Incorporating higher order network structures to improve miRNA-disease association prediction based on functional modularity.

As microRNAs (miRNAs) are involved in many essential biological processes, their abnormal expressions can serve as biomarkers and prognostic indicators to prevent the development of complex diseases, thus providing accurate early detection and prognostic evaluation. Although a number of computational methods have been proposed to predict miRNA-disease associations (MDAs) for further experimental verification, their performance is limited primarily by the inadequacy of exploiting lower order patterns characterizing known MDAs to identify missing ones from MDA networks. Hence, in this work, we present a novel prediction model, namely HiSCMDA, by incorporating higher order network structures for improved performance of MDA prediction. To this end, HiSCMDA first integrates miRNA similarity network, disease similarity network and MDA network to preserve the advantages of all these networks. After that, it identifies overlapping functional modules from the integrated network by predefining several higher order connectivity patterns of interest. Last, a path-based scoring function is designed to infer potential MDAs based on network paths across related functional modules. HiSCMDA yields the best performance across all datasets and evaluation metrics in the cross-validation and independent validation experiments. Furthermore, in the case studies, 49 and 50 out of the top 50 miRNAs, respectively, predicted for colon neoplasms and lung neoplasms have been validated by well-established databases. Experimental results show that rich higher order organizational structures exposed in the MDA network gain new insight into the MDA prediction based on higher order connectivity patterns.

Optimizing Living Material Delivery During the COVID-19 Outbreak.

The coronavirus disease 2019 (COVID-19) epidemic has spread worldwide, posing a great threat to human beings. The stay-home quarantine is an effective way to reduce physical contacts and the associated COVID-19 transmission risk, which requires the support of efficient living materials (such as meats, vegetables, grain, and oil) delivery. Notably, the presence of potential infected individuals increases the COVID-19 transmission risk during the delivery. The deliveryman may be the medium through which the virus spreads among urban residents. However, traditional delivery route optimization methods don't take the virus transmission risk into account. Here, we propose a novel living material delivery route approach considering the possible COVID-19 transmission during the delivery. A complex network-based virus transmission model is developed to simulate the possible COVID-19 infection between urban residents and the deliverymen. A bi-objective model considering the COVID-19 transmission risk and the total route length is proposed and solved by the hybrid meta-heuristics integrating the adaptive large neighborhood search and simulated annealing. The experiment was conducted in Wuhan, China to assess the performance of the proposed approach. The results demonstrate that 935 vehicles will totally travel 56,424.55 km to deliver necessary living materials to 3,154 neighborhoods, with total risk [Formula: see text]. The presented approach reduces the risk of COVID-19 transmission by 67.55% compared to traditional distance-based optimization methods. The presented approach can facilitate a well response to the COVID-19 in the transportation sector.

Information Measures for Generalized Order Statistics and Their Concomitants under General Framework from Huang-Kotz FGM Bivariate Distribution.

In this paper, we study the concomitants of dual generalized order statistics (and consequently generalized order statistics) when the parameters γ1,…,γn are assumed to be pairwise different from Huang-Kotz Farlie-Gumble-Morgenstern bivariate distribution. Some useful recurrence relations between single and product moments of concomitants are obtained. Moreover, Shannon's entropy and the Fisher information number measures are derived. Finally, these measures are extensively studied for some well-known distributions such as exponential, Pareto and power distributions. The main motivation of the study of the concomitants of generalized order statistics (as an important practical kind to order the bivariate data) under this general framework is to enable researchers in different fields of statistics to use some of the important models contained in these generalized order statistics only under this general framework. These extended models are frequently used in the reliability theory, such as the progressive type-II censored order statistics.

A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach.

