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Facial recognition technology and related research have matured over time, but research in the field of individual animal recognition is still very limited. Therefore, this article focuses on the identification of cashmere goats with similar characteristics. First, the single shot multibox detector network was used to process the dataset. Next, transfer learning was applied to learn the characteristics of the goats, as well as the loss function is composed of Triplet Loss and Label Smoothing CrossEntropy Loss function. The result of Label Smoothing CrossEntropy Loss function is fused by multiple different branches, which is convenient for classification. We added a small number of images of 24 different breeds of sheep to each cashmere goat dataset with different ID to promote the distance between training individuals, and then used the trained model to find the number of goats with the lowest recognition accuracy. The Cycle-Consistent Adversarial Network (Cycle-GAN) learned the goat dataset with a high error rate in individual identification. Unlike previous studies using the Cycle-GAN, we took the novel approach of using this network to learn and combine the features seen in photos of cashmere goats. Since the learned features were all observed in the same goats, this method achieved better results in learning the features of the goats. Finally, we found that recognition can be performed on this data with an accuracy of 93.75%. These results suggest that identification based on deep learning has a high accuracy rate, as well as great value in identifying individual cashmere goats.

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The chromatin loops in the three-dimensional (3D) structure of chromosomes are essential for the regulation of gene expression. Despite the fact that high-throughput chromatin capture techniques can identify the 3D structure of chromosomes, chromatin loop detection utilizing biological experiments is arduous and time-consuming. Therefore, a computational method is required to detect chromatin loops. Deep neural networks can form complex representations of Hi-C data and provide the possibility of processing biological datasets. Therefore, we propose a bagging ensemble one-dimensional convolutional neural network (Be-1DCNN) to detect chromatin loops from genome-wide Hi-C maps. First, to obtain accurate and reliable chromatin loops in genome-wide contact maps, the bagging ensemble learning method is utilized to synthesize the prediction results of multiple 1DCNN models. Second, each 1DCNN model consists of three 1D convolutional layers for extracting high-dimensional features from input samples and one dense layer for producing the prediction results. Finally, the prediction results of Be-1DCNN are compared to those of the existing models. The experimental results indicate that Be-1DCNN predicts high-quality chromatin loops and outperforms the state-of-the-art methods using the same evaluation metrics. The source code of Be-1DCNN is available for free at https://github.com/HaoWuLab-Bioinformatics/Be1DCNN.

Single-cell clustering is the most significant part of single-cell RNA sequencing (scRNA-seq) data analysis. One main issue facing the scRNA-seq data is noise and sparsity, which poses a great challenge for the advance of high-precision clustering algorithms. This study adopts cellular markers to identify differences between cells, which contributes to feature extraction of single cells. In this work, we propose a high-precision single-cell clustering algorithm-SCMcluster (single-cell cluster using marker genes). This algorithm integrates two cell marker databases(CellMarker database and PanglaoDB database) with scRNA-seq data for feature extraction and constructs an ensemble clustering model based on the consensus matrix. We test the efficiency of this algorithm and compare it with other eight popular clustering algorithms on two scRNA-seq datasets derived from human and mouse tissues, respectively. The experimental results show that SCMcluster outperforms the existing methods in both feature extraction and clustering performance. The source code of SCMcluster is available for free at https://github.com/HaoWuLab-Bioinformatics/SCMcluster.

Sheep detection and segmentation will play a crucial role in promoting the implementation of precision livestock farming in the future. In sheep farms, the characteristics of sheep that have the tendency to congregate and irregular contours cause difficulties for computer vision tasks, such as individual identification, behavior recognition, and weight estimation of sheep. Sheep instance segmentation is one of the methods that can mitigate the difficulties associated with locating and extracting different individuals from the same category. To improve the accuracy of extracting individual sheep locations and contours in the case of multiple sheep overlap, this paper proposed two-stage sheep instance segmentation SheepInst based on the Mask R-CNN framework, more specifically, RefineMask. Firstly, an improved backbone network ConvNeXt-E was proposed to extract sheep features. Secondly, we improved the structure of the two-stage object detector Dynamic R-CNN to precisely locate highly overlapping sheep. Finally, we enhanced the segmentation network of RefineMask by adding spatial attention modules to accurately segment irregular contours of sheep. SheepInst achieves 89.1%, 91.3%, and 79.5% in box AP, mask AP, and boundary AP metric on the test set, respectively. The extensive experiments show that SheepInst is more suitable for sheep instance segmentation and has excellent performance.