Yankai Yu

Jiajia Liu, Mengyuan Yang, Yankai Yu et al.

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.

Zhuyang Xie, Yan Yang, Yankai Yu et al.

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.