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Latent topics resonance in scientific literature and commentaries: evidences from natural language processing approach.

ABSTRACT: Resonance is generally used as a metaphor to describe the manner how the information from different sources is combined. Although it is an attractive and fundamental phenomenon in human behavior studies, most studies observed semantic resonances in well-controlled experimental settings at word level. To make up the missing link between word and document level resonances, we devoted our contributions to topic resonances in a novel and natural setting: academic commentaries. Ninety-three academic commentaries from ninety-three authors, along with their references and original papers, are analyzed by a latent Dirichlet allocation based natural language processing approach. This approach can decompose a corpus written and read by an author into several topics with different weights, which can reveal the phenomena ignored at word or document level. We found that (1) topic resonances commonly exist between commenters' fundamental input and output topics; (2) output words are re-allocated by commenters to echo salient input topics; (3) commenters are more prone to associate references which focus on the non-dominant input topics; and (4) topic resonance can even be predicted by a Hebbian-like model which matches the aforementioned findings. These findings will continue to enrich our understanding on the relationship among probe, feedback and context.

SUBMITTER: Wang T

PROVIDER: S-EPMC6019969 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundInformation pertaining to mechanisms, management and treatment of disease-causing pathogens including viruses and bacteria is readily available from research publications indexed in MEDLINE. However, identifying the literature that specifically characterises these pathogens and their properties based on experimental research, important for understanding of the molecular basis of diseases caused by these agents, requires sifting through a large number of articles to exclude incidental mentions of the pathogens, or references to pathogens in other non-experimental contexts such as public health.ObjectiveIn this work, we lay the foundations for the development of automatic methods for characterising mentions of pathogens in scientific literature, focusing on the task of identifying research that involves the experimental study of a pathogen in an experimental context. There are no manually annotated pathogen corpora available for this purpose, while such resources are necessary to support the development of machine learning-based models. We therefore aim to fill this gap, producing a large data set automatically from MEDLINE under some simplifying assumptions for the task definition, and using it to explore automatic methods that specifically support the detection of experimentally studied pathogen mentions in research publications.MethodsWe developed a pathogen mention characterisation literature data set -READBiomed-Pathogens- automatically using NCBI resources, which we make available. Resources such as the NCBI Taxonomy, MeSH and GenBank can be used effectively to identify relevant literature about experimentally researched pathogens, more specifically using MeSH to link to MEDLINE citations including titles and abstracts with experimentally researched pathogens. We experiment with several machine learning-based natural language processing (NLP) algorithms leveraging this data set as training data, to model the task of detecting papers that specifically describe experimental study of a pathogen.ResultsWe show that our data set READBiomed-Pathogens can be used to explore natural language processing configurations for experimental pathogen mention characterisation. READBiomed-Pathogens includes citations related to organisms including bacteria, viruses, and a small number of toxins and other disease-causing agents.ConclusionsWe studied the characterisation of experimentally studied pathogens in scientific literature, developing several natural language processing methods supported by an automatically developed data set. As a core contribution of the work, we presented a methodology to automatically construct a data set for pathogen identification using existing biomedical resources. The data set and the annotation code are made publicly available. Performance of the pathogen mention identification and characterisation algorithms were additionally evaluated on a small manually annotated data set shows that the data set that we have generated allows characterising pathogens of interest.Trial registrationN/A.

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Latent topics resonance in scientific literature and commentaries: evidences from natural language processing approach.

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