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Context: The retraction of research papers, for whatever reason, is a growing phenomenon. However, although retracted paper information is publicly available via publishers, it is somewhat distributed and inconsistent. Objective: The aim is to assess: (i) the extent and nature of retracted research in Computer Science (CS) (ii) the post-retraction citation behaviour of retracted works and (iii) the potential impact upon systematic reviews and mapping studies. Method: We analyse the Retraction Watch database and take citation information from the Web of Science and Google scholar. Results: We find that of the 33,955 entries in the Retraction watch database (16 May 2022), 2,816 are classified as CS, i.e., ≈ 8%. For CS, 56% of retracted papers provide little or no information as to the reasons. This contrasts with 26% for other disciplines. There is also some disparity between different publishers, a tendency for multiple versions of a retracted paper to be available beyond the Version of Record (VoR), and for new citations long after a paper is officially retracted (median = 3; maximum = 18). Systematic reviews are also impacted with ≈ 30% of the retracted papers having one or more citations from a review. Conclusions: Unfortunately, retraction seems to be a sufficiently common outcome for a scientific paper that we as a research community need to take it more seriously, e.g., standardising procedures and taxonomies across publishers and the provision of appropriate research tools. Finally, we recommend particular caution when undertaking secondary analyses and meta-analyses which are at risk of becoming contaminated by these problem primary studies. [ABSTRACT FROM AUTHOR]

Background: Peer evaluation is the cornerstone of science evaluation. In this paper, we analyze whether or not a form of peer evaluation, the pre-publication selection of the best papers in Computer Science (CS) conferences, is better than random, when considering future citations received by the papers. Methods: Considering 12 conferences (for several years), we collected the citation counts from Scopus for both the best papers and the non-best papers. For a different set of 17 conferences, we collected the data from Google Scholar. For each data set, we computed the proportion of cases whereby the best paper has more citations. We also compare this proportion for years before 2010 and after to evaluate if there is a propaganda effect. Finally, we count the proportion of best papers that are in the top 10% and 20% most cited for each conference instance. Results: The probability that a best paper will receive more citations than a non best paper is 0.72 (95% CI = 0.66, 0.77) for the Scopus data, and 0.78 (95% CI = 0.74, 0.81) for the Scholar data. There are no significant changes in the probabilities for different years. Also, 51% of the best papers are among the top 10% most cited papers in each conference/year, and 64% of them are among the top 20% most cited. Discussion: There is strong evidence that the selection of best papers in Computer Science conferences is better than a random selection, and that a significant number of the best papers are among the top cited papers in the conference. [ABSTRACT FROM AUTHOR]

The action required to stem the environmental and social implications of climate change depends crucially on how humankind shapes technology, economy, lifestyle and policy. With transport CO2 emissions accounting for about a quarter of the total, we examine the contribution of CO2 output by scientific travel. Thankfully for the reputation of the scientific community, CO2 emissions associated with the trips required to present a paper at a scientific conference account for just 0.003% of the yearly total. However, with CO2 emissions for a single conference trip amounting to 7% of an average individual’s total CO2 emissions, scientists should lead by example by demonstrating leadership in addressing the issue. [ABSTRACT FROM AUTHOR]

There is widespread debate on whether to anonymize author identities in peer review. The key argument for anonymization is to mitigate bias, whereas arguments against anonymization posit various uses of author identities in the review process. The Innovations in Theoretical Computer Science (ITCS) 2023 conference adopted a middle ground by initially anonymizing the author identities from reviewers, revealing them after the reviewer had submitted their initial reviews, and allowing the reviewer to change their review subsequently. We present an analysis of the reviews pertaining to the identification and use of author identities. Our key findings are: (I) A majority of reviewers self-report not knowing and being unable to guess the authors' identities for the papers they were reviewing. (II) After the initial submission of reviews, 7.1% of reviews changed their overall merit score and 3.8% changed their self-reported reviewer expertise. (III) There is a very weak and statistically insignificant correlation of the rank of authors' affiliations with the change in overall merit; there is a weak but statistically significant correlation with respect to change in reviewer expertise. We also conducted an anonymous survey to obtain opinions from reviewers and authors. The main findings from the 200 survey responses are: (i) A vast majority of participants favor anonymizing author identities in some form. (ii) The "middle-ground" initiative of ITCS 2023 was appreciated. (iii) Detecting conflicts of interest is a challenge that needs to be addressed if author identities are anonymized. Overall, these findings support anonymization of author identities in some form (e.g., as was done in ITCS 2023), as long as there is a robust and efficient way to check conflicts of interest. [ABSTRACT FROM AUTHOR]

Scientific progress, or scientific change, has been an important topic in the philosophy and history of science. Previous work has developed quantitative approaches to characterize the progression of science in different fields, but how individual scientists make progress through their careers is not well understood at a comprehensive scale. We characterize the regularity in the temporal dynamics of scientists' publishing behavior with computational algorithms that predict the historical emerging order of publications from individual scientists. We discover that scientists publish in ways following the processes of chaining that mirror those observed in historical word meaning extension, whereby novel ideas emerge by connecting to existing ideas that are proximal in semantic space. We report findings for predominant exemplar-based chaining that reconstructs the emerging order in the publications of 1,164 award-winning and random-sampled scientists from the fields of Physics, Chemistry, Medicine, Economics, and Computer Science over the past century. Our work provides large-scale evidence that scientists across different fields tend to share similar publishing behavior over time by taking incremental steps that build on their past research outputs. [ABSTRACT FROM AUTHOR]

