scholarly journals Two distributed semi-supervised algorithms for mining of complex networks using Giraph

2018 ◽  
Author(s):  
Erfan Farhangi Maleki ◽  
Nasser Ghadiri ◽  
Maryam Lotfi Shahreza ◽  
Zeinab Maleki
Keyword(s):  
Complex Networks ◽  
Heterogeneous Networks ◽  
Biological Networks ◽  
Biological Network ◽  
Drug Repositioning ◽  
Label Propagation ◽  
Large Graphs ◽  
The Subject ◽  
Scalable Methods

AbstractBackground and ObjectiveHeterogeneous complex networks are large graphs consisting of different types of nodes and edges. The process of mining and knowledge extraction from these networks is so complicated. Moreover, the scale of these networks is steadily increasing. Thus, scalable methods are required.MethodsIn this paper, two distributed label propagation algorithms for heterogeneous networks, namely DHLP-1 and DHLP-2 have been introduced. Biological networks are one type of the heterogeneous complex networks. As a case study, we have measured the efficiency of our proposed DHLP-1 and DHLP-2 algorithms on a biological network consisting of drugs, diseases, and targets. The subject we have studied in this network is drug repositioning but our algorithms can be used as general methods for heterogeneous networks other than the biological network.ResultsWe compared the proposed algorithms with similar non-distributed versions of them namely MINProp and Heter-LP. The experiments revealed the good performance of the algorithms in terms of running time and accuracy.

scholarly journals Reconstruction of biological networks based on life science data integration

2010 ◽  
Vol 7 (2) ◽  
Author(s):  
Benjamin Kormeier ◽  
Klaus Hippe ◽  
Patrizio Arrigo ◽  
Thoralf Töpel ◽  
Sebastian Janowski ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Data Integration ◽  
Biological Networks ◽  
Life Science ◽  
Biological Network ◽  
Network Models ◽  
Biological Data ◽  
Science Data ◽  
Biological Data Integration

SummaryFor the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and VANESA- a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

scholarly journals Drug Repurposing Using Biological Networks

Processes ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 1057
Author(s):  
Francisco Javier Somolinos ◽  
Carlos León ◽  
Sara Guerrero-Aspizua
Keyword(s):  
Computational Methods ◽  
Biological Networks ◽  
High Performance ◽  
Biological Network ◽  
Drug Repositioning ◽  
Drug Repurposing ◽  
Network Models ◽  
Biomedical Data ◽  
Multiple Targets ◽  
Medical Indication

Drug repositioning is a strategy to identify new uses for existing, approved, or research drugs that are outside the scope of its original medical indication. Drug repurposing is based on the fact that one drug can act on multiple targets or that two diseases can have molecular similarities, among others. Currently, thanks to the rapid advancement of high-performance technologies, a massive amount of biological and biomedical data is being generated. This allows the use of computational methods and models based on biological networks to develop new possibilities for drug repurposing. Therefore, here, we provide an in-depth review of the main applications of drug repositioning that have been carried out using biological network models. The goal of this review is to show the usefulness of these computational methods to predict associations and to find candidate drugs for repositioning in new indications of certain diseases.

scholarly journals A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Tomas Hruz ◽  
Markus Wyss ◽  
Christoph Lucas ◽  
Oliver Laule ◽  
Peter von Rohr ◽  
...  
Keyword(s):  
Complex System ◽  
Systems Biology ◽  
Complex Networks ◽  
Network Structure ◽  
Biological Networks ◽  
Large Graphs ◽  
Layout Algorithm ◽  
Underlying Network ◽  
Visualization Algorithms ◽  
Edge Crossings

Visualization of large complex networks has become an indispensable part of systems biology, where organisms need to be considered as one complex system. The visualization of the corresponding network is challenging due to the size and density of edges. In many cases, the use of standard visualization algorithms can lead to high running times and poorly readable visualizations due to many edge crossings. We suggest an approach that analyzes the structure of the graph first and then generates a new graph which contains specific semantic symbols for regular substructures like dense clusters. We propose a multilevel gamma-clustering layout visualization algorithm (MLGA) which proceeds in three subsequent steps: (i) a multilevel γ-clustering is used to identify the structure of the underlying network, (ii) the network is transformed to a tree, and (iii) finally, the resulting tree which shows the network structure is drawn using a variation of a force-directed algorithm. The algorithm has a potential to visualize very large networks because it uses modern clustering heuristics which are optimized for large graphs. Moreover, most of the edges are removed from the visual representation which allows keeping the overview over complex graphs with dense subgraphs.

