Progress in Whole Genome Sequencing (WGS) will soon allow a large number of individuals to have their genome fully sequenced. This lays the foundations to improve modern healthcare, enabling a new era of personalized medicine where diagnosis and treatment is tailored to the patient's genetic makeup. It also allows individuals motivated by personal curiosity to have access to their genetic information, and use it, e.g., to trace their ancestry. However, the very same progress also amplifies a number of ethical and privacy concerns, that stem from the unprecedented sensitivity of genomic information and that are not well studied. This paper presents an exploratory ethnographic study of users' perception of privacy and ethical issues with WGS, as well as their attitude toward different WGS programs. We report on a series of semi-structured interviews, involving 16 participants, and analyze the results both quantitatively and qualitatively. Our analysis shows that users exhibit common trust concerns and fear of discrimination, and demand to retain strict control over their genetic information. Finally, we highlight the need for further research in the area and follow-up studies that build on our initial findings.
Also, prior work analyzed the issue of labor discrimination in relationship to disease predisposition, mostly from the legal standpoint. We refer to the work by @cite_39 for details, along with a review of well-known rulings.
@cite_39
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The article introduces digital image restoration to the reader who is just beginning in this field, and provides a review and analysis for the reader who may already be well-versed in image restoration. The perspective on the topic is one that comes primarily from work done in the field of signal processing. Thus, many of the techniques and works cited relate to classical signal processing approaches to estimation theory, filtering, and numerical analysis. In particular, the emphasis is placed primarily on digital image restoration algorithms that grow out of an area known as "regularized least squares" methods. It should be noted, however, that digital image restoration is a very broad field, as we discuss, and thus contains many other successful approaches that have been developed from different perspectives, such as optics, astronomy, and medical imaging, just to name a few. In the process of reviewing this topic, we address a number of very important issues in this field that are not typically discussed in the technical literature. Code ownership establishes a chain of responsibility for modules in large software systems. Although prior work uncovers a link between code ownership heuristics and software quality, these heuristics rely solely on the authorship of code changes. In addition to authoring code changes, developers also make important contributions to a module by reviewing code changes. Indeed, recent work shows that reviewers are highly active in modern code review processes, often suggesting alternative solutions or providing updates to the code changes. In this paper, we complement traditional code ownership heuristics using code review activity. Through a case study of six releases of the large Qt and OpenStack systems, we find that: (1) 67 --86 of developers did not author any code changes for a module, but still actively contributed by reviewing 21 --39 of the code changes, (2) code ownership heuristics that are aware of reviewing activity share a relationship with software quality, and (3) the proportion of reviewers without expertise shares a strong, increasing relationship with the likelihood of having post-release defects. Our results suggest that reviewing activity captures an important aspect of code ownership, and should be included in approximations of it in future studies. LifeLines provide a general visualization environment for personal histories that can be applied to medical and court records, professional histories and other types of biographical data. A one screen overview shows multiple facets of the records. Aspects, for example medical conditions or legal cases, are displayed as individual time lines, while icons indicate discrete events, such as physician consultations or legal reviews. Line color and thickness illustrate relationships or significance, rescaling tools and filters allow users to focus on part of the information. LifeLines reduce the chances of missing information, facilitate spotting anomalies and trends, streamline access to details, while remaining tailorable and easily transferable between applications. The paper describes the use of LifeLines for youth records of the Maryland Department of Juvenile Justice and also for medical records. User's feedback was collected using a Visual Basic prototype for the youth record. Techniques to deal with complex records are reviewed and issues of a standard personal record format are discussed. The observation that disease associated proteins often interact with each other has fueled the development of network-based approaches to elucidate the molecular mechanisms of human disease. Such approaches build on the assumption that protein interaction networks can be viewed as maps in which diseases can be identified with localized perturbation within a certain neighborhood. The identification of these neighborhoods, or disease modules, is therefore a prerequisite of a detailed investigation of a particular pathophenotype. While numerous heuristic