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a b s t r a c tText categorization plays a crucial role in both academic and commercial platforms due to the growing demand for automatic organization of documents. Kernel-based classification algorithms such as Support Vector Machines (SVM) have become highly popular in the task of text mining. This is mainly due to their relatively high classification accuracy on several application domains as well as their ability to handle high dimensional and sparse data which is the prohibitive characteristics of textual data representation. Recently, there is an increased interest in the exploitation of background knowledge such as ontologies and corpus-based statistical knowledge in text categorization. It has been shown that, by replacing the standard kernel functions such as linear kernel with customized kernel functions which take advantage of this background knowledge, it is possible to increase the performance of SVM in the text classification domain. Based on this, we propose a novel semantic smoothing kernel for SVM. The suggested approach is based on a meaning measure, which calculates the meaningfulness of the terms in the context of classes. The documents vectors are smoothed based on these meaning values of the terms in the context of classes. Since we efficiently make use of the class information in the smoothing process, it can be considered a supervised smoothing kernel. The meaning measure is based on the Helmholtz principle from Gestalt theory and has previously been applied to several text mining applications such as document summarization and feature extraction. However, to the best of our knowledge, ours is the first study to use meaning measure in a supervised setting to build a semantic kernel for SVM. We evaluated the proposed approach by conducting a large number of experiments on well-known textual datasets and present results with respect to different experimental conditions. We compare our results with traditional kernels used in SVM such as linear kernel as well as with several corpus-based semantic kernels. Our results show that classification performance of the proposed approach outperforms other kernels.

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Ganiz, Murat Can (Dogus Author) -- Conference full title: 2014 IEEE International Symposium on Innovations in Intelligent Systems and Applications (INISTA 2014) : Alberobello, Italy, 23-25 June 2014.The bag of words (BOW) representation of documents is very common in text classification systems. However, the BOW approach ignores the position of the words in the document and more importantly, the semantic relations between the words. In this study, we present a simple semantic kernel for Support Vector Machines (SVM) algorithm. This kernel uses higher-order relations between terms in order to incorporate semantic information into the SVM. This is an easy to implement algorithm which forms a basis for future improvements. We perform a serious of experiments on different well known textual datasets. Experiment results show that classification performance improves over the traditional kernels used in SVM such as linear kernel which is commonly used in text classification

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The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions. The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and was organized in two tasks: (i) document triage task, focused on identifying scientific literature containing experimentally verified protein–protein interactions (PPIs) affected by genetic mutations and (ii) relation extraction task, focused on extracting the affected interactions (protein pairs). To assist system developers and task participants, a large-scale corpus of PubMed documents was manually annotated for this task. Ten teams worldwide contributed 22 distinct text-mining models for the document triage task, and six teams worldwide contributed 14 different text-mining systems for the relation extraction task. When comparing the text-mining system predictions with human annotations, for the triage task, the best F-score was 69.06%, the best precision was 62.89%, the best recall was 98.0% and the best average precision was 72.5%. For the relation extraction task, when taking homologous genes into account, the best F-score was 37.73%, the best precision was 46.5% and the best recall was 54.1%. Submitted systems explored a wide range of methods, from traditional rule-based, statistical and machine learning systems to state-of-the-art deep learning methods. Given the level of participation and the individual team results we find the precision medicine track to be successful in engaging the text-mining research community. In the meantime, the track produced a manually annotated corpus of 5509 PubMed documents developed by BioGRID curators and relevant for precision medicine. The data set is freely available to the community, and the specific interactions have been integrated into the BioGRID data set. In addition, this challenge provided the first results of automatically identifying PubMed articles that describe PPI affected by mutations, as well as extracting the affected relations from those articles. Still, much progress is needed for computer-assisted precision medicine text mining to become mainstream. Future work should focus on addressing the remaining technical challenges and incorporating the practical benefits of text-mining tools into real-world precision medicine information-related curation.

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