scholarly journals Extracting Graph Topological Information and Users’ Opinion

2017 ◽  
pp. 112-118 ◽  
Author(s):  
Mirko Lai ◽  
Marcella Tambuscio ◽  
Viviana Patti ◽  
Giancarlo Ruffo ◽  
Paolo Rosso
Keyword(s):  
Topological Information

Combinatorial Design of Molecule using Activity-Linked Substructural Topological Information as Applied to Antitubercular Compounds

2018 ◽  
Vol 15 (1) ◽  
pp. 67-81 ◽  
Author(s):  
Chandan Raychaudhury ◽  
Md. Imbesat Hassan Rizvi ◽  
Debnath Pal
Keyword(s):  
Biological Activities ◽  
Combinatorial Design ◽  
Combinatorial Structure ◽  
Potential Drug ◽  
Structure Generation ◽  
Topological Information ◽  
Active Compounds ◽  
Antitubercular Drugs ◽  
Topological Distance ◽  
Drug Molecules

Background: Generating a large number of compounds using combinatorial methods increases the possibility of finding novel bioactive compounds. Although some combinatorial structure generation algorithms are available, any method for generating structures from activity-linked substructural topological information is not yet reported. Objective: To develop a method using graph-theoretical techniques for generating structures of antitubercular compounds combinatorially from activity-linked substructural topological information, predict activity and prioritize and screen potential drug candidates. </P><P> Methods: Activity related vertices are identified from datasets composed of both active and inactive or, differently active compounds and structures are generated combinatorially using the topological distance distribution associated with those vertices. Biological activities are predicted using topological distance based vertex indices and a rule based method. Generated structures are prioritized using a newly defined Molecular Priority Score (MPS). Results: Studies considering a series of Acid Alkyl Ester (AAE) compounds and three known antitubercular drugs show that active compounds can be generated from substructural information of other active compounds for all these classes of compounds. Activity predictions show high level of success rate and a number of highly active AAE compounds produced high MPS score indicating that MPS score may help prioritize and screen potential drug molecules. A possible relation of this work with scaffold hopping and inverse Quantitative Structure-Activity Relationship (iQSAR) problem has also been discussed. The proposed method seems to hold promise for discovering novel therapeutic candidates for combating Tuberculosis and may be useful for discovering novel drug molecules for the treatment of other diseases as well.

scholarly journals Data-driven biological network alignment that uses topological, sequence, and functional information

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shawn Gu ◽  
Tijana Milenković
Keyword(s):  
Prediction Accuracy ◽  
Biological Network ◽  
Network Alignment ◽  
Data Driven ◽  
Sequence Information ◽  
Functional Prediction ◽  
Research Knowledge ◽  
Topological Information ◽  
Functional Knowledge ◽  
Related Proteins

Abstract Background Network alignment (NA) can transfer functional knowledge between species’ conserved biological network regions. Traditional NA assumes that it is topological similarity (isomorphic-like matching) between network regions that corresponds to the regions’ functional relatedness. However, we recently found that functionally unrelated proteins are as topologically similar as functionally related proteins. So, we redefined NA as a data-driven method called TARA, which learns from network and protein functional data what kind of topological relatedness (rather than similarity) between proteins corresponds to their functional relatedness. TARA used topological information (within each network) but not sequence information (between proteins across networks). Yet, TARA yielded higher protein functional prediction accuracy than existing NA methods, even those that used both topological and sequence information. Results Here, we propose TARA++ that is also data-driven, like TARA and unlike other existing methods, but that uses across-network sequence information on top of within-network topological information, unlike TARA. To deal with the within-and-across-network analysis, we adapt social network embedding to the problem of biological NA. TARA++ outperforms protein functional prediction accuracy of existing methods. Conclusions As such, combining research knowledge from different domains is promising. Overall, improvements in protein functional prediction have biomedical implications, for example allowing researchers to better understand how cancer progresses or how humans age.

scholarly journals GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gwenaëlle G. Lemoine ◽  
Marie-Pier Scott-Boyer ◽  
Bathilde Ambroise ◽  
Olivier Périn ◽  
Arnaud Droit
Keyword(s):  
Muscle Development ◽  
R Package ◽  
Topological Information ◽  
Old Patients ◽  
Network Modules ◽  
Extended Analysis ◽  
Networks Analysis ◽  
Underlying Processes

Abstract Background Network-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended description of each of the network modules is therefore a critical step to understand the underlying processes contributing to a disease or a phenotype. Biological integration, topology study and conditions comparison (e.g. wild vs mutant) are the main methods to do so, but to date no tool combines them all into a single pipeline. Results Here we present GWENA, a new R package that integrates gene co-expression network construction and whole characterization of the detected modules through gene set enrichment, phenotypic association, hub genes detection, topological metric computation, and differential co-expression. To demonstrate its performance, we applied GWENA on two skeletal muscle datasets from young and old patients of GTEx study. Remarkably, we prioritized a gene whose involvement was unknown in the muscle development and growth. Moreover, new insights on the variations in patterns of co-expression were identified. The known phenomena of connectivity loss associated with aging was found coupled to a global reorganization of the relationships leading to expression of known aging related functions. Conclusion GWENA is an R package available through Bioconductor (https://bioconductor.org/packages/release/bioc/html/GWENA.html) that has been developed to perform extended analysis of gene co-expression networks. Thanks to biological and topological information as well as differential co-expression, the package helps to dissect the role of genes relationships in diseases conditions or targeted phenotypes. GWENA goes beyond existing packages that perform co-expression analysis by including new tools to fully characterize modules, such as differential co-expression, additional enrichment databases, and network visualization.