scholarly journals Multiplex-Heterogeneous Network Embedding for Drug Repositioning

2021 ◽  
Author(s):  
Léo Pio-Lopez
Keyword(s):  
Heterogeneous Networks ◽  
Heterogeneous Network ◽  
Link Prediction ◽  
Drug Target ◽  
Drug Repositioning ◽  
Drug Repurposing ◽  
Network Embedding ◽  
Medical Treatments ◽  
Vector Representations

Drug repositioning (also called drug repurposing) is a strategy for identifying new therapeutic targets for existing drugs. This approach is of great importance in pharmacology as it is a faster and cheaper way to develop new medical treatments. In this paper, we present, to our knowledge, the first application of multiplex-heterogeneous network embedding to drug repositioning. Network embedding learns the vector representations of nodes, opening the whole machine learning toolbox for a wide variety of applications including link prediction, node labelling or clustering. So far, the application of network embedding for drug repositioning focused on heterogeneous networks. Our approach for drug repositioning is based on multiplex-heterogeneous network embedding. Such method allows the richness and complexity of multiplex and heterogeneous networks to be projected in the same vector space. In other words, multiplex-heterogeneous networks aggregate different multi-omics data in the same network representation. We validate the approach on a task of link prediction and on a case study for SARS-CoV2 drug repositioning. Experimental results show that our approach is highly robust and effective for finding new drug-target associations.

Polytechnic to Business Project (P2B) a Case of Innovation and Knowledge Transference

2019 ◽  
Vol 6 (1) ◽  
pp. 40-49
Author(s):  
Teresa Paiva
Keyword(s):  
Knowledge Transfer ◽  
Best Practices ◽  
Education Institution ◽  
Theoretical Background ◽  
Transfer Model ◽  
Case Study Method ◽  
Multiple Sources ◽  
The Subject ◽  
Manage Innovation

Background: The theoretical background of this article is on the model developed of knowledge transfer between universities and the industry in order to access the best practices and adapt to the study case in question regarding the model of promoting and manage innovation within the universities that best contribute with solution and projects to the business field. Objective: The development of a knowledge transfer model is the main goal of this article, supported in the best practices known and, also, to reflect in the main measurement definitions to evaluate the High Education Institution performance in this area. Methods: The method for this article development is the case study method because it allows the fully understanding of the dynamics present within a single setting, and the subject examined to comprehend what is being done and what the dynamics mean. The case study does not have a data collection method, as it is a research that may rely on multiple sources of evidence and data which should be converged. Results: Since it’s a case study this article present a fully description of the model proposed and implemented for the knowledge transfer process of the institution. Conclusion: Still in a discussion phase, this article presents as conclusions some questions and difficulties that could be pointed out, as well as some good perspectives of performed activity developed.

An Ayurvedic Visual Rehabilitation In Lebers Congenital Amaurosis - Prospective Case Study

2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Dr. Vidhyasri M ◽  
Dr. S. M. Pasha
Keyword(s):  
Marked Improvement ◽  
Clinical Case ◽  
Treatment Plan ◽  
Visual Disability ◽  
Visual Rehabilitation ◽  
Potential Risks ◽  
The Subject ◽  
Slow Frequency

Introduction: This is the case report of child who was diagnosed with LCA reported with complaints of large-amplitude, slow-frequency, roving nystagmus, frequent tendency to press on his eyes, enopthalmos, with completely normal ophthalmoscopic examination with normal appearing optic nerve and retina and has a non recordable ERG; considering this condition under the lines of Vataja Nanatmaja Vyadhi treatment was structured to render effective visual rehabilitation which showed marked results. Methods: 4 years old male child who was diagnosed with lebers congenital amaurosis was brought by his parents to Eye OPD, GAMC, Bengaluru. The presentation of this case includes bibliographic review of the subject, presentation of a clinical case and description of the importance of Ayurvedic prespective of handling of these patients. Results: The child showed improvement in fixing for light and also nystagmus showed marked improvement and there were considerable behavioural changes observed. Discussion: It is important to deepen the environment of the disease to know the possible implications in Ayurvedic management, recognize the magnitude of visual disability that our patient presents for the establishment of the treatment plan and provide an integral care of excellence in an interdisciplinary way in favor of visual rehabilitation of our patients and also help to restore quality of life with no potential risks of side effects.

