Search

Objectives: Analyze papers published in 2019 within the medical natural language processing (NLP) domain in order to select the best works of the field., Methods: We performed an automatic and manual pre-selection of papers to be reviewed and finally selected the best NLP papers of the year. We also propose an analysis of the content of NLP publications in 2019., Results: Three best papers have been selected this year including the generation of synthetic record texts in Chinese, a method to identify contradictions in the literature, and the BioBERT word representation., Conclusions: The year 2019 was very rich and various NLP issues and topics were addressed by research teams. This shows the will and capacity of researchers to move towards robust and reproducible results. Researchers also prove to be creative in addressing original issues with relevant approaches., Competing Interests: Disclosure The authors report no conflicts of interest in this work., (Georg Thieme Verlag KG Stuttgart.)

The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. Research Resource Identifiers (RRIDs) should reduce the prevalence of misidentified and contaminated cell lines in the literature by alerting researchers to cell lines that are on the list of problematic cell lines, which is maintained by the International Cell Line Authentication Committee (ICLAC) and the Cellosaurus database. To test this assertion, we text-mined the methods sections of about two million papers in PubMed Central, identifying 305,161 unique cell-line names in 150,459 articles. We estimate that 8.6% of these cell lines were on the list of problematic cell lines, whereas only 3.3% of the cell lines in the 634 papers that included RRIDs were on the problematic list. This suggests that the use of RRIDs is associated with a lower reported use of problematic cell lines., Competing Interests: ZB, TG No competing interests declared, AC runs the cell bank in Australia and heads the ICLAC consortium. MM, AB heads the RRID project, and founded SciCrunch, a company that supports the RRID project. AB develops the Cellosaurus database. IO works as a consultant for SciCrunch., (© 2019, Babic et al.)

In the era of informatization and digitization, the rapid increase in the number of scientific papers has given rise to various challenges, such as lengthy articles, difficulty in information extraction and high time costs associated with reading. Literature reading challenges for researchers are increasingly tedious and time-consuming. By utilizing the language models, the assited reading system of scientific papers has been designed to address these challenges. By adopting machine reading comprehension technology as the core, the system parses scientific texts and offers some common questions to achieve automated response capabilities. By fully utilizing the pre-trained language model PERT, the system enhances its capabilities in semantic understanding and information extraction, effectively resolving various challenges in reading scientific papers and helping readers improve the efficiency of scientific literature review. [ABSTRACT FROM AUTHOR]

PurposeIdentifying the frontiers of a specific research field is one of the most basic tasks in bibliometrics and research published in leading conferences is crucial to the data mining research community, whereas few research studies have focused on it. The purpose of this study is to detect the intellectual structure of data mining based on conference papers.Design/methodology/approachThis study takes the authoritative conference papers of the ranking 9 in the data mining field provided by Google Scholar Metrics as a sample. According to paper amount, this paper first detects the annual situation of the published documents and the distribution of the published conferences. Furthermore, from the research perspective of keywords, CiteSpace was used to dig into the conference papers to identify the frontiers of data mining, which focus on keywords term frequency, keywords betweenness centrality, keywords clustering and burst keywords.FindingsResearch showed that the research heat of data mining had experienced a linear upward trend during 2007 and 2016. The frontier identification based on the conference papers showed that there were five research hotspots in data mining, including clustering, classification, recommendation, social network analysis and community detection. The research contents embodied in the conference papers were also very rich.Originality/valueThis study detected the research frontier from leading data mining conference papers. Based on the keyword co-occurrence network, from four dimensions of keyword term frequency, betweeness centrality, clustering analysis and burst analysis, this paper identified and analyzed the research frontiers of data mining discipline from 2007 to 2016.

The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. Research Resource Identifiers (RRIDs) should reduce the prevalence of misidentified and contaminated cell lines in the literature by alerting researchers to cell lines that are on the list of problematic cell lines, which is maintained by the International Cell Line Authentication Committee (ICLAC) and the Cellosaurus database. To test this assertion, we text-mined the methods sections of about two million papers in PubMed Central, identifying 305,161 unique cell-line names in 150,459 articles. We estimate that 8.6% of these cell lines were on the list of problematic cell lines, whereas only 3.3% of the cell lines in the 634 papers that included RRIDs were on the problematic list. This suggests that the use of RRIDs is associated with a lower reported use of problematic cell lines.

