Automatically extracting relationships between entity pairs from vast biomedical texts presents a challenging research direction with substantial practical significance. For example, the correct identification of the interaction between drugs and drugs could help doctors guide patients to take the correct medication, thereby avoiding the occurrence of medical errors. However, the same statements containing different types of entity pair relationships are easily misclassified into the same category by classifiers because they share consistent semantic information. In order to solve the problems, a new Indexbased Triple Match BERT(ITM-BERT) method is proposed in this paper. Triple loss training strategy is introduced and triple data generation decision is made. If an instance has an identical opposite instance, no index is used to form the triple data. If not, the index method is used to match the global semantic information similarity, and the triple data is constructed according to the rules. After the construction is completed, the triple loss method is used for training, with the purpose of increasing the distance between different class instances, making the distance between the same class instances closer, and finally classifying the entity relationship category correctly. In this paper, our approach is validated on widely used benchmark datasets such as DDI2013, BioInfer, and AIMed. The results show that our approach is advanced compared with other models.

Several models based on deep neural networks have applied to single image super-resolution and obtained great improvements in terms of both reconstruction accuracy and computational performance. All these methods focus either on performing the super-resolution (SR) reconstruction operation in the high resolution (HR) space after upscaling with a single filter, usually bicubic interpolation, or optimizing parts of the reconstruction pipeline. Then the studies of network-based model advance to attempting to shrink the feature dimension of the nonlinear mapping considering the tradeoff between accuracy and time cost. In this paper, we present an improved convolutional neural network (CNN) architecture based on channels combination, which benefits from both quick training and accuracy gain. In addition, we propose that the feature maps can be extracted in the LR space and an efficient multi-channel convolution layer which learns an array of upscaling filters, specifically trained for each feature map, to upscale the final HR feature maps into the HR output. We explore different settings and evaluate the proposed approach using images from publicly available datasets and show that it performs significantly better (about + 0.3 dB margin on term of PSNR and + 0.03 on term of SSIM than previous works) with better visual appearance.

Hyperspectral image (HSI) is usually composed of hundreds of bands which contain very rich spatial and spectral information. However, the high-dimensional data may lead to the curse of dimensionality phenomenon when it is used for land use classification or other applications, making it difficult to be utilized effectively. In this paper, we developed a deep learning classification framework based on the spectral and spatial information of hyperspectral image. Firstly, the deep learning features in different layers could be extracted automatically. Secondly, based on the learned deep learning features, we could obtain the classification of hyperspectral image with logistic regression (LR) classifier. Finally, we compared our approach with other methods including quadratic discriminant analysis with the multilevel logistic spatial prior (QDAMLL), logistic discriminant analysis with the multilevel logistic spatial prior (logDAMLL), linear discriminant analysis with the multilevel logistic spatial prior (LDAMLL), subspace multiclass logistic regression with the multilevel logistic spatial prior (MLRsub MLL), support vector machine on extended morphological profiles (SVM/EMP), support vector machine on expectation maximization and post-regularization (SVM-EM-PR). The experimental results showed that our method obtained the optimum accuracy, which was better than the other six approaches. And the OA was up to 99.39%. Therefore, the deep convolutional neural networks (DCNNs) is a robust method for land use classification with hyperspectral image.

This paper studies and evaluates the feasibility and the performance of different level interpolations for improving spatial resolution of diffusion tensor magnetic resonance imaging (DT-MRI or DTI). In particular, the following techniques are investigated: anisotropic interpolation operating on scalar gray-level images, log-Euclidean interpolation method, and the quaternion interpolation method, which operate on diffusion tensor fields. The performance is evaluated both qualitatively and quantitatively using criteria such as tensor determinant, fractional anisotropy (FA), mean diffusivity (MD), fiber length, etc. We conclude that tensor field interpolations allow avoiding undesirable swelling effect in DTI, which is not the case with scalar gray-level interpolation, and that scalar gray-level image interpolation and log-Euclidean tensor field interpolation suffer from decrease in FA and MD, which may mislead the interpretation of the clinical parameters FA and MD. In contrast, the quaternion tensor field interpolation avoids such FA and MD decrease, which suggests its use for clinical applications.

This paper presents an efficient alternating direction method with patch-based dictionary updating, ADMDU-DEB, for sparse representation regularization framework of image deblurring. The main idea of the proposed method is to reformulate the variational problem as a linear equality constrained problem and then minimize its augmented Lagrangian function. The alternating direction method decouples the minimization by alternately iterating the pixel-based regularization and the patch-based sparse representation. Typically, accelerated sparse coding and simple dictionary updating applied in the sparse representation stage enable the whole algorithm to converge at a relatively small number of iterations. Additionally, the approach is readily extended to solve the same kind of variational problem with a nonnegativity constraint. Experimental results on benchmark test images consistently validate the superiority of the proposed approach and demonstrate that it achieves very competitive deblurring performance, compared with state-of-the-art deconvolution algorithms.

Dictionary learning based sparse modeling has been increasingly recognized as providing high performance in the restoration of noisy images. Although a number of dictionary learning algorithms have been developed, most of them attack this learning problem in its primal form, with little effort being devoted to exploring the advantage of solving this problem in a dual space. In this paper, a novel Fenchel duality based dictionary learning (FD-DL) algorithm has been proposed for the restoration of noise-corrupted images. With the restricted attention to the additive white Gaussian noise, the sparse image representation is formulated as an 2-1 minimization problem, whose dual formulation is constructed using a generalization of Fenchel’s duality theorem and solved under the augmented Lagrangian framework. The proposed algorithm has been compared with four state-of-the-art algorithms, including the local pixel grouping-principal component analysis, method of optimal directions, K-singular value decomposition, and beta process factor analysis, on grayscale natural images. Our results demonstrate that the FD-DL algorithm can effectively improve the image quality and its noisy image restoration ability is comparable or even superior to the abilities of the other four widely-used algorithms.