Motivation: The fundamental challenge of modern genetic analysis is to establish gene-phenotype correlations that are often found in the large-scale publications. Because lexical features of gene are relatively regular in text, the main challenge of these relation extraction is phenotype recognition. Due to phenotypic descriptions are often study- or author-specific, few lexicon can be used to effectively identify the entire phenotypic expressions in text, especially for plants. Results: We have proposed a pipeline for extracting phenotype, gene and their relations from biomedical literature. Combined with abbreviation revision and sentence template extraction, we improved the unsupervised word-embedding-to-sentence-embedding cascaded approach as representation learning to recognize the various broad phenotypic information in literature. In addition, the dictionary- and rule-based method was applied for gene recognition. Finally, we integrated one of famous information extraction system OLLIE to identify gene-phenotype relations. To demonstrate the applicability of the pipeline, we established two types of comparison experiment using model organism Arabidopsis thaliana. In the comparison of state-of-the-art baselines, our approach obtained the best performance (F1-Measure of 66.83%). We also applied the pipeline to 481 full-articles from TAIR gene-phenotype manual relationship dataset to prove the validity. The results showed that our proposed pipeline can cover 70.94% of the original dataset and add 373 new relations to expand it. Availability and implementation: The source code is available at http://www.wutbiolab.cn: 82/Gene-Phenotype-Relation-Extraction-Pipeline.zip. Supplementary information: Supplementary data are available at Bioinformatics online.

InDel marker detection by integration of multiple softwares using machine learning techniques.

BACKGROUND: In the biological experiments of soybean species, molecular markers are widely used to verify the soybean genome or construct its genetic map. Among a variety of molecular markers, insertions and deletions (InDels) are preferred with the advantages of wide distribution and high density at the whole-genome level. Hence, the problem of detecting InDels based on next-generation sequencing data is of great importance for the design of InDel markers. To tackle it, this paper integrated machine learning techniques with existing software and developed two algorithms for InDel detection, one is the best F-score method (BF-M) and the other is the Support Vector Machine (SVM) method (SVM-M), which is based on the classical SVM model. RESULTS: The experimental results show that the performance of BF-M was promising as indicated by the high precision and recall scores, whereas SVM-M yielded the best performance in terms of recall and F-score. Moreover, based on the InDel markers detected by SVM-M from soybeans that were collected from 56 different regions, highly polymorphic loci were selected to construct an InDel marker database for soybean. CONCLUSIONS: Compared to existing software tools, the two algorithms proposed in this work produced substantially higher precision and recall scores, and remained stable in various types of genomic regions. Moreover, based on SVM-M, we have constructed a database for soybean InDel markers and published it for academic research.

SSAT ++ : A Semantic-Aware and Versatile Makeup Transfer Network With Local Color Consistency Constraint.

The purpose of makeup transfer (MT) is to transfer makeup from a reference image to a target face while preserving the target's content. Existing methods have made remarkable progress in generating realistic results but do not perform well in terms of semantic correspondence and color fidelity. In addition, the straightforward extension of processing videos frame by frame tends to produce flickering results in most methods. These limitations restrict the applicability of previous methods in real-world scenarios. To address these issues, we propose a symmetric semantic-aware transfer network (SSAT ++ ) to improve makeup similarity and video temporal consistency. For MT, the feature fusion (FF) module first integrates the content and semantic features of the input images, producing multiscale fusion features. Then, the semantic correspondence from the reference to the target is obtained by measuring the correlation of fusion features at each position. According to semantic correspondence, the symmetric mask semantic transfer (SMST) module aligns the reference makeup features with the target content features to generate MT results. Meanwhile, the semantic correspondence from the target to the reference is obtained by transposing the correlation matrix and applied to the makeup removal task. To enhance color fidelity, we propose a novel local color loss that forces the transferred results to have the same color histogram distribution as the reference. Furthermore, a morphing simulation is designed to ensure temporal consistency for video MT without requiring additional video frame input and optical flow estimation. To evaluate the effectiveness of our SSAT ++ , extensive experiments have been conducted on the MT dataset which has a variety of makeup styles, and on the MT-Wild dataset which contains images with diverse poses and expressions. The experiments show that SSAT ++ outperforms existing MT methods through qualitative and quantitative evaluation and provides more flexible makeup control. Code and trained model will be available at https://gitee.com/sunzhaoyang0304/ssat-msp and https://github.com/Snowfallingplum/SSAT.

Multi-scale Triplet Hashing for Medical Image Retrieval.