During graduate education, postgraduates have to spend considerable time finding papers to explore the development branches of their field. However, existing paper recommendation methods focus on several attributes (title, author, keyword, venue, etc.). The network schema constructed by these attributes is extremely sparse, which easily causes the loss of important semantic paths between attributes. This results in a lack of correlations among relevant papers, which affects paper recommendation efficiency. Moreover, the relationships between multiple semantic paths can be found through common homogeneous and heterogeneous attributes. These relationships can establish many correlations among relevant papers. To address the above problems, this paper proposes a new approach to fuse multi-semantic paths into a heterogeneous educational network (HEN) for personalized paper recommendation. After data processing, a new HEN schema is built by enriching nodes and edges in heterogeneous networks. Then, different semantic meta-paths are generated by projection sub-nets. Next, a new HEN embedding method is proposed by multi-semantic path fusion to generate rich HEN node sequences. Finally, personalized paper recommendation for postgraduates by targeted path similarity. The proposed method was performed on two paper datasets in the fields of educational intergenerational mobility from 1987 to 2021 and data mining and intelligent media from 1997 to 2021. Substantial experiments demonstrate that the proposed approach is effective. [ABSTRACT FROM AUTHOR]

Keyword extraction is the task of identifying important terms or phrase that are most representative of the source document. Although the process of automatic extraction of keywords from title is an old method, it was mainly for extraction from a single web document. Our approach differs from previous research works on keyword extraction in several aspects. For those who are non-expert of the scientific fields, understating scientific research trends is difficult. The purpose of this study is to develop an automatic method of obtaining overviews of a scientific field for non-experts by capturing research trends. This empirical study excavates significant term extraction using Natural Language Processing (NLP) tools. More than 15000 titles saved in a .csv file was our dataset and scripts written in Python were our process to compare how far significant terms of scientific title corpus are similar or different to the terms available in the abstract of that same scientific article corpus. A light-weight unsupervised title extractor, Yet Another Keyword Extractor (YAKE) was used to extract the results. Based on our analysis, it can be concluded that these algorithms can be used for other fields too by the non-experts of that subject field to perform automatic extraction of significant words and understanding trends. Our algorithm could be a solution to reduce the labour-intensive manual indexing process. [ABSTRACT FROM AUTHOR]

In this era, research and development are becoming a continuous and accelerating process because technology changes rapidly with a short lifecycle. As a result, various methodologies are being developed to monitor these rapidly changing research trends; In particular, clustering method-related studies in science and technology documents are being developed with a variety of approaches. However, previous studies on document clustering methods focus on a specific field or language but do not take into consideration certain important pieces of information in science and technology documents. Therefore, this study proposes an embedding methodology that uses important content from scientific and technical documents. We took into consideration the importance of information containing core structures in science and technology documents and proposed a clustering methodology that analyzes structured and unstructured data, such as textual information, author information, and citation information. The proposed method combines both textual and structural data from the paper, using a method that focuses on screening important information by sections in science and technology documents. Then, Girvan-Newman clustering and Louvain clustering models are applied to generate embedding vectors and show evaluation results through the clustering indices. As a practical example, we applied the proposed methodology using paper data from the field of hydrogen cell vehicles. The results of this study will be effective in identifying gaps in technology for new technological development, identifying technology trends, and presenting directional information for future technology development.

Background: In the healthcare domain today, despite the substantial adoption of electronic health information systems, a significant proportion of medical reports still exist in paper-based formats. As a result, there is a significant demand for the digitization of information from these paper-based reports. However, the digitization of paper-based laboratory reports into a structured data format can be challenging due to their non-standard layouts, which includes various data types such as text, numeric values, reference ranges, and units. Therefore, it is crucial to develop a highly scalable and lightweight technique that can effectively identify and extract information from laboratory test reports and convert them into a structured data format for downstream tasks. Methods: We developed an end-to-end Natural Language Processing (NLP)-based pipeline for extracting information from paper-based laboratory test reports. Our pipeline consists of two main modules: an optical character recognition (OCR) module and an information extraction (IE) module. The OCR module is applied to locate and identify text from scanned laboratory test reports using state-of-the-art OCR algorithms. The IE module is then used to extract meaningful information from the OCR results to form digitalized tables of the test reports. The IE module consists of five sub-modules, which are time detection, headline position, line normalization, Named Entity Recognition (NER) with a Conditional Random Fields (CRF)-based method, and step detection for multi-column. Finally, we evaluated the performance of the proposed pipeline on 153 laboratory test reports collected from Peking University First Hospital (PKU1). Results: In the OCR module, we evaluate the accuracy of text detection and recognition results at three different levels and achieved an averaged accuracy of 0.93. In the IE module, we extracted four laboratory test entities, including test item name, test result, test unit, and reference value range. The overall F1 score is 0.86 on the 153 laboratory test reports collected from PKU1. With a single CPU, the average inference time of each report is only 0.78 s. Conclusion: In this study, we developed a practical lightweight pipeline to digitalize and extract information from paper-based laboratory test reports in diverse types and with different layouts that can be adopted in real clinical environments with the lowest possible computing resources requirements. The high evaluation performance on the real-world hospital dataset validated the feasibility of the proposed pipeline. [ABSTRACT FROM AUTHOR]