Informed consent is the cornerstone of human research subject protection. Many subjects sign consent documents without understanding the study purpose, procedures, risks, benefits, and their rights. Proof of comprehension is not required and rarely obtained. Understanding might improve by using an interactive system with multiple options for hearing, viewing and reading about the study and the consent form at the subject’s own pace with testing and immediate feedback. This prospective randomized study compared the IRB-approved paper ICF for an actual clinical research study with an interactive presentation of the same study and its associated consent form using an iPad device in two populations: clinical research professionals, and patients drawn from a variety of outpatient practice settings. Of the 90 participants, 69 completed the online test and survey questions the day after the session (maximum 36 hours post-session). Among research professionals (n = 14), there was a trend (p  = .07) in the direction of iPad subjects testing better on the online test (mean correct  =  77%) compared with paper subjects (mean correct  =  57%). Among patients (n = 55), iPad subjects had significantly higher test scores than standard paper consent subjects (mean correct  =  75% vs 58%, p < .001). For all subjects, the total time spent reviewing the paper consent was 13.2 minutes, significantly less than the average of 22.7 minutes total on the three components to be reviewed using the iPad (introductory video, consent form, interactive quiz). Overall satisfaction and overall enjoyment slightly favored the interactive iPad presentation. This study demonstrates that combining an introductory video, standard consent language, and an interactive quiz on a tablet-based system improves comprehension of research study procedures and risks. [ABSTRACT FROM AUTHOR]

Researchers contribute to the frontiers of knowledge by establishing facts and reaching new conclusions through systematic investigations, and by subsequently publishing the outcomes of their research findings in the form of research papers. These research publications are indicative of researchers' scientific impact. Different bibliometric indices have been proposed to measure the impact or productivity of a researcher. These indices include publication count, citation count, number of coauthors, h-index, etc. The h-index, since its inception, has been ranked as the foremost impact indicator by many studies. However, as a consequence of the various short comings identified in h-index, some variants of h-index have been proposed. For instance, one dimension which requires significant attention is determining the ability of exceptional performers in a particular research area. In our study, we have compared effectiveness of h-index and some of its recent variants in identifying the exceptional performers of a field. We have also found correlation of h-index with recently proposed indices. A high correlation indicates same effect of these indices as of h-index and low correlation means these indices make non-redundant contribution while ranking potential researchers of a field of study. So far, effectiveness of these indices has not been explored/validated on real data sets of same field. We have considered these variants/modifications of h-index along with h-index and tested on comprehensive data set for the field of Computer Science. The Award winners' data set is considered as the benchmark for the evaluation of these indices for individual researchers. Results show that there is a low correlation of these indices with h-index, and in identifying exceptional performers of a field these indices perform better than h-index. [ABSTRACT FROM AUTHOR]

The gender gap in computer science (CS) research is a well-studied problem, with an estimated ratio of 15%–30% women researchers. However, far less is known about gender representation in specific fields within CS. Here, we investigate the gender gap in one large field, computer systems. To this end, we collected data from 72 leading peer-reviewed CS conferences, totalling 6,949 accepted papers and 19,829 unique authors (2,946 women, 16,307 men, the rest unknown). We combined these data with external demographic and bibliometric data to evaluate the ratio of women authors and the factors that might affect this ratio. Our main findings are that women represent only about 10% of systems researchers, and that this ratio is not associated with various conference factors such as size, prestige, double-blind reviewing, and inclusivity policies. Author research experience also does not significantly affect this ratio, although author country and work sector do. The 10% ratio of women authors is significantly lower than the 16% in the rest of CS. Our findings suggest that focusing on inclusivity policies alone cannot address this large gap. Increasing women's participation in systems research will require addressing the systemic causes of their exclusion, which are even more pronounced in systems than in the rest of CS. [ABSTRACT FROM AUTHOR]

