Global Network Alignment

Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. 

Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures between network nodes (e.g., proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity, and structural similarity. This is efficient in resolving ties in similarity measures and in finding a combination of similarity measures yielding the largest biologically sound alignments. When used to align protein-protein interaction (PPI) networks of various species, M-GRAAL exposes the largest known functional and contiguous regions of network similarity. Hence, we use M-GRAAL’s alignments to predict functions of un-annotated proteins in yeast, human, and bacteria _C. jejuni_ and _E. coli_. Furthermore, using M-GRAAL to compare PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship and our phylogenetic tree is the same as sequenced-based one

Hybrid intelligent framework for automated medical learning

This paper investigates the automated medical learning and proposes hybrid intelligent framework, called Hybrid Automated Medical Learning (HAML). The goal is the efficient combination of several intelligent components in order to automatically learn the medical data. Multi agents system is proposed by using distributed deep learning, and knowledge graph for learning medical data. The distributed deep learning is used for efficient learning of the different agents in the system, where the knowledge graph is used for dealing with heterogeneous medical data. To demonstrate the usefulness and accuracy of the HAML framework, intensive simulations on medical data were conducted. A wide range of experiments were conducted to verify the efficiency of the proposed system. Three case studies are discussed in this research, the first case study is related to process mining, and more precisely on the ability of HAML to detect relevant patterns from event medical data. The second case study is related to smart building, and the ability of HAML to recognize the different activities of the patients. The third one is related to medical image retrieval, and the ability of HAML to find the most relevant medical images according to the image query. The results show that the developed HAML achieves good performance compared to the most up-to-date medical learning models regarding both the computational and cost the quality of returned solutions.publishedVersio

Hybrid intelligent framework for automated medical learning

This paper investigates the automated medical learning and proposes hybrid intelligent framework, called Hybrid Automated Medical Learning (HAML). The goal is the efficient combination of several intelligent components in order to automatically learn the medical data. Multi agents system is proposed by using distributed deep learning, and knowledge graph for learning medical data. The distributed deep learning is used for efficient learning of the different agents in the system, where the knowledge graph is used for dealing with heterogeneous medical data. To demonstrate the usefulness and accuracy of the HAML framework, intensive simulations on medical data were conducted. A wide range of experiments were conducted to verify the efficiency of the proposed system. Three case studies are discussed in this research, the first case study is related to process mining, and more precisely on the ability of HAML to detect relevant patterns from event medical data. The second case study is related to smart building, and the ability of HAML to recognize the different activities of the patients. The third one is related to medical image retrieval, and the ability of HAML to find the most relevant medical images according to the image query. The results show that the developed HAML achieves good performance compared to the most up-to-date medical learning models regarding both the computational and cost the quality of returned solutionspublishedVersio

Genomic scale sub-family assignment of protein domains

Many classification schemes for proteins and domains are either hierarchical or semi-hierarchical yet most databases, especially those offering genome-wide analysis, only provide assignments to sequences at one level of their hierarchy. Given an established hierarchy, the problem of assigning new sequences to lower levels of that existing hierarchy is less hard (but no less important) than the initial top level assignment which requires the detection of the most distant relationships. A solution to this problem is described here in the form of a new procedure which can be thought of as a hybrid between pairwise and profile methods. The hybrid method is a general procedure that can be applied to any pre-defined hierarchy, at any level, including in principle multiple sub-levels. It has been tested on the SCOP classification via the SUPERFAMILY database and performs significantly better than either pairwise or profile methods alone. Perhaps the greatest advantage of the hybrid method over other possible approaches to the problem is that within the framework of an existing profile library, the assignments are fully automatic and come at almost no additional computational cost. Hence it has already been applied at the SCOP family level to all genomes in the SUPERFAMILY database, providing a wealth of new data to the biological and bioinformatics communities

An ontology matching approach for semantic modeling: A case study in smart cities

This paper investigates the semantic modeling of smart cities and proposes two ontology matching frameworks, called Clustering for Ontology Matching-based Instances (COMI) and Pattern mining for Ontology Matching-based Instances (POMI). The goal is to discover the relevant knowledge by investigating the correlations among smart city data based on clustering and pattern mining approaches. The COMI method first groups the highly correlated ontologies of smart-city data into similar clusters using the generic k-means algorithm. The key idea of this method is that it clusters the instances of each ontology and then matches two ontologies by matching their clusters and the corresponding instances within the clusters. The POMI method studies the correlations among the data properties and selects the most relevant properties for the ontology matching process. To demonstrate the usefulness and accuracy of the COMI and POMI frameworks, several experiments on the DBpedia, Ontology Alignment Evaluation Initiative, and NOAA ontology databases were conducted. The results show that COMI and POMI outperform the state-of-the-art ontology matching models regarding computational cost without losing the quality during the matching process. Furthermore, these results confirm the ability of COMI and POMI to deal with heterogeneous large-scale data in smart-city environments.publishedVersio

Optimizing Ontology Alignments through NSGA-II without Using Reference Alignment

Ontology is widely used to solve the data heterogeneity problems on the semantic web, but the available ontologies could themselves introduce heterogeneity. In order to reconcile these ontologies to implement the semantic interoperability, we need to find the relationships among the entities in various ontologies, and the process of identifying them is called ontology alignment. In all the existing matching systems that use evolutionary approaches to optimize their parameters, a reference alignment between two ontologies to be aligned should be given in advance which could be very expensive to obtain especially when the scale of ontologies is considerably large. To address this issue, in this paper we propose a novel approach to utilize the NSGA-II to optimize the ontology alignments without using the reference alignment. In our approach, an adaptive aggregation strategy is presented to improve the efficiency of optimizing process and two approximate evaluation measures, namely match coverage and match ratio, are introduced to replace the classic recall and precision on reference alignment to evaluate the quality of the alignments. Experimental results show that our approach is effective and can find the solutions that are very close to those obtained by the approaches using reference alignment, and the quality of alignments is in general better than that of state of the art ontology matching systems such as GOAL and SAMBO

Sensor data fusion for the industrial artificial intelligence of things

The emergence of smart sensors, artificial intelligence, and deep learning technologies yield artificial intelligence of things, also known as the AIoT. Sophisticated cooperation of these technologies is vital for the effective processing of industrial sensor data. This paper introduces a new framework for addressing the different challenges of the AIoT applications. The proposed framework is an intelligent combination of multi-agent systems, knowledge graphs and deep learning. Deep learning architectures are used to create models from different sensor-based data. Multi-agent systems can be used for simulating the collective behaviours of the smart sensors using IoT settings. The communication among different agents is realized by integrating knowledge graphs. Different optimizations based on constraint satisfaction as well as evolutionary computation are also investigated. Experimental analysis is undertaken to compare the methodology presented to state-of-the-art AIoT technologies. We show through experimentation that our designed framework achieves good performance compared to baseline solutions.publishedVersio

Intelligent blockchain management for distributed knowledge graphs in IoT 5G environments

This article introduces a new problem of distributed knowledge graph, in IoT 5G setting. We developed an end-to-end solution for solving such problem by exploring the blockchain management and intelligent method for producing the better matching of the concepts and relations of the set of knowledge graphs. The concepts and the relations of the knowledge graphs are divided into several components, each of which contains similar concepts and relations. Instead of exploring the whole concepts and the relations of the knowledge graphs, only the representative of these components is compared during the matching process. The framework has outperformed state-of-the-art knowledge graph matching algorithms using different scenarios as input in the experiments. In addition, to confirm the usability of our suggested framework, an in-depth experimental analysis has been done; the results are very promising in both runtime and accuracy.publishedVersio