Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics

Autoimmune diseases (ADs) are a broad range of diseases in which the immune response to self-antigens causes damage or disorder of tissues, and the genetic susceptibility is regarded as the key etiology of ADs. Accumulating evidence has suggested that there are certain commonalities among different ADs. However, the theoretical research about similarity between ADs is still limited. In this work, we first computed the genetic similarity between 26 ADs based on three measurements: network similarity (NetSim), functional similarity (FunSim), and semantic similarity (SemSim), and systematically identified three significant pairs of similar ADs: rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), myasthenia gravis (MG) and autoimmune thyroiditis (AIT), and autoimmune polyendocrinopathies (AP) and uveomeningoencephalitic syndrome (Vogt-Koyanagi-Harada syndrome, VKH). Then we investigated the gene ontology terms and pathways enriched by the three significant AD pairs through functional analysis. By the cluster analysis on the similarity matrix of 26 ADs, we embedded the three significant AD pairs in three different disease clusters respectively, and the ADs of each disease cluster might have high genetic similarity. We also detected the risk genes in common among the ADs which belonged to the same disease cluster. Overall, our findings will provide significant insight in the commonalities of different ADs in genetics, and contribute to the discovery of novel biomarkers and the development of new therapeutic methods for ADs.

Quantifying emotionally grounded discursive knowledge with cognitive-affective maps

Belief systems matter for all kinds of human social interaction. People have individual cognitions and feelings concerning processes in their environment, which is why they may evaluate them differently. Belief systems can be visualized with cognitive-affective maps (CAMs; as reported by Thagard (in: McGregor (ed) EMPATHICA: A computer support system with visual representations for cognitive-affective mapping, AAAI Press, CA, 2010)). However, it is unclear whether CAMs can be constructed in an intersubjective way by different researchers attempting to map the beliefs of a third party based on qualitative text data. To scrutinize this question, we combined qualitative strategies and quantitative methods of text and network analysis in a case study examining belief networks about participation. Our data set consists of 10 sets of two empirical CAMs: the first CAM was created based on participants’ freely associating concepts related to participation in education (N = 10), the second one was created based on given text data which the participants represented as a CAM following a standardized instruction manual (N = 10). Both CAM-types were compared along three dimensions of similarity (network similarity, concept association similarity, affective similarity). On all dimensions of similarity, there was substantially higher intersubjective agreement in the text-based CAMs than in the free CAMs, supporting the viability of cognitive affective mapping as an intersubjective research method for studying the emotional coherence of belief systems and discursive knowledge. In addition, this study highlights the potential for identifying group-level differences based on how participants associate concepts.

ELRUNA

Networks model a variety of complex phenomena across different domains. In many applications, one of the most essential tasks is to align two or more networks to infer the similarities between cross-network vertices and to discover potential node-level correspondence. In this article, we propose ELRUNA ( el imination ru le-based n etwork a lignment), a novel network alignment algorithm that relies exclusively on the underlying graph structure. Under the guidance of the elimination rules that we defined, ELRUNA computes the similarity between a pair of cross-network vertices iteratively by accumulating the similarities between their selected neighbors. The resulting cross-network similarity matrix is then used to infer a permutation matrix that encodes the final alignment of cross-network vertices. In addition to the novel alignment algorithm, we improve the performance of local search , a commonly used postprocessing step for solving the network alignment problem, by introducing a novel selection method RAWSEM ( ra ndom- w alk-based se lection m ethod) based on the propagation of vertices’ mismatching across the networks. The key idea is to pass on the initial levels of mismatching of vertices throughout the entire network in a random-walk fashion. Through extensive numerical experiments on real networks, we demonstrate that ELRUNA significantly outperforms the state-of-the-art alignment methods in terms of alignment accuracy under lower or comparable running time. Moreover, ELRUNA is robust to network perturbations such that it can maintain a close-to-optimal objective value under a high level of noise added to the original networks. Finally, the proposed RAWSEM can further improve the alignment quality with a smaller number of iterations compared with the naive local search method. Reproducibility : The source code and data are available at https://tinyurl.com/uwn35an.

Beyond pairwise network similarity: exploring mediation and suppression between networks

Network similarity measures quantify how and when two networks are symmetrically related, including measures of statistical association such as pairwise distance or other correlation measures between networks or between the layers of a multiplex network, but neither can directly unveil whether there are hidden confounding network factors nor can they estimate when such correlation is underpinned by a causal relation. In this work we extend this pairwise conceptual framework to triplets of networks and quantify how and when a network is related to a second network (of the same number of nodes) directly or via the indirect mediation or interaction with a third network. Accordingly, we develop a simple and intuitive set-theoretic approach to quantify mediation and suppression between networks. We validate our theory with synthetic models and further apply it to triplets (multiplex) of real-world networks, unveiling mediation and suppression effects which emerge when considering different modes of interaction in online social networks and different routes of information processing in the nervous system.

