Motivation Enhancers are noncoding DNA fragments with high position variability and free scattering. They play an important role in controlling gene expression. As machine learning has become more widely used in identifying enhancers, a number of bioinformatic tools have been developed. Although several models for identifying enhancers and their strengths have been proposed, their accuracy and efficiency have yet to be improved. Results We propose a two-layer predictor called “iEnhancer-XG.” It comprises a one-layer predictor (for identifying enhancers) and a second classifier (for their strength) and uses “XGBoost” as a base classifier and five feature extraction methods, namely, k-Spectrum Profile, Mismatch k-tuple, Subsequence Profile, Position-specific scoring matrix (PSSM), and Pseudo dinucleotide composition (PseDNC). Each method has an independent output. We place the feature vector matrix into the ensemble learning for fusion. This experiment involves the method of “SHapley Additive explanations” to provide interpretability for the previous black box machine learning methods and improve their credibility. The accuracies of the ensemble learning method are 0.811 (first layer) and 0.657 (second layer). The rigorous 10-fold cross-validation confirms that the proposed method is significantly better than existing technologies. Availability The source code and dataset for the enhancer predictions have been uploaded to https://github.com/jimmyrate/ienhancer-xg Supplementary information Supplementary information

In recent years, due to the shortage of timber resources, it has become necessary to reduce the excessive consumption of forest resources. Non-destructive testing technology can quickly find wood defects and effectively improve wood utilization. Deep learning has achieved significant results as one of the most commonly used methods in the detection of wood knots. However, compared with convolutional neural networks in other fields, the depth of deep learning models for the detection of wood knots is still very shallow. This is because the number of samples marked in the wood detection is too small, which limits the accuracy of the final prediction of the results. In this paper, ResNet-34 is combined with transfer learning, and a new TL-ResNet34 deep learning model with 35 convolution depths is proposed to detect wood knot defects. Among them, ResNet-34 is used as a feature extractor for wood knot defects. At the same time, a new method TL-ResNet34 is proposed, which combines ResNet-34 with transfer learning. After that, the wood knot defect dataset was applied to TL-ResNet34 for testing. The results show that the detection accuracy of the dataset trained by TL-ResNet34 is significantly higher than that of other methods. This shows that the final prediction accuracy of the detection of wood knot defects can be improved by TL-ResNet34.

Wood defects are quickly identified from an optical image based on deep learning methodology, which effectively improves wood utilization. Traditional neural network techniques have not yet been employed for wood defect detection due to long training time, low recognition accuracy, and nonautomatical extraction of defect image features. In this work, a model (so-called ReSENet-18) for wood knot defect detection that combined deep learning and transfer learning is proposed. The “squeeze-and-excitation” (SE) module is firstly embedded into the “residual basic block” structure for a “SE-Basic-Block” module construction. This model has the advantages of the features that are extracted in the channel dimension, and it is fused in multiscale with original features. Instantaneously, the fully connected layer is replaced with a global average pooling; consequently, the model parameters could be reduced effectively. The experimental results show that the accuracy has reached 99.02%, meanwhile the training time is also reduced. It shows that the proposed deep convolutional neural network based on ReSENet-18 combined with transfer learning can improve the accuracy of defect recognition and has a potential application in the detection of wood knot defects.

Wood defects are quickly identified from an optical image based on deep learning methodology, which effectively improves the wood utilization. The traditional neural network technique is unemployed for the wood defect detection of optical image used, which results from a long training time, low recognition accuracy, and nonautomatic extraction of defect image features. In this paper, a wood knot defect detection model (so-called BLNN) combined deep learning is reported. Two subnetworks composed of convolutional neural networks are trained by Pytorch. By using the feature extraction capabilities of the two subnetworks and combining the bilinear join operation, the fine-grained features of the image are obtained. The experimental results show that the accuracy has reached up 99.20%, and the training time is obviously reduced with the speed of defect detection about 0.0795 s/image. It indicates that BLNN has the ability to improve the accuracy of defect recognition and has a potential application in the detection of wood knot defects.

Cell-penetrating peptides (CPPs) promote the transport of pharmacologically active molecules, such as nanoparticles, plasmid DNA and short interfering RNA. Accurate prediction of new CPPs is a prerequisite for in-depth study of such molecules. Biological experimental predictions can provide an accurate description of the penetrating properties of CPPs. However, predicting CPPs by wet laboratory experiments is both resource-intensive and time-consuming. Therefore, the development of effective calculation method prediction has become an important topic in the study of CPPs. Recently, numerous methods developed for predicting CPPs use amino acid composition, alone and the accuracies of such methods have been limited. In this study, we proposed a new CPP prediction framework, which integrates four amino acid composition features, and utilizes these features to help train Support Vector Machine (SVM) model as a classifier to predict CPPs. When performing on the training dataset CPP924, the proposed method achieves an accuracy of 92.3%, which is significantly better than the state-of-the-art methods. These results suggest that the framework can orchestrate various amino acid composition features predicted models flexibly with good performances.