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Digital Libraries

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Papers in this area

24 featured work(s)

preprint2018arXiv

The Many Shapes of Archive-It

Web archives, a key area of digital preservation, meet the needs of journalists, social scientists, historians, and government organizations. The use cases for these groups often require that they guide the archiving process themselves, selecting their own original resources, or seeds, and creating their own web archive collections. We focus on the collections within Archive-It, a subscription service started by the Internet Archive in 2005 for the purpose of allowing organizations to create their own collections of archived web pages, or mementos. Understanding these collections could be done via their user-supplied metadata or via text analysis, but the metadata is applied inconsistently between collections and some Archive-It collections consist of hundreds of thousands of seeds, making it costly in terms of time to download each memento. Our work proposes using structural metadata as an additional way to understand these collections. We explore structural features currently existing in these collections that can unveil curation and crawling behaviors. We adapt the concept of the collection growth curve for understanding Archive-It collection curation and crawling behavior. We also introduce several seed features and come to an understanding of the diversity of resources that make up a collection. Finally, we use the descriptions of each collection to identify four semantic categories of Archive-It collections. Using the identified structural features, we reviewed the results of runs with 20 classifiers and are able to predict the semantic category of a collection using a Random Forest classifier with a weighted average F1 score of 0.720, thus bridging the structural to the descriptive. Our method is useful because it saves the researcher time and bandwidth. Identifying collections by their semantic category allows further downstream processing to be tailored to these categories.

preprint2018arXiv

The many faces of mobility: Using bibliometric data to measure the movement of scientists

This paper presents a methodological framework for developing scientific mobility indicators based on bibliometric data. We identify nearly 16 million individual authors from publications covered in the Web of Science for the 2008-2015 period. Based on the information provided across individuals' publication records, we propose a general classification for analyzing scientific mobility using institutional affiliation changes. We distinguish between migrants--authors who have ruptures with their country of origin--and travelers--authors who gain additional affiliations while maintaining affiliation with their country of origin. We find that 3.7 percent of researchers who have published at least one paper over the period are mobile. Travelers represent 72.7 percent of all mobile scholars, but migrants have higher scientific impact. We apply this classification at the country level, expanding the classification to incorporate the directionality of scientists' mobility (i.e., incoming and outgoing). We provide a brief analysis to highlight the utility of the proposed taxonomy to study scholarly mobility and discuss the implications for science policy.

preprint2019arXiv

Social Cards Probably Provide For Better Understanding Of Web Archive Collections

Used by a variety of researchers, web archive collections have become invaluable sources of evidence. If a researcher is presented with a web archive collection that they did not create, how do they know what is inside so that they can use it for their own research? Search engine results and social media links are represented as surrogates, small easily digestible summaries of the underlying page. Search engines and social media have a different focus, and hence produce different surrogates than web archives. Search engine surrogates help a user answer the question "Will this link meet my information need?" Social media surrogates help a user decide "Should I click on this?" Our use case is subtly different. We hypothesize that groups of surrogates together are useful for summarizing a collection. We want to help users answer the question of "What does the underlying collection contain?" But which surrogate should we use? With Mechanical Turk participants, we evaluate six different surrogate types against each other. We find that the type of surrogate does not influence the time to complete the task we presented the participants. Of particular interest are social cards, surrogates typically found on social media, and browser thumbnails, screen captures of web pages rendered in a browser. At $p=0.0569$, and $p=0.0770$, respectively, we find that social cards and social cards paired side-by-side with browser thumbnails probably provide better collection understanding than the surrogates currently used by the popular Archive-It web archiving platform. We measure user interactions with each surrogate and find that users interact with social cards less than other types. The results of this study have implications for our web archive summarization work, live web curation platforms, social media, and more.

