Wilcoxyildirim1338

Both theoretical analysis and experimental results on synthetic and real-world datasets demonstrate our conclusions.Semisupervised learning (SSL) has been extensively studied in related literature. Despite its success, many existing learning algorithms for semisupervised problems require specific distributional assumptions, such as ``cluster assumption and ``low-density assumption, and thus, it is often hard to verify them in practice. We are interested in quantifying the effect of SSL based on kernel methods under a misspecified setting. The misspecified setting means that the target function is not contained in a hypothesis space under which some specific learning algorithm works. Practically, this assumption is mild and standard for various kernel-based approaches. Under this misspecified setting, this article makes an attempt to provide a theoretical justification on when and how the unlabeled data can be exploited to improve inference of a learning task. Our theoretical justification is indicated from the viewpoint of the asymptotic variance of our proposed two-step estimation. It is shown that the proposed pointwise nonparametric estimator has a smaller asymptotic variance than the supervised estimator using the labeled data alone. Several simulated experiments are implemented to support our theoretical results.The large-scale protein-protein interaction (PPI) data has the potential to play a significant role in the endeavor of understanding cellular processes. However, the presence of a considerable fraction of false positives is a bottleneck in realizing this potential. There have been continuous efforts to utilize complementary resources for scoring confidence of PPIs in a manner that false positive interactions get a low confidence score. Gene Ontology (GO), a taxonomy of biological terms to represent the properties of gene products and their relations, has been widely used for this purpose. We utilize GO to introduce a new set of specificity measures Relative Depth Specificity (RDS), Relative Node-based Specificity (RNS), and Relative Edge-based Specificity (RES), leading to a new family of similarity measures. We use these similarity measures to obtain a confidence score for each PPI. We evaluate the new measures using four different benchmarks. We show that all the three measures are quite effective. Notably, RNS and RES more effectively distinguish true PPIs from false positives than the existing alternatives. RES also shows a robust set-discriminating power and can be useful for protein functional clustering as well.Antibodies consisting of variable and constant regions, are a special type of proteins playing a vital role in immune system of the vertebrate. They have the remarkable ability to bind a large range of diverse antigens with extraordinary affinity and specificity. This malleability of binding makes antibodies an important class of biological drugs and biomarkers. In this article, we propose a method to identify which amino acid residues of an antibody directly interact with its associated antigen based on the features from sequence and structure. Our algorithm uses convolution neural networks (CNNs) linked with graph convolution networks (GCNs) to make use of information from both sequential and spatial neighbors to understand more about the local environment of target amino acid residue. Furthermore, we process the antigen partner of an antibody by employing an attention layer. Our method improves on the state-of-the-art methodology.Plasmids are extra-chromosomal genetic materials with important markers that affect the function and behaviour of the microorganisms supporting their environmental adaptations. Hence the identification and recovery of such plasmid sequences from assemblies is a crucial task in metagenomics analysis. In the past, machine learning approaches have been developed to separate chromosomes and plasmids. However, there is always a compromise between precision and recall in the existing classification approaches. The similarity of compositions between chromosomes and their plasmids makes it difficult to separate plasmids and chromosomes with high accuracy. However, high confidence classifications are accurate with a significant compromise of recall, and vice versa. Hence, the requirement exists to have more sophisticated approaches to separate plasmids and chromosomes accurately while retaining an acceptable trade-off between precision and recall. We present GraphPlas, a novel approach for plasmid recovery using coverage, composition and assembly graph topology. We evaluated GraphPlas on simulated and real short read assemblies with varying compositions of plasmids and chromosomes. Our experiments show that GraphPlas is able to significantly improve accuracy in detecting plasmid and chromosomal contigs on top of popular state-of-the-art plasmid detection tools.In this study, carbon nanotube (CNT) reinforced functionally graded bioactive glass scaffolds have been fabricated using additive manufacturing technique. Sol-gel method was used for the synthesis of the bioactive glass. For ink preparation, Pluronic F-127 was used as an ink carrier. Mereletinib The CNT-reinforced scaffolds were coated with the polymer polycaprolactone (PCL) using dip-coating method to improve their properties further by sealing the micro cracks. The CNT-reinforcement and polymer coating resulted in an improvement in the compressive strength of the additively manufactured scaffolds by 98% in comparison to pure bioactive glass scaffolds. Further, the morphological analysis revealed interconnected pores and their size appropriate for osteogenesis and angiogenesis. Evaluation of the in vitro bioactivity