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Register a new userCOVID-19 Literature Topic-Based Search via Hierarchical NMF
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Added by
Xia Li
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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A dataset of COVID-19-related scientific literature is compiled, combining the articles from several online libraries and selecting those with open access and full text available. Then, hierarchical nonnegative matrix factorization is used to organize literature related to the novel coronavirus into a tree structure that allows researchers to search for relevant literature based on detected topics. We discover eight major latent topics and 52 granular subtopics in the body of literature, related to vaccines, genetic structure and modeling of the disease and patient studies, as well as related diseases and virology. In order that our tool may help current researchers, an interactive website is created that organizes available literature using this hierarchical structure.
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With worldwide concerns surrounding the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is a rapidly growing body of scientific literature on the virus. Clinicians, researchers, and policy-makers need to be able to search these articles effectively. In this work, we present a zero-shot ranking algorithm that adapts to COVID-related scientific literature. Our approach filters training data from another collection down to medical-related queries, uses a neural re-ranking model pre-trained on scientific text (SciBERT), and filters the target document collection. This approach ranks top among zero-shot methods on the TREC COVID Round 1 leaderboard, and exhibits a P@5 of 0.80 and an nDCG@10 of 0.68 when evaluated on both Round 1 and 2 judgments. Despite not relying on TREC-COVID data, our method outperforms models that do. As one of the first search methods to thoroughly evaluate COVID-19 search, we hope that this serves as a strong baseline and helps in the global crisis.
Log analysis in Web search showed that user sessions often contain several different topics. This means sessions need to be segmented into parts which handle the same topic in order to give appropriate user support based on the topic, and not on a mixture of topics. Different methods have been proposed to segment a user session to different topics based on timeouts, lexical analysis, query similarity or external knowledge sources. In this paper, we study the problem in a digital library for the social sciences. We present a method based on a thesaurus and a classification system which are typical knowledge organization systems in digital libraries. Five experts evaluated our approach and rated it as good for the segmentation of search sessions into parts that treat the same topic.
Mining a set of meaningful topics organized into a hierarchy is intuitively appealing since topic correlations are ubiquitous in massive text corpora. To account for potential hierarchical topic structures, hierarchical topic models generalize flat topic models by incorporating latent topic hierarchies into their generative modeling process. However, due to their purely unsupervised nature, the learned topic hierarchy often deviates from users particular needs or interests. To guide the hierarchical topic discovery process with minimal user supervision, we propose a new task, Hierarchical Topic Mining, which takes a category tree described by category names only, and aims to mine a set of representative terms for each category from a text corpus to help a user comprehend his/her interested topics. We develop a novel joint tree and text embedding method along with a principled optimization procedure that allows simultaneous modeling of the category tree structure and the corpus generative process in the spherical space for effective category-representative term discovery. Our comprehensive experiments show that our model, named JoSH, mines a high-quality set of hierarchical topics with high efficiency and benefits weakly-supervised hierarchical text classification tasks.
Coronavirus disease (COVID-19) has been declared as a pandemic by WHO with thousands of cases being reported each day. Numerous scientific articles are being published on the disease raising the need for a service which can organize, and query them in a reliable fashion. To support this cause we present AWS CORD-19 Search (ACS), a public, COVID-19 specific, neural search engine that is powered by several machine learning systems to support natural language based searches. ACS with capabilities such as document ranking, passage ranking, question answering and topic classification provides a scalable solution to COVID-19 researchers and policy makers in their search and discovery for answers to high priority scientific questions. We present a quantitative evaluation and qualitative analysis of the system against other leading COVID-19 search platforms. ACS is top performing across these systems yielding quality results which we detail with relevant examples in this work.
We provide an up-to-date view on the knowledge management system ScienceWISE (SW) and address issues related to the automatic assignment of articles to research topics. So far, SW has been proven to be an effective platform for managing large volumes of technical articles by means of ontological concept-based browsing. However, as the publication of research articles accelerates, the expressivity and the richness of the SW ontology turns into a double-edged sword: a more fine-grained characterization of articles is possible, but at the cost of introducing more spurious relations among them. In this context, the challenge of continuously recommending relevant articles to users lies in tackling a network partitioning problem, where nodes represent articles and co-occurring concepts create edges between them. In this paper, we discuss the three research directions we have taken for solving this issue: i) the identification of generic concepts to reinforce inter-article similarities; ii) the adoption of a bipartite network representation to improve scalability; iii) the design of a clustering algorithm to identify concepts for cross-disciplinary articles and obtain fine-grained topics for all articles.
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