MMAP: a cloud computing platform for mining the maximum accuracy of predicting phenotypes from genotypes.

Accurately predicting phenotypes from genotypes holds great promise to improve health management in humans and animals, and breeding efficiency in animals and plants. Although many prediction methods have been developed, the optimal method differs across datasets due to multiple factors, including species, environments, populations and traits of interest. Studies have demonstrated that the number of genes underlying a trait and its heritability are the two key factors that determine which method fits the trait the best. In many cases, however, these two factors are unknown for the traits of interest. We developed a cloud computing platform for Mining the Maximum Accuracy of Predicting phenotypes from genotypes (MMAP) using unsupervised learning on publicly available real data and simulated data. MMAP provides a user interface to upload input data, manage projects and analyses and download the output results. The platform is free for the public to conduct computations for predicting phenotypes and genetic merit using the best prediction method optimized from many available ones, including Ridge Regression, gBLUP, compressed BLUP, Bayesian LASSO, Bayes A, B, Cpi and many more. Users can also use the platform to conduct data analyses with any methods of their choice. It is expected that extensive usage of MMAP would enrich the training data, which in turn results in continual improvement of the identification of the best method for use with particular traits. AVAILABILITY AND IMPLEMENTATION: The MMAP user manual, tutorials and example datasets are available at http://zzlab.net/MMAP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A new approach to simultaneously reducing, nitrogen doping and noble metal coating of graphene oxide via active-screen plasma.

Graphene is widely used for various applications, especially after nitrogen doping and incorporation with metal nanoparticles. Herein, a simultaneous approach to reducing, nitrogen doping and noble metals coating of graphene oxide (GO) is reported using an advanced active-screen plasma (ASP) technique. With a noble metal plate added as an extra lid of active screen cage, the corresponding noble metal, mainly or fully in pure metal state, depending on the noble metal type, as well as a minority of Fe and Cr, is deposited on GO with simultaneous reduction and nitrogen doping. The ASP treated GO exhibits varying levels of improvement in electrical property depending on the type of noble metal nanoparticles hybridized with. Specifically, ASP treated GO incorporated with Pt or Au revealed 2-4 orders of magnitude of improvement in electrical property.

[Heart rate extraction algorithm based on adaptive heart rate search model].

Photoplethysmography (PPG) is a non-invasive technique to measure heart rate at a lower cost, and it has been recently widely used in smart wearable devices. However, as PPG is easily affected by noises under high-intensity movement, the measured heart rate in sports has low precision. To tackle the problem, this paper proposed a heart rate extraction algorithm based on self-adaptive heart rate separation model. The algorithm firstly preprocessed acceleration and PPG signals, from which cadence and heart rate history were extracted respectively. A self-adaptive model was made based on the connection between the extracted information and current heart rate, and to output possible domain of the heart rate accordingly. The algorithm proposed in this article removed the interference from strong noises by narrowing the domain of real heart rate. From experimental results on the PPG dataset used in 2015 IEEE Signal Processing Cup, the average absolute error on 12 training sets was 1.12 beat per minute (bpm) (Pearson correlation coefficient: 0.996; consistency error: -0.184 bpm). The average absolute error on 10 testing sets was 3.19 bpm (Pearson correlation coefficient: 0.990; consistency error: 1.327 bpm). From experimental results, the algorithm proposed in this paper can effectively extract heart rate information under noises and has the potential to be put in usage in smart wearable devices.

LDkit: a parallel computing toolkit for linkage disequilibrium analysis.

BACKGROUND: Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing. RESULTS: We developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK 'ped + map' format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from ~77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals. CONCLUSIONS: The software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users' convenience. LDkit was written in JAVA language under cross-platform support.

SiRNA silencing efficacy prediction based on a deep architecture.

