Messenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboDecode, a deep learning framework that generates mRNA codon sequences for enhanced mRNA translation. RiboDecode introduces several advances, including direct learning from large-scale ribosome profiling data and generative exploration of a large sequence space. In silico analysis demonstrates RiboDecode’s robust predictive accuracy for unseen genes and cellular environments. In vitro experiments showed substantial improvements in protein expression, significantly outperforming past methods. In addition, RiboDecode enables mRNA design with consideration of cellular context and demonstrates robust performance across different mRNA formats, including m¹Ψ-modified and circular mRNAs, an important feature for mRNA therapeutics. In vivo mouse studies showed that optimized influenza hemagglutinin mRNAs induce ten times stronger neutralizing antibody responses against influenza virus compared to the unoptimized sequence. In an optic nerve crush model, optimized nerve growth factor mRNAs achieve equivalent neuroprotection of retinal ganglion cells at one-fifth the dose of the unoptimized sequence. Collectively, RiboDecode represents a paradigm shift from rule-based to a data-driven, context-aware approach for mRNA therapeutic applications, enabling the development of more potent and dose-efficient treatments.

Messenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboDecode, a deep learning framework that generates mRNA codon sequences for enhanced mRNA translation. RiboDecode introduces several advances, including direct learning from large-scale ribosome profiling data and generative exploration of a large sequence space. In silico analysis demonstrates RiboDecode’ s robust predictive accuracy for unseen genes and cellular environments. In vitro experiments showed substantial improvements in protein expression, significantly outperforming past methods. In addition, RiboDecode enables mRNA design with consideration of cellular context and demonstrates robust performance across different mRNA formats, including m ¹ Ψ-modified and circular mRNAs, an important feature for mRNA therapeutics. In vivo mouse studies showed that optimized influenza hemagglutinin mRNAs induce ten times stronger neutralizing antibody responses against influenza virus compared to the unoptimized sequence. In an optic nerve crush model, optimized nerve growth factor mRNAs achieve equivalent neuroprotection of retinal ganglion cells at one-fifth the dose of the unoptimized sequence. Collectively, RiboDecode represents a paradigm shift from rule-based to a data-driven, context-aware approach for mRNA therapeutic applications, enabling the development of more potent and dose-efficient treatments.

Accurate evaluation of retinopathy of prematurity (ROP) severity is vital for screening and proper treatment. Current deep-learning-based automated AI systems for assessing ROP severity do not follow clinical guidelines and are opaque. The aim of this study is to develop an interpretable AI system by mimicking the clinical screening process to determine ROP severity level. A total of 6100 RetCam Ⅲ wide-field digital retinal images were collected from Guangdong Women and Children Hospital at Panyu (PY) and Zhongshan Ophthalmic Center (ZOC). A total of 3330 images of 520 pediatric patients from PY were annotated to train an object detection model to detect lesion type and location. A total of 2770 images of 81 pediatric patients from ZOC were annotated for stage, zone, and the presence of plus disease. Integrating stage, zone, and the presence of plus disease according to clinical guidelines yields ROP severity such that an interpretable AI system was developed to provide the stage from the lesion type, the zone from the lesion location, and the presence of plus disease from a plus disease classification model. The ROP severity was calculated accordingly and compared with the assessment of a human expert. Our method achieved an area under the curve (AUC) of 0.95 (95% confidence interval [CI] 0.90–0.98) in assessing the severity level of ROP. Compared with clinical doctors, our method achieved the highest F1 score value of 0.76 in assessing the severity level of ROP. In conclusion, we developed an interpretable AI system for assessing the severity level of ROP that shows significant potential for use in clinical practice for ROP severity level screening.

Precise medical image segmentation of regions of interest (ROIs) is crucial for accurate disease diagnosis and progression assessment. However, acquiring high-quality annotated data at the pixel level poses a significant challenge due to the resource-intensive nature of this process. This scarcity of high-quality annotated data results in few-shot scenarios, which are highly prevalent in clinical applications. To address this obstacle, this paper introduces Agent-Guided SAM (AGSAM), an innovative approach that transforms the Segment Anything Model (SAM) into a fully automated segmentation method by automating prompt generation. Capitalizing on the pre-trained feature extraction and decoding capabilities of SAM-Med2D, AGSAM circumvents the need for manual prompt engineering, ensuring adaptability across diverse segmentation methods. Furthermore, the proposed feature augmentation convolution module (FACM) enhances model accuracy by promoting stable feature representations. Experimental evaluations demonstrate AGSAM’s consistent superiority over other methods across various metrics. These findings highlight AGSAM’s efficacy in tackling the challenges associated with limited annotated data while achieving high-quality medical image segmentation.