Physical Sciences and Mathematics Commons^™

Robots Still Outnumber Humans In Web Archives In 2019, But Less Than In 2015 And 2012, Himarsha R. Jayanetti, Kritika Garg, Sawood Alam, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

The significance of the web and the crucial role of web archives in its preservation highlight the necessity of understanding how users, both human and robot, access web archive content, and how best to satisfy this disparate needs of both types of users. To identify robots and humans in web archives and analyze their respective access patterns, we used the Internet Archive’s (IA) Wayback Machine access logs from 2012, 2015, and 2019, as well as Arquivo.pt’s (Portuguese Web Archive) access logs from 2019. We identified user sessions in the access logs and classified those sessions as human or robot based …

Building Datasets To Support Information Extraction And Structure Parsing From Electronic Theses And Dissertations, William A. Ingram, Jian Wu, Sampanna Yashwant Kahu, Javaid Akbar Manzoor, Bipasha Banerjee, Aman Ahuja, Muntabir Hasan Choudhury, Lamia Salsabil, Winston Shields, Edward A. Fox

Computer Science Faculty Publications

Despite the millions of electronic theses and dissertations (ETDs) publicly available online, digital library services for ETDs have not evolved past simple search and browse at the metadata level. We need better digital library services that allow users to discover and explore the content buried in these long documents. Recent advances in machine learning have shown promising results for decomposing documents into their constituent parts, but these models and techniques require data for training and evaluation. In this article, we present high-quality datasets to train, evaluate, and compare machine learning methods in tasks that are specifically suited to identify and …

Assessing The Prevalence And Archival Rate Of Uris To Git Hosting Platforms In Scholarly Publications, Emily Escamilla

Computer Science Theses & Dissertations

The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, Software Heritage is working to archive public source code, but there is value in archiving the surrounding ephemera that provide important context to the code while maintaining their original URIs. In current implementations, source code …

Fair Signposting Profile, Herbert Van De Sompel, Martin Klein, Shawn Jones, Michael L. Nelson, Simeon Warner, Anusuriya Devaraju, Robert Huber, Wilko Steinhoff, Vyacheslav Tykhonov, Luc Boruta, Enno Meijers, Stian Soiland-Reyes, Mark Wilkonson

Computer Science Faculty Publications

[First paragraph] This page details concrete recipes that platforms that host research outputs (e.g. data repositories, institutional repositories, publisher platforms, etc.) can follow to implement Signposting, a lightweight yet powerful approach to increase the FAIRness of scholarly objects.

Supporting Account-Based Queries For Archived Instagram Posts, Himarsha R. Jayanetti

Computer Science Theses & Dissertations

Social media has become one of the primary modes of communication in recent times, with popular platforms such as Facebook, Twitter, and Instagram leading the way. Despite its popularity, Instagram has not received as much attention in academic research compared to Facebook and Twitter, and its significant role in contemporary society is often overlooked. Web archives are making efforts to preserve social media content despite the challenges posed by the dynamic nature of these sites. The goal of our research is to facilitate the easy discovery of archived copies, or mementos, of all posts belonging to a specific Instagram account …

Hashes Are Not Suitable To Verify Fixity Of The Public Archived Web, Mohamed Aturban, Martin Klein, Herbert Van De Sompel, Sawood Alam, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

Web archives, such as the Internet Archive, preserve the web and allow access to prior states of web pages. We implicitly trust their versions of archived pages, but as their role moves from preserving curios of the past to facilitating present day adjudication, we are concerned with verifying the fixity of archived web pages, or mementos, to ensure they have always remained unaltered. A widely used technique in digital preservation to verify the fixity of an archived resource is to periodically compute a cryptographic hash value on a resource and then compare it with a previous hash value. If the …

Deeppatent2: A Large-Scale Benchmarking Corpus For Technical Drawing Understanding, Kehinde Ajayi, Xin Wei, Martin Gryder, Winston Shields, Jian Wu, Shawn M. Jones, Michal Kucer, Diane Oyen