BACKGROUND: Small interfering RNA (siRNA) can be used to post-transcriptional gene regulation by knocking down targeted genes. In functional genomics, biomedical research and cancer therapeutics, siRNA design is a critical research topic. Various computational algorithms have been developed to select the most effective siRNA, whereas the efficacy prediction accuracy is not so satisfactory. Many existing computational methods are based on feature engineering, which may lead to biased and incomplete features. Deep learning utilizes non-linear mapping operations to detect potential feature pattern and has been considered perform better than existing machine learning method. RESULTS: In this paper, to further improve the prediction accuracy and facilitate gene functional studies, we developed a new powerful siRNA efficacy predictor based on a deep architecture. First, we extracted hidden feature patterns from two modalities, including sequence context features and thermodynamic property. Then, we constructed a deep architecture to implement the prediction. On the available largest siRNA database, the performance of our proposed method was measured with 0.725 PCC and 0.903 AUC value. The comparative experiment showed that our proposed architecture outperformed several siRNA prediction methods. CONCLUSIONS: The results demonstrate that our deep architecture is stable and efficient to predict siRNA silencing efficacy. The method could help select candidate siRNA for targeted mRNA, and further promote the development of RNA interference.

Multi-threshold Image Segmentation based on an improved Salp Swarm Algorithm: Case study of breast cancer pathology images.

Breast cancer poses a significant risk to women's health, and it is essential to provide proper diagnostic support. Medical image processing technology is a key component of all supporting diagnostic techniques, with Image Segmentation (IS) being one of its primary steps. Among various methods, Multilevel Image Segmentation (MIS) is considered one of the most effective and straightforward approaches. Many researchers have attempted to improve the quality of image segmentation by combining different metaheuristic algorithms with MIS. However, these methods often suffer from issues such as low convergence accuracy and a proclivity for converging towards Local Optima (LO). To overcome these challenges, this study introduces an integrated approach that combines the Salp Swarm Algorithm (SSA), Slime Mould Algorithm (SMA) and Differential Evolution (DE) algorithm. In this manuscript, we introduce an innovative hybrid MIS model termed SDSSA, which leverages elements from the SSA, SMA and DE algorithms. The SDSSA model fundamentally relies on non-local means 2D histogram and 2D Kapur's entropy. To evaluate the proposed method effectively, we compare it initially with similar algorithms using the IEEE CEC2014 benchmark functions. The SDSSA showcases enhanced convergence velocity and precision relative to similar algorithms. Furthermore, this paper proposes an excellent MIS method. Subsequently, IS experiments were conducted separately at both low and high threshold levels. The test results demonstrate that the segmentation outcomes of MIS, at both low and high threshold levels, outperform other methods. This validates SDSSA as a superior segmentation technique that provides practical assistance for future research in breast cancer pathology image processing.

Winter wheat ear counting based on improved YOLOv7x and Kalman filter tracking algorithm with video streaming.

Accurate and real-time field wheat ear counting is of great significance for wheat yield prediction, genetic breeding and optimized planting management. In order to realize wheat ear detection and counting under the large-resolution Unmanned Aerial Vehicle (UAV) video, Space to depth (SPD) module was added to the deep learning model YOLOv7x. The Normalized Gaussian Wasserstein Distance (NWD) Loss function is designed to create a new detection model YOLOv7xSPD. The precision, recall, F1 score and AP of the model on the test set are 95.85%, 94.71%, 95.28%, and 94.99%, respectively. The AP value is 1.67% higher than that of YOLOv7x, and 10.41%, 39.32%, 2.96%, and 0.22% higher than that of Faster RCNN, SSD, YOLOv5s, and YOLOv7. YOLOv7xSPD is combined with the Kalman filter tracking and the Hungarian matching algorithm to establish a wheat ear counting model with the video flow, called YOLOv7xSPD Counter, which can realize real-time counting of wheat ears in the field. In the video with a resolution of 3840×2160, the detection frame rate of YOLOv7xSPD Counter is about 5.5FPS. The counting results are highly correlated with the ground truth number (R2 = 0.99), and can provide model basis for wheat yield prediction, genetic breeding and optimized planting management.