In education quality assurance, the accuracy of test data is crucial. However, there is still a problem regarding to the possibility of incorrect data filled by test taker during paper-based test. On the contrary, this problem does not appear in computer-based test. In this study, a method was proposed in order to analyze the accuracy of answer sheet filling out in paper-based test using data mining technique. A single layer of data comprehension was added within the method instead of raw data. The results of the study were a web-based program for data pre-processing and decision tree models. There were 374 instances which were analyzed. The accuracy of answer sheet filling out attained 95.19% while the accuracy of classification varied from 99.47% to 100% depend on evaluation method chosen. This study could motivate the administrators for test improvement since it preferred computer-based test to paper-based.

Background: The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract this information. This is especially challenging when the information itself resides beyond titles or abstracts. For emerging science, with a limited set of known papers of interest and an incomplete information model, this is of pressing concern. A timely example in retrospect is the identification of immune signatures (coherent sets of biomarkers) driving differential SARS-CoV-2 infection outcomes. Implementation: We built a classifier to identify papers containing domain-specific information from the document embeddings of the title and abstract. To train this classifier with limited data, we developed an iterative process leveraging pre-trained SPECTER document embeddings, SVM classifiers and web-enabled expert review to iteratively augment the training set. This training set was then used to create a classifier to identify papers containing domain-specific information. Finally, information was extracted from these papers through a semi-automated system that directly solicited the paper authors to respond via a web-based form. Results: We demonstrate a classifier that retrieves papers with human COVID-19 immune signatures with a positive predictive value of 86%. The type of immune signature (e.g., gene expression vs. other types of profiling) was also identified with a positive predictive value of 74%. Semi-automated queries to the corresponding authors of these publications requesting signature information achieved a 31% response rate. Conclusions: Our results demonstrate the efficacy of using a SVM classifier with document embeddings of the title and abstract, to retrieve papers with domain-specific information, even when that information is rarely present in the abstract. Targeted author engagement based on classifier predictions offers a promising pathway to build a semi-structured representation of such information. Through this approach, partially automated literature mining can help rapidly create semi-structured knowledge repositories for automatic analysis of emerging health threats. [ABSTRACT FROM AUTHOR]

The novel coronavirus disease — COVID-19 is a historic catastrophe that has caused many devastating impacts on human life and wellness. Researchers in academia and industry strive to understand the causes of this pandemic disease and find new therapeutics combating it. Consequently, the number of COVID-19 related publications increases rapidly, and it is too difficult for medical researchers and practitioners to keep up with the latest research and development. Literature filtering and categorization, and knowledge discovery can use text mining as a powerful tool. In this paper, we propose a text mining method to explore the categories of COVID-19 related themes and identify the standard methodologies that have been used. We discuss the potential limitations of this preliminary study and present future perspectives related to COVID-19 research. This paper provides an quantitative and qualitative mixed analysis example of using some research papers by data mining method to dig out several hidden information and set up a foundation for data scientists to develop more effective algorithms to deal with COVID-19 related problems. [ABSTRACT FROM AUTHOR]

In the digital era like today the growth of data in the database is very rapid, all things related to technology have a large contribution to data growth as well as social media, financial technology and scientific data. Therefore, topics such as big data and data mining are topics that are often discussed. Data mining is a method of extracting information through from big data to produce an information pattern or data anomaly

Automatic data processing represents the future for the development of any system, especially in scientific research. In this paper, we describe one of the automatic classification methods applied to scientific research as a supervised learning task. Throughout the process, we identify the main features that are used as keys to play a significant role in terms of predicting the new rank under the supervised learning setup. First, we propose an overview of the work that has been realized in ranking scientific research papers. Second, we evaluate and compare some of state-of-the-art for the classification by supervised learning, semi-supervised learning and non-supervised learning. During the preliminary tests, we have obtained good results for performance on realistic corpus then we have compared performance metrics, such as NDCG, MAP, GMAP, F-Measure, Precision and Recall in order to define the influential features in our work. [ABSTRACT FROM AUTHOR]

