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The timing of a behavioral response, such as a button press in reaction to a visual stimulus, is highly variable across trials. In this paper we describe a methodology for single-trial analysis of electroencephalography (EEG) which can be used to reduce the error in the estimation of the timing of the behavioral response and thus reduce the error in estimating the onset time of the stimulus. We consider a rapid serial visual presentation (RSVP) paradigm consisting of concatenated video clips and where subjects are instructed to respond when they see a predefined target. We show that a linear discriminator, with inputs distributed across sensors and time and chosen via an information theoretic feature selection criterion, can be used in conjunction with the response to yield a lower error estimate of the onset time of the target stimulus compared to the response time. We compare our results to response time and previous EEG approaches using fixed windows in time, showing that our method has the lowest estimation error. We discuss potential applications, specifically with respect to cortically-coupled computer vision based triage of large image databases.

Learning outcomes can be predicted with machine learning algorithms that assess students' online behavior data. However, there have been few generalized predictive models for a large number of blended courses in different disciplines and in different cohorts. In this study, we examined learning outcomes in terms of learning data in all of the blended courses offered at a Chinese university and proposed a new classification method of blended courses, in which students were primarily clustered on the basis of their online learning behaviors in blended courses using the expectation-maximization algorithm. Then, the blended courses were classified on the basis of the cluster of students who were present in the course and had the highest proportion. The advantage of this method is that the criteria used for classification of the blended courses are clearly defined on the basis of students' online behavior data, so it can easily be used by machine learning systems to algorithmically classify blended courses based on log data collected from a learning management system. Drawing on the classification of the blended courses, we also proposed and validated a general model using the random forest algorithm to predict learning outcomes based on students' online behaviors in blended courses with different disciplines and different cohorts. The findings of this study indicated that after blended courses were classified on the basis of students' online behavior, prediction accuracy in each category increased. The overall accuracies for Course I (380 courses out of 661 after screening), L (14 courses out of 661 after screening), A (237 courses out of 661 after screening), V (8 courses out of 661 after screening), and H (22 courses out of 661 after screening) were 38.2%, 48.4%, 42.3%, 42.4%, and 74.7%, respectively. According to these results, it was found that a prerequisite for the accurate prediction of students' learning outcomes in a blended course was that most students should be highly engaged in a variety of online learning activities rather than being focused on only one type of activity, such as only watching online videos or submitting online assignments. The prediction model achieved accuracies of 80.6%, 85.3%, 63%, 54.8%, and 14.3% for grades A, B, C, D, and F in Course H, respectively. The results demonstrated the potential of the proposed model for accurately predicting learning outcomes in blended courses. Finally, we found that there was no single online learning behavior that had a dominant effect on the prediction of students' final grades.

Cognitive diagnosis models (CDMs) are the statistical framework for cognitive diagnostic assessment in education and psychology. They generally assume that subjects' latent attributes are dichotomous--mastery or nonmastery, which seems quite deterministic. As an alternative to dichotomous attribute mastery, attention is drawn to the use of a continuous attribute mastery format in recent literature. To obtain subjects' finer-grained attribute mastery for more precise diagnosis and guidance, an equivalent but more explicit form of the partial-mastery-deterministic inputs, noisy "and" gate (DINA) model (termed continuous attribute profile [CAP]-DINA form) is proposed in this article. Its parameters estimation algorithm based on this form using Bayesian techniques with Markov chain Monte Carlo algorithm is also presented. Two simulation studies are conducted then to explore its parameter recovery and model misspecification, and the results demonstrate that the CAP-DINA form performs robustly with satisfactory efficiency in these two aspects. A real data study of the English test also indicates it has a better model fit than DINA.

Background: The ability to translate concrete manipulatives into abstract mathematical formulas can aid in the solving of mathematical word problems among students, and metacognitive prompts play a significant role in enhancing this process. Aims: Based on the concept of semantic congruence, we explored the effects of metacognitive prompts and numerical ordinality on information searching and cognitive processing, throughout the process of solving mathematical word problems among primary school students in China. Sample: Participants included 73 primary school students (38 boys and 35 girls) with normal or corrected visual acuity. Methods: This study was based on a 2 (prompt information: no-prompt, metacognitive-prompt) × 2 (number attribute: cardinal number, ordinal number) mixed experimental design. We analysed multiple eye-movement indices, such as fixation duration, saccadic amplitude, and pupil size, since they pertained to the areas of interest. Results: When solving both types of problems, pupil sizes were significantly smaller under the metacognitive-prompt condition compared with the no-prompt condition, and shorter dwell time for specific sentences, conditional on metacognitive prompts, indicated the optimization of the presented algorithm. Additionally, the levels of fixation durations and saccadic amplitudes were significantly higher when solving ordinal number word problems compared with solving ordinal number problems, indicating that primary school students were less efficient in reading and faced increased levels of difficulty when solving ordinal number problems. Conclusions: The results indicate that for Chinese upper-grade primary school students, cognitive load was lower in the metacognitive prompting condition and when solving cardinal problems, and higher when solving ordinal problems.

To improve the calibration accuracy and calibration efficiency of cognitive diagnostic computerized adaptive testing (CD-CAT) for new items and, ultimately, contribute to the widespread application of CD-CAT in practice, the current article proposed a Gini-based online calibration method that can simultaneously calibrate the Q-matrix and item parameters of new items. Three simulation studies with simulated and real item banks were conducted to investigate the performance of the proposed method and compare it with the joint estimation algorithm (JEA) and the single-item estimation (SIE) methods. The results indicated that the proposed Gini-based online calibration method yielded higher calibration efficiency than those of the SIE method and outperformed the JEA method on item calibration tasks in terms of both accuracy and efficiency under most experimental conditions.

Random item effects item response theory (IRT) models, which treat both person and item effects as random, have received much attention for more than a decade. The random item effects approach has several advantages in many practical settings. The present study introduced an explanatory multidimensional random item effects rating scale model. The proposed model was formulated under a novel parameterization of the nominal response model (NRM), and allows for flexible inclusion of person-related and item-related covariates (e.g., person characteristics and item features) to study their impacts on the person and item latent variables. A new variant of the Metropolis-Hastings Robbins-Monro (MH-RM) algorithm designed for latent variable models with crossed random effects was applied to obtain parameter estimates for the proposed model. A preliminary simulation study was conducted to evaluate the performance of the MH-RM algorithm for estimating the proposed model. Results indicated that the model parameters were well recovered. An empirical data set was analyzed to further illustrate the usage of the proposed model.

