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.

Sentence-level evidence embedding for claim verification with hierarchical attention networks

Abstract: Claim verification is generally a task of verifying the veracity of a given claim, which is critical to many downstream applications. It is cumbersome and inefficient for human fact-checkers to find consistent pieces of evidence, from which solid verdict could be inferred against the claim. In this paper, we propose a novel end-to-end hierarchical attention network focusing on learning to represent coherent evidence as well as their semantic relatedness with the claim. Our model consists of three main components: 1) A coherence-based attention layer embeds coherent evidence considering the claim and sentences from relevant articles; 2) An entailment-based attention layer attends on sentences that can semantically infer the claim on top of the first attention; and 3) An output layer predicts the verdict based on the embedded evidence. Experimental results on three public benchmark datasets show that our proposed model outperforms a set of state-of-the-art baselines.

Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method

Abstract: Background Explicit comparisons based on the semantic similarity of Gene Ontology terms provide a quantitative way to measure the functional similarity between gene products and are widely applied in large-scale genomic research via integration with other models. Previously, we presented an edge-based method, Relative Specificity Similarity (RSS), which takes the global position of relevant terms into account. However, edge-based semantic similarity metrics are sensitive to the intrinsic structure of GO and simply consider terms at the same level in the ontology to be equally specific nodes, revealing the weaknesses that could be complemented using information content (IC). Results and Conclusions Here, we used the IC-based nodes to improve RSS and proposed a new method, Hybrid Relative Specificity Similarity (HRSS). HRSS outperformed other methods in distinguishing true protein-protein interactions from false. HRSS values were divided into four different levels of confidence for protein interactions. In addition, HRSS was statistically the best at obtaining the highest average functional similarity among human-mouse orthologs. Both HRSS and the groupwise measure, simGIC, are superior in correlation with sequence and Pfam similarities. Because different measures are best suited for different circumstances, we compared two pairwise strategies, the maximum and the best-match average, in the evaluation. The former was more effective at inferring physical protein-protein interactions, and the latter at estimating the functional conservation of orthologs and analyzing the CESSM datasets. In conclusion, HRSS can be applied to different biological problems by quantifying the functional similarity between gene products. The algorithm HRSS was implemented in the C programming language, which is freely available from http://cmb.bnu.edu.cn/hrss.

GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms

Abstract: Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik's and Wang's methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ancestor node giving to its descendent nodes. GOGO can calculate functional similarities between genes and then cluster genes based on their functional similarities. Evaluations performed on multiple pathways retrieved from the saccharomyces genome database (SGD) show that GOGO can accurately and robustly cluster genes based on functional similarities. We release GOGO as a web server and also as a stand-alone tool, which allows convenient execution of the tool for a small number of GO terms or integration of the tool into bioinformatics pipelines for large-scale calculations. GOGO can be freely accessed or downloaded from http://dna.cs.miami.edu/GOGO/ .

Semantic similarity of short texts

Abstract: This paper presents a method for measuring the semantic similarity of texts using a corpus based measure of semantic word similarity and a normalized and modified versions of the Longest Common Subsequence (LCS) string matching algorithm. Existing methods for computing text similarity have focused mainly on either large documents or individual words. In this paper, we focus on computing the similarity between two sentence or between two short paragraphs. The proposed method can be exploited in a variety of applications involving textual knowledge representation and knowledge discovery. Evaluation results on two different data sets show that our method outperforms several competing methods.