DNA-encoded library (DEL) screening has revolutionized protein-ligand binding detection, enabling rapid exploration of vast chemical spaces through read count analysis. However, two critical challenges limit its effectiveness: distribution noise in low copy number regimes and systematic shifts between read counts and true binding affinities. We present DEL-Ranking, a comprehensive framework that simultaneously addresses both challenges through innovative rankingbased denoising and activity-referenced correction. Our approach introduces a dual-perspective ranking strategy combining Pair-wise Soft Rank (PSR) and Listwise Global Rank (LGR) constraints to preserve both local and global count relationships. Additionally, we develop an Activity-Referenced Correction (ARC) module that bridges the gap between read counts and binding affinities through iterative refinement and biological consistency enforcement. Another key contribution of this work is the curation and release of three comprehensive DEL datasets that uniquely combine ligand 2D sequences, 3D conformational information, and experimentally validated activity labels. We validate our framework on five diverse DEL datasets and introduce three new comprehensive datasets featuring 2D sequences, 3D structures, and activity labels. DEL-Ranking achieves state-of-the-art performance across multiple correlation metrics and demonstrates strong generalization ability across different protein targets. Importantly, our approach successfully identifies key functional groups associated with binding affinity, providing actionable insights for drug discovery.

Chemical synthesis, which is crucial for advancing material synthesis and drug discovery, impacts various sectors including environmental science and healthcare. The rise of technology in chemistry has generated extensive chemical data, challenging researchers to discern patterns and refine synthesis processes. Artificial intelligence (AI) helps by analyzing data to optimize synthesis and increase yields. However, AI faces challenges in processing literature data due to the unstructured format and diverse writing style of chemical literature. To overcome these difficulties, we introduce an end-to-end AI agent framework capable of high-fidelity extraction from extensive chemical literature. This AI agent employs large language models (LLMs) for prompt generation and iterative optimization. It functions as a chemistry assistant, automating data collection and analysis, thereby saving manpower and enhancing performance. Our framework's efficacy is evaluated using accuracy, recall, and F1 score of reaction condition data, and we compared our method with human experts in terms of content correctness and time efficiency. The proposed approach marks a significant advancement in automating chemical literature extraction and demonstrates the potential for AI to revolutionize data management and utilization in chemistry.

Deep generative models have unlocked another profound realm of human creativity. By capturing and generalizing patterns within data, we have entered the epoch of all-encompassing Artificial Intelligence for General Creativity (AIGC). Notably, diffusion models, recognized as one of the paramount generative models, materialize human ideation into tangible instances across diverse domains, encompassing imagery, text, speech, biology, and healthcare. To provide advanced and comprehensive insights into diffusion, this survey comprehensively elucidates its developmental trajectory and future directions from three distinct angles: the fundamental formulation of diffusion, algorithmic enhancements, and the manifold applications of diffusion. Each layer is meticulously explored to offer a profound comprehension of its evolution. Structured and summarized approaches are presented in https://github.com/chq1155/A-Survey-on-Generative-Diffusion-Model.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Adding to the problem, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset will be released publicly.