PLANNER: a multi-scale deep language model for the origins of replication site prediction.

Origins of replication sites (ORIs) are crucial genomic regions where DNA replication initiation takes place, playing pivotal roles in fundamental biological processes like cell division, gene expression regulation, and DNA integrity. Accurate identification of ORIs is essential for comprehending cell replication, gene expression, and mutation-related diseases. However, experimental approaches for ORI identification are often expensive and time-consuming, leading to the growing popularity of computational methods. In this study, we present PLANNER (DeeP LeArNiNg prEdictor for ORI), a novel approach for species-specific and cell-specific prediction of eukaryotic ORIs. PLANNER uses the multi-scale ktuple sequences as input and employs the DNABERT pre-training model with transfer learning and ensemble learning strategies to train accurate predictive models. Extensive empirical test results demonstrate that PLANNER achieved superior predictive performance compared to state-of-the-art approaches, including iOri-Euk, Stack-ORI, and ORI-Deep, within specific cell types and across different cell types. Furthermore, by incorporating an interpretable analysis mechanism, we provide insights into the learned patterns, facilitating the mapping from discovering important sequential determinants to comprehensively analysing their biological functions. To facilitate the widespread utilisation of PLANNER, we developed an online webserver and local stand-alone software, available at http://planner.unimelb-biotools.cloud.edu.au/ and https://github.com/CongWang3/PLANNER, respectively.

Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins.

The genome of Mycobacterium tuberculosis contains a relatively high percentage (10%) of genes that are poorly characterised because of their highly repetitive nature and high GC content. Some of these genes encode proteins of the PE/PPE family, which are thought to be involved in host-pathogen interactions, virulence, and disease pathogenicity. Members of this family are genetically divergent and challenging to both identify and classify using conventional computational tools. Thus, advanced in silico methods are needed to identify proteins of this family for subsequent functional annotation efficiently. In this study, we developed the first deep learning-based approach, termed Digerati, for the rapid and accurate identification of PE and PPE family proteins. Digerati was built upon a multipath parallel hybrid deep learning framework, which equips multi-layer convolutional neural networks with bidirectional, long short-term memory, equipped with a self-attention module to effectively learn the higher-order feature representations of PE/PPE proteins. Empirical studies demonstrated that Digerati achieved a significantly better performance (∼18-20%) than alignment-based approaches, including BLASTP, PHMMER, and HHsuite, in both prediction accuracy and speed. Digerati is anticipated to facilitate community-wide efforts to conduct high-throughput identification and analysis of PE/PPE family members. The webserver and source codes of Digerati are publicly available at http://web.unimelb-bioinfortools.cloud.edu.au/Digerati/.

LAD-Net: A Novel Light Weight Model for Early Apple Leaf Pests and Diseases Classification.

Aphids, brown spots, mosaics, rusts, powdery mildew and Alternaria blotches are common types of early apple leaf pests and diseases that severely affect the yield and quality of apples. Recently, deep learning has been regarded as the best classification model for apple leaf pests and diseases. However, these models with large parameters have difficulty providing an accurate and fast diagnosis of apple leaf pests and diseases on mobile terminals. This paper proposes a novel and real-time early apple leaf disease recognition model. AD Convolution is firstly utilized to replace standard convolution to make smaller number of parameters and calculations. Meanwhile, a LAD-Inception is built to enhance the ability of extracting multiscale features of different sizes of disease spots. Finally, the LAD-Net model is built by the LR-CBAM and the LAD-Inception modules, replacing a full connection with global average pooling to further reduce parameters. The results show that the LAD-Net, with a size of only 1.25MB, can achieve a recognition performance of 98.58%. Additionally, it is only delayed by 15.2ms on HUAWEI P40 and by 100.1ms on Jetson Nano, illustrating that the LAD-Net can accurately recognize early apple leaf pests and diseases on mobile devices in real-time, providing portable technical support.