Machine learning can be used to define subtypes of psychiatric conditions based on shared biological foundations of mental disorders. Here we analyzed cross-sectional brain images from 4,222 individuals with schizophrenia and 7038 healthy subjects pooled across 41 international cohorts from the ENIGMA, non-ENIGMA cohorts and public datasets. Using the Subtype and Stage Inference (SuStaIn) algorithm, we identify two distinct neurostructural subgroups by mapping the spatial and temporal trajectory of gray matter change in schizophrenia. Subgroup 1 was characterized by an early cortical-predominant loss with enlarged striatum, whereas subgroup 2 displayed an early subcortical-predominant loss in the hippocampus, striatum and other subcortical regions. We confirmed the reproducibility of the two neurostructural subtypes across various sample sites, including Europe, North America and East Asia. This imaging-based taxonomy holds the potential to identify individuals with shared neurobiological attributes, thereby suggesting the viability of redefining existing disorder constructs based on biological factors.

The effective design of combinatorial libraries to balance fitness and diversity facilitates the engineering of useful enzyme functions, particularly those that are poorly characterized or unknown in biology. We introduce MODIFY, a machine learning (ML) algorithm that learns from natural protein sequences to infer evolutionarily plausible mutations and predict enzyme fitness. MODIFY co-optimizes predicted fitness and sequence diversity of starting libraries, prioritizing high-fitness variants while ensuring broad sequence coverage. In silico evaluation shows that MODIFY outperforms state-of-the-art unsupervised methods in zero-shot fitness prediction and enables ML-guided directed evolution with enhanced efficiency. Using MODIFY, we engineer generalist biocatalysts derived from a thermostable cytochrome c to achieve enantioselective C-B and C-Si bond formation via a new-to-nature carbene transfer mechanism, leading to biocatalysts six mutations away from previously developed enzymes while exhibiting superior or comparable activities. These results demonstrate MODIFY's potential in solving challenging enzyme engineering problems beyond the reach of classic directed evolution.

MOTIVATION: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other nonstandard ways of representing clinical concepts. RESULTS: Here, we present a method inspired by the BLAST algorithm for biosequence alignment that screens texts for potential matches on the basis of matching k-mer counts and scores candidates based on conformance to typical patterns of spelling errors derived from 2.9 million clinical notes. Our method, the Term-BLAST-like alignment tool (TBLAT) leverages a gold standard corpus for typographical errors to implement a sequence alignment-inspired method for efficient entity linkage. We present a comprehensive experimental comparison of TBLAT with five widely used tools. Experimental results show an increase of 10% in recall on scientific publications and 20% increase in recall on EHR records (when compared against the next best method), hence supporting a significant enhancement of the entity linking task. The method can be used stand-alone or as a complement to existing approaches. AVAILABILITY AND IMPLEMENTATION: Fenominal is a Java library that implements TBLAT for named CR of Human Phenotype Ontology terms and is available at https://github.com/monarch-initiative/fenominal under the GNU General Public License v3.0.

Vehicle detection and tracking from unmanned aerial vehicles (UAVs) aerial images are among the main tasks of intelligent traffic systems. Especially in tasks with long distances, extensive backgrounds, and small objects, it increases the difficulty of localization and regression, which can easily lead to missed detections and false positives. This paper proposes a detection-based small-scale vehicle tracking framework that integrates an improved YOLOX network and the DeepSORT algorithm to address these issues. Based on the original YOLOX network, a shallow feature extraction network, 160×160 pixels, is added to enhance the ability to extract small-scale object features. A convolutional block attention module (CBAM) is inserted in front of the neck network to select crucial information for vehicle detection tasks while suppressing noncritical ones. EIoU_Loss is introduced as the bounding box regression loss function in training to speed up their convergence and improve the localization accuracy of the small objects. Furthermore, an image segmentation method is proposed to effectively reduce missed and false detection events. It divides the original high-definition image into multiple subimages, first detected and then reassembled. Finally, the improved YOLOX network is used as the detector of the DeepSORT to perform small-scale vehicle detection and tracking tasks in various traffic scenarios. Experiments show that the proposed method can significantly improve the detection accuracy of the network and effectively solve the problems of missed detection and false positives in small-scale vehicle tracking tasks in high-resolution aerial images captured by high-altitude UAVs. Significantly, the algorithm proposed in this paper has sufficient robustness for small-scale tracking tasks of aerial videos captured at different altitudes., Author(s): Heshan Zhang [1]; Xin Tan [1]; Mengwei Fan [1]; Cunshu Pan [1]; Zhanji Zheng [1]; Shuang Luo [1]; Jin Xu (corresponding author) [1] 1. Introduction With the rapid development [...]

Non-alcoholic fatty liver disease (NAFLD) is one of the most common causes of cardiometabolic diseases in overweight individuals. While liver biopsy is the current gold standard to diagnose NAFLD and magnetic resonance imaging (MRI) is a non-invasive alternative still under clinical trials, the former is invasive and the latter costly. We demonstrate electrical impedance tomography (EIT) as a portable method for detecting fatty infiltrate. We enrolled 19 overweight subjects to undergo liver MRI scans, followed by EIT measurements. The MRI images provided the a priori knowledge of the liver boundary conditions for EIT reconstruction, and the multi-echo MRI data quantified liver proton-density fat fraction (PDFF%) to validate fat infiltrate. Using the EIT electrode belts, we circumferentially injected pairwise current to the upper abdomen, followed by acquiring the resulting surface-voltage to reconstruct the liver conductivity. Pearson's correlation analyses compared EIT conductivity or MRI PDFF with body mass index, age, waist circumference, height, and weight variables. We reveal that the correlation between liver EIT conductivity or MRI PDFF with demographics is statistically insignificant, whereas liver EIT conductivity is inversely correlated with MRI PDFF (R = -0.69, p = 0.003, n = 16). As a pilot study, EIT conductivity provides a portable method for operator-independent and cost-effective detection of hepatic steatosis.

Introduction: The conventional 3-D point cloud-based deformation analysis methods, such as the shortest distance (SD), cloud-to-cloud (C2C), and multiscale model-to-model cloud comparison (M3C2), essentially regard the closest distance between two periods of point cloud data as the deformation, rather than the true position of the same point in 3-D space before and after deformation. Methods: This paper proposes a method based on the ICP algorithm to calculate the differences between the chunked multi-period point clouds to recognizes the 3-D deformations. Results and discussion: The results show that the obtained results are very close to the GNSS data but with a much larger spatial monitoring range. The accuracy is higher than that of the SD method. Moreover, we analyze the statistical relationship between the point cloud block size and the deformation vector error and determine the optimal block size. The aim of this article is to optimize the deformation analysis method and improve its accuracy to provide techniques and ideas for the wider surface deformation monitoring research field. For instance, combining this method with data from contact methods constructs a 3D overall deformation model of the mountain, enabling real-time monitoring and early warning of debris flows. [ABSTRACT FROM AUTHOR]

Immersed interface method (IIM) is a promising high-accuracy numerical scheme for the Poisson-Boltzmann model that has been widely used to study electrostatic interactions in biomolecules. However, the IIM suffers from instability and slow convergence for typical applications. In this study, we introduced both analytical interface and surface regulation into IIM to address these issues. The analytical interface setup leads to better accuracy and its convergence closely follows a quadratic manner as predicted by theory. The surface regulation further speeds up the convergence for nontrivial biomolecules. In addition, uncertainties of the numerical energies for tested systems are also reduced by about half. More interestingly, the analytical setup significantly improves the linear solver efficiency and stability by generating more precise and better-conditioned linear systems. Finally, we implemented the bottleneck linear system solver on GPUs to further improve the efficiency of the method, so it can be widely used for practical biomolecular applications. © 2019 Wiley Periodicals, Inc.

