In recent years, large language models (LLMs) such as GPT-4 have demonstrated impressive potential in a wide range of fields, including biology, genomics and healthcare. Numerous studies have attempted to apply pre-trained LLMs to single-cell data analysis within one tissue. However, when it comes to cross-tissue cell annotation, LLMs often suffer from unsatisfactory performance due to the lack of specialized biological knowledge regarding genes and tissues. In this paper, we introduce scRAG, a novel framework that incorporates advanced LLM-based RAG techniques into cross-tissue single-cell annotation. scRAG utilizes LLMs to retrieve structured triples from knowledge graphs and unstructured similar cell information from the reference cell database, and it generates candidate cell types. The framework further optimizes predictions by retrieving marker genes from both candidate cells and similar cells to refine its results. Extensive experiments on a cross-tissue dataset demonstrate that our scRAG framework outperforms various baselines, including generalist models, domain-specific methods, and trained classifiers. The source code is available at https://github.com/YuZhiyin/scRAG.

Adapting Large Language Models (LLMs) for recommendation requires careful consideration of the decoding process, given the inherent differences between generating items and natural language. Existing approaches often directly apply LLMs’ original decoding methods. However, we find these methods encounter significant challenges: 1) amplification bias—where standard length normalization inflates scores for items containing tokens with generation probabilities close to 1 (termed ghost tokens), and 2) homogeneity issue—generating multiple similar or repetitive items for a user. To tackle these challenges, we introduce a new decoding approach named Debiasing-Diversifying Decoding (D³). D³ disables length normalization for ghost tokens to alleviate amplification bias, and it incorporates a text-free assistant model to encourage tokens less frequently generated by LLMs for counteracting recommendation homogeneity. Extensive experiments on real-world datasets demonstrate the method’s effectiveness in enhancing accuracy and diversity.

Image-text matching has been a long-standing problem, which seeks to connect vision and language through semantic understanding. Due to the capability to manage large-scale raw data, unsupervised hashing-based approaches have gained prominence recently. They typically construct a semantic similarity structure using the natural distance, which subsequently guides the optimization of the hashing network. However, the similarity structure could be biased at the boundaries of semantic distributions, causing error accumulation during sequential optimization. To tackle this, we introduce a novel hashing approach termed Distribution-based Structure Mining with Consistency Learning (DEMO) for efficient image-text matching. From a statistical view, DEMO characterizes each image using multiple augmented views, which are considered as samples drawn from its intrinsic semantic distribution. Then, we employ a non-parametric distribution divergence to ensure a robust and precise similarity structure. In addition, we introduce collaborative consistency learning which not only preserves the similarity structure in the Hamming space but also encourages consistency between retrieval distribution from different directions in a self-supervised manner. Extensive experiments on several widely used datasets demonstrate that DEMO achieves superior performance compared with various state-of-the-art methods.