For medical image retrieval task, deep hashing algorithms are widely applied in large-scale datasets for auxiliary diagnosis due to the retrieval efficiency advantage of hash codes. Most of which focus on features learning, whilst neglecting the discriminate area of medical images and hierarchical similarity for deep features and hash codes. In this paper, we tackle these dilemmas with a new Multi-scale Triplet Hashing (MTH) algorithm, which can leverage multi-scale information, convolutional self-attention and hierarchical similarity to learn effective hash codes simultaneously. The MTH algorithm first designs multi-scale DenseBlock module to learn multi-scale information of medical images. Meanwhile, a convolutional self-attention mechanism is developed to perform information interaction of the channel domain, which can capture the discriminate area of medical images effectively. On top of the two paths, a novel loss function is proposed to not only conserve the category-level information of deep features and the semantic information of hash codes in the learning process, but also capture the hierarchical similarity for deep features and hash codes. Extensive experiments on the Curated X-ray Dataset, Skin Cancer MNIST Dataset and COVID-19 Radiography Dataset illustrate that the MTH algorithm can further enhance the effect of medical retrieval compared to other state-of-the-art medical image retrieval algorithms.

Making contract users safer: Towards building a Safe Browsing platform on Ethereum.

There are many papers and tools regarding the detection of unsafe contracts, but few ways for detection results to practically benefit contract users and owners. This paper presents a Blockchain Safe Browsing (BSB) platform to safely disseminate those detection results. An encrypted blacklist will be generated to provide privacy preserving user warning before they make transactions with unsafe contracts. Contract owners will be notified that there are vulnerabilities in their contracts, and they can purchase related reports which record how to exploit the vulnerabilities. The profits inspire the researchers to contribute their update-to-date lists of unsafe contracts. An effective encryption scheme is developed to guarantee that only contract owners can decrypt the encrypted reports. Extensive evaluations demonstrate that our prototype can function as intended without sacrificing user experience.

Local R-Symmetry Co-Occurrence: Characterising Leaf Image Patterns for Identifying Cultivars.

Leaf image recognition techniques have been actively researched for plant species identification. However it remains unclear whether analysing leaf patterns can provide sufficient information for further differentiating cultivars. This paper reports our attempt on cultivar recognition from leaves as a general very fine-grained pattern recognition problem, which is not only a challenging research problem but also important for cultivar evaluation, selection and production in agriculture. We propose a novel local R-symmetry co-occurrence method for characterising discriminative local symmetry patterns to distinguish subtle differences among cultivars. Through scalable and moving R-relation radius pairs, we generate a set of radius symmetry co-occurrence matrices (RsCoM)and their measures for describing the local symmetry properties of interior regions. By varying the size of the radius pair, the RsCoM measures local R-symmetry co-occurrence from global/coarse to fine scales. A new two-phase strategy of analysing the distribution of local RsCoM measures is designed to match the multiple scale appearance symmetry pattern distributions of similar cultivar leaf images. We constructed three leaf image databases, SoyCultivar, CottCultivar, and PeanCultivar, for an extensive experimental evaluation on recognition across soybean, cotton and peanut cultivars. Encouraging experimental results of the proposed method in comparison with the state-of-the-art leaf species recognition methods demonstrate the effectiveness of the proposed method for cultivar identification, which may advance the research in leaf recognition from species to cultivar.

Job Scheduling in Cloud Computing Using a Modified Harris Hawks Optimization and Simulated Annealing Algorithm.

In recent years, cloud computing technology has attracted extensive attention from both academia and industry. The popularity of cloud computing was originated from its ability to deliver global IT services such as core infrastructure, platforms, and applications to cloud customers over the web. Furthermore, it promises on-demand services with new forms of the pricing package. However, cloud job scheduling is still NP-complete and became more complicated due to some factors such as resource dynamicity and on-demand consumer application requirements. To fill this gap, this paper presents a modified Harris hawks optimization (HHO) algorithm based on the simulated annealing (SA) for scheduling jobs in the cloud environment. In the proposed HHOSA approach, SA is employed as a local search algorithm to improve the rate of convergence and quality of solution generated by the standard HHO algorithm. The performance of the HHOSA method is compared with that of state-of-the-art job scheduling algorithms, by having them all implemented on the CloudSim toolkit. Both standard and synthetic workloads are employed to analyze the performance of the proposed HHOSA algorithm. The obtained results demonstrate that HHOSA can achieve significant reductions in makespan of the job scheduling problem as compared to the standard HHO and other existing scheduling algorithms. Moreover, it converges faster when the search space becomes larger which makes it appropriate for large-scale scheduling problems.