Computer Science Faculty Publications

Recent advances in computer vision (CV) and natural language processing have been driven by exploiting big data on practical applications. However, these research fields are still limited by the sheer volume, versatility, and diversity of the available datasets. CV tasks, such as image captioning, which has primarily been carried out on natural images, still struggle to produce accurate and meaningful captions on sketched images often included in scientific and technical documents. The advancement of other tasks such as 3D reconstruction from 2D images requires larger datasets with multiple viewpoints. We introduce DeepPatent2, a large-scale dataset, providing more than 2.7 million …

Biodiversity Of Philippine Marine Fishes: A Dna Barcode Reference Library Based On Voucher Specimens, Katherine E. Bemis, Matthew G. Girard, Mudjekeewis D. Santos, Kent E. Carpenter, Jonathan R. Deeds, Diane E. Pitassy, Nicko Amor L. Flores, Elizabeth S. Hunter, Amy C. Driskell, Kenneth S. Macdonald Iii, Lee A. Weigt, Jeffrey T. Williams

Biological Sciences Faculty Publications

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased …

Claimdistiller: Scientific Claim Extraction With Supervised Contrastive Learning, Xin Wei, Md Reshad Ul Hoque, Jian Wu, Jiang Li

Computer Science Faculty Publications

The growth of scientific papers in the past decades calls for effective claim extraction tools to automatically and accurately locate key claims from unstructured text. Such claims will benefit content-wise aggregated exploration of scientific knowledge beyond the metadata level. One challenge of building such a model is how to effectively use limited labeled training data. In this paper, we compared transfer learning and contrastive learning frameworks in terms of performance, time and training data size. We found contrastive learning has better performance at a lower cost of data across all models. Our contrastive-learning-based model ClaimDistiller has the highest performance, boosting …

Progenitor Cell Isolation From Mouse Epididymal Adipose Tissue And Sequencing Library Construction, Qianglin Liu, Chaoyang Li, Yuxia Li, Leshan Wang, Xujia Zhang, Buhao Deng, Peidong Gao, Mohammad Shiri, Fozi Alkaifi, Junxing Zhao, Jacqueline M. Stephens, Constantine A. Simintiras, Joseph Francis, Jiangwen Sun, Xing Fu

Computer Science Faculty Publications

Here, we present a protocol to isolate progenitor cells from mouse epididymal visceral adipose tissue and construct bulk RNA and assay for transposase-accessible chromatin with sequencing (ATAC-seq) libraries. We describe steps for adipose tissue collection, cell isolation, and cell staining and sorting. We then detail procedures for both ATAC-seq and RNA sequencing library construction. This protocol can also be applied to other tissues and cell types directly or with minor modifications.

For complete details on the use and execution of this protocol, please refer to Liu et al. (2023).¹

*¹ Liu, Q., Li, C., Deng, B., Gao, P., …

D-Lib Magazine Pioneered Web-Based Scholarly Communication, Michael L. Nelson, Herbert Van De Sompel

Computer Science Faculty Publications

The web began with a vision of, as stated by Tim Berners-Lee in 1991, “that much academic information should be freely available to anyone”. For many years, the development of the web and the development of digital libraries and other scholarly communications infrastructure proceeded in tandem. A milestone occurred in July, 1995, when the first issue of D-Lib Magazine was published as an online, HTML-only, open access magazine, serving as the focal point for the then emerging digital library research community. In 2017 it ceased publication, in part due to the maturity of the community it served as well as …

Scholarly Big Data Quality Assessment: A Case Study Of Document Linking And Conflation With S2orc, Jian Wu, Ryan Hiltabrand, Dominik Soós, C. Lee Giles

