Convolution neural network (CNN)-based detectors have shown great performance on ship detections of synthetic aperture radar (SAR) images. However, the performance of current models has not been satisfactory enough for detecting multiscale ships and small-size ones in front of complex backgrounds. To address the problem, we propose a novel SAR ship detector based on CNN, which consist of three subnetworks: the Fusion Feature Extractor Network (FFEN), Region Proposal Network (RPN), and Refine Detection Network (RDN). Instead of using a single feature map, we fuse feature maps in bottom–up and top–down ways and generate proposals from each fused feature map in FFEN. Furthermore, we further merge features generated by the region-of-interest (RoI) pooling layer in RDN. Based on the feature representation strategy, the CNN framework constructed can significantly enhance the location and semantics information for the multiscale ships, in particular for the small ships. On the other hand, the residual block is introduced to increase the network depth, through which the detection precision could be further improved. The public SAR ship dataset (SSDD) and China Gaofen-3 satellite SAR image are used to validate the proposed method. Our method shows excellent performance for detecting the multiscale and small-size ships with respect to some competitive models and exhibits high potential in practical application.

Among many improved convolutional neural network (CNN) architectures in the optical image classification, only a few were applied in synthetic aperture radar (SAR) automatic target recognition (ATR). One main reason is that direct transfer of these advanced architectures for the optical images to the SAR images easily yields overfitting due to its limited data set and less features relative to the optical images. Thus, based on the characteristics of the SAR image, we proposed a novel deep convolutional neural network architecture named umbrella. Its framework consists of two alternate CNN-layer blocks. One block is a fusion of six 3-layer paths, which is used to extract diverse level features from different convolution layers. The other block is composed of convolution layers and pooling layers are mainly utilized to reduce dimensions and extract hierarchical feature information. The combination of the two blocks could extract rich features from different spatial scale and simultaneously alleviate overfitting. The performance of the umbrella model was validated by the Moving and Stationary Target Acquisition and Recognition (MSTAR) benchmark data set. This architecture could achieve higher than 99% accuracy for the classification of 10-class targets and higher than 96% accuracy for the classification of 8 variants of the T72 tank, even in the case of diverse positions located by targets. The accuracy of our umbrella is superior to the current networks applied in the classification of MSTAR. The result shows that the umbrella architecture possesses a very robust generalization capability and will be potential for SAR-ART.

Recently, oligomers of G-protein coupled receptors (GPCRs) have been an important topic in the GPCR fields. However, knowledge about their structures and activation mechanisms is very limited due to the absence of crystal structures reported. In this work, we used multiscale simulations to study the effects of homodimerization between different conformation states on their activation, dynamic behaviors, and allosteric communication pathways for μ-OR. The results indicated that the dimerization of one inactive monomer with either one inactive monomer or one active one could enhance its constitutive activation. However, the conformation state of the other protomer (e.g., active or inactive) can influence the activated extent. The dimerization between the two inactive protomers leads to a negative cooperativity for their activation, which should contribute to the asymmetric activation of GPCR dimers observed in some experiments. On the other hand, for the active monomer, its dimerization with one inactive receptor could alleviate its deactivation, whereby negative and positive cooperativities can be observed between the two subunits of the dimer, depending on the different regions. Observations from protein structure network (PSN) analysis indicated that the dimerization of one inactive monomer with one active one would cause a significant drop in the number of main pathways from the ligand binding pocket to the G-protein coupled region for the inactive protomer, while the impact is minor for the active protomer. But, for the active monomer or the inactive one, its dimerization with one inactive monomer would significantly change the types of residues participating in the pathway with the highest frequency.

Olfactory receptor (OR)-based bioelectronic nose is a new type of bio-affinity sensor applied for detecting numerous odorant molecules. In order to elucidate the effect of the adsorption of nanomaterial carriers on the receptor structure and its selectivity to odors, we used a systematic computation-scheme to study two OR models immobilized onto carbon nanotube. Our result indicates that there is a multistep OR-adsorption process driven by hydrophobic interaction. Many allosteric communication pathways exist between the absorbed residues and the pocket ones, leading to a significant shrinkage of the pocket. Consequently, the size-selectivity of the receptor to the odors is changed to some extent. But, the odor size and its hydrophobicity, rather than specific functional groups of the odor, still play a determinant role in binding OR, at least for the 132 odors under study. Regardless of the limitation for the odor size in initial recognition, the different-size odors could induce significant changes in the pocket conformation so that it could better match the pocket space, indicating the importance of the ligand-fit binding. Due to the CNT-induced shrinkage of the pocket, the CNT immobilization could increase the binding affinity through enhancing van der Waals interaction, in particular for the large odors.

Background: The aim of gene expression-based clinical modelling in tumorigenesis is not only to accurately predict the clinical endpoints, but also to reveal the genome characteristics for downstream analysis for the purpose of understanding the mechanisms of cancers. Most of the conventional machine learning methods involved a gene filtering step, in which tens of thousands of genes were firstly filtered based on the gene expression levels by a statistical method with an arbitrary cutoff. Although gene filtering procedure helps to reduce the feature dimension and avoid overfitting, there is a risk that some pathogenic genes important to the disease will be ignored. Results: In this study, we proposed a novel deep learning approach by combining a convolutional neural network with stationary wavelet transform (SWT-CNN) for stratifying cancer patients and predicting their clinical outcomes without gene filtering based on tumor genomic profiles. The proposed SWT-CNN overperformed the state-of-art algorithms, including support vector machine (SVM) and logistic regression (LR), and produced comparable prediction performance to random forest (RF). Furthermore, for all the cancer types, we firstly proposed a method to weight the genes with the scores, which took advantage of the representative features in the hidden layer of convolutional neural network, and then selected the prognostic genes for the Cox proportional-hazards regression. The results showed that risk stratifications can be effectively improved by using the identified prognostic genes as feature, indicating that the representative features generated by SWT-CNN can well correlate the genes with prognostic risk in cancers and be helpful for selecting the prognostic gene signatures. Conclusions: Our results indicated that gene expression-based SWT-CNN model can be an excellent tool for stratifying the prognostic risk for cancer patients. In addition, the representative features of SWT-CNN were validated to be useful for evaluating the importance of the genes in the risk stratification and can be further used to identify the prognostic gene signatures.