methods exist that successfully pinpoint disease associated modules, the basic underlying connectivity patterns remain largely unexplored. In this work we aim to fill this gap by analyzing the network properties of a comprehensive corpus of 70 complex diseases. We find that disease associated proteins do not reside within locally dense communities and instead identify connectivity significance as the most predictive quantity. This quantity inspires the design of a novel Disease Module Detection (DIAMOnD) algorithm to identify the full disease module around a set of known disease proteins. We study the performance of the algorithm using well-controlled synthetic data and systematically validate the identified neighborhoods for a large corpus of diseases. This paper presents an effective memetic approach (HEAD ) designed for coloring difficult graphs. In this algorithm a powerful tabu search is used inside a very specific population of individuals. Indeed, the main characteristic of (HEAD ) is to work with a population of only two individuals. This provides a very simple algorithm with neither selection operator nor replacement strategy. Because of its simplicity, (HEAD ) allows an easy way for managing the diversity. We focus this work on the impact of this diversity management on well-studied graphs of the DIMACS challenge benchmarks, known to be very difficult to solve. A detailed analysis is provided for three graphs on which (HEAD ) finds a legal coloring with less colors than reference algorithms: DSJC500.5 with 47 colors, DSJC1000.5 with 82 colors and flat1000_76_0 with 81 colors. The analysis performed in this work will allow to improve (HEAD ) efficiency in terms of computation time and maybe to decrease the number of needed colors for other graphs. Graph-structured data arise naturally in many different application domains. By representing data as graphs, we can capture entities (i.e., nodes) as well as their relationships (i.e., edges) with each other. Many useful insights can be derived from graph-structured data as demonstrated by an ever-growing body of work focused on graph mining. However, in the real-world, graphs can be both large - with many complex patterns - and noisy which can pose a problem for effective graph mining. An effective way to deal with this issue is to incorporate "attention" into graph mining solutions. An attention mechanism allows a method to focus on task-relevant parts of the graph, helping it to make better decisions. In this work, we conduct a comprehensive and focused survey of the literature on the emerging field of graph attention models. We introduce three intuitive taxonomies to group existing work. These are based on problem setting (type of input and output), the type of attention mechanism used, and the task (e.g., graph classification, link prediction, etc.). We motivate our taxonomies through detailed examples and use each to survey competing approaches from a unique standpoint. Finally, we highlight several challenges in the area and discuss promising directions for future work. Scholars are increasingly citing electronic “web references” which are not preserved in libraries or full text archives. WebCite is a new standard for citing web references. To “webcite” a document involves archiving the cited Web page through www.webcitation.org and citing the WebCite permalink instead of (or in addition to) the unstable live Web page. This journal has amended its “instructions for authors” accordingly, asking authors to archive cited Web pages before submitting a manuscript. Almost 200 other journals are already using the system. We discuss the rationale for WebCite, its technology, and how scholars, editors, and publishers can benefit from the service. Citing scholars initiate an archiving process of all cited Web references, ideally before they submit a manuscript. Authors of online documents and websites which are expected to be cited by others can ensure that their work is permanently available by creating an archived copy using WebCite and providing the citation information including the WebCite link on their Web document(s). Editors should ask their authors to cache all cited Web addresses (Uniform Resource Locators, or URLs) “prospectively” before submitting their manuscripts to their journal. Editors and publishers should also instruct their copyeditors to cache cited Web material if the author has not done so already. Finally, WebCite can process publisher submitted “citing articles” (submitted for example as eXtensible Markup Language [XML] documents) to automatically archive all cited Web pages shortly before or on publication. Finally, WebCite can act as a focussed crawler, caching retrospectively references of already published articles. Copyright issues are addressed by honouring respective Internet standards (robot exclusion files, no-cache and no-archive tags). Long-term preservation is ensured by agreements with libraries and digital preservation organizations. The resulting WebCite Index may also have applications for research assessment exercises, being able to measure the impact of Web services and published Web documents through access and Web citation metrics. @PARASPLIT [J Med Internet Res 2005;7(5):e60] Classification, which involves finding rules that partition a given da.ta set into disjoint groups, is one class of data mining problems. Approaches proposed so far for mining classification rules for large databases are mainly decision tree based symbolic learning