CATAD: exploring topologically associating domains from an insight of core-attachment structure.

Identifying topologically associating domains (TADs), which are considered as the basic units of chromosome structure and function, can facilitate the exploration of the 3D-structure of chromosomes. Methods have been proposed to identify TADs by detecting the boundaries of TADs or identifying the closely interacted regions as TADs, while the possible inner structure of TADs is seldom investigated. In this study, we assume that a TAD is composed of a core and its surrounding attachments, and propose a method, named CATAD, to identify TADs based on the core-attachment structure model. In CATAD, the cores of TADs are identified based on the local density and cosine similarity, and the surrounding attachments are determined based on boundary insulation. CATAD was applied to the Hi-C data of two human cell lines and two mouse cell lines, and the results show that the boundaries of TADs identified by CATAD are significantly enriched by structural proteins, histone modifications, transcription start sites and enzymes. Furthermore, CATAD outperforms other methods in many cases, in terms of the average peak, boundary tagged ratio and fold change. In addition, CATAD is robust and rarely affected by the different resolutions of Hi-C matrices. Conclusively, identifying TADs based on the core-attachment structure is useful, which may inspire researchers to explore TADs from the angles of possible spatial structures and formation process.

Combining spectral and texture feature of UAV image with plant height to improve LAI estimation of winter wheat at jointing stage.

Introduction: Leaf area index (LAI) is a critical physiological and biochemical parameter that profoundly affects vegetation growth. Accurately estimating the LAI for winter wheat during jointing stage is particularly important for monitoring wheat growth status and optimizing variable fertilization decisions. Recently, unmanned aerial vehicle (UAV) data and machine/depth learning methods are widely used in crop growth parameter estimation. In traditional methods, vegetation indices (VI) and texture are usually to estimate LAI. Plant Height (PH) unlike them, contains information about the vertical structure of plants, which should be consider. Methods: Taking Xixingdian Township, Cangzhou City, Hebei Province, China as the research area in this paper, and four machine learning algorithms, namely, support vector machine(SVM), back propagation neural network (BPNN), random forest (RF), extreme gradient boosting (XGBoost), and two deep learning algorithms, namely, convolutional neural network (CNN) and long short-term memory neural network (LSTM), were applied to estimate LAI of winter wheat at jointing stage by integrating the spectral and texture features as well as the plant height information from UAV multispectral images. Initially, Digital Surface Model (DSM) and Digital Orthophoto Map (DOM) were generated. Subsequently, the PH, VI and texture features were extracted, and the texture indices (TI) was further constructed. The measured LAI on the ground were collected for the same period and calculated its Pearson correlation coefficient with PH, VI and TI to pick the feature variables with high correlation. The VI, TI, PH and fusion were considered as the independent features, and the sample set partitioning based on joint x-y distance (SPXY) method was used to divide the calibration set and validation set of samples. Results: The ability of different inputs and algorithms to estimate winter wheat LAI were evaluated. The results showed that (1) The addition of PH as a feature variable significantly improved the accuracy of the LAI estimation, indicating that wheat plant height played a vital role as a supplementary parameter for LAI inversion modeling based on traditional indices; (2) The combination of texture features, including normalized difference texture indices (NDTI), difference texture indices (DTI), and ratio texture indices (RTI), substantially improved the correlation between texture features and LAI; Furthermore, multi-feature combinations of VI, TI, and PH exhibited superior capability in estimating LAI for winter wheat; (3) Six regression algorithms have achieved high accuracy in estimating LAI, among which the XGBoost algorithm estimated winter wheat LAI with the highest overall accuracy and best results, achieving the highest R2 (R2 = 0.88), the lowest RMSE (RMSE=0.69), and an RPD greater than 2 (RPD=2.54). Discussion: This study provided compelling evidence that utilizing XGBoost and integrating spectral, texture, and plant height information extracted from UAV data can accurately monitor LAI during the jointing stage of winter wheat. The research results will provide a new perspective for accurate monitoring of crop parameters through remote sensing.