Computer Science Faculty Publications

Recently, the Allen Institute for Artificial Intelligence released the Semantic Scholar Open Research Corpus (S2ORC), one of the largest open-access scholarly big datasets with more than 130 million scholarly paper records. S2ORC contains a significant portion of automatically generated metadata. The metadata quality could impact downstream tasks such as citation analysis, citation prediction, and link analysis. In this project, we assess the document linking quality and estimate the document conflation rate for the S2ORC dataset. Using semi-automatically curated ground truth corpora, we estimated that the overall document linking quality is high, with 92.6% of documents correctly linking to six major …

The Dsa Toolkit Shines Light Into Dark And Stormy Archives, Shawn Morgan Jones, Himarsha R. Jayanetti, Alex Osborne, Paul Koerbin, Klein Martin, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

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 …

Theory Entity Extraction For Social And Behavioral Sciences Papers Using Distant Supervision, Xin Wei, Lamia Salsabil, Jian Wu

Computer Science Faculty Publications

Theories and models, which are common in scientific papers in almost all domains, usually provide the foundations of theoretical analysis and experiments. Understanding the use of theories and models can shed light on the credibility and reproducibility of research works. Compared with metadata, such as title, author, keywords, etc., theory extraction in scientific literature is rarely explored, especially for social and behavioral science (SBS) domains. One challenge of applying supervised learning methods is the lack of a large number of labeled samples for training. In this paper, we propose an automated framework based on distant supervision that leverages entity mentions …

Streaminghub: Interactive Stream Analysis Workflows, Yasith Jayawardana, Vikas G. Ashok, Sampath Jayarathna

Computer Science Faculty Publications

Reusable data/code and reproducible analyses are foundational to quality research. This aspect, however, is often overlooked when designing interactive stream analysis workflows for time-series data (e.g., eye-tracking data). A mechanism to transmit informative metadata alongside data may allow such workflows to intelligently consume data, propagate metadata to downstream tasks, and thereby auto-generate reusable, reproducible analytic outputs with zero supervision. Moreover, a visual programming interface to design, develop, and execute such workflows may allow rapid prototyping for interdisciplinary research. Capitalizing on these ideas, we propose StreamingHub, a framework to build metadata propagating, interactive stream analysis workflows using visual programming. We conduct …

Improving Collection Understanding For Web Archives With Storytelling: Shining Light Into Dark And Stormy Archives, Shawn M. Jones

Computer Science Theses & Dissertations

Collections are the tools that people use to make sense of an ever-increasing number of archived web pages. As collections themselves grow, we need tools to make sense of them. Tools that work on the general web, like search engines, are not a good fit for these collections because search engines do not currently represent multiple document versions well. Web archive collections are vast, some containing hundreds of thousands of documents. Thousands of collections exist, many of which cover the same topic. Few collections include standardized metadata. Too many documents from too many collections with insufficient metadata makes collection understanding …

World Oceans: A Reference Handbook, Rob Tench

Libraries Faculty & Staff Publications

Book review of Newton, David, World Oceans: A Reference Handbook, ABC-CLIO. (Contemporary World Issues), Feb. 2021, ISBN 9781440875434.

Large Scale Subject Category Classification Of Scholarly Papers With Deep Attentive Neural Networks, Bharath Kandimalla, Shaurya Rohatgi, Jian Wu, C. Lee Giles

Computer Science Faculty Publications

Subject categories of scholarly papers generally refer to the knowledge domain(s) to which the papers belong, examples being computer science or physics. Subject category classification is a prerequisite for bibliometric studies, organizing scientific publications for domain knowledge extraction, and facilitating faceted searches for digital library search engines. Unfortunately, many academic papers do not have such information as part of their metadata. Most existing methods for solving this task focus on unsupervised learning that often relies on citation networks. However, a complete list of papers citing the current paper may not be readily available. In particular, new papers that have few …

Extractive Research Slide Generation Using Windowed Labeling Ranking, Athar Sefid, Prasenjit Mitra, Jian Wu, C. Lee Giles