Arabic Sentiment Classification Using Convolutional Neural Network and Differential Evolution Algorithm.

In recent years, convolutional neural network (CNN) has attracted considerable attention since its impressive performance in various applications, such as Arabic sentence classification. However, building a powerful CNN for Arabic sentiment classification can be highly complicated and time consuming. In this paper, we address this problem by combining differential evolution (DE) algorithm and CNN, where DE algorithm is used to automatically search the optimal configuration including CNN architecture and network parameters. In order to achieve the goal, five CNN parameters are searched by the DE algorithm which include convolution filter sizes that control the CNN architecture, number of filters per convolution filter size (NFCS), number of neurons in fully connected (FC) layer, initialization mode, and dropout rate. In addition, the effect of the mutation and crossover operators in DE algorithm were investigated. The performance of the proposed framework DE-CNN is evaluated on five Arabic sentiment datasets. Experiments' results show that DE-CNN has higher accuracy and is less time consuming than the state-of-the-art algorithms.

Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers.

Protein complexes are crucial in improving our understanding of the mechanisms employed by proteins. Various computational algorithms have thus been proposed to detect protein complexes from protein interaction networks. However, given massive protein interactome data obtained by high-throughput technologies, existing algorithms, especially those with additionally consideration of biological information of proteins, either have low efficiency in performing their tasks or suffer from limited effectiveness. For addressing this issue, this work proposes to detect protein complexes from a protein interaction network with high efficiency and effectiveness. To do so, the original detection task is first formulated into an optimization problem according to the intuitive properties of protein complexes. After that, the framework of alternating direction method of multipliers is applied to decompose this optimization problem into several subtasks, which can be subsequently solved in a separate and parallel manner. An algorithm for implementing this solution is then developed. Experimental results on five large protein interaction networks demonstrated that compared to state-of-the-art protein complex detection algorithms, our algorithm outperformed them in terms of both effectiveness and efficiency. Moreover, as number of parallel processes increases, one can expect an even higher computational efficiency for the proposed algorithm with no compromise on effectiveness.

Automatic hierarchy classification in venation networks using directional morphological filtering for hierarchical structure traits extraction.

The extraction of vein traits from venation networks is of great significance to the development of a variety of research fields, such as evolutionary biology. However, traditional studies normally target to the extraction of reticulate structure traits (ReSTs), which is not sufficient enough to distinguish the difference between vein orders. For hierarchical structure traits (HiSTs), only a few tools have made attempts with human assistance, and obviously are not practical for large-scale traits extraction. Thus, there is a necessity to develop the method of automated vein hierarchy classification, raising a new challenge yet to be addressed. We propose a novel vein hierarchy classification method based on directional morphological filtering to automatically classify vein orders. Different from traditional methods, our method classify vein orders from highly dense venation networks for the extraction of traits with ecological significance. To the best of our knowledge, this is the first attempt to automatically classify vein hierarchy. To evaluate the performance of our method, we prepare a soybean transmission image dataset (STID) composed of 1200 soybean leaf images and the vein orders of these leaves are manually coarsely annotated by experts as ground truth. We apply our method to classify vein orders of each leaf in the dataset. Compared with ground truth, the proposed method achieves great performance, while the average deviation on major vein is less than 5 pixels and the average completeness on second-order veins reaches 54.28%.

Quantitative Structure-Activity Relationship Model for HCVNS5B inhibitors based on an Antlion Optimizer-Adaptive Neuro-Fuzzy Inference System.