methods. The connectionist approach based on neura.l networks has been thought not well suited for data mining. One of the major reasons cited is that knowledge generated by neural networks is not explicitly represented in the form of rules suitable for verification or interpretation by humans. This paper examines this issue. With our newly developed algorithms, rules which are similar to, or more concise than those generated by the symbolic methods can be extracted from the neural networks. The data mining process using neural networks with the emphasis on rule extraction is described. ExperimenM results and comparison with previously published works are presented. Rule extraction (RE) from recurrent neural networks (RNNs) refers to finding models of the underlying RNN, typically in the form of finite state machines, that mimic the network to a satisfactory degree while having the advantage of being more transparent. RE from RNNs can be argued to allow a deeper and more profound form of analysis of RNNs than other, more or less ad hoc methods. RE may give us understanding of RNNs in the intermediate levels between quite abstract theoretical knowledge of RNNs as a class of computing devices and quantitative performance evaluations of RNN instantiations. The development of techniques for extraction of rules from RNNs has been an active field since the early 1990s. This article reviews the progress of this development and analyzes it in detail. In order to structure the survey and evaluate the techniques, a taxonomy specifically designed for this purpose has been developed. Moreover, important open research issues are identified that, if addressed properly, possibly can give the field a significant push forward. Developers always focus on delivering high-quality updates to improve, or maintain the rating of their apps. Prior work has studied user reviews by analyzing all reviews of an app. However, this app-level analysis misses the point that users post reviews to provide their feedback on a certain update. For example, two bad updates of an app with a history of good updates would not be spotted using app-level analysis. In this paper, we examine reviews at the update-level to better understand how users perceive bad updates. We focus our study on the top 250 bad updates (i.e., updates with the highest increase in the percentage of negative reviews relative to the prior updates of the app) from 26,726 updates of 2,526 top free-to-download apps in the Google Play Store. We find that feature removal and UI issues have the highest increase in the percentage of negative reviews. Bad updates with crashes and functional issues are the most likely to be fixed by a later update. However, developers often do not mention these fixes in the release notes. Our work demonstrates the necessity of an update-level analysis of reviews to capture the feelings of an app's user-base about a particular update. We analyze the dynamics of the behavior known as 'unfollow' in Twitter. We collected daily snapshots of the online relationships of 1.2 million Korean-speaking users for 51 days as well as all of their tweets. We found that Twitter users frequently unfollow. We then discover the major factors, including the reciprocity of the relationships, the duration of a relationship, the followees' informativeness, and the overlap of the relationships, which affect the decision to unfollow. We conduct interview with 22 Korean respondents to supplement the quantitative results. They unfollowed those who left many tweets within a short time, created tweets about uninteresting topics, or tweeted about the mundane details of their lives. To the best of our knowledge, this work is the first systematic study of the unfollow behavior in Twitter. There are fundamental limits to the accuracy with which one can determine the state of a quantum system. I give an overview of the main approaches to quantum state discrimination. Several strategies exist. In quantum hypothesis testing, a quantum system is prepared in a member of a known, finite set of states, and the aim is to guess which one with the minimum probability of error. Error free discrimination is also sometimes possible, if we allow for the possibility of obtaining inconclusive results. If no prior information about the state is provided, then it is impractical to try to determine it exactly, and it must be estimated instead. In addition to reviewing these various strategies, I describe connections between state discrimination, the manipulation of quantum entanglement and quantum cloning. Recent experimental work is also discussed. A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results. The machine learning provides a theoretical and methodological framework to quantify the relationship between user OoE (Quality of Experience) and network QoS (Quality of Service). This paper presents an overview of QoE-QoS correlation models based on machine learning techniques. According to the learning type, we propose a categorization of correlation models. For each category, we review the main existing works by citing deployed learning methods and model parameters (QoE measurement, QoS parameters and service type). Moreover, the survey will provide researchers with the latest trends and findings in this field. Citations are important in academic dissemination. To help researchers check the completeness of citations while authoring a paper, we introduce a citation recommendation system called RefSeer. Researchers