This research addresses the pressing challenge of weed identification in agriculture, crucial for ensuring food security in anticipation of a global population exceeding 9.7 billion by 2050. Utilizing drone imagery, we collected a dataset and proposed a customized model to achieve optimal performance. Our proposed model uses strategically modified backbone, neck, and head components, leveraging elements such as Ghost Convolution, BottleNeckCSP, and ECA (Efficient Channel Attention) layers. These modifications enhance the model’s capability to discern intricate patterns in drone imagery, ultimately leading to improved precision in weed detection. We introduce a purposefully crafted dataset to complement the model’s training, and our experiments demonstrate superior performance compared to the baseline models. Our model achieves a precision of 72.5%, recall of 68.0%, and [email protected] of 73.9, showcasing the effectiveness of our approach in enhancing detection accuracy. Leveraging a unique blend of feature extraction mechanisms, our model achieves remarkable accuracy in real-time soybean detection, outperforming established models like RT-DETR (Real-Time DEtection TransfoRmer) and YOLOv10. A detailed ablation study and comparative analysis with different YOLO versions and the transformer-based RT-DETR showcase the effectiveness of the proposed enhancements. Our work signifies a significant step towards advancing the field of precision agriculture, offering a model that is not only adaptive but also robust in identifying and localizing weeds in soybean fields.

MOTIVATION: The origins of replication sites (ORIs) are precise regions inside the DNA sequence where the replication process begins. These locations are critical for preserving the genome's integrity during cell division and guaranteeing the faithful transfer of genetic data from generation to generation. The advent of experimental techniques has aided in the discovery of ORIs in many species. Experimentation, on the other hand, is often more time-consuming and pricey than computational approaches, and it necessitates specific equipment and knowledge. Recently, ORI sites have been predicted using computational techniques like motif-based searches and artificial intelligence algorithms based on sequence characteristics and chromatin states. RESULTS: In this article, we developed ORI-Explorer, a unique artificial intelligence-based technique that combines multiple feature engineering techniques to train CatBoost Classifier for recognizing ORIs from four distinct eukaryotic species. ORI-Explorer was created by utilizing a unique combination of three traditional feature-encoding techniques and a feature set obtained from a deep-learning neural network model. The ORI-Explorer has significantly outperformed current predictors on the testing dataset. Furthermore, by employing the sophisticated SHapley Additive exPlanation method, we give crucial insights that aid in comprehending model success, highlighting the most relevant features vital for forecasting cell-specific ORIs. ORI-Explorer is also intended to aid community-wide attempts in discovering potential ORIs and developing innovative verifiable biological hypotheses. AVAILABILITY AND IMPLEMENTATION: The used datasets along with the source code are made available through https://github.com/Z-Abbas/ORI-Explorer and https://zenodo.org/record/8358679.

MOTIVATION: The investigation of DNA methylation can shed light on the processes underlying human well-being and help determine overall human health. However, insufficient coverage makes it challenging to implement single-stranded DNA methylation sequencing technologies, highlighting the need for an efficient prediction model. Models are required to create an understanding of the underlying biological systems and to project single-cell (methylated) data accurately. RESULTS: In this study, we developed positional features for predicting CpG sites. Positional characteristics of the sequence are derived using data from CpG regions and the separation between nearby CpG sites. Multiple optimized classifiers and different ensemble learning approaches are evaluated. The OPTUNA framework is used to optimize the algorithms. The CatBoost algorithm followed by the stacking algorithm outperformed existing DNA methylation identifiers. AVAILABILITY AND IMPLEMENTATION: The data and methodologies used in this study are openly accessible to the research community. Researchers can access the positional features and algorithms used for predicting CpG site methylation patterns. To achieve superior performance, we employed the CatBoost algorithm followed by the stacking algorithm, which outperformed existing DNA methylation identifiers. The proposed iCpG-Pos approach utilizes only positional features, resulting in a substantial reduction in computational complexity compared to other known approaches for detecting CpG site methylation patterns. In conclusion, our study introduces a novel approach, iCpG-Pos, for predicting CpG site methylation patterns. By focusing on positional features, our model offers both accuracy and efficiency, making it a promising tool for advancing DNA methylation research and its applications in human health and well-being.