preprint2018arXiv

The Off-Topic Memento Toolkit

Web archive collections are created with a particular purpose in mind. A curator selects seeds, or original resources, which are then captured by an archiving system and stored as archived web pages, or mementos. The systems that build web archive collections are often configured to revisit the same original resource multiple times. This is incredibly useful for understanding an unfolding news story or the evolution of an organization. Unfortunately, over time, some of these original resources can go off-topic and no longer suit the purpose for which the collection was originally created. They can go off-topic due to web site redesigns, changes in domain ownership, financial issues, hacking, technical problems, or because their content has moved on from the original topic. Even though they are off-topic, the archiving system will still capture them, thus it becomes imperative to anyone performing research on these collections to identify these off-topic mementos. Hence, we present the Off-Topic Memento Toolkit, which allows users to detect off-topic mementos within web archive collections. The mementos identified by this toolkit can then be separately removed from a collection or merely excluded from downstream analysis. The following similarity measures are available: byte count, word count, cosine similarity, Jaccard distance, Sørensen-Dice distance, Simhash using raw text content, Simhash using term frequency, and Latent Semantic Indexing via the gensim library. We document the implementation of each of these similarity measures. We possess a gold standard dataset generated by manual analysis, which contains both off-topic and on-topic mementos. Using this gold standard dataset, we establish a default threshold corresponding to the best F1 score for each measure. We also provide an overview of potential future directions that the toolkit may take.

preprint2019arXiv

h-Index Manipulation by Undoing Merges

The h-index is an important bibliographic measure used to assess the performance of researchers. Dutiful researchers merge different versions of their articles in their Google Scholar profile even though this can decrease their h-index. In this article, we study the manipulation of the h-index by undoing such merges. In contrast to manipulation by merging articles (van Bevern et al. [Artif. Intel. 240:19-35, 2016]) such manipulation is harder to detect. We present numerous results on computational complexity (from linear-time algorithms to parameterized computational hardness results) and empirically indicate that at least small improvements of the h-index by splitting merged articles are unfortunately easily achievable.

preprint2019arXiv

CupQ: A New Clinical Literature Search Engine

A new clinical literature search engine, called CupQ, is presented. It aims to help clinicians stay updated with medical knowledge. Although PubMed is currently one of the most widely used digital libraries for biomedical information, it frequently does not return clinically relevant results. CupQ utilizes a ranking algorithm that filters non-medical journals, compares semantic similarity between queries, and incorporates journal impact factor and publication date. It organizes search results into useful categories for medical practitioners: reviews, guidelines, and studies. Qualitative comparisons suggest that CupQ may return more clinically relevant information than PubMed. CupQ is available at https://cupq.io/.

preprint2019arXiv

Do disruption index indicators measure what they propose to measure? The comparison of several indicator variants with assessments by peers

Recently, Wu, Wang, and Evans (2019) and Bu, Waltman, and Huang (2019) proposed a new family of indicators, which measure whether a scientific publication is disruptive to a field or tradition of research. Such disruptive influences are characterized by citations to a focal paper, but not its cited references. In this study, we are interested in the question of convergent validity, i.e., whether these indicators of disruption are able to measure what they propose to measure ('disruptiveness'). We used external criteria of newness to examine convergent validity: in the post-publication peer review system of F1000Prime, experts assess papers whether the reported research fulfills these criteria (e.g., reports new findings). This study is based on 120,179 papers from F1000Prime published between 2000 and 2016. In the first part of the study we discuss the indicators. Based on the insights from the discussion, we propose alternate variants of disruption indicators. In the second part, we investigate the convergent validity of the indicators and the (possibly) improved variants. Although the results of a factor analysis show that the different variants measure similar dimensions, the results of regression analyses reveal that one variant (DI5) performs slightly better than the others.

preprint2020arXiv

menoci: Lightweight Extensible Web Portal enabling FAIR Data Management for Biomedical Research Projects

Background: Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability. Results: We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform. Conclusions: Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.

preprint2019arXiv

Viewing Computer Science through Citation Analysis; Salton and Bergmark Redux

Computer science has experienced dramatic growth and diversification over the last twenty years. Towards a current understanding of the structure of this discipline, we analyze a cohort of the computer science literature using the DBLP database. For insight on the features of this cohort and the relationship within its components, we constructed article level clusters based on either direct citations or co-citations, and reconciled them to major and minor subject categories in the Scopus All Science Journal Classification (ASJC). We described complementary insights from clustering by direct citation and co-citation, and both point to the increase in computer science publications and their scope. Our analysis shows cross-category clusters, some that interact with external fields, such as the biological sciences, while others remain inward looking.

