scholarly journals Generating Extractive Summaries of Scientific Paradigms

2013 ◽  
Vol 46 ◽  
pp. 165-201 ◽  
Author(s):  
V. Qazvinian ◽  
D. R. Radev ◽  
S. M. Mohammad ◽  
B. Dorr ◽  
D. Zajic ◽  
...  
Keyword(s):  
Text Mining ◽  
Community Detection ◽  
Question Answering ◽  
Scientific Literature ◽  
Dependency Parsing ◽  
Scientific Paradigms ◽  
Unique Information ◽  
Technical Material ◽  
Scientific Topic

Researchers and scientists increasingly find themselves in the position of having to quickly understand large amounts of technical material. Our goal is to effectively serve this need by using bibliometric text mining and summarization techniques to generate summaries of scientific literature. We show how we can use citations to produce automatically generated, readily consumable, technical extractive summaries. We first propose C-LexRank, a model for summarizing single scientific articles based on citations, which employs community detection and extracts salient information-rich sentences. Next, we further extend our experiments to summarize a set of papers, which cover the same scientific topic. We generate extractive summaries of a set of Question Answering (QA) and Dependency Parsing (DP) papers, their abstracts, and their citation sentences and show that citations have unique information amenable to creating a summary.

scholarly journals Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Chris Bauer ◽  
Ralf Herwig ◽  
Matthias Lienhard ◽  
Paul Prasse ◽  
Tobias Scheffer ◽  
...  
Keyword(s):  
Text Mining ◽  
Knowledge Base ◽  
Survival Data ◽  
Scientific Literature ◽  
Entity Recognition ◽  
Literature Mining ◽  
Cancer Drugs ◽  
Classical Text ◽  
Anti Cancer ◽  
Cancer Types

Abstract Background There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap. Conclusions Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.

scholarly journals PaperBLAST: Text-mining papers for information about homologs

2017 ◽  
Author(s):  
Morgan N. Price ◽  
Adam P. Arkin
Keyword(s):  
Text Mining ◽  
Genome Sequencing ◽  
Full Text ◽  
Large Scale ◽  
Scientific Literature ◽  
Protein Sequences ◽  
Protein Coding ◽  
Link Protein ◽  
Protein Coding Genes ◽  
Link Type

AbstractLarge-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources that link protein sequences to scientific articles (Swiss-Prot, GeneRIF, and EcoCyc). PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/.

A Text Mining Approach for Definition Question Answering

2006 ◽  
pp. 76-86 ◽  
Author(s):  
Claudia Denicia-Carral ◽  
Manuel Montes-y-Gómez ◽  
Luis Villaseñor-Pineda ◽  
René García Hernández
Keyword(s):  
Text Mining ◽  
Question Answering

Events Automatic Extraction from Arabic Texts

2020 ◽  
pp. 1686-1704
Author(s):  
Emna Hkiri ◽  
Souheyl Mallat ◽  
Mounir Zrigui
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Text Mining ◽  
Machine Translation ◽  
Language Processing ◽  
Question Answering ◽  
Arabic Language ◽  
Event Extraction ◽  
Mining Machine ◽  
Open Domain

The event extraction task consists in determining and classifying events within an open-domain text. It is very new for the Arabic language, whereas it attained its maturity for some languages such as English and French. Events extraction was also proved to help Natural Language Processing tasks such as Information Retrieval and Question Answering, text mining, machine translation etc… to obtain a higher performance. In this article, we present an ongoing effort to build a system for event extraction from Arabic texts using Gate platform and other tools.

Automatic Genre-Specific Text Classification

2011 ◽  
pp. 120-127
Author(s):  
Xiaoyan Yu ◽  
Manas Tungare ◽  
Weiguo Fan ◽  
Manuel Pérez-Quiñones ◽  
Edward A. Fox ◽  
...  
Keyword(s):  
Text Mining ◽  
Text Classification ◽  
Information Needs ◽  
Question Answering ◽  
Class Schedule ◽  
Semistructured Documents ◽  
Linkage Information ◽  
Filter Noise ◽  
Topic Tracking ◽  
Course Syllabus

Starting with a vast number of unstructured or semistructured documents, text mining tools analyze and sift through them to present to users more valuable information specific to their information needs. The technologies in text mining include information extraction, topic tracking, summarization, categorization/ classification, clustering, concept linkage, information visualization, and question answering [Fan, Wallace, Rich, & Zhang, 2006]. In this chapter, we share our hands-on experience with one specific text mining task — text classification [Sebastiani, 2002]. Information occurs in various formats, and some formats have a specific structure or specific information that they contain: we refer to these as `genres’. Examples of information genres include news items, reports, academic articles, etc. In this paper, we deal with a specific genre type, course syllabus. A course syllabus is such a genre, with the following commonly-occurring fields: title, description, instructor’s name, textbook details, class schedule, etc. In essence, a course syllabus is the skeleton of a course. Free and fast access to a collection of syllabi in a structured format could have a significant impact on education, especially for educators and life-long learners. Educators can borrow ideas from others’ syllabi to organize their own classes. It also will be easy for life-long learners to find popular textbooks and even important chapters when they would like to learn a course on their own. Unfortunately, searching for a syllabus on the Web using Information Retrieval [Baeza-Yates & Ribeiro-Neto, 1999] techniques employed by a generic search engine often yields too many non-relevant search result pages (i.e., noise) — some of these only provide guidelines on syllabus creation; some only provide a schedule for a course event; some have outgoing links to syllabi (e.g. a course list page of an academic department). Therefore, a well-designed classifier for the search results is needed, that would help not only to filter noise out, but also to identify more relevant and useful syllabi.

scholarly journals Using Machine Learning and Text Mining in Question Answering

2007 ◽  
pp. 415-423 ◽  
Author(s):  
Antonio Juárez-González ◽  
Alberto Téllez-Valero ◽  
Claudia Denicia-Carral ◽  
Manuel Montes-y-Gómez ◽  
Luis Villaseñor-Pineda
Keyword(s):  
Machine Learning ◽  
Text Mining ◽  
Question Answering

scholarly journals Extracting kinetic information from literature with KineticRE

2015 ◽  
Vol 12 (4) ◽  
pp. 56-68
Author(s):  
Ana Alão Freitas ◽  
Hugo Costa ◽  
Isabel Rocha
Keyword(s):  
Text Mining ◽  
Metabolic Networks ◽  
Scientific Literature ◽  
Kluyveromyces Lactis ◽  
Relevant Information ◽  
Text Documents ◽  
Kinetic Information ◽  
Mining Tool ◽  
Text Mining Tool

Summary To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

scholarly journals Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer

2017 ◽  
Vol 33 (24) ◽  
pp. 3973-3981 ◽  
Author(s):  
Simon Baker ◽  
Imran Ali ◽  
Ilona Silins ◽  
Sampo Pyysalo ◽  
Yufan Guo ◽  
...  
Keyword(s):  
Text Mining ◽  
Scientific Literature ◽  
Cancer Hallmarks

Terminological resources for text mining over biomedical scientific literature

2011 ◽  
Vol 52 (2) ◽  
pp. 107-114 ◽  
Author(s):  
Fabio Rinaldi ◽  
Kaarel Kaljurand ◽  
Rune Sætre
Keyword(s):  
Text Mining ◽  
Scientific Literature
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