Mengyuan Yang

Yidan Sun, Mengying Zhu, Feiyue Chen et al.

Large language models (LLMs) have demonstrated impressive performance in text generation tasks; however, their embedding spaces often suffer from the isotropy problem, resulting in poor discrimination of domain-specific terminology, particularly in legal and financial contexts. This weakness in terminology-level representation can severely hinder downstream tasks such as legal judgment prediction or financial risk analysis, where subtle semantic distinctions are critical. To address this problem, we propose TermGPT, a multi-level contrastive fine-tuning framework designed for terminology adaptation. We first construct a sentence graph to capture semantic and structural relations, and generate semantically consistent yet discriminative positive and negative samples based on contextual and topological cues. We then devise a multi-level contrastive learning approach at both the sentence and token levels, enhancing global contextual understanding and fine-grained terminology discrimination. To support robust evaluation, we construct the first financial terminology dataset derived from official regulatory documents. Experiments show that TermGPT outperforms existing baselines in term discrimination tasks within the finance and legal domains.

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.