Background: Predicting the drug response of the cancer diseases through the cellular perturbation signatures under the action of specific compounds is very important in personalized medicine. In the process of testing drug responses to the cancer, traditional experimental methods have been greatly hampered by the cost and sample size. At present, the public availability of large amounts of gene expression data makes it a challenging task to use machine learning methods to predict the drug sensitivity. Results: In this study, we introduced the WRFEN-XGBoost cell viability prediction algorithm based on LINCS-L1000 cell signatures. We integrated the LINCS-L1000, CTRP and Achilles datasets and adopted a weighted fusion algorithm based on random forest and elastic net for key gene selection. Then the FEBPSO algorithm was introduced into XGBoost learning algorithm to predict the cell viability induced by the drugs. The proposed method was compared with some new methods, and it was found that our model achieved good results with 0.83 Pearson correlation. At the same time, we completed the drug sensitivity validation on the NCI60 and CCLE datasets, which further demonstrated the effectiveness of our method. Conclusions: The results showed that our method was conducive to the elucidation of disease mechanisms and the exploration of new therapies, which greatly promoted the progress of clinical medicine.

Shallow water bathymetry is of great significance in understanding, managing, and protecting coastal ecological environments. Many studies have shown that both empirical models and deep learning models can achieve promising results from satellite imagery bathymetry inversion. However, the spectral information available today in multispectral or/and hyperspectral satellite images has not been explored thoroughly in many models. The Band-optimized Bidirectional Long Short-Term Memory (BoBiLSTM) model proposed in this paper feeds only the optimized bands and band ratios to the deep learning model, and a series of experiments were conducted in the shallow waters of Molokai Island, Hawaii, using hyperspectral satellite imagery (PRISMA) and multispectral satellite imagery (Sentinel-2) with ICESat-2 data and multibeam scan data as training data, respectively. The experimental results of the BoBiLSTM model demonstrate its robustness over other compared models. For example, using PRISMA data as the source image, the BoBiLSTM model achieves RMSE values of 0.82 m (using ICESat-2 as the training data) and 1.43 m (using multibeam as the training data), respectively, and because of using the bidirectional strategy, the inverted bathymetry reaches as far as a depth of 25 m. More importantly, the BoBiLSTM model does not overfit the data in general, which is one of its advantages over many other deep learning models. Unlike other deep learning models, which require a large amount of training data and all available bands as the inputs, the BoBiLSTM model can perform very well using equivalently less training data and a handful of bands and band ratios. With ICESat-2 data becoming commonly available and covering many shallow water regions around the world, the proposed BoBiLSTM model holds potential for bathymetry inversion for any region around the world where satellite images and ICESat-2 data are available.

Hyperspectral data usually consists of hundreds of narrow spectral bands and provides more detailed spectral characteristics compared to commonly used multispectral data in remote sensing applications. However, highly correlated spectral bands in hyperspectral data lead to computational complexity, which limits many applications or traditional methods when applied to hyperspectral data. The dimensionality reduction of hyperspectral data becomes one of the most important pre-processing steps in hyperspectral data analysis. Recently, deep reinforcement learning (DRL) has been introduced to hyperspectral data band selection (BS); however, the current DRL methods for hyperspectral data BS simply remove redundant bands, lack the significance analysis for the selected bands, and the reward mechanisms used in DRL only take basic forms in general. In this paper, a new reward mechanism strategy has been proposed, and Double Deep Q-Network (DDQN) is introduced during BS using DRL to improve the network stabilities and avoid local optimum. To verify the effect of the proposed BS method, land cover classification experiments were designed and carried out to analyze and compare the proposed method with other BS methods. In the land cover classification experiments, the overall accuracy (OA) of the proposed method can reach 98.37%, the average accuracy (AA) is 95.63%, the kappa coefficient (Kappa) is 97.87%. Overall, the proposed method is superior to other BS methods. Experiments have also shown that the proposed method works not only for airborne hyperspectral data (AVIRIS and HYDICE), but also for hyperspectral satellite data, such as PRISMA data. When hyperspectral data is applied to similar applications, the proposed BS method could be a candidate for the BS preprocessing options.