Background: Finding duplicates is an important phase of systematic review. However, no consensus regarding the methods to find duplicates has been provided. This study aims to describe a pragmatic strategy of combining auto- and hand-searching duplicates in systematic review and to evaluate the prevalence and characteristics of duplicates. Methods and Findings: Literatures regarding portal vein thrombosis (PVT) and Budd-Chiari syndrome (BCS) were searched by the PubMed, EMBASE, and Cochrane library databases. Duplicates included one index paper and one or more redundant papers. They were divided into type-I (duplicates among different databases) and type-II (duplicate publications in different journals/issues) duplicates. For type-I duplicates, reference items were further compared between index and redundant papers. Of 10936 papers regarding PVT, 2399 and 1307 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 11.0% (1201/10936) and 6.1% (665/10936), respectively. They included 3431 type-I and 275 type-II duplicates. Of 11403 papers regarding BCS, 3275 and 2064 were identified as auto- and hand-searched duplicates, respectively. The prevalence of auto- and hand-searched redundant papers was 14.4% (1640/11403) and 9.1% (1039/11403), respectively. They included 5053 type-I and 286 type-II duplicates. Most of type-I duplicates were identified by auto-searching method (69.5%, 2385/3431 in PVT literatures; 64.6%, 3263/5053 in BCS literatures). Nearly all type-II duplicates were identified by hand-searching method (94.9%, 261/275 in PVT literatures; 95.8%, 274/286 in BCS literatures). Compared with those identified by auto-searching method, type-I duplicates identified by hand-searching method had a significantly higher prevalence of wrong items (47/2385 versus 498/1046, p<0.0001 in PVT literatures; 30/3263 versus 778/1790, p<0.0001 in BCS literatures). Most of wrong items originated from EMBASE database. Conclusion: Given the inadequacy of a single strategy of auto-searching method, a combined strategy of auto- and hand-searching methods should be employed to find duplicates in systematic review. [ABSTRACT FROM AUTHOR]

A ‘Sleeping Beauty in Science’ is a publication that goes unnoticed (‘sleeps’) for a long time and then, almost suddenly, attracts a lot of attention (‘is awakened by a prince’). The aim of this paper is to present a general methodology to investigate (1) important properties of Sleeping Beauties such as the time-dependent distribution, author characteristics, journals and fields, and (2) the cognitive environment of Sleeping Beauties. We are particularly interested to find out to what extent Sleeping Beauties are application-oriented and thus are potential Sleeping Innovations. In this study we focus primarily on physics (including materials science and astrophysics) and present first results for chemistry and for engineering & computer science. We find that more than half of the SBs are application-oriented. To study the cognitive environments of Sleeping Beauties we develop a new approach in which the cognitive environment of the SBs is analyzed, based on the mapping of Sleeping Beauties using their citation links and conceptual relations, particularly co-citation mapping. In this way we investigate the research themes in which the SBs are ‘used’ and possible causes of why the premature work in the SBs becomes topical, i.e., the trigger of the awakening of the SBs. This approach is tested with a blue skies SB and an application-oriented SB. We think that the mapping procedures discussed in this paper are not only important for bibliometric analyses. They also provide researchers with useful, interactive tools to discover both relevant older work as well as new developments, for instance in themes related to Sleeping Beauties that are also Sleeping Innovations. [ABSTRACT FROM AUTHOR]

: In computational science literature including, e.g., bioinformatics, computational statistics or machine learning, most published articles are devoted to the development of “new methods”, while comparison studies are generally appreciated by readers but surprisingly given poor consideration by many journals. This paper stresses the importance of neutral comparison studies for the objective evaluation of existing methods and the establishment of standards by drawing parallels with clinical research. The goal of the paper is twofold. Firstly, we present a survey of recent computational papers on supervised classification published in seven high-ranking computational science journals. The aim is to provide an up-to-date picture of current scientific practice with respect to the comparison of methods in both articles presenting new methods and articles focusing on the comparison study itself. Secondly, based on the results of our survey we critically discuss the necessity, impact and limitations of neutral comparison studies in computational sciences. We define three reasonable criteria a comparison study has to fulfill in order to be considered as neutral, and explicate general considerations on the individual components of a “tidy neutral comparison study”. R codes for completely replicating our statistical analyses and figures are available from the companion website http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/plea2013. [ABSTRACT FROM AUTHOR]

Science advances by pushing the boundaries of the adjacent possible. While the global scientific enterprise grows at an exponential pace, at the mesoscopic level the exploration and exploitation of research ideas are reflected through the rise and fall of research fields. The empirical literature has largely studied such dynamics on a case-by-case basis, with a focus on explaining how and why communities of knowledge production evolve. Although fields rise and fall on different temporal and population scales, they are generally argued to pass through a common set of evolutionary stages. To understand the social processes that drive these stages beyond case studies, we need a way to quantify and compare different fields on the same terms. In this paper we develop techniques for identifying common patterns in the evolution of scientific fields and demonstrate their usefulness using 1.5 million preprints from the arXiv repository covering 175 research fields spanning Physics, Mathematics, Computer Science, Quantitative Biology and Quantitative Finance. We show that fields consistently follow a rise and fall pattern captured by a two parameters right-tailed Gumbel temporal distribution. We introduce a field-specific re-scaled time and explore the generic properties shared by articles and authors at the creation, adoption, peak, and decay evolutionary phases. We find that the early phase of a field is characterized by disruptive works mixing of cognitively distant fields written by small teams of interdisciplinary authors, while late phases exhibit the role of specialized, large teams building on the previous works in the field. This method provides foundations to quantitatively explore the generic patterns underlying the evolution of research fields in science, with general implications in innovation studies. [ABSTRACT FROM AUTHOR]