Exploring a novel HE image segmentation technique for glioblastoma: A hybrid slime mould and differential evolution approach.

Glioblastoma is a primary brain tumor with high incidence and mortality rates, posing a significant threat to human health. It is crucial to provide necessary diagnostic assistance for its management. Among them, Multi-threshold Image Segmentation (MIS) is considered the most efficient and intuitive method in image processing. In recent years, many scholars have combined different metaheuristic algorithms with MIS to improve the quality of Image Segmentation (IS). Slime Mould Algorithm (SMA) is a metaheuristic approach inspired by the foraging behavior of slime mould populations in nature. In this investigation, we introduce a hybridized variant named BDSMA, aimed at overcoming the inherent limitations of the original algorithm. These limitations encompass inadequate exploitation capacity and a tendency to converge prematurely towards local optima when dealing with complex multidimensional problems. To bolster the algorithm's optimization prowess, we integrate the original algorithm with a robust exploitative operator called Differential Evolution (DE). Additionally, we introduce a strategy for handling solutions that surpass boundaries. The incorporation of an advanced cooperative mixing model accelerates the convergence of BDSMA, refining its precision and preventing it from becoming trapped in local optima. To substantiate the effectiveness of our proposed approach, we conduct a comprehensive series of comparative experiments involving 30 benchmark functions. The results of these experiments demonstrate the superiority of our method in terms of both convergence speed and precision. Moreover, within this study, we propose a MIS technique. This technique is subsequently employed to conduct experiments on IS at both low and high threshold levels. The effectiveness of the BDSMA-based MIS technique is further showcased through its successful application to the medical image of brain glioblastoma. The evaluation of these experimental outcomes, utilizing image quality metrics, conclusively underscores the exceptional efficacy of the algorithm we have put forth.

Research on weed identification in soybean fields based on the lightweight segmentation model DCSAnet.

Weeds can compete with crops for sunlight, water, space and various nutrients, which can affect the growth of crops.In recent years, people have started to use self-driving agricultural equipment, robots, etc. for weeding work and use of drones for weed identification and spraying of weeds with herbicides, and the effectiveness of these mobile weeding devices is largely limited by the superiority of weed detection capability. To improve the weed detection capability of mobile weed control devices, this paper proposes a lightweight weed segmentation network model DCSAnet that can be better applied to mobile weed control devices. The whole network model uses an encoder-decoder structure and the DCA module as the main feature extraction module. The main body of the DCA module is based on the reverse residual structure of MobileNetV3, effectively combines asymmetric convolution and depthwise separable convolution, and uses a channel shuffle strategy to increase the randomness of feature extraction. In the decoding stage, feature fusion utilizes the high-dimensional feature map to guide the aggregation of low-dimensional feature maps to reduce feature loss during fusion and increase the accuracy of the model. To validate the performance of this network model on the weed segmentation task, we collected a soybean field weed dataset containing a large number of weeds and crops and used this dataset to conduct an experimental study of DCSAnet. The results showed that our proposed DCSAnet achieves an MIoU of 85.95% with a model parameter number of 0.57 M and the highest segmentation accuracy in comparison with other lightweight networks, which demonstrates the effectiveness of the model for the weed segmentation task.

A new population initialization of metaheuristic algorithms based on hybrid fuzzy rough set for high-dimensional gene data feature selection.

In the realm of modern medicine and biology, vast amounts of genetic data with high complexity are available. However, dealing with such high-dimensional data poses challenges due to increased processing complexity and size. Identifying critical genes to reduce data dimensionality is essential. The filter-wrapper hybrid method is a commonly used approach in feature selection. Most of these methods employ filters such as MRMR and ReliefF, but the performance of these simple filters is limited. Rough set methods, on the other hand, are a type of filter method that outperforms traditional filters. Simultaneously, many studies have pointed out the crucial importance of good initialization strategies for the performance of the metaheuristic algorithm (a type of wrapper-based method). Combining these two points, this paper proposes a novel filter-wrapper hybrid method for high-dimensional feature selection. To be specific, we utilize the variant of bWOA (binary Whale Optimization Algorithm) based on Hybrid Fuzzy Rough Set to perform attribute reduction, and the reduced attributes are used as prior knowledge to initialize the population. We then employ metaheuristics for further feature selection based on this initialized population. We conducted experiments using five different algorithms on 14 UCI datasets. The experiment results show that after applying the initialization method proposed in this article, the performance of five enhanced algorithms, has shown significant improvement. Particularly, the improved bMFO using our initialization method: fuzzy_bMFO outperformed six currently advanced algorithms, indicating that our initialization method for metaheuristic algorithms is suitable for high-dimensional feature selection tasks.