To enhance the accuracy of lightweight CNN classification models in analyzing fish feeding behavior, this paper addresses the image quality issues caused by external environmental factors and lighting conditions, such as low contrast and uneven illumination, by proposing a Multi-step Image Pre-enhancement Strategy (MIPS). This strategy includes three critical steps: initially, images undergo a preliminary processing using the Multi-Scale Retinex with Color Restoration (MSRCR) algorithm, effectively reducing the impact of water surface reflections and enhancing the visual effect of the images; secondly, the Multi-Metric-Driven Contrast Limited Adaptive Histogram Equalization (mdc) technique is applied to further improve image contrast, especially in areas of low contrast, by adjusting the local contrast levels to enhance the clarity of the image details; finally, Unsharp Masking (UM) technology is employed to sharpen the images, emphasizing their edges to increase the clarity of the image details, thereby significantly improving the overall image quality. Experimental results on a custom dataset have confirmed that this pre-enhancement strategy significantly boosts the accuracy of various CNN-based classification models, particularly for lightweight CNN models, and drastically reduces the time required for model training compared to the use of advanced ResNet models. This research provides an effective technical route for improving the accuracy and efficiency of an image-based analysis of fish feeding behavior in complex environments.

With the release of the draft genome of the grass carp, researches on the grass carp from the genetic level and the further molecular mechanisms of economically valuable physiological behaviors have gained great attention. In this paper, we integrated a large number of genomic, genetic and some other data resources and established a web-based grass carp genomic visualization database (GCGVD). To view these data more effectively, we visualized grass carp and zebrafish gene collinearity and genetic linkage map using Scalable Vector Graphics (SVG) format in the browser, and genomic annotations by JBrowse. Furthermore, we carried out some preliminary study on a whole-genome alternative splicing (AS) of the grass carp. The RNA-seq reads of 15 samples were aligned to the reference genome of the grass carp by Bowtie2 software. RNA-seq reads of each sample and density map of reads were also exhibited in JBrowse. Additionally, we designed a universal grass carp genome annotation data model to improve the retrieval speed and scalability. Compared with the published database GCGD previously, we newly added the visualization of some more genomic annotations, conserved domain and RNA-seq reads aligned to the reference genome. GCGVD can be accessed at http://122.1 12.216.104.

In order to achieve fast and accurate detection of Gannan navel orange fruits with different ripeness levels in a natural environment under all-weather scenarios and then to realise automated harvesting of Gannan navel oranges, this paper proposes a YOLOv5-NMM (YOLOv5 with Navel orange Measure Model) object detection model based on the improvement in the original YOLOv5 model. Based on the changes in the phenotypic characteristics of navel oranges and the Chinese national standard GB/T 21488-2008, the maturity of Gannan navel oranges is tested. And it addresses and improves the problems of occlusion, dense distribution, small target size, rainy days, and light changes in the detection of navel orange fruits. Firstly, a new detection head of 160 × 160 feature maps is constructed in the detection layer to improve the multi-scale target detection layer of YOLOv5 and to increase the detection accuracy of the different maturity levels of Gannan navel oranges of small sizes. Secondly, a convolutional block attention module is incorporated in its backbone layer to capture the correlations between features in different dimensions to improve the perceptual ability of the model. Then, the weighted bidirectional feature pyramid network structure is integrated into the Neck layer to improve the fusion efficiency of the network on the feature maps and reduce the amount of computation. Lastly, in order to reduce the loss of the target of the Gannan Navel Orange due to occlusion and overlapping, the detection frame is used to remove redundancy using the Soft-NMS algorithm to remove redundant candidate frames. The results show that the accuracy rate, recall rate, and average accuracy of the improved YOLOv5-NMM model are 93.2%, 89.6%, and 94.2%, respectively, and the number of parameters is only 7.2 M. Compared with the mainstream network models, such as Faster R-CNN, YOLOv3, the original model of YOLOv5, and YOLOv7-tiny, it is superior in terms of the accuracy rate, recall rate, and average accuracy mean, and also performs well in terms of the detection rate and memory occupation. This study shows that the YOLOv5-NMM model can effectively identify and detect the ripeness of Gannan navel oranges in natural environments, which provides an effective exploration of the automated harvesting of Gannan navel orange fruits.