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Register a new userEmbedding-based Scientific Literature Discovery in a Text Editor Application
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Added by
Onur G\\\"ok\\c{c}e
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Each claim in a research paper requires all relevant prior knowledge to be discovered, assimilated, and appropriately cited. However, despite the availability of powerful search engines and sophisticated text editing software, discovering relevant papers and integrating the knowledge into a manuscript remain complex tasks associated with high cognitive load. To define comprehensive search queries requires strong motivation from authors, irrespective of their familiarity with the research field. Moreover, switching between independent applications for literature discovery, bibliography management, reading papers, and writing text burdens authors further and interrupts their creative process. Here, we present a web application that combines text editing and literature discovery in an interactive user interface. The application is equipped with a search engine that couples Boolean keyword filtering with nearest neighbor search over text embeddings, providing a discovery experience tuned to an authors manuscript and his interests. Our application aims to take a step towards more enjoyable and effortless academic writing. The demo of the application (https://SciEditorDemo2020.herokuapp.com/) and a short video tutorial (https://youtu.be/pkdVU60IcRc) are available online.
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The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 6 million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve information from the rapidly growing corpora on COVID-19. These engines lack extraction and visualization tools necessary to retrieve and interpret complex relations inherent to scientific literature. Moreover, because these engines mainly rely upon semantic information, their ability to capture complex global relationships across documents is limited, which reduces the quality of similarity-based article recommendations for users. In this work, we present the COVID-19 Knowledge Graph (CKG), a heterogeneous graph for extracting and visualizing complex relationships between COVID-19 scientific articles. The CKG combines semantic information with document topological information for the application of similar document retrieval. The CKG is constructed using the latent schema of the data, and then enriched with biomedical entity information extracted from the unstructured text of articles using scalable AWS technologies to form relations in the graph. Finally, we propose a document similarity engine that leverages low-dimensional graph embeddings from the CKG with semantic embeddings for similar article retrieval. Analysis demonstrates the quality of relationships in the CKG and shows that it can be used to uncover meaningful information in COVID-19 scientific articles. The CKG helps power www.cord19.aws and is publicly available.
As a research community grows, more and more papers are published each year. As a result there is increasing demand for improved methods for finding relevant papers, automatically understanding the key ideas and recommending potential methods for a target problem. Despite advances in search engines, it is still hard to identify new technologies according to a researchers need. Due to the large variety of domains and extremely limited annotated resources, there has been relatively little work on leveraging natural language processing in scientific recommendation. In this proposal, we aim at making scientific recommendations by extracting scientific terms from a large collection of scientific papers and organizing the terms into a knowledge graph. In preliminary work, we trained a scientific term extractor using a small amount of annotated data and obtained state-of-the-art performance by leveraging large amount of unannotated papers through applying multiple semi-supervised approaches. We propose to construct a knowledge graph in a way that can make minimal use of hand annotated data, using only the extracted terms, unsupervised relational signals such as co-occurrence, and structural external resources such as Wikipedia. Latent relations between scientific terms can be learned from the graph. Recommendations will be made through graph inference for both observed and unobserved relational pairs.
Identification of new concepts in scientific literature can help power faceted search, scientific trend analysis, knowledge-base construction, and more, but current methods are lacking. Manual identification cannot keep up with the torrent of new publications, while the precision of existing automatic techniques is too low for many applications. We present an unsupervised concept extraction method for scientific literature that achieves much higher precision than previous work. Our approach relies on a simple but novel intuition: each scientific concept is likely to be introduced or popularized by a single paper that is disproportionately cited by subsequent papers mentioning the concept. From a corpus of computer science papers on arXiv, we find that our method achieves a Precision@1000 of 99%, compared to 86% for prior work, and a substantially better precision-yield trade-off across the top 15,000 extractions. To stimulate research in this area, we release our code and data (https://github.com/allenai/ForeCite).
Literature search is critical for any scientific research. Different from Web or general domain search, a large portion of queries in scientific literature search are entity-set queries, that is, multiple entities of possibly different types. Entity-set queries reflect users need for finding documents that contain multiple entities and reveal inter-entity relationships and thus pose non-trivial challenges to existing search algorithms that model each entity separately. However, entity-set queries are usually sparse (i.e., not so repetitive), which makes ineffective many supervised ranking models that rely heavily on associated click history. To address these challenges, we introduce SetRank, an unsupervised ranking framework that models inter-entity relationships and captures entity type information. Furthermore, we develop a novel unsupervised model selection algorithm, based on the technique of weighted rank aggregation, to automatically choose the parameter settings in SetRank without resorting to a labeled validation set. We evaluate our proposed unsupervised approach using datasets from TREC Genomics Tracks and Semantic Scholars query log. The experiments demonstrate that SetRank significantly outperforms the baseline unsupervised models, especially on entity-set queries, and our model selection algorithm effectively chooses suitable parameter settings.
The Geant4 reference paper published in Nuclear Instruments and Methods A in 2003 has become the most cited publication in the whole Nuclear Science and Technology category of Thomson-Reuters Journal Citation Reports. It is currently the second most cited article among the publications authored by two major research institutes, CERN and INFN. An overview of Geant4 presence (and absence) in scholarly literature is presented; the patterns of Geant4 citations are quantitatively examined and discussed.
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