Exploration of GH94 Sequence Space for Enzyme Discovery Reveals a Novel Glucosylgalactose Phosphorylase Specificity

The substantial increase in DNA sequencing efforts has led to a rapid expansion of available sequences in glycoside hydrolase families. The ever-increasing sequence space presents considerable opportunities for the search for enzymes with novel functionalities. In this work, the sequence-function space of glycoside hydrolase family 94 (GH94) was explored in detail, using a combined approach of phylogenetic analysis and sequence similarity networks. The identification and experimental screening of unknown clusters led to the discovery of an enzyme from the soil bacterium Paenibacillus polymyxa that acts as a 4-O-β-d -glucosyl-d -galactose phosphorylase (GGalP), a specificity that has not been reported to date. Detailed characterization of GGalP revealed that its kinetic parameters were consistent with those of other known phosphorylases. Furthermore, the enzyme could be used for production of the rare disaccharides 4-O-β-d -glucosyl-d -galactose and 4-O-β-d -glucosyl-l -arabinose. Our current work highlights the power of rational sequence space exploration in the search for novel enzyme specificities, as well as the potential of phosphorylases for rare disaccharide synthesis.     

Transmission line detection in aerial images: An instance segmentation approach based on multitask neural networks

Camera-based transmission line detection (TLD) is a fundamental and crucial task for automatically patrolling powerlines by aircraft. Motivated by instance segmentation, a TLD algorithm is proposed in this paper with a novel deep neural network, i.e., CableNet. The network structure is designed based on fully convolutional networks (FCNs) with two major improvements, considering the specific appearance characteristics of transmission lines. First, overlaying dilated convolutional layers and spatial convolutional layers are configured to better represent continuous long and thin cable shapes. Second, two branches of outputs are arranged to generate multidimensional feature maps for instance segmentation. Thus, cable pixels can be detected and assigned cable IDs simultaneously. Multiple experiments are conducted on aerial images, and the results show that the proposed algorithm obtains reliable detection performance and is superior to traditional TLD methods. Meanwhile, segmented pixels can be accurately identified as cable instances, contributing to line fitting for further applications.     

Neural network-based flight control systems: Present and future

As the first review in this field, this paper presents an in-depth mathematical view of Intelligent Flight Control Systems (IFCSs), particularly those based on artificial neural networks. The rapid evolution of IFCSs in the last two decades in both the methodological and technical aspects necessitates a comprehensive view of them to better demonstrate the current stage and the crucial remaining steps towards developing a truly intelligent flight management unit. To this end, in this paper, we will provide a detailed mathematical view of Neural Network (NN)-based flight control systems and the challenging problems that still remain. The paper will cover both the model-based and model-free IFCSs. The model-based methods consist of the basic feedback error learning scheme, the pseudocontrol strategy, and the neural backstepping method. Besides, different approaches to analyze the closed-loop stability in IFCSs, their requirements, and their limitations will be discussed in detail. Various supplementary features, which can be integrated with a basic IFCS such as the fault-tolerance capability, the consideration of system constraints, and the combination of NNs with other robust and adaptive elements like disturbance observers, would be covered, as well. On the other hand, concerning model-free flight controllers, both the indirect and direct adaptive control systems including indirect adaptive control using NN-based system identification, the approximate dynamic programming using NN, and the reinforcement learning-based adaptive optimal control will be carefully addressed. Finally, by demonstrating a well-organized view of the current stage in the development of IFCSs, the challenging issues, which are critical to be addressed in the future, are thoroughly identified. As a result, this paper can be considered as a comprehensive road map for all researchers interested in the design and development of intelligent control systems, particularly in the field of aerospace applications.     

Retinal microaneurysms detection using adversarial pre-training with unlabeled multimodal images

The detection of retinal microaneurysms is crucial for the early detection of important diseases such as diabetic retinopathy. However, the detection of these lesions in retinography, the most widely available retinal imaging modality, remains a very challenging task. This is mainly due to the tiny size and low contrast of the microaneurysms in the images. Consequently, the automated detection of microaneurysms usually relies on extensive ad-hoc processing. In this regard, although microaneurysms can be more easily detected using fluorescein angiography, this alternative imaging modality is invasive and not adequate for regular preventive screening.In this work, we propose a novel deep learning methodology that takes advantage of unlabeled multimodal image pairs for improving the detection of microaneurysms in retinography. In particular, we propose a novel adversarial multimodal pre-training consisting in the prediction of fluorescein angiography from retinography using generative adversarial networks. This pre-training allows learning about the retina and the microaneurysms without any manually annotated data. Additionally, we also propose to approach the microaneurysms detection as a heatmap regression, which allows an efficient detection and precise localization of multiple microaneurysms. To validate and analyze the proposed methodology, we perform an exhaustive experimentation on different public datasets. Additionally, we provide relevant comparisons against different state-of-the-art approaches. The results show a satisfactory performance of the proposal, achieving an Average Precision of 64.90%, 31.36%, and 33.55% in the E-Ophtha, ROC, and DDR public datasets. Overall, the proposed approach outperforms existing deep learning alternatives while providing a more straightforward detection method that can be effectively applied to raw unprocessed retinal images.     