Bibliographic analysis has been a very powerful tool in evaluating the effective contributions of a researcher and determining his/her future research potential. The lack of an absolute quantification of the author’s scientific contributions by the existing measurement system hampers the decision-making process. In this paper, a new metric system, Absolute index (Ab-index), has been proposed that allows a more objective comparison of the contributions of a researcher. The Ab-index takes into account the impact of research findings while keeping in mind the physical and intellectual contributions of the author(s) in accomplishing the task. The Ab-index and h-index were calculated for 10 highly cited geneticists and molecular biologist and 10 young researchers of biological sciences and compared for their relationship to the researchers input as a primary author. This is the first report of a measuring method clarifying the contributions of the first author, corresponding author, and other co-authors and the sharing of credit in a logical ratio. A java application has been developed for the easy calculation of the Ab-index. It can be used as a yardstick for comparing the credibility of different scientists competing for the same resources while the Productivity index (Pr-index), which is the rate of change in the Ab-index per year, can be used for comparing scientists of different age groups. The Ab-index has clear advantage over other popular metric systems in comparing scientific credibility of young scientists. The sum of the Ab-indices earned by individual researchers of an institute per year can be referred to as Pr-index of the institute. [ABSTRACT FROM AUTHOR]

Using the InCites tool of Thomson Reuters, this study compares normalized citation impact values calculated for China, Japan, France, Germany, United States, and the UK throughout the time period from 1981 to 2010. InCites offers a unique opportunity to study the normalized citation impacts of countries using (i) a long publication window (1981 to 2010), (ii) a differentiation in (broad or more narrow) subject areas, and (iii) allowing for the use of statistical procedures in order to obtain an insightful investigation of national citation trends across the years. Using four broad categories, our results show significantly increasing trends in citation impact values for France, the UK, and especially Germany across the last thirty years in all areas. The citation impact of papers from China is still at a relatively low level (mostly below the world average), but the country follows an increasing trend line. The USA exhibits a stable pattern of high citation impact values across the years. With small impact differences between the publication years, the US trend is increasing in engineering and technology but decreasing in medical and health sciences as well as in agricultural sciences. Similar to the USA, Japan follows increasing as well as decreasing trends in different subject areas, but the variability across the years is small. In most of the years, papers from Japan perform below or approximately at the world average in each subject area. [ABSTRACT FROM AUTHOR]

Divide-and-conquer dividing by a half recurrences, of the form x n = a · x ⌈ n / 2 ⌉ + a · x ⌊ n / 2 ⌋ + p (n) , n ⩾ 2 , appear in many areas of applied mathematics, from the analysis of algorithms to the optimization of phylogenetic balance indices. These equations are usually "solved" by means of a Master Theorem that provides a bound for the growing order of xn, but not the solution's explicit expression. In this paper we give a finite explicit expression for this solution, in terms of the binary decomposition of n, when the independent term p(n) is a polynomial in ⌈n/2⌉ and ⌊n/2⌋. As an application, we obtain explicit formulas for several sequences of interest in phylogenetics, combinatorics, and computer science, for which no such formulas were known so far: for instance, for the Total Cophenetic index and the rooted Quartet index of the maximally balanced bifurcating phylogenetic trees with n leaves, and the sum of the bitwise AND operator applied to pairs of complementary numbers up to n. [ABSTRACT FROM AUTHOR]

Network diffusion processes or how information spreads through networks have been widely examined in numerous disciplines such as epidemiology, physics, sociology, politics, or computer science. In this paper, we extend previous developments by considering a generalization of the diffusion by considering the possibility of differences in the speed of diffusion and reduction depending on the forces' directions. In this situation, the differential speed of diffusion produces deviations from the standard solution around the average of the initial conditions in the network. In fact, this asymmetry gives rise to non-linear dynamics in which, contrary to the symmetric case, the final solution depends on the topology of the graph as well as on the distribution of the initial values. Counter-intuitively, less central nodes in the network are able to exert a higher influence on the final solution. This behavior applies also for different simulated networks such as random, small-world, and scale-free. We show an example of this kind of asymmetric diffusion process in a real case. To do so, we use a network of US Boards of Directors, where boards are the nodes and the directors working for more than one board, are the links. Changes in the proportion of women serving on each board are influenced by the gradient between adjacent boards. We also show that there is an asymmetry: the gradient is reduced at a slower (faster) rhythm if the board has less (more) women than neighboring boards. We are able to quantify the accumulated effect of this asymmetry from 2000 to 2015 in the overall proportion of women on boards, in a 4.7 percentage points (the proportion should have been an 14.61% instead of the observed 9.93% in 2015). [ABSTRACT FROM AUTHOR]

Objective: Despite substantial investment in Electronic Medical Record (EMR) systems there has been little research to evaluate them. Our aim was to evaluate changes in efficiency and quality of services after the introduction of a purpose built EMR system, and to assess its acceptability by the doctors, nurses and patients using it. Methods: We compared a nine month period before and after the introduction of an EMR system in a large sexual health service, audited a sample of records in both periods and undertook anonymous surveys of both staff and patients. Results: There were 9,752 doctor consultations (in 5,512 consulting hours) in the Paper Medical Record (PMR) period and 9,145 doctor consultations (in 5,176 consulting hours in the EMR period eligible for inclusion in the analysis. There were 5% more consultations per hour seen by doctors in the EMR period compared to the PMR period (rate ratio = 1.05; 95% confidence interval, 1.02, 1.08) after adjusting for type of consultation. The qualitative evaluation of 300 records for each period showed no difference in quality (P>0.17). A survey of clinicians demonstrated that doctors and nurses preferred the EMR system (P<0.01) and a patient survey in each period showed no difference in satisfaction of their care (97% for PMR, 95% for EMR, P = 0.61). Conclusion: The introduction of an integrated EMR improved efficiency while maintaining the quality of the patient record. The EMR was popular with staff and was not associated with a decline in patient satisfaction in the clinical care provided. [ABSTRACT FROM AUTHOR]

