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Abstract Systematic reviews and meta-analyses are essential tools in contemporary evidence-based medicine, synthesizing evidence from various sources to better inform clinical decision-making. However, the conclusions from different meta-analyses on the same topic can be discrepant, which has raised concerns about their reliability. One reason is that the result of a meta-analysis is sensitive to factors such as study inclusion/exclusion criteria and model assumptions. The arm-based meta-analysis model is growing in importance due to its advantage of including single-arm studies and historical controls with estimation efficiency and its flexibility in drawing conclusions with both marginal and conditional effect measures. Despite its benefits, the inference may heavily depend on the heterogeneity parameters that reflect design and model assumptions. This article aims to evaluate the robustness of meta-analyses using the arm-based model within a Bayesian framework. Specifically, we develop a tipping point analysis of the between-arm correlation parameter to assess the robustness of meta-analysis results. Additionally, we introduce some visualization tools to intuitively display its impact on meta-analysis results. We demonstrate the application of these tools in three real-world meta-analyses, one of which includes single-arm studies.

Abstract Background Emotions after surviving cancer can be complicated. The survivors may have gained new strength to continue life, but some of them may begin to deal with complicated feelings and emotional stress due to trauma and fear of cancer recurrence. The widespread use of Twitter for socializing has been the alternative medium for data collection compared to traditional studies of mental health, which primarily depend on information taken from medical staff with their consent. These social media data, to a certain extent, reflect the users’ psychological state. However, Twitter also contains a mix of noisy and genuine tweets. The process of manually identifying genuine tweets is expensive and time-consuming. Methods We stream the data using cancer as a keyword to filter the tweets with cancer-free and use post-traumatic stress disorder (PTSD) related keywords to reduce the time spent on the annotation task. Convolutional Neural Network (CNN) learns the representations of the input to identify cancer survivors with PTSD. Results The results present that the proposed CNN can effectively identify cancer survivors with PTSD. The experiments on real-world datasets show that our model outperforms the baselines and correctly classifies the new tweets. Conclusions PTSD is one of the severe anxiety disorders that could affect individuals who are exposed to traumatic events, including cancer. Cancer survivors are at risk of short-term or long-term effects on physical and psycho-social well-being. Therefore, the evaluation and treatment of PTSD are essential parts of cancer survivorship care. It will act as an alarming system by detecting the PTSD presence based on users’ postings on Twitter.

Abstract In this introduction, we first summarize the Fourth International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019) held on October 26, 2019 in conjunction with the 18th International Semantic Web Conference (ISWC 2019) in Auckland, New Zealand, and then briefly introduce seven research articles included in this supplement issue, covering the topics on Knowledge Graph, Ontology-Powered Analytics, and Deep Learning.

Abstract Background Information on protein-protein interactions affected by mutations is very useful for understanding the biological effect of mutations and for developing treatments targeting the interactions. In this study, we developed a natural language processing (NLP) based machine learning approach for extracting such information from literature. Our aim is to identify journal abstracts or paragraphs in full-text articles that contain at least one occurrence of a protein-protein interaction (PPI) affected by a mutation. Results Our system makes use of latest NLP methods with a large number of engineered features including some based on pre-trained word embedding. Our final model achieved satisfactory performance in the Document Triage Task of the BioCreative VI Precision Medicine Track with highest recall and comparable F1-score. Conclusions The performance of our method indicates that it is ideally suited for being combined with manual annotations. Our machine learning framework and engineered features will also be very helpful for other researchers to further improve this and other related biological text mining tasks using either traditional machine learning or deep learning based methods.

