Search

The off-target activities within the CRISPR-Cas9 system remains a formidable barrier to its broader application and development. Recent advancements have highlighted the potential of deep learning models in predicting these off-target effects, yet they encounter significant hurdles including imbalances within datasets and the intricacies associated with encoding schemes and model architectures. To surmount these challenges, our study innovatively introduces an Efficiency and Specificity-Based (ESB) class rebalancing strategy, specifically devised for datasets featuring mismatches-only off-target instances, marking a pioneering approach in this realm. Furthermore, through a meticulous evaluation of various One-hot encoding schemes alongside numerous hybrid neural network models, we discern that encoding and models of moderate complexity ideally balance performance and efficiency. On this foundation, we advance a novel hybrid model, the CRISPR-MCA, which capitalizes on multi-feature extraction to enhance predictive accuracy. The empirical results affirm that the ESB class rebalancing strategy surpasses five conventional methods in addressing extreme dataset imbalances, demonstrating superior efficacy and broader applicability across diverse models. Notably, the CRISPR-MCA model excels in off-target effect prediction across four distinct mismatches-only datasets and significantly outperforms contemporary state-of-the-art models in datasets comprising both mismatches and indels. In summation, the CRISPR-MCA model, coupled with the ESB rebalancing strategy, offers profound insights and a robust framework for future explorations in this field. Author summary: In the field of gene editing, the application of deep learning technologies holds significant promise for predicting off-target effects in the CRISPR-Cas9 system. Nevertheless, one of the primary challenges encountered is the extreme imbalance among classes within the off-target datasets, which severely hampers the predictive accuracy for certain classes. Furthermore, as an array of sequence encoding methods continue to evolve, there has been a corresponding increase in model complexity. Addressing these issues, we introduce a novel Efficiency and Specificity-Based (ESB) class rebalancing strategy designed to mitigate the impact of class imbalance. Additionally, we assess the influence of six encoding schemes and four distinct architectural approaches on the prediction performance, employing four benchmark datasets for validation. Building upon these insights, we have developed a new hybrid model, termed CRISPR-MCA. Our experimental results demonstrate that the ESB strategy significantly surpasses the performance of existing baseline methods across multiple models. Moreover, the CRISPR-MCA model exhibits robust performance on two distinct types of datasets, affirming its effectiveness in enhancing the accuracy of deep learning predictions for off-target activities. [ABSTRACT FROM AUTHOR]

The Remote Sensing Image Change Captioning (RSICC) has recently emerged in the field of remote sensing image interpretation; it aims to automatically predict natural language captions of significant semantic changes in bi-temporal remote sensing images. Recent studies of RSICC have improved the accuracy of change captions of bi-temporal remote sensing images to a large extent. Nevertheless, there still remain challenges in multi-scale perception of ground objects and feature enhancement of bi-temporal remote sensing images. To address these challenges and further improve the accuracy of RSICC, a novel deep learning–based end-to-end scale-wised feature enhancement network (SFEN) is proposed in this paper. SFEN integrates four efficient blocks: 1) the siamese backbone network (SBN) to extract initial features of bi-temporal remote sensing images, 2) the siamese receptive field fusion (SRFF) block to explicitly capture multi-scale semantic information of ground objects in bi-temporal feature maps, 3) the siamese global feature enhancement (SGFE) block to adaptively enhance key information and filtering redundant features of bi-temporal feature maps in both channel and spatial dimensions, 4) the change caption decoder (CCD) to map bi-temporal feature maps into natural language. The SFEN aims to precisely capture significant semantic information of ground objects in bi-temporal remote sensing images and predict accurate change captions. Experimental results on LEVIR-CC dataset demonstrate our SFEN outperforms recent state-of-the-art (SOTA) approach in RSICC by 5.2% on CIDEr-D and achieves a new SOTA. [ABSTRACT FROM AUTHOR]

Acute, high-dose radiation exposure results in life-threatening acute radiation syndrome (ARS) and debilitating delayed effects of acute radiation exposure (DEARE). The DEARE are a set of chronic multi-organ illnesses that can result in early death due to malignancy and other diseases. Animal models have proven essential in understanding the natural history of ARS and DEARE and licensure of medical countermeasures (MCM) according to the FDA Animal Rule. Our lab has developed models of hematopoietic (H)-ARS and DEARE in inbred C57BL/6J and Jackson Diversity Outbred (JDO) mice of both sexes and various ages and have used these models to identify mechanisms of radiation damage and effective MCMs. Herein, aggregate data from studies conducted over decades in our lab, consisting of 3,250 total-body lethally irradiated C57BL/6J young adult mice and 1,188 H-ARS survivors from these studies, along with smaller datasets in C57BL/6J pediatric and geriatric mice and JDO mice, were examined for lifespan and development of thymic lymphoma in survivors up to 3 years of age. Lifespan was found to be significantly shortened in H-ARS survivors compared to age-matched nonirradiated controls in all four models. Males and females exhibited similar lifespans except in the young adult C57BL/ 6J model where males survived longer than females after 16 months of age. The incidence of thymic lymphoma was increased in H-ARS survivors from the young adult and pediatric C57BL/ 6J models. Consistent with our findings in H-ARS, geriatric mice appeared more radioresistant than other models, with a lifespan and thymic lymphoma incidence more similar to nonirradiated controls than other models. Increased levels of multiple pro-inflammatory cytokines in DEARE bone marrow and serum correlated with shortened lifespan and malignancy, consistent with other animal models and human data. Of interest, G-CSF levels in bone marrow and serum 8-11 months after irradiation were significantly increased in females. Importantly, treatment with granulopoietic cytokine MCM for radiomitigation of H-ARS did not influence the long-term survival rate or incidence of thymic lymphoma in any model. Taken together, these findings indicate that the lifespan of H-ARS survivors was significantly decreased regardless of age at time of exposure or genetic diversity, and was unaffected by earlier treatment with granulopoietic cytokines for radiomitigation of H-ARS. [ABSTRACT FROM AUTHOR]