Distributed Systems architectures are becoming the standard computational model for processing and transportation of information, especially for Cloud Computing environments. The increase in demand for application processing and data management from enterprise and end-user workloads continues to move from a single-node client-server architecture to a distributed multitier design where data processing and transmission are segregated. Software development must considerer the orchestration required to provision its core components in order to deploy the services efficiently in many independent, loosely coupled—physically and virtually interconnected—data centers spread geographically, across the globe. This network routing challenge can be modeled as a variation of the Travelling Salesman Problem (TSP). This paper proposes a new optimization algorithm for optimum route selection using Algorithmic Information Theory. The Kelly criterion for a Shannon-Bernoulli process is used to generate a reliable quantitative algorithm to find a near optimal solution tour. The algorithm is then verified by comparing the results with benchmark heuristic solutions in 3 test cases. A statistical analysis is designed to measure the significance of the results between the algorithms and the entropy function can be derived from the distribution. The tested results shown an improvement in the solution quality by producing routes with smaller length and time requirements. The quality of the results proves the flexibility of the proposed algorithm for problems with different complexities without relying in nature-inspired models such as Genetic Algorithms, Ant Colony, Cross Entropy, Neural Networks, 2opt and Simulated Annealing. The proposed algorithm can be used by applications to deploy services across large cluster of nodes by making better decision in the route design. The findings in this paper unifies critical areas in Computer Science, Mathematics and Statistics that many researchers have not explored and provided a new interpretation that advances the understanding of the role of entropy in decision problems encoded in Turing Machines. [ABSTRACT FROM AUTHOR]

The progress of science increasingly relies on machine learning (ML) and machines work alongside humans in various domains of science. This study investigates the team structure of ML-related projects and analyzes the contribution of ML to scientific knowledge production under different team structure, drawing on bibliometric analyses of 25,000 scientific publications in various disciplines. Our regression analyses suggest that (1) interdisciplinary collaboration between domain scientists and computer scientists as well as the engagement of interdisciplinary individuals who have expertise in both domain and computer sciences are common in ML-related projects; (2) the engagement of interdisciplinary individuals seem more important in achieving high impact and novel discoveries, especially when a project employs computational and domain approaches interdependently; and (3) the contribution of ML and its implication to team structure depend on the depth of ML. [ABSTRACT FROM AUTHOR]

A bridge role metric model is put forward in this paper. Compared with previous metric models, our solution of a large-scale object-oriented software system as a complex network is inherently more realistic. To acquire nodes and links in an undirected network, a new model that presents the crucial connectivity of a module or the hub instead of only centrality as in previous metric models is presented. Two previous metric models are described for comparison. In addition, it is obvious that the fitting curve between the results and degrees can well be fitted by a power law. The model represents many realistic characteristics of actual software structures, and a hydropower simulation system is taken as an example. This paper makes additional contributions to an accurate understanding of module design of software systems and is expected to be beneficial to software engineering practices. [ABSTRACT FROM AUTHOR]

Encouraging women to pursue STEM employment is frequently touted as a means of reducing the gender wage gap. We examine whether the attributes of computer science workers–who account for nearly half of those working in STEM jobs–explain the persistent gender wage gap in computer science, using American Community Survey (ACS) data from 2009 to 2019. Our analysis focuses on working-age respondents between the ages of 22 and 60 who had a college degree and were employed full-time. We use ordinary least squares (OLS) regression of logged wages on observed characteristics, before turning to regression decomposition techniques to estimate what proportion of the gender wage gap would remain if men and women were equally rewarded for the same attributes–such as parenthood or marital status, degree field, or occupation. Women employed in computer science jobs earned about 86.6 cents for every dollar that men earned–a raw gender gap that is smaller than it is for the overall labor force (where it was 82 percent). Controlling for compositional effects (family attributes, degree field and occupation) narrows the gender wage gap, though women continue to earn 9.1 cents per dollar less than their male counterparts. But differential returns to family characteristics and human capital measures account for almost two-thirds of the gender wage gap in computer science jobs. Women working in computer science receive both a marriage and parenthood premium relative to unmarried or childless women, but these are significantly smaller than the bonus that married men and fathers receive over their childless and unmarried peers. Men also receive sizable wage premiums for having STEM degrees in computer science and engineering when they work in computer science jobs, advantages that do not accrue to women. Closing the gender wage gap in computer science requires treating women more like men, not just increasing their representation. [ABSTRACT FROM AUTHOR]

