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.

Protein–protein interactions (PPIs) are essential for most living organisms’ process. Thus, detecting PPIs is extremely important to understand the molecular mechanisms of biological systems. Although many PPIs data have been generated by high-throughput technologies for a variety of organisms, the whole interatom is still far from complete. In addition, the high-throughput technologies for detecting PPIs has some unavoidable defects, including time consumption, high cost, and high error rate. In recent years, with the development of machine learning, computational methods have been broadly used to predict PPIs, and can achieve good prediction rate. In this paper, we present here PCVMZM, a computational method based on a Probabilistic Classification Vector Machines (PCVM) model and Zernike moments (ZM) descriptor for predicting the PPIs from protein amino acids sequences. Specifically, a Zernike moments (ZM) descriptor is used to extract protein evolutionary information from Position-Specific Scoring Matrix (PSSM) generated by Position-Specific Iterated Basic Local Alignment Search Tool (PSI-BLAST). Then, PCVM classifier is used to infer the interactions among protein. When performed on PPIs datasets of Yeast and H. Pylori, the proposed method can achieve the average prediction accuracy of 94.48% and 91.25%, respectively. In order to further evaluate the performance of the proposed method, the state-of-the-art support vector machines (SVM) classifier is used and compares with the PCVM model. Experimental results on the Yeast dataset show that the performance of PCVM classifier is better than that of SVM classifier. The experimental results indicate that our proposed method is robust, powerful and feasible, which can be used as a helpful tool for proteomics research.

Protein‐protein interactions (PPIs), as an important molecular process within cells, are of pivotal importance in the biochemical function of cells. Although high‐throughput experimental techniques have matured, enabling researchers to detect large amounts of PPIs, it has unavoidable disadvantages, such as having a high cost and being time consuming. Recent studies have demonstrated that PPIs can be efficiently detected by computational methods. Therefore, in this study, we propose a novel computational method to predict PPIs using only protein sequence information. This method was developed based on a deep learning algorithm‐stacked sparse autoencoder (SSAE) combined with a Legendre moment (LM) feature extraction technique. Finally, a probabilistic classification vector machine (PCVM) classifier is used to implement PPI prediction. The proposed method was performed on human, unbalanced‐human, H. pylori , and S. cerevisiae datasets with 5‐fold cross‐validation and yielded very high predictive accuracies of 98.58%, 97.71%, 93.76%, and 96.55%, respectively. To further evaluate the performance of our method, we compare it with the support vector machine‐ (SVM‐) based method. The experimental results indicate that the PCVM‐based method is obviously preferable to the SVM‐based method. Our results have proven that the proposed method is practical, effective, and robust.

Vehicle detection and classification are very important for analysis of vehicle behavior in intelligent transportation system, urban computing, etc. In this paper, an approach based on convolutional neural networks (CNNs) has been applied for vehicle classification. In order to achieve a more accurate classification, we removed the unrelated background as much as possible based on a trained object detection model. In addition, an unsupervised pretraining approach has been introduced to better initialize CNNs parameters to enhance the classification performance. Through the data enhancement on manual labeled images, we got 2000 labeled images in each category of motorcycle, transporter, passenger, and others, with 1400 samples for training and 600 samples for testing. Then, we got 17395 unlabeled images for layer-wise unsupervised pretraining convolutional layers. A remarkable accuracy of 93.50% is obtained, demonstrating the high classification potential of our approach.

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. 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. 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.

For the task of time-series data classification (TSC), some methods directly classify raw time-series (TS) data. However, certain sequence features are not evident in the time domain and the human brain can extract visual features based on visualization to classify data. Therefore, some researchers have converted TS data to image data and used image processing methods for TSC. While human perceptionconsists of a combination of human senses from different aspects, existing methods only use sequence features or visualization features. Therefore, this paper proposes a framework for TSC based on fusion features (TSC-FF) of sequence features extracted from raw TS and visualization features extracted from Area Graphs converted from TS. Deep learning methods have been proven to be useful tools for automatically learning features from data; therefore, we use long short-term memory with an attention mechanism (LSTM-A) to learn sequence features and a convolutional neural network with an attention mechanism (CNN-A) for visualization features, in order to imitate the human brain. In addition, we use the simplest visualization method of Area Graph for visualization features extraction, avoiding loss of information and additional computational cost. This article aims to prove that using deep neural networks to learn features from different aspects and fusing them can replace complex, artificially constructed features, as well as remove the bias due to manually designed features, in order to avoid the limitations of domain knowledge. Experiments on several open data sets show that the framework achieves promising results, compared with other methods.