A novel method for Pu-erh tea face traceability identification based on improved MobileNetV3 and triplet loss.

Ensuring the traceability of Pu-erh tea products is crucial in the production and sale of tea, as it is a key means to ensure their quality and safety. The common approach used in traceability systems is the utilization of bound Quick Response (QR) codes or Near Field Communication (NFC) chips to track every link in the supply chain. However, counterfeiting risks still persist, as QR codes or NFC chips can be copied and inexpensive products can be fitted into the original packaging. To address this issue, this paper proposes a tea face verification model called TeaFaceNet for traceability verification. The aim of this model is to improve the traceability of Pu-erh tea products by quickly identifying counterfeit products and enhancing the credibility of Pu-erh tea. The proposed method utilizes an improved MobileNetV3 combined with Triplet Loss to verify the similarity between two input tea face images with different texture features. The recognition accuracy of the raw tea face dataset, ripe tea face dataset and mixed tea face dataset of the TeaFaceNet network were 97.58%, 98.08% and 98.20%, respectively. Accurate verification of tea face was achieved using the optimal threshold. In conclusion, the proposed TeaFaceNet model presents a promising approach to enhance the traceability of Pu-erh tea products and combat counterfeit products. The robustness and generalization ability of the model, as evidenced by the experimental results, highlight its potential for improving the accuracy of Pu-erh tea face recognition and enhancing the credibility of Pu-erh tea in the market. Further research in this area is warranted to advance the traceability of Pu-erh tea products and ensure their quality and safety.

An end-to-end seed vigor prediction model for imbalanced samples using hyperspectral image.

Hyperspectral imaging is a key technology for non-destructive detection of seed vigor presently due to its capability to capture variations of optical properties in seeds. As the seed vigor data depends on the actual germination rate, it inevitably results in an imbalance between positive and negative samples. Additionally, hyperspectral image (HSI) suffers from feature redundancy and collinearity due to its inclusion of hundreds of wavelengths. It also creates a challenge to extract effective wavelength information in feature selection, however, which limits the ability of deep learning to extract features from HSI and accurately predict seed vigor. Accordingly, in this paper, we proposed a Focal-WAResNet network to predict seed vigor end-to-end, which improves the network performance and feature representation capability, and improves the accuracy of seed vigor prediction. Firstly, the focal loss function is utilized to adjust the loss weights of different sample categories to solve the problem of sample imbalance. Secondly, a WAResNet network is proposed to select characteristic wavelengths and predict seed vigor end-to-end, focusing on wavelengths with higher network weights, which enhance the ability of seed vigor prediction. To validate the effectiveness of this method, this study collected HSI of maize seeds for experimental verification, providing a reference for plant breeding. The experimental results demonstrate a significant improvement in classification performance compared to other state-of-the-art methods, with an accuracy up to 98.48% and an F1 score of 95.9%.

An intent classification method for questions in "Treatise on Febrile diseases" based on TinyBERT-CNN fusion model.