In 1979 Haralick famously introduced a method for analyzing the texture of an image: a set of statistics extracted from the co-occurrence matrix. In this paper we investigate novel sets of texture descriptors extracted from the co-occurrence matrix; in addition, we compare and combine different strategies for extending these descriptors. The following approaches are compared: the standard approach proposed by Haralick, two methods that consider the co-occurrence matrix as a three-dimensional shape, a gray-level run-length set of features and the direct use of the co-occurrence matrix projected onto a lower dimensional subspace by principal component analysis. Texture descriptors are extracted from the co-occurrence matrix evaluated at multiple scales. Moreover, the descriptors are extracted not only from the entire co-occurrence matrix but also from subwindows. The resulting texture descriptors are used to train a support vector machine and ensembles. Results show that our novel extraction methods improve the performance of standard methods. We validate our approach across six medical datasets representing different image classification problems using the Wilcoxon signed rank test. The source code used for the approaches tested in this paper will be available at: http://www.dei.unipd.it/wdyn/?IDsezione=3314&IDgruppo_pass=124&preview=. [ABSTRACT FROM AUTHOR]

In this paper, we develop two automated authorship attribution schemes, one based on Multiple Discriminant Analysis (MDA) and the other based on a Support Vector Machine (SVM). The classification features we exploit are based on word frequencies in the text. We adopt an approach of preprocessing each text by stripping it of all characters except a-z and space. This is in order to increase the portability of the software to different types of texts. We test the methodology on a corpus of undisputed English texts, and use leave-one-out cross validation to demonstrate classification accuracies in excess of 90%. We further test our methods on the Federalist Papers, which have a partly disputed authorship and a fair degree of scholarly consensus. And finally, we apply our methodology to the question of the authorship of the Letter to the Hebrews by comparing it against a number of original Greek texts of known authorship. These tests identify where some of the limitations lie, motivating a number of open questions for future work. An open source implementation of our methodology is freely available for use at https://github.com/matthewberryman/author-detection. [ABSTRACT FROM AUTHOR]

Searching for new high temperature superconductors has long been a key research issue. Fe-based superconductors attract researchers' attention due to their high transition temperature, strong irreversibility field, and excellent crystallographic symmetry. By using doping methods and dopant levels, different types of new Fe-based superconductors are synthesized. The transition temperature is a key indicator to measure whether new superconductors are high temperature superconductors. However, the condition for measuring transition temperature are strict, and the measurement process is dangerous. There is a strong relationship between the lattice parameters and the transition temperature of Fe-based superconductors. To avoid the difficulties in measuring transition temperature, in this paper, we adopt a machine learning method to build a model based on the lattice parameters to predict the transition temperature of Fe-based superconductors. The model results are in accordance with available transition temperatures, showing 91.181% accuracy. Therefore, we can use the proposed model to predict unknown transition temperatures of Fe-based superconductors. [ABSTRACT FROM AUTHOR]

Understanding the dynamics of research production and collaboration may reveal better strategies for scientific careers, academic institutions, and funding agencies. Here we propose the use of a large and multidisciplinary database of scientific curricula in Brazil, namely, the Lattes Platform, to study patterns of scientific production and collaboration. Detailed information about publications and researchers is available in this database. Individual curricula are submitted by the researchers themselves so that coauthorship is unambiguous. Researchers can be evaluated by scientific productivity, geographical location and field of expertise. Our results show that the collaboration network is growing exponentially for the last three decades, with a distribution of number of collaborators per researcher that approaches a power-law as the network gets older. Moreover, both the distributions of number of collaborators and production per researcher obey power-law behaviors, regardless of the geographical location or field, suggesting that the same universal mechanism might be responsible for network growth and productivity. We also show that the collaboration network under investigation displays a typical assortative mixing behavior, where teeming researchers (i.e., with high degree) tend to collaborate with others alike. [ABSTRACT FROM AUTHOR]

The influence of the statistical properties of the network on the knowledge diffusion has been extensively studied. However, the structure evolution and the knowledge generation processes are always integrated simultaneously. By introducing the Cobb-Douglas production function and treating the knowledge growth as a cooperative production of knowledge, in this paper, we present two knowledge-generation dynamic evolving models based on different evolving mechanisms. The first model, named “HDPH model,” adopts the hyperedge growth and the hyperdegree preferential attachment mechanisms. The second model, named “KSPH model,” adopts the hyperedge growth and the knowledge stock preferential attachment mechanisms. We investigate the effect of the parameters on the total knowledge stock of the two models. The hyperdegree distribution of the HDPH model can be theoretically analyzed by the mean-field theory. The analytic result indicates that the hyperdegree distribution of the HDPH model obeys the power-law distribution and the exponent is . Furthermore, we present the distributions of the knowledge stock for different parameters . The findings indicate that our proposed models could be helpful for deeply understanding the scientific research cooperation. [ABSTRACT FROM AUTHOR]

