arXiv subjects

Yankai Yu

Publications and source records attributed to Yankai Yu.

3 recordsLinked to original sources

arXiv2025

A Multi-Layered Framework for Modeling Human Biology: From Basic AI Agents to a Full-Body AI Agent

We envision the Full-Body AI Agent as a comprehensive AI system designed to simulate, analyze, and optimize the dynamic processes of the human body across multiple biological levels. By integrating computational models, machine learning tools, and experimental platforms, this system aims to replicate and predict both physiological and pathological processes, ranging from molecules and cells to tissues, organs, and entire body systems. Central to the Full-Body AI Agent is its emphasis on integration and coordination across these biological levels, enabling analysis of how molecular changes influence cellular behaviors, tissue responses, organ function, and systemic outcomes. With a focus on biological functionality, the system is designed to advance the understanding of disease mechanisms, support the development of therapeutic interventions, and enhance personalized medicine. We propose two specialized implementations to demonstrate the utility of this framework: (1) the metastasis AI Agent, a multi-scale metastasis scoring system that characterizes tumor progression across the initiation, dissemination, and colonization phases by integrating molecular, cellular, and systemic signals; and (2) the drug AI Agent, a system-level drug development paradigm in which a drug AI-Agent dynamically guides preclinical evaluations, including organoids and chip-based models, by providing full-body physiological constraints. This approach enables the predictive modeling of long-term efficacy and toxicity beyond what localized models alone can achieve. These two agents illustrate the potential of Full-Body AI Agent to address complex biomedical challenges through multi-level integration and cross-scale reasoning.

q-bio.TO↗

arXiv2024

Exploring Temporal Event Cues for Dense Video Captioning in Cyclic Co-learning

Dense video captioning aims to detect and describe all events in untrimmed videos. This paper presents a dense video captioning network called Multi-Concept Cyclic Learning (MCCL), which aims to: (1) detect multiple concepts at the frame level, using these concepts to enhance video features and provide temporal event cues; and (2) design cyclic co-learning between the generator and the localizer within the captioning network to promote semantic perception and event localization. Specifically, we perform weakly supervised concept detection for each frame, and the detected concept embeddings are integrated into the video features to provide event cues. Additionally, video-level concept contrastive learning is introduced to obtain more discriminative concept embeddings. In the captioning network, we establish a cyclic co-learning strategy where the generator guides the localizer for event localization through semantic matching, while the localizer enhances the generator's event semantic perception through location matching, making semantic perception and event localization mutually beneficial. MCCL achieves state-of-the-art performance on the ActivityNet Captions and YouCook2 datasets. Extensive experiments demonstrate its effectiveness and interpretability.

cs.CV↗

arXiv2024

Advancing bioinformatics with large language models: components, applications and perspectives

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of artificial neural networks with numerous parameters, trained on large amounts of unlabeled input using self-supervised or semi-supervised learning. However, their potential for solving bioinformatics problems may even exceed their proficiency in modeling human language. In this review, we will provide a comprehensive overview of the essential components of large language models (LLMs) in bioinformatics, spanning genomics, transcriptomics, proteomics, drug discovery, and single-cell analysis. Key aspects covered include tokenization methods for diverse data types, the architecture of transformer models, the core attention mechanism, and the pre-training processes underlying these models. Additionally, we will introduce currently available foundation models and highlight their downstream applications across various bioinformatics domains. Finally, drawing from our experience, we will offer practical guidance for both LLM users and developers, emphasizing strategies to optimize their use and foster further innovation in the field.

q-bio.QM↗