Computer Science Faculty Publications

Presentation slides generated from original research papers provide an efficient form to present research innovations. Manually generating presentation slides is labor-intensive. We propose a method to automatically generates slides for scientific articles based on a corpus of 5000 paper-slide pairs compiled from conference proceedings websites. The sentence labeling module of our method is based on SummaRuNNer, a neural sequence model for extractive summarization. Instead of ranking sentences based on semantic similarities in the whole document, our algorithm measures the importance and novelty of sentences by combining semantic and lexical features within a sentence window. Our method outperforms several baseline methods …

Automatic Metadata Extraction Incorporating Visual Features From Scanned Electronic Theses And Dissertations, Muntabir Hasan Choudhury, Himarsha R. Jayanetti, Jian Wu, William A. Ingram, Edward A. Fox

Computer Science Faculty Publications

Electronic Theses and Dissertations (ETDs) contain domain knowledge that can be used for many digital library tasks, such as analyzing citation networks and predicting research trends. Automatic metadata extraction is important to build scalable digital library search engines. Most existing methods are designed for born-digital documents, so they often fail to extract metadata from scanned documents such as ETDs. Traditional sequence tagging methods mainly rely on text-based features. In this paper, we propose a conditional random field (CRF) model that combines text-based and visual features. To verify the robustness of our model, we extended an existing corpus and created a …

Reflection And Transmission Of Electromagnetic Pulses At A Planar Dielectric Interface: Theory And Quantum Lattice Simulations, Abhay K. Ram, George Vahala, Linda Vahala, Min Soe

Electrical & Computer Engineering Faculty Publications

There is considerable interest in the application of quantum information science to advance computations in plasma physics. A particular point of curiosity is whether it is possible to take advantage of quantum computers to speed up numerical simulations relative to conventional computers. Many of the topics in fusion plasma physics are classical in nature. In order to implement them on quantum computers, it will require couching a classical problem in the language of quantum mechanics. Electromagnetic waves are routinely used in fusion experiments to heat a plasma or to generate currents in the plasma. The propagation of electromagnetic waves is …

A Framework For Verifying The Fixity Of Archived Web Resources, Mohamed Aturban

Computer Science Theses & Dissertations

The number of public and private web archives has increased, and we implicitly trust content delivered by these archives. Fixity is checked to ensure that an archived resource has remained unaltered (i.e., fixed) since the time it was captured. Currently, end users do not have the ability to easily verify the fixity of content preserved in web archives. For instance, if a web page is archived in 1999 and replayed in 2019, how do we know that it has not been tampered with during those 20 years? In order for the users of web archives to verify that archived web …

Bootstrapping Web Archive Collections From Micro-Collections In Social Media, Alexander C. Nwala

Computer Science Theses & Dissertations

In a Web plagued by disappearing resources, Web archive collections provide a valuable means of preserving Web resources important to the study of past events. These archived collections start with seed URIs (Uniform Resource Identifiers) hand-selected by curators. Curators produce high quality seeds by removing non-relevant URIs and adding URIs from credible and authoritative sources, but this ability comes at a cost: it is time consuming to collect these seeds. The result of this is a shortage of curators, a lack of Web archive collections for various important news events, and a need for an automatic system for generating seeds. …

A Heuristic Baseline Method For Metadata Extraction From Scanned Electronic Theses And Dissertations, Muntabir H. Choudhury, Jian Wu, William A. Ingam, Edward A. Fox

Computer Science Faculty Publications

Extracting metadata from scholarly papers is an important text mining problem. Widely used open-source tools such as GROBID are designed for born-digital scholarly papers but often fail for scanned documents, such as Electronic Theses and Dissertations (ETDs). Here we present a preliminary baseline work with a heuristic model to extract metadata from the cover pages of scanned ETDs. The process started with converting scanned pages into images and then text files by applying OCR tools. Then a series of carefully designed regular expressions for each field is applied, capturing patterns for seven metadata fields: titles, authors, years, degrees, academic programs, …

Acknowledgement Entity Recognition In Cord-19 Papers, Jian Wu, Pei Wang, Xin Wei, Sarah Rajtmajer, C. Lee Giles, Christopher Griffin