Modern computing architecture based on the separation of memory and processing leads to a well known problem called the von Neumann bottleneck, a restrictive limit on the data bandwidth between CPU and RAM. This paper introduces a new approach to computing we call AHaH computing where memory and processing are combined. The idea is based on the attractor dynamics of volatile dissipative electronics inspired by biological systems, presenting an attractive alternative architecture that is able to adapt, self-repair, and learn from interactions with the environment. We envision that both von Neumann and AHaH computing architectures will operate together on the same machine, but that the AHaH computing processor may reduce the power consumption and processing time for certain adaptive learning tasks by orders of magnitude. The paper begins by drawing a connection between the properties of volatility, thermodynamics, and Anti-Hebbian and Hebbian (AHaH) plasticity. We show how AHaH synaptic plasticity leads to attractor states that extract the independent components of applied data streams and how they form a computationally complete set of logic functions. After introducing a general memristive device model based on collections of metastable switches, we show how adaptive synaptic weights can be formed from differential pairs of incremental memristors. We also disclose how arrays of synaptic weights can be used to build a neural node circuit operating AHaH plasticity. By configuring the attractor states of the AHaH node in different ways, high level machine learning functions are demonstrated. This includes unsupervised clustering, supervised and unsupervised classification, complex signal prediction, unsupervised robotic actuation and combinatorial optimization of procedures–all key capabilities of biological nervous systems and modern machine learning algorithms with real world application. [ABSTRACT FROM AUTHOR]

Constraints arise naturally in many scientific experiments/studies such as in, epidemiology, biology, toxicology, etc. and often researchers ignore such information when analyzing their data and use standard methods such as the analysis of variance (ANOVA). Such methods may not only result in a loss of power and efficiency in costs of experimentation but also may result poor interpretation of the data. In this paper we discuss constrained statistical inference in the context of linear mixed effects models that arise naturally in many applications, such as in repeated measurements designs, familial studies and others. We introduce a novel methodology that is broadly applicable for a variety of constraints on the parameters. Since in many applications sample sizes are small and/or the data are not necessarily normally distributed and furthermore error variances need not be homoscedastic (i.e. heterogeneity in the data) we use an empirical best linear unbiased predictor (EBLUP) type residual based bootstrap methodology for deriving critical values of the proposed test. Our simulation studies suggest that the proposed procedure maintains the desired nominal Type I error while competing well with other tests in terms of power. We illustrate the proposed methodology by re-analyzing a clinical trial data on blood mercury level. The methodology introduced in this paper can be easily extended to other settings such as nonlinear and generalized regression models. [ABSTRACT FROM AUTHOR]

Data-driven and machine learning based approaches for detecting, categorising and measuring abusive content such as hate speech and harassment have gained traction due to their scalability, robustness and increasingly high performance. Making effective detection systems for abusive content relies on having the right training datasets, reflecting a widely accepted mantra in computer science: Garbage In, Garbage Out. However, creating training datasets which are large, varied, theoretically-informed and that minimize biases is difficult, laborious and requires deep expertise. This paper systematically reviews 63 publicly available training datasets which have been created to train abusive language classifiers. It also reports on creation of a dedicated website for cataloguing abusive language data hatespeechdata.com. We discuss the challenges and opportunities of open science in this field, and argue that although more dataset sharing would bring many benefits it also poses social and ethical risks which need careful consideration. Finally, we provide evidence-based recommendations for practitioners creating new abusive content training datasets. [ABSTRACT FROM AUTHOR]

This paper proposed a novel bionic selective visual attention mechanism to quickly select regions that contain salient objects to reduce calculations. Firstly, lateral inhibition filtering, inspired by the limulus’ ommateum, is applied to filter low-frequency noises. After the filtering operation, we use Artificial Bee Colony (ABC) algorithm based selective visual attention mechanism to obtain the interested object to carry through the following recognition operation. In order to eliminate the camera motion influence, this paper adopted ABC algorithm, a new optimization method inspired by swarm intelligence, to calculate the motion salience map to integrate with conventional visual attention. To prove the feasibility and effectiveness of our method, several experiments were conducted. First the filtering results of lateral inhibition filter were shown to illustrate its noise reducing effect, then we applied the ABC algorithm to obtain the motion features of the image sequence. The ABC algorithm is proved to be more robust and effective through the comparison between ABC algorithm and popular Particle Swarm Optimization (PSO) algorithm. Except for the above results, we also compared the classic visual attention mechanism and our ABC algorithm based visual attention mechanism, and the experimental results of which further verified the effectiveness of our method. [ABSTRACT FROM AUTHOR]

Background: Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. Method: This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. Results: The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. Conclusion: The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid. [ABSTRACT FROM AUTHOR]

Identifying metaphorical language-use (e.g., sweet child) is one of the challenges facing natural language processing. This paper describes three novel algorithms for automatic metaphor identification. The algorithms are variations of the same core algorithm. We evaluate the algorithms on two corpora of Reuters and the New York Times articles. The paper presents the most comprehensive study of metaphor identification in terms of scope of metaphorical phrases and annotated corpora size. Algorithms’ performance in identifying linguistic phrases as metaphorical or literal has been compared to human judgment. Overall, the algorithms outperform the state-of-the-art algorithm with 71% precision and 27% averaged improvement in prediction over the base-rate of metaphors in the corpus. [ABSTRACT FROM AUTHOR]