Abstract argumentation has become one of the important fields of artificial intelligence. This paper proposes a dual-neighborhood tabu search (DNTS) method specifically designed to find a single stable extension in abstract argumentation frameworks. The proposed algorithm implements an improved dual-neighborhood strategy incorporating a fast neighborhood evaluation method. In addition, by introducing techniques such as tabu and perturbation, this algorithm is able to jump out of the local optimum, which significantly improves the performance of the algorithm. In order to evaluate the effectiveness of the method, the performance of the algorithm on more than 300 randomly generated benchmark datasets was studied and compared with the algorithm in the literature. In the experiment, DNTS outperforms the other method regarding time consumption in more than 50 instances and surpasses the other meta-heuristic method in the number of solved cases. Further analysis shows that the initialization method, the tabu strategy, and the perturbation technique help guarantee the efficiency of the proposed DNTS. [ABSTRACT FROM AUTHOR]

Inspired by the idea of game learning, this paper studies the Cournot game model of the multi-oligopoly market and studies the realization of the Nash equilibrium by using adaptive differential evolution algorithm based on relaxation strategies. The realization path of Nash equilibrium is attained through an adaptive differential evolution based on a relaxation strategy procedure applied to an objective function with best response dynamics. Among them, the objective function is derived from the sum of the payoff changes of each oligopoly under best response decisions. And theoretically proved that the Nash equilibrium is the optimal solution of the objective function. [ABSTRACT FROM AUTHOR]

Background: Many studies have investigated the transfer of skills between laparoscopic and robot-assisted surgery (RAS). These studies have considered time, error, and clinical outcomes in the assessment of skill transfer. However, little is known about the specific operations of the surgeon. Clutch control use is an important skill in RAS. Therefore, the present study aimed to propose a novel objective algorithm based on computer vision that can automatically evaluate a surgeon's clutch use. Additionally, the study aimed to evaluate the correlation between clutch metrics and surgical skill on different surgical robot platforms. Methods: The robotic surgery training center of Wuhan University trained 30 laparoscopic surgeons as the study group between 2023 and 2024. Laparoscopic surgeons were trained by combining robotic simulator exercises and RAS animal experiments. During the training, video and hand movement data were collected. Hand movements identified by a skin-color model were combined with labeling information to classify clutch use. The metrics were validated on different robotic platforms (dv-Trainer, EDGE MP1000, Toumai™ MT1000, and DaVinci Xi system) and among surgeons with different surgical skill levels. Results: On the robotic simulator, clutch accuracy in the expert group was significantly higher than in the study group for all tasks. No significant differences were observed in the number of clutches between the expert and study groups. In the RAS experiment, the number of clutches decreased significantly for both study and expert groups. The accuracy was maintained at a high level in the expert group but decreased rapidly in the study group. Conclusions: We proposed a new objective assessment of surgical skills, clutch use metrics, in cross-platform RAS. Additionally, we verified that the metrics significantly correlated with the surgical skill levels of the surgeons. [ABSTRACT FROM AUTHOR]

Space-time fusion is an economical and efficient way to solve "space-time contradiction". Among all kinds of space-time fusion methods, Fit-FC space-time fusion method based on weight Function is widely used. However, this method is based on the linear model to depict the phase change, but the phase change in the real scene is complicated, and the linear model is difficult to accurately capture the phase change, resulting in the spectral distortion of the fusion image. In addition, pixel-by-pixel scanning with moving Windows leads to inefficiency issues, limiting its use in large-scale and long-term tasks. To overcome these limitations, this paper developed a simple and fast adaptive remote sensing image Spatio-Temporal fusion method based on Fit-FC, called Adapt Lasso-Fit-FC (AL-FF). Firstly, the sparse characteristics of time phase change between images are explored, and a time phase change estimation model based on sparse regression is constructed, which overcomes the fuzzy problem of fusion image caused by the failure of linear regression to capture complex nonlinear time phase transition in the weighted Function method, making the algorithm better at capturing details. Secondly, an adaptive window selection Function is established to overcome the problem of manually setting parameters on different data sets, improve the convenience of the algorithm and robustness of the application on different data sets, and make the algorithm simpler and more efficient. Finally, the improved AL-FF algorithm is compared with other algorithms to verify the performance improvement. Compared with the current advanced Spatio-Temporal fusion methods, AL-FF algorithm has stronger detail capture ability and can generate more accurate fusion results. In addition, the computational efficiency is significantly improved, and the efficiency is increased by more than 20 times compared with the current mainstream method. [ABSTRACT FROM AUTHOR]

We study a class of chance constrained programs (CCPs) where the underlying distribution is modeled by a Gaussian mixture model. As the original work, Hu et al. (IISE Trans 54(12):1117–1130, 2022. https://doi.org/10.1080/24725854.2021.2001608) developed a spatial branch-and-bound (B &B) algorithm to solve the problems. In this paper, we propose an enhanced procedure to speed up the computation of B &B algorithm. We design an enhanced pruning strategy that explores high-potential domains and an augmented branching strategy that prevents redundant computations. We integrate the new strategies into original framework to develop an enhanced B &B algorithm, and illustrate how the enhanced algorithm improves on the original approach. Furthermore, we extend the enhanced B &B framework to handle the CCPs with multiple chance constraints, which is not considered in the previous work. We evaluate the performance of our new algorithm through extensive numerical experiments and apply it to solve a real-world portfolio selection problem. [ABSTRACT FROM AUTHOR]

