Weak signal identification with semantic web mining

We investigate an automated identification of weak signals according to Ansoff to improve strategic planning and technological forecasting. Literature shows that weak signals can be found in the organization's environment and that they appear in different contexts. We use internet information to represent organization's environment and we select these websites that are related to a given hypothesis. In contrast to related research, a methodology is provided that uses latent semantic indexing (LSI) for the identification of weak signals. This improves existing knowledge based approaches because LSI considers the aspects of meaning and thus, it is able to identify similar textual patterns in different contexts. A new weak signal maximization approach is introduced that replaces the commonly used prediction modeling approach in LSI. It enables to calculate the largest number of relevant weak signals represented by singular value decomposition (SVD) dimensions. A case study identifies and analyses weak signals to predict trends in the field of on-site medical oxygen production. This supports the planning of research and development (R&D) for a medical oxygen supplier. As a result, it is shown that the proposed methodology enables organizations to identify weak signals from the internet for a given hypothesis. This helps strategic planners to react ahead of time

Text Analytics for Android Project

Most advanced text analytics and text mining tasks include text classification, text clustering, building ontology, concept/entity extraction, summarization, deriving patterns within the structured data, production of granular taxonomies, sentiment and emotion analysis, document summarization, entity relation modelling, interpretation of the output. Already existing text analytics and text mining cannot develop text material alternatives (perform a multivariant design), perform multiple criteria analysis, automatically select the most effective variant according to different aspects (citation index of papers (Scopus, ScienceDirect, Google Scholar) and authors (Scopus, ScienceDirect, Google Scholar), Top 25 papers, impact factor of journals, supporting phrases, document name and contents, density of keywords), calculate utility degree and market value. However, the Text Analytics for Android Project can perform the aforementioned functions. To the best of the knowledge herein, these functions have not been previously implemented; thus this is the first attempt to do so. The Text Analytics for Android Project is briefly described in this article

Large-Scale Online Semantic Indexing of Biomedical Articles via an Ensemble of Multi-Label Classification Models

Background: In this paper we present the approaches and methods employed in order to deal with a large scale multi-label semantic indexing task of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge of 2014. Methods: The main contribution of this work is a multi-label ensemble method that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms. Some secondary contributions include a study on the temporal aspects of the BioASQ corpus (observations apply also to the BioASQ's super-set, the PubMed articles collection) and the proper adaptation of the algorithms used to deal with this challenging classification task. Results: The ensemble method we developed is compared to other approaches in experimental scenarios with subsets of the BioASQ corpus giving positive results. During the BioASQ 2014 challenge we obtained the first place during the first batch and the third in the two following batches. Our success in the BioASQ challenge proved that a fully automated machine-learning approach, which does not implement any heuristics and rule-based approaches, can be highly competitive and outperform other approaches in similar challenging contexts

Chi-square-based scoring function for categorization of MEDLINE citations

Objectives: Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Methods: Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Results: Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine learning algorithms (support vector machines, decision trees, na\"ive Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine learning algorithms. Conclusions: We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.Comment: 34 pages, 2 figure

The devices, experimental scaffolds, and biomaterials ontology (DEB): a tool for mapping, annotation, and analysis of biomaterials' data

The size and complexity of the biomaterials literature makes systematic data analysis an excruciating manual task. A practical solution is creating databases and information resources. Implant design and biomaterials research can greatly benefit from an open database for systematic data retrieval. Ontologies are pivotal to knowledge base creation, serving to represent and organize domain knowledge. To name but two examples, GO, the gene ontology, and CheBI, Chemical Entities of Biological Interest ontology and their associated databases are central resources to their respective research communities. The creation of the devices, experimental scaffolds, and biomaterials ontology (DEB), an open resource for organizing information about biomaterials, their design, manufacture, and biological testing, is described. It is developed using text analysis for identifying ontology terms from a biomaterials gold standard corpus, systematically curated to represent the domain's lexicon. Topics covered are validated by members of the biomaterials research community. The ontology may be used for searching terms, performing annotations for machine learning applications, standardized meta-data indexing, and other cross-disciplinary data exploitation. The input of the biomaterials community to this effort to create data-driven open-access research tools is encouraged and welcomed.Preprin