GATCDA: Predicting circRNA-Disease Associations Based on Graph Attention Network

CircRNAs (circular RNAs) are a class of non-coding RNA molecules with a closed circular structure. CircRNAs are closely related to the occurrence and development of diseases. Due to the time-consuming nature of biological experiments, computational methods have become a better way to predict the interactions between circRNAs and diseases. In this study, we developed a novel computational method called GATCDA utilizing a graph attention network (GAT) to predict circRNA–disease associations with disease symptom similarity, network similarity, and information entropy similarity for both circRNAs and diseases. GAT learns representations for nodes on a graph by an attention mechanism, which assigns different weights to different nodes in a neighborhood. Considering that the circRNA–miRNA–mRNA axis plays an important role in the generation and development of diseases, circRNA–miRNA interactions and disease–mRNA interactions were adopted to construct features, in which mRNAs were related to 88% of miRNAs. As demonstrated by five-fold cross-validation, GATCDA yielded an AUC value of 0.9011. In addition, case studies showed that GATCDA can predict unknown circRNA–disease associations. In conclusion, GATCDA is a useful method for exploring associations between circRNAs and diseases.

DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization

Background In the development of science and technology, there are increasing evidences that there are some associations between lncRNAs and human diseases. Therefore, finding these associations between them will have a huge impact on our treatment and prevention of some diseases. However, the process of finding the associations between them is very difficult and requires a lot of time and effort. Therefore, it is particularly important to find some good methods for predicting lncRNA-disease associations (LDAs). Results In this paper, we propose a method based on dual sparse collaborative matrix factorization (DSCMF) to predict LDAs. The DSCMF method is improved on the traditional collaborative matrix factorization method. To increase the sparsity, the L2,1-norm is added in our method. At the same time, Gaussian interaction profile kernel is added to our method, which increase the network similarity between lncRNA and disease. Finally, the AUC value obtained by the experiment is used to evaluate the quality of our method, and the AUC value is obtained by the ten-fold cross-validation method. Conclusions The AUC value obtained by the DSCMF method is 0.8523. At the end of the paper, simulation experiment is carried out, and the experimental results of prostate cancer, breast cancer, ovarian cancer and colorectal cancer are analyzed in detail. The DSCMF method is expected to bring some help to lncRNA-disease associations research. The code can access the https://github.com/Ming-0113/DSCMF website.

A Study Internet of Things Is A Revolutionary Approach for Future Technology Enhancement

The creation is pushing ahead on a quick leap, and the recognition goes to regularly developing innovation. One such idea is Internet of things with which robotization is never again an augmented simulation. IOT interfaces different nonliving articles through the web and empowers them to impart data to their locale system to computerize forms for people and makes their lives simpler. The paper shows what's to come difficulties of IoT ,, for example, the specialized (network , similarity and life span , guidelines , insightful investigation and activities , security), business ( venture , unassuming income model and so forth ), cultural (evolving requests , new gadgets, cost, client certainty and so forth ) and lawful difficulties ( laws, guidelines, methodology, approaches and so on ). An area additionally examines the different fantasies that may hamper the advancement of Internet of things, security of information being the most basic factor of all. An idealistic way to deal with individuals in embracing the unfurling changes brought by IOT will likewise benefit in its development. Internet of Things (IoT) is a new paradigm that has changed the traditional way of living into a high tech life style. Smart city, smart homes, pollution control, energy saving, smart transportation, smart industries are such transformations due to IoT. A lot of crucial research studies and investigations have been done in order to enhance the technology through IoT. However, there are still a lot of challenges and issues that need to be addressed to achieve the full potential of IoT. These challenges and issues must be considered from various aspects of IoT such as applications, challenges, enabling technologies, social and environmental impacts etc. The main goal of this review article is to provide a detailed discussion from both technological and social perspective. The article discusses different challenges and key issues of IoT, architecture and important application domains. Also, the article bring into light the existing literature and illustrated their contribution in different aspects of IoT. Moreover, the importance of big data and its analysis with respect to IoT has been discussed. This article would help the readers and researcher to understand the IoT and its applicability to the real world.

Social network characteristics and alcohol use by ethnic origin: An ego-based network study on peer similarity, social relationships, and co-existing drinking habits among young Swedes

The study explores how social network determinants relate to the prevalence and frequency of alcohol use among peer dyads. It is studied how similar alcohol habits co-exist among persons (egos) and their peers (alters) when socio-demographic similarity (e.g., in ethnic origin), network composition and other socio-cultural aspects were considered. Data was ego-based responses derived from a Swedish national survey with a cohort of 23-year olds. The analytical sample included 7987 ego-alter pairs, which corresponds to 2071 individuals (egos). A so-called dyadic design was applied i.e., all components of the analysis refer to ego-alter pairs (dyads). Multilevel multinomial-models were used to analyse similarity in alcohol habits in relation to ego-alter similarity in ethnic background, religious beliefs, age, sex, risk-taking, educational level, closure in network, duration, and type of relationship, as well as interactions between ethnicity and central network characteristics. Ego-alter similarity in terms of ethnic origin, age and sex was associated with ego-alter similarity in alcohol use. That both ego and alters were non-religious and were members of closed networks also had an impact on similarity in alcohol habits. It was concluded that network similarity might be an explanation for the co-existence of alcohol use among members of peer networks.