Individual tree detection in urban areas using unmanned air vehicles (UAVs) RGB imagery poses challenges due to the diverse shapes and structures of urban trees and the complexity of urban forests. The digital surface model (DSM) provides elevation data, and the fusion of UAV RGB imagery with elevation data has emerged as a promising approach for tree detection. Here, we constructed a novel network structure based on the faster region-based convolutional neural network (Faster R-CNN) to detect camphor trees in urban environments using RGB-DSM data. First, an attention fusion module was proposed to effectively fuse the RGB and DSM features by leveraging their complementarity. Second, the bidirectional feature pyramid network (BiFPN) was introduced to enhance the model performance in detecting camphor tree crowns of varying sizes. The results showed that our approach could effectively detect urban camphor trees and achieved an AP of 85.7%. Notably, our approach yielded an AP of 81.3% in urban green spaces. The analysis indicated that our approach was feasible for detecting camphor trees in urban areas and demonstrated its potential to facilitate urban forestry research and applications. [ABSTRACT FROM AUTHOR]

Since the 1950s, when the Turing Test was introduced, there has been notable progress in machine language intelligence. Language modeling, crucial for AI development, has evolved from statistical to neural models over the last two decades. Recently, transformer-based Pre-trained Language Models (PLM) have excelled in Natural Language Processing (NLP) tasks by leveraging large-scale training corpora. Increasing the scale of these models enhances performance significantly, introducing abilities like context learning that smaller models lack. The advancement in Large Language Models, exemplified by the development of ChatGPT, has made significant impacts both academically and industrially, capturing widespread societal interest. This survey provides an overview of the development and prospects from Large Language Models (LLM) to Large Multimodal Models (LMM). It first discusses the contributions and technological advancements of LLMs in the field of natural language processing, especially in text generation and language understanding. Then, it turns to the discussion of LMMs, which integrates various data modalities such as text, images, and sound, demonstrating advanced capabilities in understanding and generating cross-modal content, paving new pathways for the adaptability and flexibility of AI systems. Finally, the survey highlights the prospects of LMMs in terms of technological development and application potential, while also pointing out challenges in data integration, cross-modal understanding accuracy, providing a comprehensive perspective on the latest developments in this field. [ABSTRACT FROM AUTHOR]

Stress wave technology is very suitable for detecting internal defects of standing trees, logs, and wood and has gradually become the mainstream technology in this research field. Usually, 12 sensors are positioned equidistantly around the cross-section of tree trunks in order to obtain enough stress wave signals. However, the arrangement of sensors is time-consuming and laborious, and maintaining the accuracy of stress wave imaging under sparse signals is a challenging problem. In this paper, a novel stress wave hybrid imaging method based on compressive sensing and elliptic interpolation is proposed. The spatial structure of the defective area is reconstructed by using the advantages of compressive sensing in sparse signal representation and solution of stress waves, and the healthy area is reconstructed by using the elliptic space interpolation method. Then, feature points are selected and mixed for imaging. The comparative experimental results show that the overall imaging accuracy of the proposed method reaches 89.7%, and the high-quality imaging effect can be guaranteed when the number of sensors is reduced to 10, 8, or even 6. [ABSTRACT FROM AUTHOR]

Tea diseases have an extremely serious impact on tea plantations and related industries. Traditional methods for disease detection in the dynamic and complex tea plantation environment are inefficient and unsatisfactory. This study proposed that a YOLOv7-tiny-based model enhanced the fine-grained detection of tea tree diseases. By integrating CoordConv and ECA channel attention mechanisms, this model achieved higher spatial recognition capability in convolutional feature maps and reduced the effect of background noise on feature recognition. Further improvements included the use of a normalized Wasserstein distance metric and decoupled heads to improve the detection of small spots. A new anchor frame was generated using the K-means algorithm based on the specificity of tea spots to improve the accuracy and generalizability of the model. Comparative analysis shows that the model outperforms the existing models Faster R-CNN, SSD, YOLOv5s, YOLO-Tea, YOLOv7-tiny, and YOLOv7, with an average accuracy improvement of 5.9 percentage points to 93%. The improved model could be applied to tea disease monitoring. [ABSTRACT FROM AUTHOR]