Summary: In the process of evolution, the multi‐target Firefly algorithm has a single learning strategy and is easy to fall into premature convergence, resulting in poor comprehensive performance of the algorithm. To solve this problem, a multi‐objective firefly algorithm (MOFA‐LM) combining logistic mapping and Cauchy mutation is proposed in this article. To improve the uneven distribution of the initial population, the initial population with good ergodicity is generated by logistic mapping. Aiming at the problem that the population is easy to fall into local optimal, Cauchy mutation can generate relatively large disturbance when fireflies are updating their positions, which makes it easier to jump out of the local optimal value with a wide range of individual optimization, effectively improve the optimization accuracy of the algorithm, overcome the premature convergence of the algorithm and maintain the convergence of the population. In the experimental part, the proposed algorithm is compared with some multi‐objective optimization algorithms in 19 benchmark test functions, and the effectiveness of the strategy added by MOFA‐LM is verified. The results show that MOFA‐LM has obvious advantages over other algorithms in improving population convergence and distribution. [ABSTRACT FROM AUTHOR]

Intelligent identification of the different lithology of outcrops has been a major research challenge in the field of geology. The manual identification of outcrop lithology is labor-intensive and lacks systematicity and consistency. Intelligent lithology identification based on deep convolutional neural networks can significantly reduce such workload and also serves as the foundation for intelligent outcrop research. In this paper, we propose a workflow based on the DeepLabV3+ semantic segmentation neural network algorithm. The algorithm can intelligently identify the lithology of outcrop photos obtained by unmanned aerial vehicle (UAV) oblique photography. Based on this workflow, we can complete the tasks of dataset creation, model training, intelligent identification of outcrop lithology, and model accuracy evaluation. The dataset used in this paper is composed of high-resolution photos of the Fugu Tiansheng Bridge Shihezi Formation profile collected by UAV, which are annotated with three major categories and five subcategories of lithology. Then, we input the data into four types of neural networks, including a fully convolutional network (FCN), SegNet, U-Net, and DeepLabV3+, for training. The results indicate that the recognition accuracies of the four neural network algorithms, FCN, SegNet, U-Net, and DeepLabV3+, for outcrop lithology classification tasks based on UAV oblique photography images are 90.81%, 90.44%, 92.03%, and 93.88%, respectively. Among such algorithms, the DeepLabV3+ semantic segmentation neural network algorithm is reliable and accurate, and can provide a basis for intelligent lithology recognition. This is fundamental for promoting the automation, intelligence, and digitalization of geological outcrop research. [ABSTRACT FROM AUTHOR]

This study presents a novel bridge anomaly detection approach that employs the reconstruction error and structural similarity of an unsupervised convolutional auto-encoder. The presence of structural damage in a bridge typically results in changes in its vibration signals, and thus, the use of these signals for structural damage detection (SDD) has been widely investigated, with many methods relying on supervised learning. However, such existing SDD methods based on the supervised learning require prior knowledge of the damage states and cannot process monitoring data in real-time, thereby limiting their application to in-service bridges. To address this challenge, the authors propose the use of a convolutional auto-encoder as the reconstruction algorithm for real-time vibration signals. The auto-encoder is trained using normal signals and then used to reconstruct new inputs (either normal or abnormal). Two damage indicators (reconstruction error and structural similarity) are then calculated based on the reconstruction results and clustered to detect abnormal signals. The proposed approach was applied to the detection of various abnormalities in the old ADA Bridge, the results were 100% accurate, and about a 10% increase in accuracy was observed when compared to other control experiments. These results demonstrate the effectiveness of the proposed approach, with the auto-encoder achieving excellent reconstruction results for normal signals and clear discrepancies for abnormal signals. The proposed method was also validated on a cable-stayed bridge and an arch bridge, demonstrating its wide applicability in bridge anomaly detection. [ABSTRACT FROM AUTHOR]

The Tree-Seed Algorithm (TSA) has been effective in addressing a multitude of optimization issues. However, it has faced challenges with early convergence and difficulties in managing high-dimensional, intricate optimization problems. To tackle these shortcomings, this paper introduces a TSA variant (DTSA). DTSA incorporates a suite of methodological enhancements that significantly bolster TSA's capabilities. It introduces the PSO-inspired seed generation mechanism, which draws inspiration from Particle Swarm Optimization (PSO) to integrate velocity vectors, thereby enhancing the algorithm's ability to explore and exploit solution spaces. Moreover, DTSA's adaptive velocity adaptation mechanism based on count parameters employs a counter to dynamically adjust these velocity vectors, effectively curbing the risk of premature convergence and strategically reversing vectors to evade local optima. DTSA also integrates the trees population integrated evolutionary strategy, which leverages arithmetic crossover and natural selection to bolster population diversity, accelerate convergence, and improve solution accuracy. Through experimental validation on the IEEE CEC 2014 benchmark functions, DTSA has demonstrated its enhanced performance, outperforming recent TSA variants like STSA, EST-TSA, fb-TSA, and MTSA, as well as established benchmark algorithms such as GWO, PSO, BOA, GA, and RSA. In addition, the study analyzed the best value, mean, and standard deviation to demonstrate the algorithm's efficiency and stability in handling complex optimization issues, and DTSA's robustness and efficiency are proven through its successful application in five complex, constrained engineering scenarios, demonstrating its superiority over the traditional TSA by dynamically optimizing solutions and overcoming inherent limitations. [ABSTRACT FROM AUTHOR]

To overcome incomplete point cloud data obtained from laser scanners scanning complex surfaces, multi-viewpoint cloud data needs to be aligned for use. A hybrid improved SAC-IA with a KD-ICP algorithm is proposed for local point cloud alignment optimization. The scanned point cloud data is preprocessed with statistical filtering, as well as uniform down-sampling. The sampling consistency initial alignment (SAC-IA) algorithm is improved by introducing a dissimilarity vector for point cloud initial alignment. In addition, the iterative closest point (ICP) algorithm is improved by incorporating bidirectional KD-tree to form the KD-ICP algorithm for fine point cloud alignment. Finally, the algorithms are compared in terms of runtime and alignment accuracy. The implementation of the algorithms is based on the Visual Studio 2013 software configurating point cloud library environment for testing experiments and practical experiments. The overall alignment method can be 40%~50% faster in terms of running speed. The improved SAC-IA algorithm provides better transformed poses, combined with the KD-ICP algorithm to select the corresponding nearest neighbor pairs, which improves the accuracy, as well as the applicability of the alignment. [ABSTRACT FROM AUTHOR]

Limited gene capture efficiency and spot size of spatial transcriptome (ST) data pose significant challenges in cell-type characterization. The heterogeneity and complexity of cell composition in the mammalian brain make it more challenging to accurately annotate ST data from brain. Many algorithms attempt to characterize subtypes of neuron by integrating ST data with single-nucleus RNA sequencing (snRNA-seq) or single-cell RNA sequencing. However, assessing the accuracy of these algorithms on Stereo-seq ST data remains unresolved. Here, we benchmarked 9 mapping algorithms using 10 ST datasets from four mouse brain regions in two different resolutions and 24 pseudo-ST datasets from snRNA-seq. Both actual ST data and pseudo-ST data were mapped using snRNA-seq datasets from the corresponding brain regions as reference data. After comparing the performance across different areas and resolutions of the mouse brain, we have reached the conclusion that both robust cell-type decomposition and SpatialDWLS demonstrated superior robustness and accuracy in cell-type annotation. Testing with publicly available snRNA-seq data from another sequencing platform in the cortex region further validated our conclusions. Altogether, we developed a workflow for assessing suitability of mapping algorithm that fits for ST datasets, which can improve the efficiency and accuracy of spatial data annotation. [ABSTRACT FROM AUTHOR]

