Zhenyu Wang

Joongwon Chae, Zhenyu Wang, Ijaz Gul et al.

Recent advancements in protein structure prediction, particularly AlphaFold2, have revolutionized structural biology by achieving near-experimental accuracy ($\text{average RMSD} < 1.5\textÅ$). However, the computational demands of these models (approximately 30 minutes per protein on an RTX 4090) significantly limit their application in high-throughput protein screening. While large language models like ESM (Evolutionary Scale Modeling) have shown promise in extracting structural information directly from protein sequences, rapid assessment of protein structure quality for large-scale analyses remains a major challenge. We introduce pLDDT-Predictor, a high-speed protein screening tool that achieves a $250,000\times$ speedup compared to AlphaFold2 by leveraging pre-trained ESM2 protein embeddings and a Transformer architecture. Our model predicts AlphaFold2's pLDDT (predicted Local Distance Difference Test) scores with a Pearson correlation of 0.7891 and processes proteins in just 0.007 seconds on average. Using a comprehensive dataset of 1.5 million diverse protein sequences (ranging from 50 to 2048 amino acids), we demonstrate that pLDDT-Predictor accurately classifies high-confidence structures (pLDDT $>$ 70) with 91.2\% accuracy and achieves an MSE of 84.8142 compared to AlphaFold2's predictions. The source code and pre-trained models are freely available at https://github.com/jw-chae/pLDDT_Predictor, enabling the research community to perform rapid, large-scale protein structure quality assessments.

Haichao Shi, Peng Li, Bo Wang et al.

Recently it has shown that the policy-gradient methods for reinforcement learning have been utilized to train deep end-to-end systems on natural language processing tasks. What's more, with the complexity of understanding image content and diverse ways of describing image content in natural language, image captioning has been a challenging problem to deal with. To the best of our knowledge, most state-of-the-art methods follow a pattern of sequential model, such as recurrent neural networks (RNN). However, in this paper, we propose a novel architecture for image captioning with deep reinforcement learning to optimize image captioning tasks. We utilize two networks called "policy network" and "value network" to collaboratively generate the captions of images. The experiments are conducted on Microsoft COCO dataset, and the experimental results have verified the effectiveness of the proposed method.