Text Mining and Management Tools for Resource Construction and Validation in the Life Sciences

In this talk, I am concerned with the question of what it really takes to move forward in the age of information, along the well knowln progression of human understanding, or data-information-knowledge-truth. After an overview of research directions of our group at KAIST, I present four text mining and management tools for resource construction and validation: Automatic gene summary generation, e3db construction, pathway validation by logical inference, and the system that taps into the evolutionary aspect of the Gene Ontology with colored graphs

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

A study on text-score disagreement in online reviews

In this paper, we focus on online reviews and employ artificial intelligence tools, taken from the cognitive computing field, to help understanding the relationships between the textual part of the review and the assigned numerical score. We move from the intuitions that 1) a set of textual reviews expressing different sentiments may feature the same score (and vice-versa); and 2) detecting and analyzing the mismatches between the review content and the actual score may benefit both service providers and consumers, by highlighting specific factors of satisfaction (and dissatisfaction) in texts. To prove the intuitions, we adopt sentiment analysis techniques and we concentrate on hotel reviews, to find polarity mismatches therein. In particular, we first train a text classifier with a set of annotated hotel reviews, taken from the Booking website. Then, we analyze a large dataset, with around 160k hotel reviews collected from Tripadvisor, with the aim of detecting a polarity mismatch, indicating if the textual content of the review is in line, or not, with the associated score. Using well established artificial intelligence techniques and analyzing in depth the reviews featuring a mismatch between the text polarity and the score, we find that -on a scale of five stars- those reviews ranked with middle scores include a mixture of positive and negative aspects. The approach proposed here, beside acting as a polarity detector, provides an effective selection of reviews -on an initial very large dataset- that may allow both consumers and providers to focus directly on the review subset featuring a text/score disagreement, which conveniently convey to the user a summary of positive and negative features of the review target.Comment: This is the accepted version of the paper. The final version will be published in the Journal of Cognitive Computation, available at Springer via http://dx.doi.org/10.1007/s12559-017-9496-

ADAPTS: An Intelligent Sustainable Conceptual Framework for Engineering Projects

This paper presents a conceptual framework for the optimization of environmental sustainability in engineering projects, both for products and industrial facilities or processes. The main objective of this work is to propose a conceptual framework to help researchers to approach optimization under the criteria of sustainability of engineering projects, making use of current Machine Learning techniques. For the development of this conceptual framework, a bibliographic search has been carried out on the Web of Science. From the selected documents and through a hermeneutic procedure the texts have been analyzed and the conceptual framework has been carried out. A graphic representation pyramid shape is shown to clearly define the variables of the proposed conceptual framework and their relationships. The conceptual framework consists of 5 dimensions; its acronym is ADAPTS. In the base are: (1) the Application to which it is intended, (2) the available DAta, (3) the APproach under which it is operated, and (4) the machine learning Tool used. At the top of the pyramid, (5) the necessary Sensing. A study case is proposed to show its applicability. This work is part of a broader line of research, in terms of optimization under sustainability criteria.Telefónica Chair “Intelligence in Networks” of the University of Seville (Spain