Life Cycle Assessment (LCA) has been used to evaluate the life-cycle Greenhouse Gas (GHG) emissions of pulp and paper production, and most previous studies rely on process-based models for specific product types (e.g., printing paper), industry-average data, or information from a few mills. In this work, a data-mining approach is used to quantify GHG emissions intensities of different paper products manufactured by the U.S. mills. Facility-level emission data collected from publically available governmental databases and mill-level production data collected from the private sector were integrated to track the GHG emissions for different product lines and paper products in mills (in total, 165 mills were matched and analyzed). The results highlight the ranges of GHG emissions intensities by different product groups and categories, and can be used as a transparent data source for LCA practitioners, policymakers, and the pulp and paper industry to perform further analysis on carbon accounting and strategic planning for GHG mitigation. [ABSTRACT FROM AUTHOR]

This paper introduces CORE, a widely used scholarly service, which provides access to the world's largest collection of open access research publications, acquired from a global network of repositories and journals. CORE was created with the goal of enabling text and data mining of scientific literature and thus supporting scientific discovery, but it is now used in a wide range of use cases within higher education, industry, not-for-profit organisations, as well as by the general public. Through the provided services, CORE powers innovative use cases, such as plagiarism detection, in market-leading third-party organisations. CORE has played a pivotal role in the global move towards universal open access by making scientific knowledge more easily and freely discoverable. In this paper, we describe CORE's continuously growing dataset and the motivation behind its creation, present the challenges associated with systematically gathering research papers from thousands of data providers worldwide at scale, and introduce the novel solutions that were developed to overcome these challenges. The paper then provides an in-depth discussion of the services and tools built on top of the aggregated data and finally examines several use cases that have leveraged the CORE dataset and services. [ABSTRACT FROM AUTHOR]

Representing a strong instrument of control and feedback used by top management executives, regulators institutions or independent bodies, the audit, its methods and techniques incite the interest of specialists, professionals, professors and researchers from all socio-economic activities. The way domain experts write about audit itself is often reflected in the manner in which they choose the keywords for the title and for the article. This study is a detailed analysis of assignment to the specific thematic areas of articles published in "Financial Audit" journal, for all public appearances in electronic format from the period 2003-2015. The study is different from other similar researches by the methodology and the type of information extracted addressed. The main purpose is to identify the most used keywords in the title and content of articles published over time and insight traceability to future research directions. The conclusions of the analysis from this article give a comprehensive picture of audit multidisciplinary, thus providing researchers, on several economic fields, an image about the content of the publication, quality information for readers, authors and future authors.

Waste paper recycling is an important way to realize the environmental protection development of the papermaking industry. The quality of the pulp will affect the pulp sales of the secondary fiber paper mills. The waste paper pulp can be adjusted by controlling the pulping process working conditions, but the working conditions of the waste paper pulping process have too many parameters. And the parameters are coupled with each other, it is difficult to control. In order to find the best working conditions and improve the quality of the pulp, this study uses the association rules algorithm to optimize the parameters for the waste paper pulping process. These parameters are power of refiner, waste paper concentration of refiner, the volume of slurry that enters deinked process, deinking agent amount, deinking time, deinking temperature, bleaching agent amount, bleaching time, and bleaching temperature. The test results show that the qualified rate of the pulp produced under the improved working conditions is 92.56%, an increase of 6.93%, and the average electricity consumption per ton of pulp is reduced by 5.76 kWh/t. In addition to potential economic benefits, this method can reduce carbon emissions. [ABSTRACT FROM AUTHOR]

This document is an editorial note introducing a special issue of the journal Electronics on the topic of "Trends and Applications in Information Systems and Technologies." The note highlights the importance of information technologies in reshaping business models and improving operational efficiency. It also discusses the challenges associated with information systems, such as cybersecurity issues and data-centric decision-making processes. The special issue includes fourteen selected papers covering topics such as the adoption of blockchain technology, digital business solutions, ICT penetration, processing and information extraction in information systems, and innovative applications of information systems. The note concludes by expressing the hope that readers will find the special issue informative and inspiring for further research. [Extracted from the article]