preprint2020arXiv

Automating Software Citation using GitCite

The ability to cite software and give credit to its authors and contributors is increasingly important. While the number of online open-source software repositories has grown rapidly over the past few years, few are being properly cited when used due to the difficulty of creating appropriate citations and the lack of automated techniques. This paper presents GitCite, a model for software citation with version control which enables citations to be inferred for any project component based on a small number of explicit citations attached to subdirectories/files, and an implementation that integrates with Git and GitHub. The implementation includes a browser extension and a local executable tool, which enable citations to be added/modified/deleted to software project repositories and managed through functions such as fork/merge/copy.

preprint2020arXiv

A Novel Approach to Predicting Exceptional Growth in Research

The prediction of exceptional or surprising growth in research is an issue with deep roots and few practical solutions. In this study we develop and validate a novel approach to forecasting growth in highly specific research communities. Each research community is represented by a cluster of papers. Multiple indicators were tested, and a composite indicator was created that predicts which research communities will experience exceptional growth over the next three years. The accuracy of this predictor was tested using hundreds of thousands of community-level forecasts and was found to exceed the performance benchmarks established in Intelligence Advanced Research Projects Activity's (IARPA) Foresight Using Scientific Exposition (FUSE) program in six of nine major fields in science. Furthermore, ten of eleven disciplines within the Computing Technologies field met the benchmarks. Specific detailed forecast examples are given and evaluated, and a critical evaluation of the forecasting approach is also provided.

preprint2020arXiv

Mapping the co-evolution of artificial intelligence, robotics, and the internet of things over 20 years (1998-2017)

Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas offers competitive intelligence for researchers, managers, policy makers, and others. The resulting data-driven decision support helps set proper research and development (R&D) priorities; develop future S&T investment strategies; monitor key authors, organizations, or countries; perform effective research program assessment; and implement cutting-edge education/training efforts. This paper presents new funding, publication, and scholarly network metrics and visualizations that were validated via expert surveys. The metrics and visualizations exemplify the emergence and convergence of three areas of strategic interest: artificial intelligence (AI), robotics, and internet of things (IoT) over the last 20 years (1998-2017). For 32,716 publications and 4,497 NSF awards, we identify their conceptual space (using the UCSD map of science), geospatial network, and co-evolution landscape. The findings demonstrate how the transition of knowledge (through cross-discipline publications and citations) and the emergence of new concepts (through term bursting) create a tangible potential for interdisciplinary research and new disciplines.

preprint2020arXiv

Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature

During the current century, each major coronavirus outbreak has triggered a quick surge of academic publications on this topic. The spike in research publications following the 2019 Novel Coronavirus (Covid-19), however, has been like no other. The global crisis caused by the Covid-19 pandemic has mobilised scientific efforts in an unprecedented way. In less than five months, more than 12,000 research items have been indexed while the number increasing every day. With the crisis affecting all aspects of life, research on Covid-19 seems to have become a focal point of interest across many academic disciplines. Here, scientometric aspects of the Covid-19 literature are analysed and contrasted with those of the two previous major Coronavirus diseases, i.e. SARS and MERS. The focus is on the co-occurrence of key-terms, bibliographic coupling and citation relations of journals and collaborations between countries. Certain recurring patterns across all three literatures were discovered. All three outbreaks have commonly generated three distinct and major cohort of studies: (i) studies linked to the public health response and epidemic control, (ii) studies associated with the chemical constitution of the virus and (iii) studies related to treatment, vaccine and clinical care. While studies affiliated with the category (i) seem to have been the first to emerge, they overall received least numbers of citations compared to those of the two other categories. Covid-19 studies seem to have been distributed across a broader variety of journals and subject areas. Clear links are observed between the geographical origins of each outbreak or the local geographical severity of each outbreak and the magnitude of research originated from regions. Covid-19 studies also display the involvement of authors from a broader variety of countries compared to SARS and MRS.

