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Motivation Recently, deep learning has become the mainstream methodology for drug–target binding affinity prediction. However, two deficiencies of the existing methods restrict their practical applications. On the one hand, most existing methods ignore the individual information of sequence elements, resulting in poor sequence feature representations. On the other hand, without prior biological knowledge, the prediction of drug–target binding regions based on attention weights of a deep neural network could be difficult to verify, which may bring adverse interference to biological researchers. Results We propose a novel Multi-Functional and Robust Drug–Target binding Affinity prediction (MFR-DTA) method to address the above issues. Specifically, we design a new biological sequence feature extraction block, namely BioMLP, that assists the model in extracting individual features of sequence elements. Then, we propose a new Elem-feature fusion block to refine the extracted features. After that, we construct a Mix-Decoder block that extracts drug–target interaction information and predicts their binding regions simultaneously. Last, we evaluate MFR-DTA on two benchmarks consistently with the existing methods and propose a new dataset, sc-PDB, to better measure the accuracy of binding region prediction. We also visualize some samples to demonstrate the locations of their binding sites and the predicted multi-scale interaction regions. The proposed method achieves excellent performance on these datasets, demonstrating its merits and superiority over the state-of-the-art methods. Availability and implementation https://github.com/JU-HuaY/MFR. [ABSTRACT FROM AUTHOR]

Face anti-spoofing (FAS) is crucial for safe and reliable biometric systems. In recent years, deep neural networks have been proven to be very effective for FAS as compared with classical approaches. However, deep learning-based FAS methods are data-driven and use learning-based features only. It is a legitimate question to ask whether hand-crafted features can provide any complementary information to a deep learning-based FAS method. To answer this question, we propose a two-stream network that consists of a convolutional network and a local difference network. To be specific, we first build a texture extraction convolutional block to calculate the gradient magnitude at each pixel of an input image. Our experiments demonstrate that additional liveness cues can be captured by the proposed method. Second, we design an attention fusion module to combine the features obtained from the RGB domain and gradient magnitude domain, aiming for discriminative information mining and information redundancy elimination. Finally, we advocate a simple binary facial mask supervision strategy for further performance boost. The proposed network has only 2.79M parameters and the inference speed is up to 118 frames per second, which makes it very convenient for real-time FAS systems. The experimental results obtained on several well-known benchmarking datasets demonstrate the merits and superiority of the proposed method over the state-of-the-art approaches. [ABSTRACT FROM AUTHOR]

As an essential task in protein structure and function prediction, protein fold recognition has attracted increasing attention. The majority of the existing machine learning-based protein fold recognition approaches strongly rely on handcrafted features, which depict the characteristics of different protein folds; however, effective feature extraction methods still represent the bottleneck for further performance improvement of protein fold recognition. As a powerful feature extractor, deep convolutional neural network (DCNN) can automatically extract discriminative features for fold recognition without human intervention, which has demonstrated an impressive performance on protein fold recognition. Despite the encouraging progress, DCNN often acts as a black box, and as such, it is challenging for users to understand what really happens in DCNN and why it works well for protein fold recognition. In this study, we explore the intrinsic mechanism of DCNN and explain why it works for protein fold recognition using a visual explanation technique. More specifically, we first trained a VGGNet-based DCNN model, termed VGGNet-FE, which can extract fold-specific features from the predicted protein residue–residue contact map for protein fold recognition. Subsequently, based on the trained VGGNet-FE, we implemented a new contact-assisted predictor, termed VGGfold, for protein fold recognition; we then visualized what features were extracted by each of the convolutional layers in VGGNet-FE using a deconvolution technique. Furthermore, we visualized the high-level semantic information, termed fold-discriminative region, of a predicted contact map from the localization map obtained from the last convolutional layer of VGGNet-FE. It is visually confirmed that VGGNet-FE could effectively extract distinct fold-discriminative regions for different types of protein folds, thereby accounting for the improved performance of VGGfold for protein fold recognition. In summary, this study is of great significance for both understanding the working principle of DCNNs in protein fold recognition and exploring the relationship between the predicted protein contact map and protein tertiary structure. This proposed visualization method is flexible and applicable to address other DCNN-based bioinformatics and computational biology questions. The online web server of VGGfold is freely available at http://csbio.njust.edu.cn/bioinf/vggfold/. [ABSTRACT FROM AUTHOR]

The infrared and visible image fusion task aims to generate a single image that preserves complementary features and reduces redundant information from different modalities. Although convolutional neural networks (CNNs) can effectively extract local features and obtain better fusion performance, the size of the receptive field limits its feature extraction ability. Thus, the Transformer architecture has gradually become mainstream to extract global features. However, current Transformer-based fusion methods ignore the enhancement of details, which is important to image fusion tasks and other downstream vision tasks. To this end, a new super feature attention mechanism and the wavelet-guided pooling operation are applied to the fusion network to form a novel fusion network, termed SFPFusion. Specifically, super feature attention is able to establish long-range dependencies of images and to fully extract global features. The extracted global features are processed by wavelet-guided pooling to fully extract multi-scale base information and to enhance the detail features. With the powerful representation ability, only simple fusion strategies are utilized to achieve better fusion performance. The superiority of our method compared with other state-of-the-art methods is demonstrated in qualitative and quantitative experiments on multiple image fusion benchmarks. [ABSTRACT FROM AUTHOR]

• This paper proposes a novel global refined local binary pattern (GRLBP) by analyzing the nature of the distribution of pixel intensity in local neighborhoods. • GRLBP consists of two descriptors termed as magnitude refined local sign binary pattern (MRLBP_S) and center refined local magnitude binary pattern (CRLBP_M). • MRLBP_S distinguishes local neighborhoods with contrast differences by using global magnitude anchors to refine local sign patterns. • CRLBP_M identifies local neighborhoods with gray differences by employing global central gray anchors to refine local magnitude patterns. • RLBP has obvious advantages in classification performance, computational complexity, and feature dimension. Local binary pattern (LBP) and its variants have been successfully applied in texture feature extraction. However, it is hard for most LBP-based methods to effectively describe and distinguish the local neighborhoods with similar structures (that is, the calculated feature patterns are identical) but different contrasts or grayscales. To alleviate such problems, we propose a novel global refined local binary pattern (GRLBP) by analyzing the nature of pixel intensity distribution in local neighborhoods. GRLBP consists of two descriptors called magnitude refined local sign binary pattern (MRLBP_S) and center refined local magnitude binary pattern (CRLBP_M). MRLBP_S distinguishes local neighborhoods with contrast differences by using global magnitude anchors to refine local sign patterns. And CRLBP_M identifies local neighborhoods with grayscale differences by employing global central grayscale anchors to refine local magnitude patterns. Finally, frequency histograms of MRLBP_S and CRLBP_M from each image are cascaded to generate the GRLBP. Extensive experimental results on seven benchmark texture databases: Outex, CUReT, KTH-TIPS, UMD, UIUC, KTH-T2b, and DTD demonstrate that the proposed GRLBP can represent the detailed information of texture images. Furthermore, compared with state-of-the-art LBP variants, GRLBP has competitive advantages in classification accuracy, feature dimension, and computational complexity, respectively. [ABSTRACT FROM AUTHOR]