Semantic similarity

About: Semantic similarity is a research topic. Over the lifetime, 14605 publications have been published within this topic receiving 364659 citations. The topic is also known as: semantic relatedness.

An efficient approach based on multi-sources information to predict circRNA–disease associations using deep convolutional neural network

Abstract: Motivation Emerging evidence indicates that circular RNA (circRNA) plays a crucial role in human disease. Using circRNA as biomarker gives rise to a new perspective regarding our diagnosing of diseases and understanding of disease pathogenesis. However, detection of circRNA-disease associations by biological experiments alone is often blind, limited to small scale, high cost and time consuming. Therefore, there is an urgent need for reliable computational methods to rapidly infer the potential circRNA-disease associations on a large scale and to provide the most promising candidates for biological experiments. Results In this article, we propose an efficient computational method based on multi-source information combined with deep convolutional neural network (CNN) to predict circRNA-disease associations. The method first fuses multi-source information including disease semantic similarity, disease Gaussian interaction profile kernel similarity and circRNA Gaussian interaction profile kernel similarity, and then extracts its hidden deep feature through the CNN and finally sends them to the extreme learning machine classifier for prediction. The 5-fold cross-validation results show that the proposed method achieves 87.21% prediction accuracy with 88.50% sensitivity at the area under the curve of 86.67% on the CIRCR2Disease dataset. In comparison with the state-of-the-art SVM classifier and other feature extraction methods on the same dataset, the proposed model achieves the best results. In addition, we also obtained experimental support for prediction results by searching published literature. As a result, 7 of the top 15 circRNA-disease pairs with the highest scores were confirmed by literature. These results demonstrate that the proposed model is a suitable method for predicting circRNA-disease associations and can provide reliable candidates for biological experiments. Availability and implementation The source code and datasets explored in this work are available at https://github.com/look0012/circRNA-Disease-association. Supplementary information Supplementary data are available at Bioinformatics online.

Semantic Context Enhances the Early Auditory Encoding of Natural Speech

Abstract: Speech perception involves the integration of sensory input with expectations based on the context of that speech. Much debate surrounds the issue of whether or not prior knowledge feeds back to affect early auditory encoding in the lower levels of the speech processing hierarchy, or whether perception can be best explained as a purely feedforward process. Although there has been compelling evidence on both sides of this debate, experiments involving naturalistic speech stimuli to address these questions have been lacking. Here, we use a recently introduced method for quantifying the semantic context of speech and relate it to a commonly used method for indexing low-level auditory encoding of speech. The relationship between these measures is taken to be an indication of how semantic context leading up to a word influences how its low-level acoustic and phonetic features are processed. We record EEG from human participants (both male and female) listening to continuous natural speech and find that the early cortical tracking of a word's speech envelope is enhanced by its semantic similarity to its sentential context. Using a forward modeling approach, we find that prediction accuracy of the EEG signal also shows the same effect. Furthermore, this effect shows distinct temporal patterns of correlation depending on the type of speech input representation (acoustic or phonological) used for the model, implicating a top-down propagation of information through the processing hierarchy. These results suggest a mechanism that links top-down prior information with the early cortical entrainment of words in natural, continuous speech.SIGNIFICANCE STATEMENT During natural speech comprehension, we use semantic context when processing information about new incoming words. However, precisely how the neural processing of bottom-up sensory information is affected by top-down context-based predictions remains controversial. We address this discussion using a novel approach that indexes a word's similarity to context and how well a word's acoustic and phonetic features are processed by the brain at the time of its utterance. We relate these two measures and show that lower-level auditory tracking of speech improves for words that are more related to their preceding context. These results suggest a mechanism that links top-down prior information with bottom-up sensory processing in the context of natural, narrative speech listening.

Evaluating distributed word representations for capturing semantics of biomedical concepts

Abstract: Recently there is a surge in interest in learning vector representations of words using huge corpus in unsupervised manner. Such word vector representations, also known as word embedding, have been shown to improve the performance of machine learning models in several NLP tasks. However efficiency of such representation has not been systematically evaluated in biomedical domain. In this work our aim is to compare the performance of two state-of-the-art word embedding methods, namely word2vec and GloVe on a basic task of reflecting semantic similarity and relatedness of biomedical concepts. For this, vector representations of all unique words in the corpus of more than 1 million full-length research articles in biomedical domain are obtained from the two methods. These word vectors are evaluated for their ability to reflect semantic similarity and semantic relatedness of word-pairs in a benchmark data set of manually curated semantic similar and related words available at http:// rxinformatics.umn.edu. We observe that parameters of these models do affect their ability to capture lexicosemantic properties and word2vec with particular language modeling seems to perform better than others.

Leveraging terminological structure for object reconciliation

Abstract: It has been argued that linked open data is the major benefit of semantic technologies for the web as it provides a huge amount of structured data that can be accessed in a more effective way than web pages. While linked open data avoids many problems connected with the use of expressive ontologies such as the knowledge acquisition bottleneck, data heterogeneity remains a challenging problem. In particular, identical objects may be referred to by different URIs in different data sets. Identifying such representations of the same object is called object reconciliation. In this paper, we propose a novel approach to object reconciliation that is based on an existing semantic similarity measure for linked data. We adapt the measure to the object reconciliation problem, present exact and approximate algorithms that efficiently implement the methods, and provide a systematic experimental evaluation based on a benchmark dataset. As our main result, we show that the use of light-weight ontologies and schema information significantly improves object reconciliation in the context of linked open data.

Description and Evaluation of Semantic Similarity Measures Approaches

Abstract: In recent years, semantic similarity measure has a great interest in Semantic Web and Natural Language Processing (NLP). Several similarity measures have been developed, being given the existence of a structured knowledge representation offered by ontologies and corpus which enable semantic interpretation of terms. Semantic similarity measures compute the similarity between concepts/terms included in knowledge sources in order to perform estimations. This paper discusses the existing semantic similarity methods based on structure, information content and feature approaches. Additionally, we present a critical evaluation of several categories of semantic similarity approaches based on two standard benchmarks. The aim of this paper is to give an efficient evaluation of all these measures which help researcher and practitioners to select the measure that best fit for their requirements.