Background: Symmetrical and coordinated dental and alveolar arches are crucial for achieving proper occlusion. This study aimed to explore the association between dental and dentoalveolar arch forms in children with both normal occlusion and malocclusion. Methods: 209 normal occlusion subjects (5–13 years, mean 8.48 years) and 199 malocclusion subjects (5–12 years, mean 8.19 years) were included. The dentoalveolar arch form was characterized by the smoothest projected curve representing the layered contour of the buccal alveolar bone, referred to as the LiLo curve. Subsequently, a polynomial function was utilized to assess dental and dentoalveolar arch forms. To facilitate separate analyses of shape (depth/width ratio) and size (depth and width), the widths of dental and dentoalveolar arch forms were normalized. The normalized dental and dentoalveolar arch forms (shapes) were further classified into 6 groups, termed dental/dentoalveolar arch clusters, using the k-means algorithm. Results: The association between dental and dentoalveolar arch clusters was found to be one-to-many rather than one-to-one. The mismatch between dental and dentoalveolar arch forms is common in malocclusion, affecting 11.4% of the maxilla and 9.2% of the mandible, respectively. Conclusions: There are large individual variations in the association between dental and dentoalveolar arch forms. Early orthodontic treatment may play an active role in coordinating the relationship between the dental and dentoalveolar arch forms. [ABSTRACT FROM AUTHOR]

Addressing the challenges of high model complexity, low generalization capability, and suboptimal detection performance in most algorithms for crop leaf disease detection, the paper propose a lightweight enhanced YOLOv8 algorithm. First, by incorporating the advantages of GhostNet's feature redundancy reduction and MobileNet's ability to fuse diverse channel features using the concept of Group Convolution, the paper enhance the backbone network. This improves the network's ability to extract critical features from a multitude of similar redundant feature maps. Second, to improve detection accuracy while reducing model parameters and computational load, the paper introduce the slim-Neck module. Finally, addressing the issue where detection head parameters and computations account for over half of the model, the paper restructure the Head using the concept of shared parameters and integrate convolution blocks that enhance multi-scale information recognition. Results from multiple experiments, averaged for consistency, indicate that compared to the original YOLOv8 algorithm, the improved algorithm achieves an increase in mAP50 from 86% to 87.3% and mAP50:95 from 67% to 68.6%. The model's size is a mere 5.45 MB, and the computational parameter GFLOPs is reduced from 8.1 to 5.5, even lower than the most lightweight YOLOv5. In comparison to other large-model algorithms, this model also demonstrates strong competitiveness in detection accuracy. [ABSTRACT FROM AUTHOR]

A digital Image Compression Encryption Method (ICEM) is proposed in this work by using the Compressed Sensing (CS), two-dimensional Logistic-adjusted-Sine map, the piecewise asymptotic deterministic system, dynamic diffusion and Hilbert-Logistic permutation. The plain image is pre-processed by a two-dimensional discrete wavelet transform to obtain four kinds of frequency components HH , HL , LH and LL . Dynamic diffusion and the CS are used to process low and high-frequency components, respectively, and then the results are combined to obtain an intermediate cryptographic image. In the process of CS, a measurement matrix is generated by a piecewise asymptotic deterministic random system and a chaotic sequence. To obtain the encrypted image, an improved Hilbert-Logistic permutation method is used to disturb the pixel position of the intermediate cryptographic image. The SHA-256 is utilized to generate the required keys for the encryption process. The proposed ICEM has the ability to resist chosen-plaintext and known-plaintext attacks as the key is selected dynamically. By using the CS the time and space complexity of the algorithm are reduced. It is shown in experimental results that the proposed scheme has good key sensitivity, decryption speed, fast encryption and large key space, and high robustness and security. [ABSTRACT FROM AUTHOR]

Aiming at the problems of the poor robustness and universality of traditional contour matching algorithms in engineering applications, a method for improving the surface defect detection of industrial products based on contour matching algorithms is detailed in this paper. Based on the image pyramid optimization method, a three-level matching method is designed, which can quickly obtain the candidate pose of the target contour at the top of the image pyramid, combining the integral graph and the integration graph acceleration strategy based on weak classification. It can quickly obtain the rough positioning and rough angle of the target contour, which greatly improves the performance of the algorithm. In addition, to solve the problem that a large number of duplicate candidate points will be generated when the target candidate points are expanded, a method to obtain the optimal candidate points in the neighborhood of the target candidate points is designed, which can guarantee the matching accuracy and greatly reduce the calculation amount. In order to verify the effectiveness of the algorithm, functional test experiments were designed for template building function and contour matching function, including uniform illumination condition, nonlinear condition and contour matching detection under different conditions. The results show that: (1) Under uniform illumination conditions, the detection accuracy can be maintained at about 93%. (2) Under nonlinear illumination conditions, the detection accuracy can be maintained at about 91.84%. (3) When there is an external interference source, there will be a false detection or no detection, and the overall defect detection rate remains above 94%. It is verified that the proposed method can meet the application requirements of common defect detection, and has good robustness and meets the expected functional requirements of the algorithm, providing a strong technical guarantee and data support for the design of embedded image sensors in the later stage. [ABSTRACT FROM AUTHOR]

In response to the complexity of the Jacobian matrix inversion process in the power flow algorithm for AC/DC microgrids, leading to large memory requirements and susceptibility to convergence issues, a novel power flow algorithm based on an improved unified iteration method for AC/DC microgrids is proposed. Firstly, the fundamental equations of the unified iteration method and the characteristics of DC systems are analyzed. The reactive power correction terms and voltage phase correction differences are removed from the modified equations of the unified iteration method, and result in a reduction in the order of the Jacobian matrix in the power flow algorithm. Subsequently, the improved IEEE 11-node system is subjected to simulation verification to attain precise power flow solutions for hybrid AC/DC microgrids. The theoretical analysis identifies the main influencing parameters of active and reactive power errors and assesses their impact factors. Finally, experimental validation of the improved power flow algorithm is carried out on a physical platform, clarifying the applicability range of the proposed method. The research results indicate that within allowable error margins, the proposed approach reduces the difficulty of Jacobian matrix inversion, resulting in an 80% increase in computational speed compared to the unified iteration method. It is suitable for microgrid systems with short electrical distances and small magnitudes of node voltage amplitudes and phase differences. [ABSTRACT FROM AUTHOR]