can use it to find related works to cited while authoring papers. It can also be used by reviewers to check the completeness of a paper's references. RefSeer presents both topic based global recommendation and also citation-context based local recommendation. By evaluating the quality of recommendation, we show that such recommendation system can recommend citations with good precision and recall. We also show that our recommendation system is very efficient and scalable. Human Desoxyribo-Nucleic Acid (DNA) sequences offer a wealth of information that reveal, among others, predisposition to various diseases and paternity relations. The breadth and personalized nature of this information highlights the need for privacy-preserving protocols. In this paper, we present a new error-resilient privacy-preserving string searching protocol that is suitable for running private DNA queries. This protocol checks if a short template (e.g., a string that describes a mutation leading to a disease), known to one party, is present inside a DNA sequence owned by another party, accounting for possible errors and without disclosing to each party the other party's input. Each query is formulated as a regular expression over a finite alphabet and implemented as an automaton. As the main technical contribution, we provide a protocol that allows to execute any finite state machine in an oblivious manner, requiring a communication complexity which is linear both in the number of states and the length of the input string. Recent work on mid-level visual representations aims to capture information at the level of complexity higher than typical "visual words", but lower than full-blown semantic objects. Several approaches [5,6,12,23] have been proposed to discover mid-level visual elements, that are both 1) representative, i.e., frequently occurring within a visual dataset, and 2) visually discriminative. However, the current approaches are rather ad hoc and difficult to analyze and evaluate. In this work, we pose visual element discovery as discriminative mode seeking, drawing connections to the the well-known and well-studied mean-shift algorithm [2, 1, 4, 8]. Given a weakly-labeled image collection, our method discovers visually-coherent patch clusters that are maximally discriminative with respect to the labels. One advantage of our formulation is that it requires only a single pass through the data. We also propose the Purity-Coverage plot as a principled way of experimentally analyzing and evaluating different visual discovery approaches, and compare our method against prior work on the Paris Street View dataset of [5]. We also evaluate our method on the task of scene classification, demonstrating state-of-the-art performance on the MIT Scene-67 dataset. When we write or prepare to write a research paper, we always have appropriate references in mind. However, there are most likely references we have missed and should have been read and cited. As such a good citation recommendation system would not only improve our paper but, overall, the efficiency and quality of literature search. Usually, a citation's context contains explicit words explaining the citation. Using this, we propose a method that "translates" research papers into references. By considering the citations and their contexts from existing papers as parallel data written in two different "languages", we adopt the translation model to create a relationship between these two "vocabularies". Experiments on both CiteSeer and CiteULike dataset show that our approach outperforms other baseline methods and increase the precision, recall and f-measure by at least 5 to 10 , respectively. In addition, our approach runs much faster in the both training and recommending stage, which proves the effectiveness and the scalability of our work. Reading academic paper is a daily task for researchers and graduate students. However, reading effectively can be challenging, particularly for novices in scientific research. For example, when readers are reading the related work section that cites a fair number of references in limited page space, they often need to flip back and forth between the text and the references and may also frequently search elsewhere for more information about the references. This increases the difficulty of understanding a paper. In this paper, we propose a narrative visualization system that helps the reading of academic papers. As a first step, we adopt narrative visualization to present literature review as interactive slides. Specifically, we propose a narrative structure with three levels of granularities that the reader can drill down or roll up freely. The logic flow of a slideshow can be organized based on the paper's presentation or citations. We demonstrate the effectiveness of our system through several case studies and user studies. The results show that the system allows users to quickly track and glance related work, making paper reading more effective and enjoyable. Provides a systematic account of the subject area, concentrating on the most recent advances in the field. While the focus is on practical considerations, both theoretical and practical issues are explored. Among the advances covered are: regularized discriminant analysis and bootstrap-based assessment of the performance of a sample-based discriminant rule and extensions of discriminant analysis motivated by problems in statistical image analysis. Includes over 1,200 references in the bibliography.