Moth–flame optimization-based algorithm with synthetic dynamic PPI networks for discovering protein complexes

A seed expansion-based method to identify essential proteins by integrating protein-protein interaction sub-networks and multiple biological characteristics

BACKGROUND

The identification of essential proteins is of great significance in biology and pathology. However, protein-protein interaction (PPI) data obtained through high-throughput technology include a high number of false positives. To overcome this limitation, numerous computational algorithms based on biological characteristics and topological features have been proposed to identify essential proteins.

RESULTS

In this paper, we propose a novel method named SESN for identifying essential proteins. It is a seed expansion method based on PPI sub-networks and multiple biological characteristics. Firstly, SESN utilizes gene expression data to construct PPI sub-networks. Secondly, seed expansion is performed simultaneously in each sub-network, and the expansion process is based on the topological features of predicted essential proteins. Thirdly, the error correction mechanism is based on multiple biological characteristics and the entire PPI network. Finally, SESN analyzes the impact of each biological characteristic, including protein complex, gene expression data, GO annotations, and subcellular localization, and adopts the biological data with the best experimental results. The output of SESN is a set of predicted essential proteins.

CONCLUSIONS

The analysis of each component of SESN indicates the effectiveness of all components. We conduct comparison experiments using three datasets from two species, and the experimental results demonstrate that SESN achieves superior performance compared to other methods.

DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding

Biological functions of a cell are typically carried out through protein complexes. The detection of protein complexes is therefore of great significance for understanding the cellular organizations and protein functions. In the past decades, many computational methods have been proposed to detect protein complexes. However, most of the existing methods just search the local topological information to mine dense subgraphs as protein complexes, ignoring the global topological information. To tackle this issue, we propose the DPCMNE method to detect protein complexes via multi-level network embedding. It can preserve both the local and global topological information of biological networks. First, DPCMNE employs a hierarchical compressing strategy to recursively compress the input protein-protein interaction (PPI) network into multi-level smaller PPI networks. Then, a network embedding method is applied on these smaller PPI networks to learn protein embeddings of different levels of granularity. The embeddings learned from all the compressed PPI networks are concatenated to represent the final protein embeddings of the original input PPI network. Finally, a core-attachment based strategy is adopted to detect protein complexes in the weighted PPI network constructed by the pairwise similarity of protein embeddings. To assess the efficiency of our proposed method, DPCMNE is compared with other eight clustering algorithms on two yeast datasets. The experimental results show that the performance of DPCMNE outperforms those state-of-the-art complex detection methods in terms of F1 and F1+Acc. Furthermore, the results of functional enrichment analysis indicate that protein complexes detected by DPCMNE are more biologically significant in terms of P-score.

An Improved Memetic Algorithm for Detecting Protein Complexes in Protein Interaction Networks

Identifying the protein complexes in protein-protein interaction (PPI) networks is essential for understanding cellular organization and biological processes. To address the high false positive/negative rates of PPI networks and detect protein complexes with multiple topological structures, we developed a novel improved memetic algorithm (IMA). IMA first combines the topological and biological properties to obtain a weighted PPI network with reduced noise. Next, it integrates various clustering results to construct the initial populations. Furthermore, a fitness function is designed based on the five topological properties of the protein complexes. Finally, we describe the rest of our IMA method, which primarily consists of four steps: selection operator, recombination operator, local optimization strategy, and updating the population operator. In particular, IMA is a combination of genetic algorithm and a local optimization strategy, which has a strong global search ability, and searches for local optimal solutions effectively. The experimental results demonstrate that IMA performs much better than the base methods and existing state-of-the-art techniques. The source code and datasets of the IMA can be found at https://github.com/RongquanWang/IMA.

An Improved Moth-Flame Optimization Algorithm with Adaptation Mechanism to Solve Numerical and Mechanical Engineering Problems

Moth-flame optimization (MFO) algorithm inspired by the transverse orientation of moths toward the light source is an effective approach to solve global optimization problems. However, the MFO algorithm suffers from issues such as premature convergence, low population diversity, local optima entrapment, and imbalance between exploration and exploitation. In this study, therefore, an improved moth-flame optimization (I-MFO) algorithm is proposed to cope with canonical MFO's issues by locating trapped moths in local optimum via defining memory for each moth. The trapped moths tend to escape from the local optima by taking advantage of the adapted wandering around search (AWAS) strategy. The efficiency of the proposed I-MFO is evaluated by CEC 2018 benchmark functions and compared against other well-known metaheuristic algorithms. Moreover, the obtained results are statistically analyzed by the Friedman test on 30, 50, and 100 dimensions. Finally, the ability of the I-MFO algorithm to find the best optimal solutions for mechanical engineering problems is evaluated with three problems from the latest test-suite CEC 2020. The experimental and statistical results demonstrate that the proposed I-MFO is significantly superior to the contender algorithms and it successfully upgrades the shortcomings of the canonical MFO.

A Combination Strategy of Feature Selection Based on an Integrated Optimization Algorithm and Weighted K-Nearest Neighbor to Improve the Performance of Network Intrusion Detection

With the widespread use of the Internet, network security issues have attracted more and more attention, and network intrusion detection has become one of the main security technologies. As for network intrusion detection, the original data source always has a high dimension and a large amount of data, which greatly influence the efficiency and the accuracy. Thus, both feature selection and the classifier then play a significant role in raising the performance of network intrusion detection. This paper takes the results of classification optimization of weighted K-nearest neighbor (KNN) with those of the feature selection algorithm into consideration, and proposes a combination strategy of feature selection based on an integrated optimization algorithm and weighted KNN, in order to improve the performance of network intrusion detection. Experimental results show that the weighted KNN can increase the efficiency at the expense of a small amount of the accuracy. Thus, the proposed combination strategy of feature selection based on an integrated optimization algorithm and weighted KNN can then improve both the efficiency and the accuracy of network intrusion detection.

An Improved Moth-Flame Optimization Algorithm for Engineering Problems

In this paper, an improved moth-flame optimization algorithm (IMFO) is presented to solve engineering problems. Two novel effective strategies composed of Lévy flight and dimension-by-dimension evaluation are synchronously introduced into the moth-flame optimization algorithm (MFO) to maintain a great global exploration ability and effective balance between the global and local search. The search strategy of Lévy flight is used as a regulator of the moth-position update mechanism of global search to maintain a good research population diversity and expand the algorithm’s global search capability, and the dimension-by-dimension evaluation mechanism is added, which can effectively improve the quality of the solution and balance the global search and local development capability. To substantiate the efficacy of the enhanced algorithm, the proposed algorithm is then tested on a set of 23 benchmark test functions. It is also used to solve four classical engineering design problems, with great progress. In terms of test functions, the experimental results and analysis show that the proposed method is effective and better than other well-known nature-inspired algorithms in terms of convergence speed and accuracy. Additionally, the results of the solution of the engineering problems demonstrate the merits of this algorithm in solving challenging problems with constrained and unknown search spaces.