Advances in computer image recognition have significantly impacted many industries, including healthcare, security and autonomous systems. This paper aims to explore the potential of improving image algorithms to enhance computer image recognition. Specifically, we will focus on regression methods as a means to improve the accuracy and efficiency of identifying images. In this study, we will analyze various regression techniques and their applications in computer image recognition, as well as the resulting performance improvements through detailed examples and data analysis. This paper deals with the problems related to visual image processing in outdoor unstructured environment. Finally, the heterogeneous patterns are converted into the same pattern, and the heterogeneous patterns are extracted from the fusion features of data modes. The simulation results show that the perception ability and recognition ability of outdoor image recognition in complex environment are improved. [ABSTRACT FROM AUTHOR]

Quantum computing has made many important achievements in the field of cryptanalysis. However, due to the limitations of current physical system and technology, the realization of large-scale universal quantum computers is a long way off. Currently, small-scale quantum computers are easier to implement than large-scale universal quantum computers. Distributed quantum computing proposes an implementation architecture, which attempts to break down large-scale tasks into many sub-tasks distributed across multiple small-scale quantum computers. How to use small-scale quantum computers with fewer qubits and shallower quantum depths to complete large-scale tasks and improve the success rate of attacking symmetric cryptosystems is our concern. In this paper, we propose a distributed exact Simon's algorithm, apply it to achieve quantum key recovery attacks on single-permutation-based pseudorandom cryptographic schemes with classical birthday bound security, and estimate the quantum resources of quantum circuits. Furthermore, we combine distributed exact Grover's algorithm and distributed exact Simon's algorithm to achieve quantum key recovery attacks on two-permutation-based pseudorandom cryptographic schemes with classical beyond birthday bound security and estimate the corresponding quantum resources. Our results show that (1) our algorithms are exact which means that the theoretical success probability of attacking pseudorandom cryptographic schemes is 100%; (2) the depth of circuit is in polynomial time which means that the theoretical depth of attacking symmetric cryptosystems is exponentially accelerated relative to the previous results; (3) the qubits of circuit don't increase significantly. Our work is of great importance. It could lead to the rapid realization of effective quantum attacks against symmetric cryptosystems on small-scale quantum computers. [ABSTRACT FROM AUTHOR]

The ongoing COVID-19 pandemic remains a significant threat, emphasizing the critical importance of mask-wearing to reduce infection risks. However, existing methods for mask detection encounter challenges such as identifying small targets and achieving high accuracy. In this paper, we present an enhanced YOLOv7 model tailored for mask-wearing detection. we employing a Generative Adversarial Network (GAN) to augment the original dataset, introducing the Convolutional Block Attention Module (CBAM) mechanism into the YOLOv7 model to enhance its small target detection capabilities, and replacing the model's activation function with Parametric Rectified Linear Unit (FReLU) to improve overall performance. Experimental validation on a dataset showcases an average precision of 97.8% and a real-time inference speed of 64 frames per second (fps), meeting the real-time mask-wearing detection requirements effectively. [ABSTRACT FROM AUTHOR]

In Currently, research in the field of infrared road object detection is primarily focused on enhancing model performance and robustness to address the challenges posed by complex real-world driving scenarios. In response to these challenges, this paper proposes an infrared road object detection algorithm based on an attention mechanism. By incorporating the CPCA module, which utilizes attention mechanisms, into the YOLOv8s model, the algorithm enhances the model's focus on unobstructed areas and highly illuminated sections, extracting crucial feature information to improve both accuracy and robustness. Additionally, the original model's downsampling layer is replaced with the Context Grided Network Block Downsampling (CGBD) module, which not only preserves feature edge information but also effectively handles local and contextual features, thereby enhancing the overall feature capturing capabilities of the model. To address the issue of equal aspect ratios in the model's original loss function, the proposed algorithm adopts the superior Weighted Intersection over Union (WIoU). This not only addresses the shortcomings of the original loss function (CIoU) but also demonstrates increased sensitivity in classification tasks. Experimental results show that the improved algorithm, compared to YOLOv8s, achieves a 1.4% increase in mean average precision (mAP), along with notable improvements in precision and recall. Furthermore, when compared to mainstream model algorithms, the enhanced model significantly outperforms in infrared road object detection tasks, providing validation of its effectiveness. [ABSTRACT FROM AUTHOR]

Aiming at the problem that the offline screening method of traditional slurry fineness detection is inefficient and cannot be fed back to the upstream grinding system in time, in order to develop the fineness automatic detection technology, an improved surface fitting algorithm called MLTS-LS algorithm (the Moving Least Trimmed Square - Least Square algorithm) is proposed, which performs surface fitting on the slurry fineness data to achieve the purpose of rapid detection of slurry fineness. Firstly, the three-dimensional discrete data of slurry fineness was collected by fineness detection test. Secondly, the surface fitting evaluation indexes of "nearest", "linear", "cubic", "V4" and the traditional least squares method are calculated and analyzed, and an improved interpolation algorithm proposed. Finally, the "MLTS-LS" algorithm is applied to the fitting of three-dimensional discrete data of slurry fineness. The results show that the sum variance and mean square deviation values of the "MLTS-LS" algorithm are significantly smaller than those of other algorithms, and the determination coefficient value and the correction coefficient value are close to 1, indicating that the "MLTS-LS" algorithm has a good fitting effect on the three-dimensional discrete data of slurry fineness. [ABSTRACT FROM AUTHOR]

With the development of machine vision technology, visual inspection technology has been widely used in many fields. Among them, the 3D visual detection technology based on line structured light has attracted the attention of relevant scholars because of its advantages of the easy acquisition of image information and high detection accuracy. Therefore, applying machine vision technology to the field of three‐dimensional weld inspection can improve the inspection effect, so a machine vision technology based on simulation analysis was proposed. First, the model parameter calibration and algorithm of the structured light imaging system are studied, and then a structured light‐based torque converter weld height detection system is designed and related models are constructed. Finally, the detection accuracy and speed of the constructed 3D vision measurement system are verified. The results show that the calibration parameters obtained by the optimization algorithm of this study are as t1 follows, focal length = 17.16376; u0 = 1798.55439; v0 = 1276.85505; r1 = 0.14072; r2 Secondly, in the comparative experiment, the height of the wave crest coordinates of the measurement results of the three‐dimensional detection system of the torque converter weld seam in the global feature extraction process based on the machine vision technology based on simulation analysis is 9.1330 mm, and the maximum error value is 1.0403 mm; As a result of the calibration algorithm, the peak coordinate height is 10.3526 mm, and the maximum error value is 2.7482 mm. The error of the research system is better than Zhang Zhengyou's calibration method. The research content has important reference value for improving the three‐dimensional inspection effect of torque converter welds. [ABSTRACT FROM AUTHOR]

