Structuralizing biomedical abstracts with discriminative linguistic features

Which structure of academic articles do referees pay more attention to?: perspective of peer review and full-text of academic articles

Purpose

The purpose of this paper is to explore which structures of academic articles referees would pay more attention to, what specific content referees focus on, and whether the distribution of PRC is related to the citations.

Design/methodology/approach

Firstly, utilizing the feature words of section title and hierarchical attention network model (HAN) to identify the academic article structures. Secondly, analyzing the distribution of PRC in different structures according to the position information extracted by rules in PRC. Thirdly, analyzing the distribution of feature words of PRC extracted by the Chi-square test and TF-IDF in different structures. Finally, four correlation analysis methods are used to analyze whether the distribution of PRC in different structures is correlated to the citations.

Findings

The count of PRC distributed in Materials and Methods and Results section is significantly more than that in the structure of Introduction and Discussion, indicating that referees pay more attention to the Material and Methods and Results. The distribution of feature words of PRC in different structures is obviously different, which can reflect the content of referees' concern. There is no correlation between the distribution of PRC in different structures and the citations.

Research limitations/implications

Due to the differences in the way referees write peer review reports, the rules used to extract position information cannot cover all PRC.

Originality/value

The paper finds a pattern in the distribution of PRC in different academic article structures proving the long-term empirical understanding. It also provides insight into academic article writing: researchers should ensure the scientificity of methods and the reliability of results when writing academic article to obtain a high degree of recognition from referees.

A model for the identification of the functional structures of unstructured abstracts in the social sciences

Purpose

Reorganising unstructured academic abstracts according to a certain logical structure can help scholars not only extract valid information quickly but also facilitate the faceted search of academic literature. This study aims to build a high-performance model for identifying of the functional structures of unstructured abstracts in the social sciences.

Design/methodology/approach

This study first investigated the structuring of abstracts in academic articles in the field of social sciences, using large-scale statistical analyses. Then, the functional structures of sentences in the abstract in a corpus of more than 3.5 million abstracts were identified from sentence classification and sequence tagging by using several models based on either machine learning or a deep learning approach, and the results were compared.

Findings

The results demonstrate that the functional structures of sentences in abstracts in social science manuscripts include the background, purpose, methods, results and conclusions. The experimental results show that the bidirectional encoder representation from transformers exhibited the best performance, the overall F1 score of which was 86.23%.

Originality/value

The data set of annotated social science abstract is generated and corresponding models are trained on the basis of the data set, both of which are available on Github (https://github.com/Academic-Abstract-Knowledge-Mining/SSCI_Abstract_Structures_Identification). Based on the optimised model, a Web application for the identification of the functional structures of abstracts and their faceted search in social sciences was constructed to enable rapid and convenient reading, organisation and fine-grained retrieval of academic abstracts.

Large Scale Subject Category Classification of Scholarly Papers With Deep Attentive Neural Networks

Subject categories of scholarly papers generally refer to the knowledge domain(s) to which the papers belong, examples being computer science or physics. Subject category classification is a prerequisite for bibliometric studies, organizing scientific publications for domain knowledge extraction, and facilitating faceted searches for digital library search engines. Unfortunately, many academic papers do not have such information as part of their metadata. Most existing methods for solving this task focus on unsupervised learning that often relies on citation networks. However, a complete list of papers citing the current paper may not be readily available. In particular, new papers that have few or no citations cannot be classified using such methods. Here, we propose a deep attentive neural network (DANN) that classifies scholarly papers using only their abstracts. The network is trained using nine million abstracts from Web of Science (WoS). We also use the WoS schema that covers 104 subject categories. The proposed network consists of two bi-directional recurrent neural networks followed by an attention layer. We compare our model against baselines by varying the architecture and text representation. Our best model achieves micro-F1 measure of 0.76 with F1 of individual subject categories ranging from 0.50 to 0.95. The results showed the importance of retraining word embedding models to maximize the vocabulary overlap and the effectiveness of the attention mechanism. The combination of word vectors with TFIDF outperforms character and sentence level embedding models. We discuss imbalanced samples and overlapping categories and suggest possible strategies for mitigation. We also determine the subject category distribution in CiteSeerX by classifying a random sample of one million academic papers.