"Treatise on Febrile Diseases" is an important classic book in the academic history of Chinese material medica. Based on the knowledge map of traditional Chinese medicine established by the study of "Treatise on Febrile Diseases", a question-answering system of traditional Chinese medicine was established to help people better understand and use traditional Chinese medicine. Intention classification is the basis of the question-answering system of traditional Chinese medicine, but as far as we know, there is no research on question intention classification based on "Treatise on Febrile Diseases". In this paper, the intent classification research is carried out based on the Chinese material medica-related content materials in "Treatise on Febrile Diseases" as data. Most of the existing models perform well on long text classification tasks, with high costs and a lot of memory requirements. However, the intent classification data of this paper has the characteristics of short text, a small amount of data, and unbalanced categories. In response to these problems, this paper proposes a knowledge distillation-based bidirectional Transformer encoder combined with a convolutional neural network model (TinyBERT-CNN), which is used for the task of question intent classification in "Treatise on Febrile Diseases". The model used TinyBERT as an embedding and encoding layer to obtain the global vector information of the text and then completed the intent classification by feeding the encoded feature information into the CNN. The experimental results indicated that the model outperformed other models in terms of accuracy, recall, and F1 values of 96.4%, 95.9%, and 96.2%, respectively. The experimental results prove that the model proposed in this paper can effectively classify the intent of the question sentences in "Treatise on Febrile Diseases", and provide technical support for the question-answering system of "Treatise on Febrile Diseases" later.

An accelerated sine mapping whale optimizer for feature selection.

An improved whale optimization algorithm (SWEWOA) is presented for global optimization issues. Firstly, the sine mapping initialization strategy (SS) is used to generate the population. Secondly, the escape energy (EE) is introduced to balance the exploration and exploitation of WOA. Finally, the wormhole search (WS) strengthens the capacity for exploitation. The hybrid design effectively reinforces the optimization capability of SWEWOA. To prove the effectiveness of the design, SWEWOA is performed in two test sets, CEC 2017 and 2022, respectively. The advantage of SWEWOA is demonstrated in 26 superior comparison algorithms. Then a new feature selection method called BSWEWOA-KELM is developed based on the binary SWEWOA and kernel extreme learning machine (KELM). To verify its performance, 8 high-performance algorithms are selected and experimentally studied in 16 public datasets of different difficulty. The test results demonstrate that SWEWOA performs excellently in selecting the most valuable features for classification problems.

A classification method for soybean leaf diseases based on an improved ConvNeXt model.

Deep learning technologies have enabled the development of a variety of deep learning models that can be used to detect plant leaf diseases. However, their use in the identification of soybean leaf diseases is currently limited and mostly based on machine learning methods. In this investigation an enhanced deep learning network model was developed to recognize soybean leaf diseases more accurately. The improved network model consists of three parts: feature extraction, attention calculation, and classification. The dataset used was first diversified through data augmentation operations such as random masking to enhance network robustness. An attention module was then used to generate feature maps at various depths. This increased the network's focus on discriminative features, reduced background noise, and enabled the use of the LeakyReLu activation function in the attention module to prevent situations in which neurons fail to learn when the input is negative. Finally, the extracted features were then integrated using a fully connected layer, and the predicted disease category inferred to improve the classification accuracy of soybean leaf diseases. The average recognition accuracy of the improved network model for soybean leaf diseases was 85.42% both higher than the six deep learning comparison models (ConvNeXt (66.41%), ResNet50 (72.22%), Swin Transformer (77.00%), MobileNetV3 (67.27%), ShuffleNetV2 (59.89%), and SqueezeNet (72.92%)), thus proving the effectiveness of the improved method.The model proposed in this paper was also tested on the grapevine leaf dataset, and the performance ability of the improved network model remained due to other common network models, and overall the proposed network model was very effective in leaf disease identification.

Research on Field Soybean Weed Identification Based on an Improved UNet Model Combined With a Channel Attention Mechanism.

