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- Digital libraries (3)
- Text mining (3)
- Electronic theses and dissertations (2)
- Heuristic method (2)
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- Metadata (2)
- Metadata extraction (2)
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Articles 1 - 13 of 13
Full-Text Articles in Cataloging and Metadata
Foundation Models In Bioinformatics, Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang
Foundation Models In Bioinformatics, Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang
Computer Science Faculty Publications
With the adoption of foundation models (FMs), artificial intelligence (AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges, such as pre-training frameworks, model evaluation and interpretability. FMs demonstrate notable proficiency in managing large-scale, unlabeled datasets, because experimental procedures are costly and labor intensive. In various downstream tasks, FMs have consistently achieved noteworthy results, demonstrating high levels of accuracy in representing biological entities. A new era in computational biology has been ushered in by the application of FMs, focusing on both general and specific biological issues. In this review, we introduce recent advancements in bioinformatics FMs …
The Invisible Influencer In Information Infrastructure, Herbert Van De Sompel, Michael L. Nelson
The Invisible Influencer In Information Infrastructure, Herbert Van De Sompel, Michael L. Nelson
Computer Science Faculty Publications
The UPS Prototype was a proof-of-concept web portal built in preparation for the Universal Preprint Service Meeting held in October 1999 in Santa Fe, New Mexico. The portal provided search functionality for a set of metadata records that had been aggregated from a range of repositories that hosted preprints, working papers, and technical reports. Every search result was overlaid with a dynamically generated menu, called an SFX-menu, that provided a selection of value-adding links for the described scholarly work. The meeting eventually led to the Open Archives Initiative and its Protocol for Metadata Harvesting (OAI-PMH), which remains widely used in …
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
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 …
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
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 …
Streaminghub: Interactive Stream Analysis Workflows, Yasith Jayawardana, Vikas G. Ashok, Sampath Jayarathna
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 …
Theory Entity Extraction For Social And Behavioral Sciences Papers Using Distant Supervision, Xin Wei, Lamia Salsabil, Jian Wu
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 …
Large Scale Subject Category Classification Of Scholarly Papers With Deep Attentive Neural Networks, Bharath Kandimalla, Shaurya Rohatgi, Jian Wu, C. Lee Giles
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 …
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
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 …
A Heuristic Baseline Method For Metadata Extraction From Scanned Electronic Theses And Dissertations, Muntabir H. Choudhury, Jian Wu, William A. Ingam, Edward A. Fox
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, …
Smartcitecon: Implicit Citation Context Extraction From Academic Literature Using Unsupervised Learning, Chenrui Gao, Haoran Cui, Li Zhang, Jiamin Wang, Wei Lu, Jian Wu
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 …
Acknowledgement Entity Recognition In Cord-19 Papers, Jian Wu, Pei Wang, Xin Wei, Sarah Rajtmajer, C. Lee Giles, Christopher Griffin
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 …
Opening Books And The National Corpus Of Graduate Research, William A. Ingram, Edward A. Fox, Jian Wu
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. …
A Survey Of Archival Replay Banners, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson
A Survey Of Archival Replay Banners, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson
Computer Science Faculty Publications
We surveyed various archival systems to compare and contrast different techniques used to implement an archival replay banner. We found that inline plain HTML injection is the most common approach, but prone to style conflicts. Iframe-based banners are also very common and while they do not have style conflicts, they suffer from screen real estate wastage and limited design choices. Custom Elements-based banners are promising, but due to being a new web standard, these are not yet widely deployed.