The objective of the paper is to show that electroosmotic flow might play an important role in the intracellular transport of biomolecules. The paper presents two mathematical models describing the role of electroosmosis in the transport of the negatively charged messenger proteins to the negatively charged nucleus and in the recovery of the fluorescence after photobleaching. The parameters of the models were derived from the extensive review of the literature data. Computer simulations were performed within the COMSOL 4.2a software environment. The first model demonstrated that the presence of electroosmosis might intensify the flux of messenger proteins to the nucleus and allow the efficient transport of the negatively charged phosphorylated messenger proteins against the electrostatic repulsion of the negatively charged nucleus. The second model revealed that the presence of the electroosmotic flow made the time of fluorescence recovery dependent on the position of the bleaching spot relative to cellular membrane. The magnitude of the electroosmotic flow effect was shown to be quite substantial, i.e. increasing the flux of the messengers onto the nucleus up to 4-fold relative to pure diffusion and resulting in the up to 3-fold change in the values of fluorescence recovery time, and therefore the apparent diffusion coefficient determined from the fluorescence recovery after photobleaching experiments. Based on the results of the modeling and on the universal nature of the electroosmotic flow, the potential wider implications of electroosmotic flow in the intracellular and extracellular biological processes are discussed. Both models are available for download at ModelDB. [ABSTRACT FROM AUTHOR]

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data. [ABSTRACT FROM AUTHOR]

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/. [ABSTRACT FROM AUTHOR]

In this paper, we introduce a biologically inspired model to generate complex networks. In contrast to many other construction procedures for growing networks introduced so far, our method generates networks from one-dimensional symbol sequences that are related to the so called Collatz problem from number theory. The major purpose of the present paper is, first, to derive a symbol sequence from the Collatz problem, we call the step sequence, and investigate its structural properties. Second, we introduce a construction procedure for growing networks that is based on these step sequences. Third, we investigate the structural properties of this new network class including their finite scaling and asymptotic behavior of their complexity, average shortest path lengths and clustering coefficients. Interestingly, in contrast to many other network models including the small-world network from Watts & Strogatz, we find that CS graphs become ‘smaller’ with an increasing size. [ABSTRACT FROM AUTHOR]

Information diffusion has been widely discussed in various disciplines including sociology, economics, physics or computer science. In this paper, we generalize the linear threshold model in signed networks consisting of both positive and negative links. We analyze the dynamics of the spread of information based on balance theory, and find that a signed network can generate path dependence while structural balance can help remove the path dependence when seeded with balanced initialized active nodes. Simulation shows that the diffusion of information based on positive links contradicts that based on negative links. More positive links in signed networks are more likely to activate nodes and remove path dependence, but they can reduce predictability that is based on active states. We also find that a balanced structure can facilitate both the magnitude and speed of information diffusion, remove the path dependence, and cause polarization. [ABSTRACT FROM AUTHOR]

In recent years, with the development of computer science, deep learning is held as competent enough to solve the problem of inference and learning in high dimensional space. Therefore, it has received unprecedented attention from both the academia and the business community. Compared with CPU/GPU, FPGA has attracted much attention for its high-energy efficiency, short development cycle and reconfigurability in the aspect of deep learning algorithm. However, because of the limited research on OpenCL optimization on FPGA of deep learning algorithms, OpenCL tools and models applied to CPU/GPU cannot be directly used on FPGA. This makes it difficult for software programmers to use FPGA when implementing deep learning algorithms for a rewarding performance. To solve this problem, this paper proposed an OpenCL computational model based on FPGA template architecture to optimize the time-consuming convolution layer in deep learning. The comparison between the program applying the computational model and the corresponding optimization program provided by Xilinx indicates that the former is 8-40 times higher than the latter in terms of performance. [ABSTRACT FROM AUTHOR]

Privacy-aware intersection set computation (PISC) can be modeled as secure multi-party computation. The basic idea is to compute the intersection of input sets without leaking privacy. Furthermore, PISC should be sufficiently flexible to recommend approximate intersection items. In this paper, we reveal two previously unpublished attacks against PISC, which can be used to reveal and link one input set to another input set, resulting in privacy leakage. We coin these as Set Linkage Attack and Set Reveal Attack. We then present a lightweight and flexible PISC scheme (LiPISC) and prove its security (including against Set Linkage Attack and Set Reveal Attack). [ABSTRACT FROM AUTHOR]

With an increasing emphasis on network security, much more attentions have been attracted to the vulnerability of complex networks. In this paper, the fractal dimension, which can reflect space-filling capacity of networks, is redefined as the origin moment of the edge betweenness to obtain a more reasonable evaluation of vulnerability. The proposed model combining multiple evaluation indexes not only overcomes the shortage of average edge betweenness’s failing to evaluate vulnerability of some special networks, but also characterizes the topological structure and highlights the space-filling capacity of networks. The applications to six US airline networks illustrate the practicality and effectiveness of our proposed method, and the comparisons with three other commonly used methods further validate the superiority of our proposed method. [ABSTRACT FROM AUTHOR]