Computer Science Faculty Publications

Acknowledgements are ubiquitous in scholarly papers. Existing acknowledgement entity recognition methods assume all named entities are acknowledged. Here, we examine the nuances between acknowledged and named entities by analyzing sentence structure. We develop an acknowledgement extraction system, AckExtract based on open-source text mining software and evaluate our method using manually labeled data. AckExtract uses the PDF of a scholarly paper as input and outputs acknowledgement entities. Results show an overall performance of F₁=0.92. We built a supplementary database by linking CORD-19 papers with acknowledgement entities extracted by AckExtract including persons and organizations and find that only up to …

Smartcitecon: Implicit Citation Context Extraction From Academic Literature Using Unsupervised Learning, Chenrui Gao, Haoran Cui, Li Zhang, Jiamin Wang, Wei Lu, Jian Wu

Computer Science Faculty Publications

We introduce SmartCiteCon (SCC), a Java API for extracting both explicit and implicit citation context from academic literature in English. The tool is built on a Support Vector Machine (SVM) model trained on a set of 7,058 manually annotated citation context sentences, curated from 34,000 papers in the ACL Anthology. The model with 19 features achieves F₁=85.6%. SCC supports PDF, XML, and JSON files out-of-box, provided that they are conformed to certain schemas. The API supports single document processing and batch processing in parallel. It takes about 12–45 seconds on average depending on the format to process a …

Opening Books And The National Corpus Of Graduate Research, William A. Ingram, Edward A. Fox, Jian Wu

Computer Science Faculty Publications

Virginia Tech University Libraries, in collaboration with Virginia Tech Department of Computer Science and Old Dominion University Department of Computer Science, request $505,214 in grant funding for a 3-year project, the goal of which is to bring computational access to book-length documents, demonstrating that with Electronic Theses and Dissertations (ETDs). The project is motivated by the following library and community needs. (1) Despite huge volumes of book-length documents in digital libraries, there is a lack of models offering effective and efficient computational access to these long documents. (2) Nationwide open access services for ETDs generally function at the metadata level. …

Aggregating Private And Public Web Archives Using The Mementity Framework, Matthew R. Kelly

Computer Science Theses & Dissertations

Web archives preserve the live Web for posterity, but the content on the Web one cares about may not be preserved. The ability to access this content in the future requires the assurance that those sites will continue to exist on the Web until the content is requested and that the content will remain accessible. It is ultimately the responsibility of the individual to preserve this content, but attempting to replay personally preserved pages segregates archived pages by individuals and organizations of personal, private, and public Web content. This is misrepresentative of the Web as it was. While the Memento …

The Right To Human Intervention: Law, Ethics And Artificial Intelligence, Maria Kanellopoulou - Botti, Fereniki Panagopoulou, Maria Nikita, Anastasia Michailaki

Computer Ethics - Philosophical Enquiry (CEPE) Proceedings

The paper analyses the new right of human intervention in use of information technology, automatization processes and advanced algorithms in individual decision-making activities. Art. 22 of the new General Data Protection Regulation (GDPR) provides that the data subject has the right not to be subject to a fully automated decision on matters of legal importance to her interests, hence the data subject has a right to human intervention in this kind of decisions.

Legal And Technical Issues For Text And Data Mining In Greece, Maria Kanellopoulou - Botti, Marinos Papadopoulos, Christos Zampakolas, Paraskevi Ganatsiou

Computer Ethics - Philosophical Enquiry (CEPE) Proceedings

Web harvesting and archiving pertains to the processes of collecting from the web and archiving of works that reside on the Web. Web harvesting and archiving is one of the most attractive applications for libraries which plan ahead for their future operation. When works retrieved from the Web are turned into archived and documented material to be found in a library, the amount of works that can be found in said library can be far greater than the number of works harvested from the Web. The proposed participation in the 2019 CEPE Conference aims at presenting certain issues related to …