Tabular data: Deep learning is not all you need

A key element in solving real-life data science problems is selecting the types of models to use. Tree ensemble models (such as XGBoost) are usually recommended for classification and regression problems with tabular data. However, several deep learning models for tabular data have recently been proposed, claiming to outperform XGBoost for some use cases. This paper explores whether these deep models should be a recommended option for tabular data by rigorously comparing the new deep models to XGBoost on various datasets. In addition to systematically comparing their performance, we consider the tuning and computation they require. Our study shows that XGBoost outperforms these deep models across the datasets, including the datasets used in the papers that proposed the deep models. We also demonstrate that XGBoost requires much less tuning. On the positive side, we show that an ensemble of deep models and XGBoost performs better on these datasets than XGBoost alone.     

基于K-means和SOM的水下传感器数据采集方法

随着海洋资源勘探和海洋污染物监控工作的开展，水文数据的监测和采集等已经成为重要的研究方向。其中，水下无线传感器网络在水文数据采集过程中起着举足轻重的作用。本文研究的是水下无线传感器二维监测网络模型中，传感器节点数据采集的问题，其设计方法是通过自组织映射（Self-organizing mapping，SOM）对传感器节点进行路径最优化处理，结合优化的路径图形和K-means算法找到路径内部聚合点，利用聚合点和传感器的节点得到传感器通信半径内的数据采集点，最后通过SOM得到水下机器人（Autonomous underwater vehicle，AUV）到各个数据采集点采集数据的最优路径。经过实验验证，在水下1 200 m×1 750 m范围内布置52个传感器节点的情景下，数据采集点相比于传感器节点路径规划采用相同的采集顺序得到的路径优化了6.7%；对数据采集点重新进行自组织路径规划得到的路径比传感器结点路径的最优解提高了12.2%。增加传感器节点的数量，其结果也大致相同，因此采用该方法可以提高水下机器人采集数据的效率。     

A novel adaptive sampling based methodology for feasible region identification of compute intensive models using artificial neural network

Identification of feasible region of operations in multivariate processes is a problem of interest in several fields. This is particularly challenging when the process model is black-box in nature and/or is computationally expensive, as analytical solutions are not available and the number of possible model evaluations is limited. An efficient methodology is required to identify samples where the model is evaluated for developing a computationally efficient surrogate model. In this work, an artificial neural network based surrogate model is proposed which is integrated with a statistical-based approach (Jack-knifing) to estimate the variance of the surrogate model prediction. This allows implementation of an adaptive sampling approach where new samples are identified close to the feasible region boundary or in regions of high prediction uncertainty. The proposed approach performs better than a previously published kriging based method for different dimensionality case studies.     

Quasi‐Bayesian Estimation of Time‐Varying Volatility in DSGE Models

We propose a novel quasi‐Bayesian Metropolis‐within‐Gibbs algorithm that can be used to estimate drifts in the shock volatilities of a linearized dynamic stochastic general equilibrium (DSGE) model. The resulting volatility estimates differ from the existing approaches in two ways. First, the time variation enters non‐parametrically, so that our approach ensures consistent estimation in a wide class of processes, thereby eliminating the need to specify the volatility law of motion and alleviating the risk of invalid inference due to mis‐specification. Second, the conditional quasi‐posterior of the drifting volatilities is available in closed form, which makes inference straightforward and simplifies existing algorithms. We apply our estimation procedure to a standard DSGE model and find that the estimated volatility paths are smoother compared to alternative stochastic volatility estimates. Moreover, we demonstrate that our procedure can deliver statistically significant improvements to the density forecasts of the DSGE model compared to alternative methods.     

Mixture ratio modeling of dynamic systems

Any knowledge extraction relies (possibly implicitly) on a hypothesis about the modelled-data dependence. The extracted knowledge ultimately serves to a decision-making (DM). DM always faces uncertainty and this makes probabilistic modelling adequate. The inspected black-box modeling deals with “universal” approximators of the relevant probabilistic model. Finite mixtures with components in the exponential family are often exploited. Their attractiveness stems from their flexibility, the cluster interpretability of components and the existence of algorithms for processing high-dimensional data streams. They are even used in dynamic cases with mutually dependent data records while regression and auto-regression mixture components serve to the dependence modeling. These dynamic models, however, mostly assume data-independent component weights, that is, memoryless transitions between dynamic mixture components. Such mixtures are not universal approximators of dynamic probabilistic models. Formally, this follows from the fact that the set of finite probabilistic mixtures is not closed with respect to the conditioning, which is the key estimation and predictive operation. The paper overcomes this drawback by using ratios of finite mixtures as universally approximating dynamic parametric models. The paper motivates them, elaborates their approximate Bayesian recursive estimation and reveals their application potential.