N6-methyladenosine (m6A) is a common post-transcriptional alteration that plays a critical function in a variety of biological processes. Although experimental approaches for identifying m6A sites have been developed and deployed, they are currently expensive for transcriptome-wide m6A identification. Some computational strategies for identifying m6A sites have been presented as an effective complement to the experimental procedure. However, their performance still requires improvement. In this study, we have proposed a novel tool called DL-m6A for the identification of m6A sites in mammals using deep learning based on different encoding schemes. The proposed tool uses three encoding schemes which give the required contextual feature representation to the input RNA sequence. Later these contextual feature vectors individually go through several neural network layers for shallow feature extraction after which they are concatenated to a single feature vector. The concatenated feature map is then used by several other layers to extract the deep features so that the insight features of the sequence can be used for the prediction of m6A sites. The proposed tool is firstly evaluated on the tissue-specific dataset and later on a full transcript dataset. To ensure the generalizability of the tool we assessed the proposed model by training it on a full transcript dataset and test on the tissue-specific dataset. The achieved results by the proposed model have outperformed the existing tools. The results demonstrate that the proposed tool can be of great use for the biology experts and therefore a freely accessible web-server is created which can be accessed at: http://nsclbio.jbnu.ac.kr/tools/DL-m6A/.

N6-methyladenine (6mA), is amongst the most prevalent post-transcriptional epigenetic changes and is crucial for several cellular functions and disease development. Therefore, a thorough knowledge of cellular processes and other potential functional pathways depends on the proper identification of 6mA modifications. Although we have a number of experimental methods for identifying 6mA-modification sites, computational prediction has emerged as a substitute method as a result of the expensive and labor-intensive nature of experimental methods. Considering this, it is of utmost importance to develop a reliable and effective approach for N6-methy1adenine identification. To categorize genome-wide 6mA locations, numerous computational models have previously been proposed, but there is still potential for advancement in their ability to anticipate 6mA sites. Therefore, we developed a technique using Transformers and neural networks for the accurate prediction of 6mA modification sites in Homo sapiens and Mus musculus genomes and obtained high accuracy of 96.5% and 96.86%, respectively using 5-fold cross-validation technique, and 93.75% on Homo sapiens independent test set. The outcomes demonstrate that the presented model outperforms current approaches in terms of all assessment metrics.

An important post-transcriptional alteration is 5-methylcytosine (m5C). It has become more prevalent as technology has advanced in many different RNAs. Previous research has shown that m5C is crucial for many biological processes, including tRNA recognition, RNA stability and the metabolic process of RNA. Traditional detection processes are expensive and time-consuming. As a result, computer models are frequently employed to locate the m5C locations. It is possible to create an effective prediction model because of deep learning’s extensive computing capabilities. Therefore, developing a reliable computational method for predicting RNA modification sites is essential. In this work, we have proposed a CapsuleNet-based architecture for the classification of m5C sites. The one-hot technique is used to convert biological sequences into numerical data. The CNN model is then given the numerical data in order to extract the concealed information. Further, this concealed information is shared with the CapsuleNet framework to get the m5C sites classified. The proposed architecture is evaluated on the human m5C dataset. CapsuleNet-based architecture has demonstrated improved results when compared with already available predictors.

MOTIVATION: DNA N6-methyladenine (6mA) has been demonstrated to have an essential function in epigenetic modification in eukaryotic species in recent research. 6mA has been linked to various biological processes. It's critical to create a new algorithm that can rapidly and reliably detect 6mA sites in genomes to investigate their biological roles. The identification of 6mA marks in the genome is the first and most important step in understanding the underlying molecular processes, as well as their regulatory functions. RESULTS: In this article, we proposed a novel computational tool called i6mA-Caps which CapsuleNet based a framework for identifying the DNA N6-methyladenine sites. The proposed framework uses a single encoding scheme for numerical representation of the DNA sequence. The numerical data is then used by the set of convolution layers to extract low-level features. These features are then used by the capsule network to extract intermediate-level and later high-level features to classify the 6mA sites. The proposed network is evaluated on three datasets belonging to three genomes which are Rosaceae, Rice and Arabidopsis thaliana. Proposed method has attained an accuracy of 96.71%, 94% and 86.83% for independent Rosaceae dataset, Rice dataset and A.thaliana dataset respectively. The proposed framework has exhibited improved results when compared with the existing top-of-the-line methods. AVAILABILITY AND IMPLEMENTATION: A user-friendly web-server is made available for the biological experts which can be accessed at: http://nsclbio.jbnu.ac.kr/tools/i6mA-Caps/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.