With the progress of manufacturing capability and the requirements of modern project construction clustering and safety, unmanned technology has become a major development direction for construction machinery. The study analyzes the defects of the ACO applied to path planning, uses the basic ant colony method combined with the APF algorithm to construct comprehensive heuristic information to improve the efficiency of the initial iteration, and adds a pseudo‐random proportional transfer rule to improve its transfer rule, in addition to proposing an optimal ant pheromone release rule to ensure that the pheromone update can effectively improve the effect of the later iteration. In the 20 × 20 raster map, the optimal path of both the basic and potential field ant colony algorithms is 31.52, while the basic ant colony algorithm does not converge to the optimal path after 200 iterations in the 30 × 30 raster map, and the comparison algorithm converges to the optimal path after 156 iterations, while the potential field ant colony algorithm converges to the optimal path after 25 iterations at 47.52. And the potential field ant colony The potential field ant colony algorithm converges to the optimal path of 47.52 after 25 iterations, and the number of turns in both raster maps of different sizes is only about 50% of the basic ant colony algorithm, which is also better than that of the comparison algorithm. The proposed algorithm improves the ability of the ant colony algorithm to explore and exploit raster maps, enhances its path planning capability, and improves the construction efficiency well in practical applications. [ABSTRACT FROM AUTHOR]

Summary: In order to achieve efficiency extremum of power conversion independent of parameter values and operational mode, an adaptive dual‐controller on‐line efficiency optimization method is presented in this paper. Firstly, based on tri‐modal analysis for four‐switch buck‐boost (FSBB) converter, efficiency extremum analysis is given and existed for such this converter. Then, adaptive dual controller on‐line efficiency seeking algorithm is shown to adaptive two variables for efficiency optimization and output voltage regulation. Furthermore, perturb and observe detector is described to realize control variables decoupling of dual‐controller and to prevent the instability of the whole system during the algorithm tuning process and to improve the algorithm speed of the dual controller. The proposed method is model independent and does not depend on the circuit parameter values. The detail implement of algorithm and performance analysis is given, and the experimental platform and experimental results are put forward to verify the effectiveness of the algorithm. [ABSTRACT FROM AUTHOR]

Motivation There are many clustered transcriptionally active regions in the human genome, in which the transcription complex cannot immediately terminate transcription at the upstream gene termination site, but instead continues to transcribe intergenic regions and downstream genes, resulting in read-through transcripts. Several studies have demonstrated the regulatory roles of read-through transcripts in tumorigenesis and development. However, limited by the read length of next-generation sequencing, discovery of read-through transcripts has been slow. For long but also erroneous third-generation sequencing data, this study developed a novel minimizer sketch algorithm to accurately and quickly identify read-through transcripts. Results Readon initially splits the reference sequence into distinct active regions. It employs a sliding window approach within each region, calculates minimizers, and constructs the specialized structured arrays for query indexing. Following initial alignment anchor screening of candidate read-through transcripts, further confirmation steps are executed. Comparative assessments against existing software reveal Readon's superior performance on both simulated and validated real data. Additionally, two downstream tools are provided: one for predicting whether a read-through transcript is likely to undergo nonsense-mediated decay or encodes a protein, and another for visualizing splicing patterns. Availability and implementation Readon is freely available on GitHub (https://github.com/Bulabula45/Readon). [ABSTRACT FROM AUTHOR]

As the fields of engineering, energy, and geology become increasingly complex, decision makers face escalating challenges that require skilled solutions to meet practical production needs. Evolutionary algorithms, inspired by biological evolution, have emerged as powerful methods for tackling intricate optimization problems without relying on gradient data. Among these, the tree-seed algorithm (TSA) distinguishes itself due to its unique mechanism and efficient searching capabilities. However, an imbalance between its exploitation and exploration phases can lead it to be stuck in local optima, impeding the discovery of globally optimal solutions. This study introduces an improved TSA that incorporates water-cycling and quantum rotation-gate mechanisms. These enhancements assist the algorithm in escaping local peaks and achieving a more harmonious balance between its exploitation and exploration phases. Comparative experimental evaluations, using the CEC 2017 benchmarks and a well-known metaheuristic algorithm, demonstrate the upgraded algorithm's faster convergence rate and enhanced ability to locate global optima. Additionally, its application in optimizing reservoir production models underscores its superior performance compared to competing methods, further validating its real-world optimization capabilities. [ABSTRACT FROM AUTHOR]

The besiege and conquer algorithm has shown excellent performance in single-objective optimization problems. However, there is no literature on the research of the BCA algorithm on multi-objective optimization problems. Therefore, this paper proposes a new multi-objective besiege and conquer algorithm to solve multi-objective optimization problems. The grid mechanism, archiving mechanism, and leader selection mechanism are integrated into the BCA to estimate the Pareto optimal solution and approach the Pareto optimal frontier. The proposed algorithm is tested with MOPSO, MOEA/D, and NSGAIII on the benchmark function IMOP and ZDT. The experiment results show that the proposed algorithm can obtain competitive results in terms of the accuracy of the Pareto optimal solution. [ABSTRACT FROM AUTHOR]

Train wheels are crucial components for ensuring the safety of trains. The accurate and fast identification of wheel tread defects is necessary for the timely maintenance of wheels, which is essential for achieving the premise of conditional repair. Image-based detection methods are commonly used for detecting tread defects, but they still have issues with the misdetection of water stains and the leaking of small defects. In this paper, we address the challenges posed by the detection of wheel tread defects by proposing improvements to the YOLOv8 model. Firstly, the impact of water stains on tread defect detection is avoided by optimising the structure of the detection layer. Secondly, an improved SPPCSPC module is introduced to enhance the detection of small targets. Finally, the SIoU loss function is used to accelerate the convergence speed of the network, which ensures defect recognition accuracy with high operational efficiency. Validation was performed on the constructed tread defect dataset. The results demonstrate that the enhanced YOLOv8 model in this paper outperforms the original network and significantly improves the tread defect detection indexes. The average precision, accuracy, and recall reached 96.95%, 96.30%, and 95.31%. [ABSTRACT FROM AUTHOR]