Abstract Background In recent years, deep learning methods have been applied to many natural language processing tasks to achieve state-of-the-art performance. However, in the biomedical domain, they have not out-performed supervised word sense disambiguation (WSD) methods based on support vector machines or random forests, possibly due to inherent similarities of medical word senses. Results In this paper, we propose two deep-learning-based models for supervised WSD: a model based on bi-directional long short-term memory (BiLSTM) network, and an attention model based on self-attention architecture. Our result shows that the BiLSTM neural network model with a suitable upper layer structure performs even better than the existing state-of-the-art models on the MSH WSD dataset, while our attention model was 3 or 4 times faster than our BiLSTM model with good accuracy. In addition, we trained “universal” models in order to disambiguate all ambiguous words together. That is, we concatenate the embedding of the target ambiguous word to the max-pooled vector in the universal models, acting as a “hint”. The result shows that our universal BiLSTM neural network model yielded about 90 percent accuracy. Conclusion Deep contextual models based on sequential information processing methods are able to capture the relative contextual information from pre-trained input word embeddings, in order to provide state-of-the-art results for supervised biomedical WSD tasks.

Abstract Background Dietary supplements (DSs) are widely used. However, consumers know little about the safety and efficacy of DSs. There is a growing interest in accessing health information online; however, health information, especially online information on DSs, is scattered with varying levels of quality. In our previous work, we prototyped a web application, ALOHA, with interactive graph-based visualization to facilitate consumers’ browsing of the integrated DIetary Supplement Knowledge base (iDISK) curated from scientific resources, following an iterative user-centered design (UCD) process. Methods Following UCD principles, we carried out two design iterations to enrich the functionalities of ALOHA and enhance its usability. For each iteration, we conducted a usability assessment and design session with a focus group of 8–10 participants and evaluated the usability with a modified System Usability Scale (SUS). Through thematic analysis, we summarized the identified usability issues and conducted a heuristic evaluation to map them to the Gerhardt-Powals’ cognitive engineering principles. We derived suggested improvements from each of the usability assessment session and enhanced ALOHA accordingly in the next design iteration. Results The SUS score in the second design iteration decreased to 52.2 ± 11.0 from 63.75 ± 7.2 in our original work, possibly due to the high number of new functionalities we introduced. By refining existing functionalities to make the user interface simpler, the SUS score increased to 64.4 ± 7.2 in the third design iteration. All participants agreed that such an application is urgently needed to address the gaps in how DS information is currently organized and consumed online. Moreover, most participants thought that the graph-based visualization in ALOHA is a creative and visually appealing format to obtain health information. Conclusions In this study, we improved a novel interactive visualization platform, ALOHA, for the general public to obtain DS-related information through two UCD design iterations. The lessons learned from the two design iterations could serve as a guide to further enhance ALOHA and the development of other knowledge graph-based applications. Our study also showed that graph-based interactive visualization is a novel and acceptable approach to end-users who are interested in seeking online health information of various domains.

Abstract Background There is strong scientific evidence linking obesity and overweight to the risk of various cancers and to cancer survivorship. Nevertheless, the existing online information about the relationship between obesity and cancer is poorly organized, not evidenced-based, of poor quality, and confusing to health information consumers. A formal knowledge representation such as a Semantic Web knowledge base (KB) can help better organize and deliver quality health information. We previously presented the OC-2-KB (Obesity and Cancer to Knowledge Base), a software pipeline that can automatically build an obesity and cancer KB from scientific literature. In this work, we investigated crowdsourcing strategies to increase the number of ground truth annotations and improve the quality of the KB. Methods We developed a new release of the OC-2-KB system addressing key challenges in automatic KB construction. OC-2-KB automatically extracts semantic triples in the form of subject-predicate-object expressions from PubMed abstracts related to the obesity and cancer literature. The accuracy of the facts extracted from scientific literature heavily relies on both the quantity and quality of the available ground truth triples. Thus, we incorporated a crowdsourcing process to improve the quality of the KB. Results We conducted two rounds of crowdsourcing experiments using a new corpus with 82 obesity and cancer-related PubMed abstracts. We demonstrated that crowdsourcing is indeed a low-cost mechanism to collect labeled data from non-expert laypeople. Even though individual layperson might not offer reliable answers, the collective wisdom of the crowd is comparable to expert opinions. We also retrained the relation detection machine learning models in OC-2-KB using the crowd annotated data and evaluated the content of the curated KB with a set of competency questions. Our evaluation showed improved performance of the underlying relation detection model in comparison to the baseline OC-2-KB. Conclusions We presented a new version of OC-2-KB, a system that automatically builds an evidence-based obesity and cancer KB from scientific literature. Our KB construction framework integrated automatic information extraction with crowdsourcing techniques to verify the extracted knowledge. Our ultimate goal is a paradigm shift in how the general public access, read, digest, and use online health information.

