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Mobile phones are rapidly becoming the most widespread and popular form of communication; thus, they are also the most important attack target of malware. The amount of malware in mobile phones is increasing exponentially and poses a serious security threat. Google’s Android is the most popular smart phone platforms in the world and the mechanisms of permission declaration access control cannot identify the malware. In this paper, we proposed an ensemble machine learning system for the detection of malware on Android devices. More specifically, four groups of features including permissions, monitoring system events, sensitive API and permission rate are extracted to characterize each Android application (app). Then an ensemble random forest classifier is learned to detect whether an app is potentially malicious or not. The performance of our proposed method is evaluated on the actual data set using tenfold cross-validation. The experimental results demonstrate that the proposed method can achieve a highly accuracy of 89.91%. For further assessing the performance of our method, we compared it with the state-of-the-art support vector machine classifier. Comparison results demonstrate that the proposed method is extremely promising and could provide a cost-effective alternative for Android malware detection. [ABSTRACT FROM AUTHOR]

Background: Drug repositioning, meanings finding new uses for existing drugs, which can accelerate the processing of new drugs research and development. Various computational methods have been presented to predict novel drug–disease associations for drug repositioning based on similarity measures among drugs and diseases. However, there are some known associations between drugs and diseases that previous studies not utilized. Methods: In this work, we develop a deep gated recurrent units model to predict potential drug–disease interactions using comprehensive similarity measures and Gaussian interaction profile kernel. More specifically, the similarity measure is used to exploit discriminative feature for drugs based on their chemical fingerprints. Meanwhile, the Gaussian interactions profile kernel is employed to obtain efficient feature of diseases based on known disease-disease associations. Then, a deep gated recurrent units model is developed to predict potential drug–disease interactions. Results: The performance of the proposed model is evaluated on two benchmark datasets under tenfold cross-validation. And to further verify the predictive ability, case studies for predicting new potential indications of drugs were carried out. Conclusion: The experimental results proved the proposed model is a useful tool for predicting new indications for drugs or new treatments for diseases, and can accelerate drug repositioning and related drug research and discovery. [ABSTRACT FROM AUTHOR]

Many life activities and key functions in organisms are maintained by different types of protein–protein interactions (PPIs). In order to accelerate the discovery of PPIs for different species, many computational methods have been developed. Unfortunately, even though computational methods are constantly evolving, efficient methods for predicting PPIs from protein sequence information have not been found for many years due to limiting factors including both methodology and technology. Inspired by the similarity of biological sequences and languages, developing a biological language processing technology may provide a brand new theoretical perspective and feasible method for the study of biological sequences. In this paper, a pure biological language processing model is proposed for predicting protein–protein interactions only using a protein sequence. The model was constructed based on a feature representation method for biological sequences called bio-to-vector (Bio2Vec) and a convolution neural network (CNN). The Bio2Vec obtains protein sequence features by using a "bio-word" segmentation system and a word representation model used for learning the distributed representation for each "bio-word". The Bio2Vec supplies a frame that allows researchers to consider the context information and implicit semantic information of a bio sequence. A remarkable improvement in PPIs prediction performance has been observed by using the proposed model compared with state-of-the-art methods. The presentation of this approach marks the start of "bio language processing technology," which could cause a technological revolution and could be applied to improve the quality of predictions in other problems. [ABSTRACT FROM AUTHOR]

Background: Self-interacting Proteins (SIPs) plays a critical role in a series of life function in most living cells. Researches on SIPs are important part of molecular biology. Although numerous SIPs data be provided, traditional experimental methods are labor-intensive, time-consuming and costly and can only yield limited results in real-world needs. Hence,it's urgent to develop an efficient computational SIPs prediction method to fill the gap. Deep learning technologies have proven to produce subversive performance improvements in many areas, but the effectiveness of deep learning methods for SIPs prediction has not been verified. Results: We developed a deep learning model for predicting SIPs by constructing a Stacked Long Short-Term Memory (SLSTM) neural network that contains "dropout". We extracted features from protein sequences using a novel feature extraction scheme that combined Zernike Moments (ZMs) with Position Specific Weight Matrix (PSWM). The capability of the proposed approach was assessed on S.erevisiae and Human SIPs datasets. The result indicates that the approach based on deep learning can effectively resist data skew and achieve good accuracies of 95.69 and 97.88%, respectively. To demonstrate the progressiveness of deep learning, we compared the results of the SLSTM-based method and the celebrated Support Vector Machine (SVM) method and several other well-known methods on the same datasets. Conclusion: The results show that our method is overall superior to any of the other existing state-of-the-art techniques. As far as we know, this study first applies deep learning method to predict SIPs, and practical experimental results reveal its potential in SIPs identification. [ABSTRACT FROM AUTHOR]