series of pilot studies and questionnaires. Our initial results indicate that there are many research questions to be explored and that the relationships between personal memory, context and content for these tasks is complex and fascinating

    General scores for accessibility and inequality measures in urban areas

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    In the last decades, the acceleration of urban growth has led to an unprecedented level of urban interactions and interdependence. This situation calls for a significant effort among the scientific community to come up with engaging and meaningful visualizations and accessible scenario simulation engines. The present paper gives a contribution in this direction by providing general methods to evaluate accessibility in cities based on public transportation data. Through the notion of isochrones, the accessibility quantities proposed measure the performance of transport systems at connecting places and people in urban systems. Then we introduce scores rank cities according to their overall accessibility. We highlight significant inequalities in the distribution of these measures across the population, which are found to be strikingly similar across various urban environments. Our results are released through the interactive platform: www.citychrone.org, aimed at providing the community at large with a useful tool for awareness and decision-making
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