A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton’s resilience against CLCuD

Mixed Data Imputation Using Generative Adversarial Networks

Missing values are common in real-world datasets and pose a significant challenge to the performance of statistical and machine learning models. Generally, missing values are imputed using statistical methods, such as the mean, median, mode, or machine learning approaches. These approaches are limited to either numerical or categorical data. Imputation in mixed datasets that contain both numerical and categorical attributes is challenging and has received little attention. Machine learning-based imputation algorithms usually require a large amount of training data. However, obtaining such data is difficult. Furthermore, no considerate work has been conducted in the literature that focuses on the effects of the training and testing size with increasing amounts of missing data. To address this gap, we proposed that increasing the amount of training data will improve imputation performance. We first used generative adversarial network (GAN) methods to increase the amount of training data. We considered two state-of-the-art GANs (tabular and conditional tabular) to add synthetic samples using observed data with different synthetic sample ratios. We then used three state-of-the-art imputation models that can handle mixed data: MissForest, multivariate imputation by chained equations, and denoising auto encoder (DAE). We proposed robust experimental setups on four publicly available datasets with different training-testing data divisions that have increasing missingness ratios. Extensive experimental results show that incorporating synthetic samples with training data achieves better performance compared to the baseline methods for mixed data imputation in both categorical and numerical variables, especially for large missingness ratios

Infant Low Birth Weight Prediction Using Graph Embedding Features

Low Birth weight (LBW) infants pose a serious public health concern worldwide in both the short and long term for infants and their mothers. Infant weight prediction prior to birth can help to identify risk factors and reduce the risk of infant morbidity and mortality. Although many Machine Learning (ML) algorithms have been proposed for LBW prediction using maternal features and produced considerable model performance, their performance needs to be improved so that they can be adapted in real-world clinical settings. Existing algorithms used for LBW classification often fail to capture structural information from the tabular dataset of patients with different complications. Therefore, to improve the LBW classification performance, we propose a solution by transforming the tabular data into a knowledge graph with the aim that patients from the same class (normal or LBW) exhibit similar patterns in the graphs. To achieve this, several features related to each node are extracted such as node embedding using node2vec algorithm, node degree, node similarity, nearest neighbors, etc. Our method is evaluated on a real-life dataset obtained from a large cohort study in the United Arab Emirates which contains data from 3453 patients. Multiple experiments were performed using the seven most commonly used ML models on the original dataset, graph features, and a combination of features, respectively. Experimental results show that our proposed method achieved the best performance with an area under the curve of 0.834 which is over 6% improvement compared to using the original risk factors without transforming them into knowledge graphs. Furthermore, we provide the clinical relevance of the proposed model that are important for the model to be adapted in clinical settings