Christophersenfisher6527

Furthermore, a novel policy network with an attention module is proposed to extract the hidden information of AUV dynamics. The simulation environment with time-varying dynamics is established, and the simulation results reveal the effectiveness of our proposed method.Deep learning has become the most powerful machine learning tool in the last decade. However, how to efficiently train deep neural networks remains to be thoroughly solved. The widely used minibatch stochastic gradient descent (SGD) still needs to be accelerated. As a promising tool to better understand the learning dynamic of minibatch SGD, the information bottleneck (IB) theory claims that the optimization process consists of an initial fitting phase and the following compression phase. Based on this principle, we further study typicality sampling, an efficient data selection method, and propose a new explanation of how it helps accelerate the training process of the deep networks. We show that the fitting phase depicted in the IB theory will be boosted with a high signal-to-noise ratio of gradient approximation if the typicality sampling is appropriately adopted. Furthermore, this finding also implies that the prior information of the training set is critical to the optimization process, and the better use of the most important data can help the information flow through the bottleneck faster. 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. selleck kinase inhibitor 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.