Aiming at the problem that it is difficult to identify two types of weeds, grass weeds and broadleaf weeds, in complex field environments, this paper proposes a semantic segmentation method with an improved UNet structure and an embedded channel attention mechanism SE module. First, to eliminate the semantic gap between low-dimensional semantic features and high-dimensional semantic features, the UNet model structure is modified according to the characteristics of different types of weeds, and the feature maps after the first five down sampling tasks are restored to the same original image through the deconvolution layer. Hence, the final feature map used for prediction is obtained by the fusion of the upsampling feature map and the feature maps containing more low-dimensional semantic information in the first five layers. In addition, ResNet34 is used as the backbone network, and the channel attention mechanism SE module is embedded to improve useful features. The channel weight is determined, noise is suppressed, soybean and grass weeds are identified, and broadleaf weeds are extracted through digital image morphological processing, and segmented images of soybean plants, grass weeds and broadleaf weeds are generated. Moreover, compared with the standard semantic segmentation models, FCN, UNet, and SegNet, the experimental results show that the overall performance of the model in this paper is the best. The average intersection ratio and average pixel recognition rate in a complex field environment are 0.9282 and 96.11%, respectively. On the basis of weed classification, the identified weeds are further refined into two types of weeds to provide technical support for intelligent precision variable weed spraying.

Multi-Threshold Image Segmentation of Maize Diseases Based on Elite Comprehensive Particle Swarm Optimization and Otsu.

Maize is a major global food crop and as one of the most productive grain crops, it can be eaten; it is also a good feed for the development of animal husbandry and essential raw material for light industry, chemical industry, medicine, and health. Diseases are the main factor limiting the high and stable yield of maize. Scientific and practical identification is a vital link to reduce the damage of diseases and accurate segmentation of disease spots is one of the fundamental techniques for disease identification. However, one single method cannot achieve a good segmentation effect to meet the diversity and complexity of disease spots. In order to solve the shortcomings of noise interference and oversegmentation in the Otsu segmentation method, a non-local mean filtered two-dimensional histogram was used to remove the noise in disease images and a new elite strategy improved comprehensive particle swarm optimization (PSO) method was used to find the optimal segmentation threshold of the objective function in this study. The experimental results of segmenting three kinds of maize foliar disease images show that the segmentation effect of this method is better than other similar algorithms and it has better convergence and stability.

Quality Assessment of Protein Docking Models Based on Graph Neural Network.

Protein docking provides a structural basis for the design of drugs and vaccines. Among the processes of protein docking, quality assessment (QA) is utilized to pick near-native models from numerous protein docking candidate conformations, and it directly determines the final docking results. Although extensive efforts have been made to improve QA accuracy, it is still the bottleneck of current protein docking systems. In this paper, we presented a Deep Graph Attention Neural Network (DGANN) to evaluate and rank protein docking candidate models. DGANN learns inter-residue physio-chemical properties and structural fitness across the two protein monomers in a docking model and generates their probabilities of near-native models. On the ZDOCK decoy benchmark, our DGANN outperformed the ranking provided by ZDOCK in terms of ranking good models into the top selections. Furthermore, we conducted comparative experiments on an independent testing dataset, and the results also demonstrated the superiority and generalization of our proposed method.

Synthesis and in-vitro antibacterial properties of a functionally graded Ag impregnated composite surface.

Silver is considered promising in medical devices to prevent infection due to its excellent properties of broad antibacterial spectrum and persistent antibacterial activity. Herein, silver impregnated functionally graded composite surfaces have been developed by a novel duplex plasma deposition technique, which combines the double glow sputtering process and active screen plasma nitriding process. The composite surfaces include a surface antibacterial layer and a bottom supporting layer, which are deposited simultaneously. The functionally graded structure endows the composite surfaces with antibacterial activity, combined with improved wear resistance. The multilayer structures were observed by scanning electron microscopy, and the graded distribution of silver and nitrogen was verified by glow discharge optical emission spectroscopy. X-ray diffraction and X-ray photoelectron spectroscopy were used to analyze the microstructures and chemical states of the components. Results from physical properties tests indicated that the composite surfaces have increased hardness, lower contact angles, excellent scratch resistance and wear resistance. The in-vitro antibacterial tests using the Gram-negative E. coli. NCTC 10418 also showed that over 99% of bacteria were killed after 5 h contacting with the composite surface.