preprint2020arXiv

Are papers addressing certain diseases perceived where these diseases are prevalent? The proposal to use Twitter data as social-spatial sensors

We propose to use Twitter data as social-spatial sensors. This study deals with the question whether research papers on certain diseases are perceived by people in regions (worldwide) that are especially concerned by the diseases. Since (some) Twitter data contain location information, it is possible to spatially map the activity of Twitter users referring to certain papers (e.g., dealing with tuberculosis). The resulting maps reveal whether heavy activity on Twitter is correlated with large numbers of people having certain diseases. In this study, we focus on tuberculosis, human immunodeficiency virus (HIV), and malaria, since the World Health Organization ranks these diseases as the top three causes of death worldwide by a single infectious agent. The results of the social-spatial Twitter maps (and additionally performed regression models) reveal the usefulness of the proposed sensor approach. One receives an impression of how research papers on the diseases have been perceived by people in regions that are especially concerned by the diseases. Our study demonstrates a promising approach for using Twitter data for research evaluation purposes beyond simple counting of tweets.

preprint2020arXiv

Accelerating COVID-19 Differential Diagnosis with Explainable Ultrasound Image Analysis

Controlling the COVID-19 pandemic largely hinges upon the existence of fast, safe, and highly-available diagnostic tools. Ultrasound, in contrast to CT or X-Ray, has many practical advantages and can serve as a globally-applicable first-line examination technique. We provide the largest publicly available lung ultrasound (US) dataset for COVID-19 consisting of 106 videos from three classes (COVID-19, bacterial pneumonia, and healthy controls); curated and approved by medical experts. On this dataset, we perform an in-depth study of the value of deep learning methods for differential diagnosis of COVID-19. We propose a frame-based convolutional neural network that correctly classifies COVID-19 US videos with a sensitivity of 0.98+-0.04 and a specificity of 0.91+-08 (frame-based sensitivity 0.93+-0.05, specificity 0.87+-0.07). We further employ class activation maps for the spatio-temporal localization of pulmonary biomarkers, which we subsequently validate for human-in-the-loop scenarios in a blindfolded study with medical experts. Aiming for scalability and robustness, we perform ablation studies comparing mobile-friendly, frame- and video-based architectures and show reliability of the best model by aleatoric and epistemic uncertainty estimates. We hope to pave the road for a community effort toward an accessible, efficient and interpretable screening method and we have started to work on a clinical validation of the proposed method. Data and code are publicly available.

preprint2020arXiv

A SIR epidemic model for citation dynamics

The study of citations in the scientific literature crosses the boundaries between the traditional branches of science and stands on its own as a most profitable research field dubbed the `science of science'. Although the understanding of the citation histories of individual papers involves many intangible factors, the basic assumption that citations beget citations can explain most features of the empirical citation patterns. Here we use the SIR epidemic model as a mechanistic model for the citation dynamics of well-cited papers published in selected journals of the American Physical Society. The estimated epidemiological parameters offer insight on unknown quantities as the size of the community that could cite a paper and its ultimate impact on that community. We find a good, though imperfect, agreement between the rank of the journals obtained using the epidemiological parameters and the impact factor rank.

preprint2020arXiv

Algorithmic labeling in hierarchical classifications of publications: Evaluation of bibliographic fields and term weighting approaches

Algorithmic classifications of research publications can be used to study many different aspects of the science system, such as the organization of science into fields, the growth of fields, interdisciplinarity, and emerging topics. How to label the classes in these classifications is a problem that has not been thoroughly addressed in the literature. In this study we evaluate different approaches to label the classes in algorithmically constructed classifications of research publications. We focus on two important choices: the choice of (1) different bibliographic fields and (2) different approaches to weight the relevance of terms. To evaluate the different choices, we created two baselines: one based on the Medical Subject Headings in MEDLINE and another based on the Science-Metrix journal classification. We tested to what extent different approaches yield the desired labels for the classes in the two baselines. Based on our results we recommend extracting terms from titles and keywords to label classes at high levels of granularity (e.g. topics). At low levels of granularity (e.g. disciplines) we recommend extracting terms from journal names and author addresses. We recommend the use of a new approach, term frequency to specificity ratio, to calculate the relevance of terms.