Abstract Background In the past few years, neural word embeddings have been widely used in text mining. However, the vector representations of word embeddings mostly act as a black box in downstream applications using them, thereby limiting their interpretability. Even though word embeddings are able to capture semantic regularities in free text documents, it is not clear how different kinds of semantic relations are represented by word embeddings and how semantically-related terms can be retrieved from word embeddings. Methods To improve the transparency of word embeddings and the interpretability of the applications using them, in this study, we propose a novel approach for evaluating the semantic relations in word embeddings using external knowledge bases: Wikipedia, WordNet and Unified Medical Language System (UMLS). We trained multiple word embeddings using health-related articles in Wikipedia and then evaluated their performance in the analogy and semantic relation term retrieval tasks. We also assessed if the evaluation results depend on the domain of the textual corpora by comparing the embeddings of health-related Wikipedia articles with those of general Wikipedia articles. Results Regarding the retrieval of semantic relations, we were able to retrieve semanti. Meanwhile, the two popular word embedding approaches, Word2vec and GloVe, obtained comparable results on both the analogy retrieval task and the semantic relation retrieval task, while dependency-based word embeddings had much worse performance in both tasks. We also found that the word embeddings trained with health-related Wikipedia articles obtained better performance in the health-related relation retrieval tasks than those trained with general Wikipedia articles. Conclusion It is evident from this study that word embeddings can group terms with diverse semantic relations together. The domain of the training corpus does have impact on the semantic relations represented by word embeddings. We thus recommend using domain-specific corpus to train word embeddings for domain-specific text mining tasks.

Abstract In this editorial, we first summarize the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017) held on November 13, 2017 in Kansas City, Missouri, U.S.A., and then briefly introduce 13 research articles included in this supplement issue, covering topics such as Semantic Integration, Deep Learning, Knowledge Base Construction, and Natural Language Processing.

Abstract In this editorial, we first summarize the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018) held on December 3, 2018 in conjunction with the 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018) in Madrid, Spain, and then briefly introduce five research articles included in this supplement issue, covering topics including Data Analytics, Data Visualization, Text Mining, and Ontology Evaluation.

After publication of this supplement article [1], it was brought to our attention that the Results section of the abstract contained a partial sentence.

Abstract Purpose This study aims to explore the incidence of hypoglycemia in patients with type 2 diabetes mellitus (T2DM) and the influence of hypoglycemia on the specific quality of life in T2DM patients. Methods It was a comparative cross-sectional study consisting of 519 T2DM patients in Xi'an, China and patients were investigated by self-reported hypoglycemia and specific quality of life questionnaires from September 2019 to January 2020. Descriptive analysis, t-test, Chi-square test, hierarchical regression analysis and stepwise multiple regression analysis were applied to assess the influence of hypoglycemia on the specific quality of life. Results The incidence of hypoglycemia in T2DM patients was 32.18%. The mean score of specific quality of life in diabetes without hypoglycemia was 57.33 ± 15.36 and was 61.56 ± 17.50 in those with hypoglycemia, which indicated that hypoglycemia had a serious impact on the quality of life of diabetics (t = − 5.172, p = 0.000). In the Univariate analysis of specific quality of life, age, education background, marital status, living status, duration of diabetes, monthly income per capita were independent and significant factors associated with specific quality of life of two groups of T2DM patients (p