of the scaffolds after immersion in simulated body fluid (SBF) confirmed the formation of hydroxyapatite (HA). Further, the cellular studies showed good cell viability and initiation of osteogensis. These results demonstrate the potential of these scaffolds for bone tissue engineering applications.Recent studies have investigated bilateral gaits based on the causality analysis of kinetic (or kinematic) signals recorded using both feet. However, these approaches have not considered the influence of their simultaneous causation, which might lead to inaccurate causality inference. Furthermore, the causal interaction of these signals has not been investigated within their frequency domain. Therefore, in this study we attempted to employ a causal-decomposition approach to analyze bilateral gait. The vertical ground reaction force (VGRF) signals of Parkinson's disease (PD) patients and healthy control (HC) individuals were taken as an example to illustrate this method. To achieve this, we used ensemble empirical mode decomposition to decompose the left and right VGRF signals into intrinsic mode functions (IMFs) from the high to low frequency bands. The causal interaction strength (CIS) between each pair of IMFs was then assessed through the use of their instantaneous phase dependency. The results show that the CISes between pairwise IMFs decomposed in the high frequency band of VGRF signals can not only markedly distinguish PD patients from HC individuals, but also found a significant correlation with disease progression, while other pairwise IMFs were not able to produce this. In sum, we found for the first time that the frequency specific causality of bilateral gait may reflect the health status and disease progression of individuals. This finding may help to understand the underlying mechanisms of walking and walking-related diseases, and offer broad applications in the fields of medicine and engineering.To avoid severe limited-view artifacts in reconstructed CT images, current multi-row detector CT (MDCT) scanners with a single x-ray source-detector assembly need to limit table translation speeds such that the pitch p (viz., normalized table translation distance per gantry rotation) is lower than 1.5. When p > 1.5, it remains an open question whether one can reconstruct clinically useful helical CT images without severe artifacts. In this work, we show that a synergistic use of advanced techniques in conventional helical filtered backprojection, compressed sensing, and more recent deep learning methods can be properly integrated to enable accurate reconstruction up to p = 4 without significant artifacts for single source MDCT scans.This paper proposes a new method for joint design of radiofrequency (RF) and gradient waveforms in Magnetic Resonance Imaging (MRI), and applies it to the design of 3D spatially tailored saturation and inversion pulses. The joint design of both waveforms is characterized by the ODE Bloch equations, to which there is no known direct solution. Existing approaches therefore typically rely on simplified problem formulations based on, e.g., the small-tip approximation or constraining the gradient waveforms to particular shapes, and often apply only to specific objective functions for a narrow set of design goals (e.g., ignoring hardware constraints). This paper develops and exploits an auto-differentiable Bloch simulator to directly compute Jacobians of the (Bloch-simulated) excitation pattern with respect to RF and gradient waveforms. This approach is compatible with arbitrary sub-differentiable loss functions, and optimizes the RF and gradients directly without restricting the waveform shapes. For computational efficiency, we derive and implement explicit Bloch simulator Jacobians (approximately halving computation time and memory usage). To enforce hardware limits (peak RF, gradient, and slew rate), we use a change of variables that makes the 3D pulse design problem effectively unconstrained; we then optimize the resulting problem directly using the proposed auto-differentiation framework. We demonstrate our approach with two kinds of 3D excitation pulses that cannot be easily designed with conventional approaches Outer-volume saturation (90° flip angle), and inner-volume inversion.Due to lack of data, overfitting ubiquitously exists in real-world applications of deep neural networks (DNNs). We propose advanced dropout, a model-free methodology, to mitigate overfitting and improve the performance of DNNs. The advanced dropout technique applies a model-free and easily implemented distribution with parametric prior, and adaptively adjusts dropout rate. Specifically, the distribution parameters are optimized by stochastic gradient variational Bayes in order to carry out an end-to-end training. We evaluate the effectiveness of the advanced dropout against nine dropout techniques on seven computer vision datasets (five small-scale datasets and two large-scale datasets) with various base models. The advanced dropout outperforms all the referred techniques on all the datasets.We further compare the effectiveness ratios and find that advanced dropout achieves the highest one on most cases. Next, we conduct a set of analysis of dropout rate characteristics, including convergence of the adaptive dropout rate, the learned distributions of dropout masks, and a comparison with dropout rate generation without an explicit distribution. In addition, the ability of overfitting prevention is evaluated and confirmed. Finally, we extend the application of the advanced dropout to uncertainty inference, network pruning, text classification, and regression. The proposed advanced dropout is also superior to the corresponding referred methods.