scholarly journals Techniques for Mitigating the Effects of Smoke Taint While Maintaining Quality in Wine Production: A Review

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1672
Author(s):  
Ysadora A. Mirabelli-Montan ◽  
Matteo Marangon ◽  
Antonio Graça ◽  
Christine M. Mayr Marangon ◽  
Kerry L. Wilkinson
Keyword(s):  
Global Perspective ◽  
Wine Industry ◽  
Wine Production ◽  
Specific Data ◽  
Main Research ◽  
Initial Severity ◽  
The Subject ◽  
Available Information

Smoke taint has become a prominent issue for the global wine industry as climate change continues to impact the length and extremity of fire seasons around the world. Although the issue has prompted a surge in research on the subject in recent years, no singular solution has yet been identified that is capable of maintaining the quality of wine made from smoke-affected grapes. In this review, we summarize the main research on smoke taint, the key discoveries, as well as the prevailing uncertainties. We also examine methods for mitigating smoke taint in the vineyard, in the winery, and post production. We assess the effectiveness of remediation methods (proposed and actual) based on available research. Our findings are in agreement with previous studies, suggesting that the most viable remedies for smoke taint are still the commercially available activated carbon fining and reverse osmosis treatments, but that the quality of the final treated wines is fundamentally dependent on the initial severity of the taint. In this review, suggestions for future studies are introduced for improving our understanding of methods that have thus far only been preliminarily investigated. We select regions that have already been subjected to severe wildfires, and therefore subjected to smoke taint (particularly Australia and California) as a case study to inform other wine-producing countries that will likely be impacted in the future and suggest specific data collection and policy implementation actions that should be taken, even in countries that have not yet been impacted by smoke taint. Ultimately, we streamline the available information on the topic of smoke taint, apply it to a global perspective that considers the various stakeholders involved, and provide a launching point for further research on the topic.

scholarly journals Influence of Hydrogeochemistry on Tunnel Drainage in Evaporitic Formations: El Regajal Tunnel Case Study (Aranjuez, Spain)

2021 ◽  
Vol 13 (3) ◽  
pp. 1505
Author(s):  
Ignacio Menéndez Pidal ◽  
Jose Antonio Mancebo Piqueras ◽  
Eugenio Sanz Pérez ◽  
Clemente Sáenz Sanz
Keyword(s):  
High Speed ◽  
Civil Engineering ◽  
Saturation Index ◽  
The Subject ◽  
Under Construction ◽  
Underground Flow ◽  
Very High ◽  
Over Time

Many of the large number of underground works constructed or under construction in recent years are in unfavorable terrains facing unusual situations and construction conditions. This is the case of the subject under study in this paper: a tunnel excavated in evaporitic rocks that experienced significant karstification problems very quickly over time. As a result of this situation, the causes that may underlie this rapid karstification are investigated and a novel methodology is presented in civil engineering where the use of saturation indices for the different mineral specimens present has been crucial. The drainage of the rock massif of El Regajal (Madrid-Toledo, Spain, in the Madrid-Valencia high-speed train line) was studied and permitted the in-situ study of the hydrogeochemical evolution of water flow in the Miocene evaporitic materials of the Tajo Basin as a full-scale testing laboratory, that are conforms as a whole, a single aquifer. The work provides a novel methodology based on the calculation of activities through the hydrogeochemical study of water samples in different piezometers, estimating the saturation index of different saline materials and the dissolution capacity of the brine, which is surprisingly very high despite the high electrical conductivity. The circulating brine appears unsaturated with respect to thenardite, mirabilite, epsomite, glauberite, and halite. The alteration of the underground flow and the consequent renewal of the water of the aquifer by the infiltration water of rain and irrigation is the cause of the hydrogeochemical imbalance and the modification of the characteristics of the massif. These modifications include very important loss of material by dissolution, altering the resistance of the terrain and the increase of the porosity. Simultaneously, different expansive and recrystallization processes that decrease the porosity of the massif were identified in the present work. The hydrogeochemical study allows the evolution of these phenomena to be followed over time, and this, in turn, may facilitate the implementation of preventive works in civil engineering.

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