Scanning ion conductance microscopy (SICM) enables the non-invasive three-dimensional imaging of live cells and other structures in physiological environments. However, when imaging complex samples, SICM faces challenges such as having a low temporal resolution during slow scanning and a reduced signal-to-noise ratio during fast scanning, making it difficult to simultaneously improve both temporal and spatial resolution. To address these issues, this paper proposes an algorithm for enhancing image resolution under high-speed scanning. Firstly, scanning images are preprocessed using a median filtering algorithm to remove the salt-and-pepper noise generated during high-speed scanning. Next, the Canny edge detection algorithm is employed to extract the edges of the image targets. To avoid blurring the edges, the new edge-directed interpolation (NEDI) algorithm is then used to fill the edges, while non-edge areas are filled using bilinear interpolation, thereby enhancing the image resolution. Finally, the peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM) are used to analyze the imaging of articular chondrocytes. The results show that under a scanning speed of 480 nm/ms, the proposed algorithm improves the temporal resolution of imaging by 60% compared to traditional 2× resolution imaging, increases the peak signal-to-noise ratio of the scanning images by 7 dB, and achieves a structural similarity of 0.97. Therefore, the proposed algorithm effectively removes noise during high-speed scanning and improves the SICM scanning imaging resolution, thereby avoiding the reduction in temporal resolution when scanning larger resolution samples and effectively enhancing the performance of SICM scanning imaging. [ABSTRACT FROM AUTHOR]

Simon's problem is one of the most important problems demonstrating the power of quantum algorithms, as it greatly inspired the proposal of Shor's algorithm. The generalized Simon's problem is a natural extension of Simon's problem and also a special hidden subgroup problem: Given a function f : { 0 , 1 } n → { 0 , 1 } m , it is promised that there exists a hidden subgroup S ≤ Z 2 n of rank k such that for any x , y ∈ { 0 , 1 } n , f (x) = f (y) iff x ⊕ y ∈ S . The goal of generalized Simon's problem is to find the hidden subgroup S. In this paper, we present two key contributions. Firstly, we characterize the structure of the generalized Simon's problem in distributed scenario and introduce a corresponding distributed quantum algorithm. Secondly, we refine the algorithm to ensure exactness due to the application of quantum amplitude amplification technique. Our algorithm offers exponential speedup compared to the distributed classical algorithm. When contrasted with the quantum algorithm for the generalized Simon's problem, our algorithm's oracle requires fewer qubits, thus making it easier to be physically implemented. Particularly, the exact distributed quantum algorithm we develop for the generalized Simon's problem outperforms the best previously proposed distributed quantum algorithm for Simon's problem in terms of generalizability and exactness. [ABSTRACT FROM AUTHOR]

Introduction: Obesity is associated with an increased risk of nonalcoholic fatty liver disease (NAFLD). While Magnetic Resonance Imaging (MRI) is a non-invasive gold standard to detect fatty liver, we demonstrate a low-cost and portable electrical impedance tomography (EIT) approach with circumferential abdominal electrodes for liver conductivity measurements. Methods and Results: A finite element model (FEM) was established to simulate decremental liver conductivity in response to incremental liver lipid content. To validate the FEM simulation, we performed EIT imaging on an ex vivo porcine liver in a non-conductive tank with 32 circumferentially-embedded electrodes, demonstrating a high-resolution output given a priori information on location and geometry. To further examine EIT capacity in fatty liver detection, we performed EIT measurements in age- and gender-matched New Zealand White rabbits (3 on normal, 3 on high-fat diets). Liver conductivity values were significantly distinct following the high-fat diet (p = 0.003 vs. normal diet, n=3), accompanied by histopathological evidence of hepatic fat accumulation. We further assessed EIT imaging in human subjects with MRI quantification for fat volume fraction based on Dixon procedures, demonstrating average liver conductivity of 0.331 S/m for subjects with low Body-Mass Index (BMI < 25 kg/m²) and 0.286 S/m for high BMI (> 25 kg/m²). Conclusion: We provide both the theoretical and experimental framework for a multi-scale EIT strategy to detect liver lipid content. Our preliminary studies pave the way to enhance the spatial resolution of EIT as a marker for fatty liver disease and metabolic syndrome.

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. Computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here, we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: (1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. (2) The highly different accessibilities in the membrane and water regions are addressed with a two-step, two-probe grid-labeling procedure. (3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 Å for globular proteins is a very reasonable default value for membrane protein simulations. It gives the best compromise in reproducing the explicit water distributions in membrane channel proteins, at least in the water accessible pore/channel regions. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe good agreement with the experimental results.

Continuum solvent models, particularly those based on the Poisson-Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one-sided and two-sided methods with both first-order and second-order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces. These efforts prompted us to develop an efficient approximated one-dimensional method, which is to fit the surface field one dimension at a time, for biomolecular applications without much compromise in accuracy. We also developed a surface-to-atom force partition scheme given a level set representation of analytical molecular surfaces to facilitate their applications to molecular simulations. Testing of these fitting methods in the dielectric boundary force calculations shows that the second-order methods, including the one-dimensional method, consistently perform among the best in the molecular test cases. Finally, the timing analysis shows the approximated one-dimensional method is far more efficient than standard second-order methods in the PBE force calculations. © 2017 Wiley Periodicals, Inc.

While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata, samples that have challenged short-read assembly approaches. The FALCON-based assemblies are substantially more contiguous and complete than alternate short- or long-read approaches. The phased diploid assembly enabled the study of haplotype structure and heterozygosities between homologous chromosomes, including the identification of widespread heterozygous structural variation within coding sequences.

In response to the low matching accuracy of stereo matching algorithms in image regions with specular reflection, this paper proposes a multidimensional fusion stereo matching algorithm named MFANet. The algorithm embeds a multispectral attention module into the residual feature extraction network, utilizing two‐dimensional discrete cosine transforms to extract frequency features. In the pyramid pooling module, a coordinated attention mechanism is introduced to capture relevant positional information. In the cost aggregation part, the MFANet algorithm incorporates a three‐dimensional attention mechanism, focusing on the more important semantic information in high‐level features. By combining detailed information from low‐level features, semantic information from high‐level features, and contextual information, the algorithm generates features that are more conducive to disparity prediction. The MFANet algorithm is evaluated on three standard datasets (SceneFlow, KITTI2015, and KITTI2012). Experimental results demonstrate its robustness against specular reflection interference, accurate prediction of disparities in specular reflection pathological regions, and promising application prospects. [ABSTRACT FROM AUTHOR]

In this paper, we propose a sparse least squares (SLS) optimization model for solving multilinear equations, in which the sparsity constraint on the solutions can effectively reduce storage and computation costs. By employing variational properties of the sparsity set, along with differentiation properties of the objective function in the SLS model, the first-order optimality conditions are analysed in terms of the stationary points. Based on the equivalent characterization of the stationary points, we propose the Newton Hard-Threshold Pursuit (NHTP) algorithm and establish its locally quadratic convergence under some regularity conditions. Numerical experiments conducted on simulated datasets including cases of Completely Positive(CP)-tensors and symmetric strong M-tensors illustrate the efficiency of our proposed NHTP method. [ABSTRACT FROM AUTHOR]