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Peach diseases seriously affect peach yield and people's health. The precise identification of peach diseases and the segmentation of the diseased areas can provide the basis for disease control and treatment. However, the complex background and imbalanced samples bring certain challenges to the segmentation and recognition of lesion area, and the hard samples and imbalance samples can lead to a decline in classification of foreground class and background class. In this paper we applied deep network models (Mask R-CNN and Mask Scoring R-CNN) for segmentation and recognition of peach diseases. Mask R-CNN and Mask Scoring R-CNN are classic instance segmentation models. Using instance segmentation model can obtain the disease names, disease location and disease segmentation, and the foreground area is the basic feature for next segmentation. Focal Loss can solve the problems caused by difficult samples and imbalance samples, and was used for this dataset to improve segmentation accuracy. Experimental results show that Mask Scoring R-CNN with Focal Loss function can improve recognition rate and segmentation accuracy comparing to Mask Scoring R-CNN with CE loss or comparing to Mask R-CNN. When ResNet50 is used as the backbone network based on Mask R-CNN, the segmentation accuracy of segm_mAP_50 increased from 0.236 to 0.254. When ResNetx101 is used as the backbone network, the segmentation accuracy of segm_mAP_50 increased from 0.452 to 0.463. In summary, this paper used Focal Loss on Mask R-CNN and Mask Scoring R-CNN to generate better mAP of segmentation and output more detailed information about peach diseases. [ABSTRACT FROM AUTHOR]

Biological pathways play important roles in the development of complex diseases, such as cancers, which are multifactorial complex diseases that are usually caused by multiple disorders gene mutations or pathway. It has become one of the most important issues to analyze pathways combining multiple types of high-throughput data, such as genomics and proteomics, to understand the mechanisms of complex diseases. In this paper, we propose a method for constructing the pathway network of gene phenotype and find out disease pathogenesis pathways through the analysis of the constructed network. The specific process of constructing the network includes, firstly, similarity calculation between genes expressing data combined with phenotypic mutual information and GO ontology information, secondly, calculating the correlation between pathways based on the similarity between differential genes and constructing the pathway network, and, finally, mining critical pathways to identify diseases. Experimental results on Breast Cancer Dataset using this method show that our method is better. In addition, testing on an alternative dataset proved that the key pathways we found were more accurate and reliable as biological markers of disease. These results show that our proposed method is effective. [ABSTRACT FROM AUTHOR]

Genetic algorithm is easy to fall into local optimal solution. Simulated annealing algorithm may accept nonoptimal solution at a certain probability to jump out of local optimal solution. On the other hand, lack of communication among genes in MapReduce platform based genetic algorithm, the high-performance distributed computing technologies or platforms can further increase the execution efficiency of these traditional genetic algorithms. To this end, we propose a novel Phoenix++ based new genetic algorithm involving mechanism of simulated annealing. Simulated annealing genetic algorithm has two distinctive characteristics. First, it is the synthesis of the conventional genetic algorithm and the simulated annealing algorithm. This characteristic guarantees our proposed algorithm has a higher probability of getting the global optimal solution than traditional genetic algorithms. The other is that our algorithm is a parallel algorithm running on the high-performance parallel platform Phoenix++ instead of a conventional serial genetic algorithm. Phoenix++ implements the MapReduce programming model that processes and generates large data sets with our parallel, distributed algorithm on a cluster. The experiments indicate that the convergence speed of GA algorithm is significantly faster after adding the simulated annealing algorithm on Phoenix++ platform. [ABSTRACT FROM AUTHOR]

Detecting and controlling tea pests promptly are crucial for safeguarding tea production quality. Due to the insufficient feature extraction ability of traditional CNN-based methods, they face challenges such as inaccuracy and inefficiency of detecting pests in dense and mimicry scenarios. This study proposes an end-to-end tea pest detection and segmentation framework, TeaPest-Transfiner (TP-Transfiner), based on Mask Transfiner to address the challenge of detecting and segmenting pests in mimicry and dense scenarios. In order to improve the feature extraction inability and weak accuracy of traditional convolution modules, this study proposes three strategies. Firstly, a deformable attention block is integrated into the model, which consists of deformable convolution and self-attention using the key content only term. Secondly, the FPN architecture in the backbone network is improved with a more effective feature-aligned pyramid network (FaPN). Lastly, focal loss is employed to balance positive and negative samples during the training period, and parameters are adapted to the dataset distribution. Furthermore, to address the lack of tea pest images, a dataset called TeaPestDataset is constructed, which contains 1,752 images and 29 species of tea pests. Experimental results on the TeaPestDataset show that the proposed TP-Transfiner model achieves state-of-the-art performance compared with other models, attaining a detection precision (AP50) of 87.211% and segmentation performance of 87.381%. Notably, the model shows a significant improvement in segmentation average precision (mAP) by 9.4% and a reduction in model size by 30% compared to the state-of-the-art CNN-based model Mask R-CNN. Simultaneously, TP-Transfiner's lightweight module fusion maintains fast inference speeds and a compact model size, demonstrating practical potential for pest control in tea gardens, especially in dense and mimicry scenarios., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Wu, He, Rong, Liang, Xu, Ni and Dong.)

Identifying drug-disease associations is integral to drug development. Computationally prioritizing candidate drug-disease associations has attracted growing attention due to its contribution to reducing the cost of laboratory screening. Drug-disease associations involve different association types, such as drug indications and drug side effects. However, the existing models for predicting drug-disease associations merely concentrate on independent tasks: recommending novel indications to benefit drug repositioning, predicting potential side effects to prevent drug-induced risk, or only determining the existence of drug-disease association. They ignore crucial prior knowledge of the correlations between different association types. Since the Comparative Toxicogenomics Database (CTD) annotates the drug-disease associations as therapeutic or marker/mechanism, we consider predicting the two types of association. To this end, we propose a collective matrix factorization-based multi-task learning method (CMFMTL) in this paper. CMFMTL handles the problem as multi-task learning where each task is to predict one type of association, and two tasks complement and improve each other by capturing the relatedness between them. First, drug-disease associations are represented as a bipartite network with two types of links representing therapeutic effects and non-therapeutic effects. Then, CMFMTL, respectively, approximates the association matrix regarding each link type by matrix tri-factorization, and shares the low-dimensional latent representations for drugs and diseases in the two related tasks for the goal of collective learning. Finally, CMFMTL puts the two tasks into a unified framework and an efficient algorithm is developed to solve our proposed optimization problem. In the computational experiments, CMFMTL outperforms several state-of-the-art methods both in the two tasks. Moreover, case studies show that CMFMTL helps to find out novel drug-disease associations that are not included in CTD, and simultaneously predicts their association types., (Copyright © 2020 Huang, Qiu, Li, Liu and Ni.)