In recent years Bregman iterative method (or related augmented Lagrangian method) has shown to be an efficient optimization technique for various inverse problems. In this paper, we propose a two-level Bregman Method with dictionary updating for highly undersampled magnetic resonance (MR) image reconstruction. The outer-level Bregman iterative procedure enforces the sampled k-space data constraints, while the inner-level Bregman method devotes to updating dictionary and sparse representation of small overlapping image patches, emphasizing local structure adaptively. Modified sparse coding stage and simple dictionary updating stage applied in the inner minimization make the whole algorithm converge in a relatively small number of iterations, and enable accurate MR image reconstruction from highly undersampled k-space data. Experimental results on both simulated MR images and real MR data consistently demonstrate that the proposed algorithm can efficiently reconstruct MR images and present advantages over the current state-of-the-art reconstruction approach.

This paper proposes a sparse representation of an image using discrete delta-u functions. A delta-u function is defined as the product of a Kronecker delta function and a step function. Based on the sparse representation, we have developed a novel and effective method for reconstructing an image from limited-angle projections. The method first estimates the parameters of the sparse representation from the incomplete projection data, and then directly calculates the image to be reconstructed. Experiments have shown that the proposed method can effectively recover the missing data and reconstruct images more accurately than the total-variation (TV) regularized reconstruction method.

MOTIVATION: Reproducibility analyses of biologically relevant microarray studies have mostly focused on overlap of detected biomarkers or correlation of differential expression evidences across studies. For clinical utility, direct inter-study prediction (i.e. to establish a prediction model in one study and apply to another) for disease diagnosis or prognosis prediction is more important. Normalization plays a key role for such a task. Traditionally, sample-wise normalization has been a standard for inter-array and inter-study normalization. For gene-wise normalization, it has been implemented for intra-study or inter-study predictions in a few papers while its rationale, strategy and effect remain unexplored. RESULTS: In this article, we investigate the effect of gene-wise normalization in microarray inter-study prediction. Gene-specific intensity discrepancies across studies are commonly found even after proper sample-wise normalization. We explore the rationale and necessity of gene-wise normalization. We also show that the ratio of sample sizes in normal versus diseased groups can greatly affect the performance of gene-wise normalization and an analytical method is developed to adjust for the imbalanced ratio effect. Both simulation results and applications to three lung cancer and two prostate cancer data sets, considering both binary classification and survival risk predictions, showed significant and robust improvement of the new adjustment. A calibration scheme is developed to apply the ratio-adjusted gene-wise normalization for prospective clinical trials. The number of calibration samples needed is estimated from existing studies and suggested for future applications. The result has important implication to the translational research of microarray as a practical disease diagnosis and prognosis prediction tool.

BACKGROUND: The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular network affects the evolution of its member proteins remains unclear. RESULTS: In this work, the functional and evolutionary modularity of Homo sapiens (H. sapiens) metabolic network were investigated from a topological point of view. Network decomposition shows that the metabolic network is organized in a highly modular core-periphery way, in which the core modules are tightly linked together and perform basic metabolism functions, whereas the periphery modules only interact with few modules and accomplish relatively independent and specialized functions. Moreover, over half of the modules exhibit co-evolutionary feature and belong to specific evolutionary ages. Peripheral modules tend to evolve more cohesively and faster than core modules do. CONCLUSION: The correlation between functional, evolutionary and topological modularity suggests that the evolutionary history and functional requirements of metabolic systems have been imprinted in the architecture of metabolic networks. Such systems level analysis could demonstrate how the evolution of genes may be placed in a genome-scale network context, giving a novel perspective on molecular evolution.

BACKGROUND: The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks. RESULTS: In this work, metabolic networks of 75 organisms were investigated from a topological point of view. Network decomposition of three microbes (Escherichia coli, Aeropyrum pernix and Saccharomyces cerevisiae) shows that almost all of the sub-networks exhibit a highly modularized bow-tie topological pattern similar to that of the global metabolic networks. Moreover, these small bow-ties are hierarchically nested into larger ones and collectively integrated into a large metabolic network, and important features of this modularity are not observed in the random shuffled network. In addition, such a bow-tie pattern appears to be present in certain chemically isolated functional modules and spatially separated modules including carbohydrate metabolism, cytosol and mitochondrion respectively. CONCLUSION: The highly modularized bow-tie pattern is present at different levels and scales, and in different chemical and spatial modules of metabolic networks, which is likely the result of the evolutionary process rather than a random accident. Identification and analysis of such a pattern is helpful for understanding the design principles and facilitate the modelling of metabolic networks.

A new approach for correcting bias field in magnetic resonance (MR) images is proposed using the mathematical model of singularity function analysis (SFA), which represents a discrete signal or its spectrum as a weighted sum of singularity functions. Through this model, an MR image's low spatial frequency components corrupted by a smoothly varying bias field are first removed, and then reconstructed from its higher spatial frequency components not polluted by bias field. The thus reconstructed image is then used to estimate bias field for final image correction. The approach does not rely on the assumption that anatomical information in MR images occurs at higher spatial frequencies than bias field. The performance of this approach is evaluated using both simulated and real clinical MR images.