The global prevalence of hepatitis C Virus (HCV) is approximately 3% and one-fifth of all HCV carriers live in the Middle East, where Egypt has the highest global incidence of HCV infection. Quantitative structure-activity relationship (QSAR) models were used in many applications for predicting the potential effects of chemicals on human health and environment. The adaptive neuro-fuzzy inference system (ANFIS) is one of the most popular regression methods for building a nonlinear QSAR model. However, the quality of ANFIS is influenced by the size of the descriptors, so descriptor selection methods have been proposed, although these methods are affected by slow convergence and high time complexity. To avoid these limitations, the antlion optimizer was used to select relevant descriptors, before constructing a nonlinear QSAR model based on the PIC50 and these descriptors using ANFIS. In our experiments, 1029 compounds were used, which comprised 579 HCVNS5B inhibitors (PIC50 < ~14) and 450 non-HCVNS5B inhibitors (PIC50 > ~14). The experimental results showed that the proposed QSAR model obtained acceptable accuracy according to different measures, where [Formula: see text] was 0.952 and 0.923 for the training and testing sets, respectively, using cross-validation, while [Formula: see text] was 0.8822 using leave-one-out (LOO).

Automatic Detection of Galaxy Type From Datasets of Galaxies Image Based on Image Retrieval Approach.

This paper presents a new approach for the automatic detection of galaxy morphology from datasets based on an image-retrieval approach. Currently, there are several classification methods proposed to detect galaxy types within an image. However, in some situations, the aim is not only to determine the type of galaxy within the queried image, but also to determine the most similar images for query image. Therefore, this paper proposes an image-retrieval method to detect the type of galaxies within an image and return with the most similar image. The proposed method consists of two stages, in the first stage, a set of features is extracted based on shape, color and texture descriptors, then a binary sine cosine algorithm selects the most relevant features. In the second stage, the similarity between the features of the queried galaxy image and the features of other galaxy images is computed. Our experiments were performed using the EFIGI catalogue, which contains about 5000 galaxies images with different types (edge-on spiral, spiral, elliptical and irregular). We demonstrate that our proposed approach has better performance compared with the particle swarm optimization (PSO) and genetic algorithm (GA) methods.

Analysis of Bioactive Amino Acids from Fish Hydrolysates with a New Bioinformatic Intelligent System Approach.

The current economics of the fish protein industry demand rapid, accurate and expressive prediction algorithms at every step of protein production especially with the challenge of global climate change. This help to predict and analyze functional and nutritional quality then consequently control food allergies in hyper allergic patients. As, it is quite expensive and time-consuming to know these concentrations by the lab experimental tests, especially to conduct large-scale projects. Therefore, this paper introduced a new intelligent algorithm using adaptive neuro-fuzzy inference system based on whale optimization algorithm. This algorithm is used to predict the concentration levels of bioactive amino acids in fish protein hydrolysates at different times during the year. The whale optimization algorithm is used to determine the optimal parameters in adaptive neuro-fuzzy inference system. The results of proposed algorithm are compared with others and it is indicated the higher performance of the proposed algorithm.

Bar charts detection and analysis in biomedical literature of PubMed Central.

Bar charts are crucial to summarize and present multi-faceted data sets in biomedical publications. Quantitative information carried by bar charts is of great interest to scientists and practitioners, which make it valuable to parse bar charts. This fact together with the abundance of bar chart images and their shared common patterns gives us a good candidates for automated image mining and parsing. We demonstrate a workflow to analyze bar charts and give a few feasible solutions to apply it. We are able to detect bar segments and panels with a promising performance in terms of both accuracy and recall, and we also perform extensive experiments to identify the entities of bar charts in the images of biomedical literature collected from PubMed Central. While we cannot provide a complete instance of the application using our method, we present evidence that this kind of image mining is feasible.

Multiobjective optimization of evacuation routes in stadium using superposed potential field network based ACO.

Multiobjective evacuation routes optimization problem is defined to find out optimal evacuation routes for a group of evacuees under multiple evacuation objectives. For improving the evacuation efficiency, we abstracted the evacuation zone as a superposed potential field network (SPFN), and we presented SPFN-based ACO algorithm (SPFN-ACO) to solve this problem based on the proposed model. In Wuhan Sports Center case, we compared SPFN-ACO algorithm with HMERP-ACO algorithm and traditional ACO algorithm under three evacuation objectives, namely, total evacuation time, total evacuation route length, and cumulative congestion degree. The experimental results show that SPFN-ACO algorithm has a better performance while comparing with HMERP-ACO algorithm and traditional ACO algorithm for solving multi-objective evacuation routes optimization problem.