Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Bibliometric Survey on Incremental Learning in Text Classification Algorithms for False Information Detection

The false information or misinformation over the web has severe effects on people, business and society as a whole. Therefore, detection of misinformation has become a topic of research among many researchers. Detecting misinformation of textual articles is directly connected to text classification problem. With the massive and dynamic generation of unstructured textual documents over the web, incremental learning in text classification has gained more popularity. This survey explores recent advancements in incremental learning in text classification and review the research publications of the area from Scopus, Web of Science, Google Scholar, and IEEE databases and perform quantitative analysis by using methods such as publication statistics, collaboration degree, research network analysis, and citation analysis. The contribution of this study in incremental learning in text classification provides researchers insights on the latest status of the research through literature survey, and helps the researchers to know the various applications and the techniques used recently in the field

A Novel Distributed Representation of News (DRNews) for Stock Market Predictions

In this study, a novel Distributed Representation of News (DRNews) model is developed and applied in deep learning-based stock market predictions. With the merit of integrating contextual information and cross-documental knowledge, the DRNews model creates news vectors that describe both the semantic information and potential linkages among news events through an attributed news network. Two stock market prediction tasks, namely the short-term stock movement prediction and stock crises early warning, are implemented in the framework of the attention-based Long Short Term-Memory (LSTM) network. It is suggested that DRNews substantially enhances the results of both tasks comparing with five baselines of news embedding models. Further, the attention mechanism suggests that short-term stock trend and stock market crises both receive influences from daily news with the former demonstrates more critical responses on the information related to the stock market {\em per se}, whilst the latter draws more concerns on the banking sector and economic policies.Comment: 25 page

Overcoming data scarcity of Twitter: using tweets as bootstrap with application to autism-related topic content analysis

Notwithstanding recent work which has demonstrated the potential of using Twitter messages for content-specific data mining and analysis, the depth of such analysis is inherently limited by the scarcity of data imposed by the 140 character tweet limit. In this paper we describe a novel approach for targeted knowledge exploration which uses tweet content analysis as a preliminary step. This step is used to bootstrap more sophisticated data collection from directly related but much richer content sources. In particular we demonstrate that valuable information can be collected by following URLs included in tweets. We automatically extract content from the corresponding web pages and treating each web page as a document linked to the original tweet show how a temporal topic model based on a hierarchical Dirichlet process can be used to track the evolution of a complex topic structure of a Twitter community. Using autism-related tweets we demonstrate that our method is capable of capturing a much more meaningful picture of information exchange than user-chosen hashtags.Comment: IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, 201

Towards cross-lingual alerting for bursty epidemic events

Background: Online news reports are increasingly becoming a source for event based early warning systems that detect natural disasters. Harnessing the massive volume of information available from multilingual newswire presents as many challenges as opportunities due to the patterns of reporting complex spatiotemporal events. Results: In this article we study the problem of utilising correlated event reports across languages. We track the evolution of 16 disease outbreaks using 5 temporal aberration detection algorithms on text-mined events classified according to disease and outbreak country. Using ProMED reports as a silver standard, comparative analysis of news data for 13 languages over a 129 day trial period showed improved sensitivity, F1 and timeliness across most models using cross-lingual events. We report a detailed case study analysis for Cholera in Angola 2010 which highlights the challenges faced in correlating news events with the silver standard. Conclusions: The results show that automated health surveillance using multilingual text mining has the potential to turn low value news into high value alerts if informed choices are used to govern the selection of models and data sources. An implementation of the C2 alerting algorithm using multilingual news is available at the BioCaster portal http://born.nii.ac.jp/?page=globalroundup

The Application of Text Mining and Data Visualization Techniques to Textual Corpus Exploration

Unstructured data in the digital universe is growing rapidly and shows no evidence of slowing anytime soon. With the acceleration of growth in digital data being generated and stored on the World Wide Web, the prospect of information overload is much more prevalent now than it has been in the past. As a preemptive analytic measure, organizations across many industries have begun implementing text mining techniques to analyze such large sources of unstructured data. Utilizing various text mining techniques such as n -gram analysis, document and term frequency analysis, correlation analysis, and topic modeling methodologies, this research seeks to develop a tool to allow analysts to maneuver effectively and efficiently through large corpuses of potentially unknown textual data. Additionally, this research explores two notional data exploration scenarios through a large corpus of text data, each exhibiting unique navigation methods analysts may elect to take. Research concludes with the validation of inferential results obtained through each corpus’s exploration scenario