Cancer Research Trend Analysis Based on Fusion Feature Representation

Machine learning models can automatically discover biomedical research trends and promote the dissemination of information and knowledge. Text feature representation is a critical and challenging task in natural language processing. Most methods of text feature representation are based on word representation. A good representation can capture semantic and structural information. In this paper, two fusion algorithms are proposed, namely, the Tr-W2v and Ti-W2v algorithms. They are based on the classical text feature representation model and consider the importance of words. The results show that the effectiveness of the two fusion text representation models is better than the classical text representation model, and the results based on the Tr-W2v algorithm are the best. Furthermore, based on the Tr-W2v algorithm, trend analyses of cancer research are conducted, including correlation analysis, keyword trend analysis, and improved keyword trend analysis. The discovery of the research trends and the evolution of hotspots for cancers can help doctors and biological researchers collect information and provide guidance for further research.

Fast and scalable neural embedding models for biomedical sentence classification

Background

Biomedical literature is expanding rapidly, and tools that help locate information of interest are needed. To this end, a multitude of different approaches for classifying sentences in biomedical publications according to their coarse semantic and rhetoric categories (e.g., Background, Methods, Results, Conclusions) have been devised, with recent state-of-the-art results reported for a complex deep learning model. Recent evidence showed that shallow and wide neural models such as fastText can provide results that are competitive or superior to complex deep learning models while requiring drastically lower training times and having better scalability. We analyze the efficacy of the fastText model in the classification of biomedical sentences in the PubMed 200k RCT benchmark, and introduce a simple pre-processing step that enables the application of fastText on sentence sequences. Furthermore, we explore the utility of two unsupervised pre-training approaches in scenarios where labeled training data are limited.

Results

Our fastText-based methodology yields a state-of-the-art F1 score of.917 on the PubMed 200k benchmark when sentence ordering is taken into account, with a training time of only 73 s on standard hardware. Applying fastText on single sentences, without taking sentence ordering into account, yielded an F1 score of.852 (training time 13 s). Unsupervised pre-training of N-gram vectors greatly improved the results for small training set sizes, with an increase of F1 score of.21 to.74 when trained on only 1000 randomly picked sentences without taking sentence ordering into account.

Conclusions

Because of it’s ease of use and performance, fastText should be among the first choices of tools when tackling biomedical text classification problems with large corpora. Unsupervised pre-training of N-gram vectors on domain-specific corpora also makes it possible to apply fastText when labeled training data are limited.

Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease

Neurodegenerative disorders such as Parkinson's and Alzheimer's disease are devastating and costly illnesses, a source of major global burden. In order to provide successful interventions for patients and reduce costs, both causes and pathological processes need to be understood. The ApiNATOMY project aims to contribute to our understanding of neurodegenerative disorders by manually curating and abstracting data from the vast body of literature amassed on these illnesses. As curation is labour-intensive, we aimed to speed up the process by automatically highlighting those parts of the PDF document of primary importance to the curator. Using techniques similar to those of summarisation, we developed an algorithm that relies on linguistic, semantic and spatial features. Employing this algorithm on a test set manually corrected for tool imprecision, we achieved a macro F 1 -measure of 0.51, which is an increase of 132% compared to the best bag-of-words baseline model. A user based evaluation was also conducted to assess the usefulness of the methodology on 40 unseen publications, which reveals that in 85% of cases all highlighted sentences are relevant to the curation task and in about 65% of the cases, the highlights are sufficient to support the knowledge curation task without needing to consult the full text. In conclusion, we believe that these are promising results for a step in automating the recognition of curation-relevant sentences. Refining our approach to pre-digest papers will lead to faster processing and cost reduction in the curation process.

Database URL

https://github.com/KHP-Informatics/NapEasy.