New Method of Fault Knowledge Acquisition of Electronic Equipment

2014 ◽  
Vol 496-500 ◽  
pp. 931-934
Author(s):  
Zhi Cheng Huo ◽  
Qi Shun Sun ◽  
Feng Jun Qi ◽  
Guo Bao Ding
Keyword(s):  
Knowledge Acquisition ◽  
Electronic Equipment ◽  
New Method ◽  
Topological Information ◽  
Amplifier Circuit ◽  
C Language ◽  
Transistor Amplifier ◽  
Analog System ◽  
Non Linear ◽  
Electric Equipment

For the problems like discreteness, tolerance, non-linear of the parts, acquiring the fault knowledge of analog system in electric equipment is hard. This method realized the process of KA automatization through the combination of PSPICE software and C language and taking command lines as combining site. Using the batch file, the programs will form some topological information and parameter information about the fault states of a circuit system each time. The result of a experiment about an Basic Transistor Amplifier circuit proves its feasibility.

Combining contextual, temporal and topological information for unsupervised link prediction in social networks

2018 ◽  
Vol 156 ◽  
pp. 129-137 ◽  
Author(s):  
Carlos Pedro Muniz ◽  
Ronaldo Goldschmidt ◽  
Ricardo Choren
Keyword(s):  
Social Networks ◽  
Link Prediction ◽  
Topological Information

Incremental Community Detection on Large Complex Attributed Network

2021 ◽  
Vol 15 (6) ◽  
pp. 1-20
Author(s):  
Zhe Chen ◽  
Aixin Sun ◽  
Xiaokui Xiao
Keyword(s):  
Community Detection ◽  
Large Scale ◽  
Network Data ◽  
Topological Information ◽  
Community Membership ◽  
Attributed Network ◽  
Benchmark Datasets ◽  
Modularity Maximization ◽  
Large Scale Networks

Community detection on network data is a fundamental task, and has many applications in industry. Network data in industry can be very large, with incomplete and complex attributes, and more importantly, growing. This calls for a community detection technique that is able to handle both attribute and topological information on large scale networks, and also is incremental. In this article, we propose inc-AGGMMR, an incremental community detection framework that is able to effectively address the challenges that come from scalability, mixed attributes, incomplete values, and evolving of the network. Through construction of augmented graph, we map attributes into the network by introducing attribute centers and belongingness edges. The communities are then detected by modularity maximization. During this process, we adjust the weights of belongingness edges to balance the contribution between attribute and topological information to the detection of communities. The weight adjustment mechanism enables incremental updates of community membership of all vertices. We evaluate inc-AGGMMR on five benchmark datasets against eight strong baselines. We also provide a case study to incrementally detect communities on a PayPal payment network which contains users with transactions. The results demonstrate inc-AGGMMR’s effectiveness and practicability.

scholarly journals Graph Convolutional Network and Convolutional Neural Network Based Method for Predicting lncRNA-Disease Associations

Cells ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 1012 ◽  
Author(s):  
Xuan ◽  
Pan ◽  
Zhang ◽  
Liu ◽  
Sun
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Heterogeneous Network ◽  
Heterogeneous Data ◽  
Superior Performance ◽  
Convolutional Network ◽  
Topological Information ◽  
Disease Pair ◽  
Disease Associations ◽  
The Right

Aberrant expressions of long non-coding RNAs (lncRNAs) are often associated with diseases and identification of disease-related lncRNAs is helpful for elucidating complex pathogenesis. Recent methods for predicting associations between lncRNAs and diseases integrate their pertinent heterogeneous data. However, they failed to deeply integrate topological information of heterogeneous network comprising lncRNAs, diseases, and miRNAs. We proposed a novel method based on the graph convolutional network and convolutional neural network, referred to as GCNLDA, to infer disease-related lncRNA candidates. The heterogeneous network containing the lncRNA, disease, and miRNA nodes, is constructed firstly. The embedding matrix of a lncRNA-disease node pair was constructed according to various biological premises about lncRNAs, diseases, and miRNAs. A new framework based on a graph convolutional network and a convolutional neural network was developed to learn network and local representations of the lncRNA-disease pair. On the left side of the framework, the autoencoder based on graph convolution deeply integrated topological information within the heterogeneous lncRNA-disease-miRNA network. Moreover, as different node features have discriminative contributions to the association prediction, an attention mechanism at node feature level is constructed. The left side learnt the network representation of the lncRNA-disease pair. The convolutional neural networks on the right side of the framework learnt the local representation of the lncRNA-disease pair by focusing on the similarities, associations, and interactions that are only related to the pair. Compared to several state-of-the-art prediction methods, GCNLDA had superior performance. Case studies on stomach cancer, osteosarcoma, and lung cancer confirmed that GCNLDA effectively discovers the potential lncRNA-disease associations.

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