preprint2020arXiv

Bibliometric analysis of the world scientific production in Chemical Engineering during 2000-2011. Part 3: Analysis of research trends and hot topics

A comprehensive bibliometric analysis of the scientific production of Chemical Engineering area has been carried out using the Web of Science database for the period 2000-2011 through three complementary studies. Part 3 has analyzed the distribution of words in article titles, keyword plus and author keywords of both total scientific production and the 1,000 most cited publications. The main areas of Chemical Engineering have been identified; they are mainly related to chemical reaction engineering such as catalysis, reactors, kinetics, and unit operations such as adsorption. Furthermore, a total of ten hotspots in the area have been identified: hydrogen as a new energy vector, wastewater treatments, carbon dioxide (capture and sequestration), photocatalysis, nanoparticles, biodiesel, nanotubes, ionic liquids, advanced oxidation processes, membranes, fuel cells and the use of biomass as raw material (e.g. bioethanol, energy production, etc.). Results obtained suggest thematic areas and research trends can be easier analyzed through the most cited publications, decreasing significantly the time necessary for these analyses. Words in article title, keyword plus and author keywords are complementary, however, author keywords are suggested as the source of most useful data. Compared to other strategies, the author keywords are more valuable for identifying research areas and trends, and the total number of words to be analyzed is lower. Whatever the case, authors recommend a revision of the results obtained by experts in the area to avoid inaccurate results and get the most meaningful information.

preprint2021arXiv

Mining the online infosphere: A survey

The evolution of AI-based system and applications had pervaded everyday life to make decisions that have momentous impact on individuals and society. With the staggering growth of online data, often termed as the Online Infosphere it has become paramount to monitor the infosphere to ensure social good as the AI-based decisions are severely dependent on it. The goal of this survey is to provide a comprehensive review of some of the most important research areas related to infosphere, focusing on the technical challenges and potential solutions. The survey also outlines some of the important future directions. We begin by discussions focused on the collaborative systems that have emerged within the infosphere with a special thrust on Wikipedia. In the follow up we demonstrate how the infosphere has been instrumental in the growth of scientific citations and collaborations thus fueling interdisciplinary research. Finally, we illustrate the issues related to the governance of the infosphere such as the tackling of the (a) rising hateful and abusive behavior and (b) bias and discrimination in different online platforms and news reporting.

preprint2020arXiv

Bibliometric analysis of world scientific production in Chemical Engineering during 2000-2011. Part 1: Analysis of total scientific production

A comprehensive bibliometric analysis of Chemical Engineering area has been carried out through the analysis of the scientific production covered in Web of Science during the period 2000-2011. Three complementary studies have been carried out. Part 1 analyzes total scientific production in the area. An important displacement of the scientific production to the Far East has occurred, mainly by the increase in publications from China (the world most productive country since 2008) but also from countries such as India and Iran. Although the share of publications from Europe, and especially from North America, have been decreased significantly, United States is still the country with the highest number of articles among the 1,000 most cited (31.5%), followed by Germany (8.4%) and China (7.5%). Switzerland, Italy, Netherlands, Singapore and Spain outstands as the countries with the highest number of cites per article and year and average impact factors of their publications. The international collaboration in the area is considerably high, especially within European countries (>40% publications are in international collaboration). The scientific production of the area is concentrated in a few journals (top 10 journals publishing around 30% publications and top 25 journals, around 50%) and publishers (Elsevier, Wiley-Blackwell, Taylor & Francis and the American Chemical Society). The countries with the highest number of institutions among the top 100 most productive are China and United States (12 each), followed by France (9), Japan (7) and United Kingdom (7). The top five institutions were from France, China, India, United States and Russia.

preprint2020arXiv

Bibliometric analysis of the world scientific production in Chemical Engineering during 2000-2011. Part 2: Analysis of the 1,000 most cited publications

A comprehensive bibliometric analysis of the scientific production of Chemical Engineering area has been carried out using the Web of Science database for the period 2000-2011 through three complementary studies. Part 2 demonstrated a displacement of the most cited publications to the Far East, especially due to China, however, this displacement is less important to that observed for total scientific production (Part 1). United States is still the country with the highest number of articles among the 1,000 most cited (31.5%), largely above what expected from their number of publications, followed by Germany (8.4%) and China (7.5%). The international collaboration, at least globally, seems not being an important issue for producing highly cited papers. In fact, only two from the top 25 most cited papers were international collaborations (8%). Furthermore, a large share of reviews among the 1,000 most cited papers (65%) has been observed. Although the number of institutions with more publications among the most cited in the area are from United States, the two institutions with the highest cited papers are CNRS (France) and CSIC (Spain). The most cited papers are highly concentrated in a few journals: around half of the most cited papers were published in five journals. Generally, the most cited papers are published in journals with high impact factors, however, there is also a significant number of highly cited papers published in journals with low or not having impact factor.

preprint2021arXiv

Looking Through Glass: Knowledge Discovery from Materials Science Literature using Natural Language Processing

Most of the knowledge in materials science literature is in the form of unstructured data such as text and images. Here, we present a framework employing natural language processing, which automates text and image comprehension and precision knowledge extraction from inorganic glasses' literature. The abstracts are automatically categorized using latent Dirichlet allocation (LDA), providing a way to classify and search semantically linked publications. Similarly, a comprehensive summary of images and plots are presented using the 'Caption Cluster Plot' (CCP), which provides direct access to the images buried in the papers. Finally, we combine the LDA and CCP with the chemical elements occurring in the manuscript to present an 'Elemental map', a topical and image-wise distribution of chemical elements in the literature. Overall, the framework presented here can be a generic and powerful tool to extract and disseminate material-specific information on composition-structure-processing-property dataspaces, allowing insights into fundamental problems relevant to the materials science community and accelerated materials discovery.

preprint2021arXiv

Attitudes toward Open Access, Open Peer Review, and Altmetrics among Contributors to Spanish Scholarly Journals

This paper aims to gain a better understanding of the perspectives of contributors to Spanish academic journals regarding open access, open peer review, and altmetrics. It also explores how age, gender, professional experience, career history, and perception and use of social media influence authors opinions toward these developments in scholarly publishing. A sample of contributors (n-1254) to Spanish academic journals was invited to participate in a survey about the aforementioned topics. The response rate was 24 per cent (n-295). Contributors to Spanish scholarly journals hold a favourable opinion of open access but were more cautious about open peer review and altmetrics. Younger and female scholars were more reluctant to accept open peer review practices. A positive attitude toward social networks did not necessarily translate into enthusiasm for emerging trends in scholarly publishing. Despite this, ResearchGate users were more aware of altmetrics.

preprint2021arXiv

The inconsistency of h-index: a mathematical analysis

Citation distributions are lognormal. We use 30 lognormally distributed synthetic series of numbers that simulate real series of citations to investigate the consistency of the h index. Using the lognormal cumulative distribution function, the equation that defines the h index can be formulated; this equation shows that h has a complex dependence on the number of papers (N). We also investigate the correlation between h and the number of papers exceeding various citation thresholds, from 5 to 500 citations. The best correlation is for the 100 threshold but numerous data points deviate from the general trend. The size-independent indicator h/N shows no correlation with the probability of publishing a paper exceeding any of the citation thresholds. In contrast with the h index, the total number of citations shows a high correlation with the number of papers exceeding the thresholds of 10 and 50 citations; the mean number of citations correlates with the probability of publishing a paper that exceeds any level of citations. Thus, in synthetic series, the number of citations and the mean number of citations are much better indicators of research performance than h and h/N. We discuss that in real citation distributions there are other difficulties.

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