De novo peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models encode the observed mass spectra into latent representations from which peptides are predicted auto-regressively. However, the issue of missing fragmentation, attributable to factors such as suboptimal fragmentation efficiency and instrumental constraints, presents a formidable challenge in practical applications. To tackle this obstacle, we propose a novel computational paradigm called $\underline{\textbf{L}}$atent $\underline{\textbf{I}}$mputation before $\underline{\textbf{P}}$rediction (LIPNovo). LIPNovo is devised to compensate for missing fragmentation information within observed spectra before executing the final peptide prediction. Rather than generating raw missing data, LIPNovo performs imputation in the latent space, guided by the theoretical peak profile of the target peptide sequence. The imputation process is conceptualized as a set-prediction problem, utilizing a set of learnable peak queries to reason about the relationships among observed peaks and directly generate the latent representations of theoretical peaks through optimal bipartite matching. In this way, LIPNovo manages to supplement missing information during inference and thus boosts performance. Despite its simplicity, experiments on three benchmark datasets demonstrate that LIPNovo outperforms state-of-the-art methods by large margins. Code is available at https://github.com/usr922/LIPNovo.

Vision-language foundation models (VLMs) have shown great potential in feature transfer and generalization across a wide spectrum of medical-related downstream tasks. However, fine-tuning these models is resource-intensive due to their large number of parameters. Prompt tuning has emerged as a viable solution to mitigate memory usage and reduce training time while maintaining competitive performance. Nevertheless, the challenge is that existing prompt tuning methods cannot precisely distinguish different kinds of medical concepts, which miss essentially specific disease-related features across various medical imaging modalities in medical image classification tasks. We find that Large Language Models (LLMs), trained on extensive text corpora, are particularly adept at providing this specialized medical knowledge. Motivated by this, we propose incorporating LLMs into the prompt tuning process. Specifically, we introduce the CILMP, Conditional Intervention of Large Language Models for Prompt Tuning, a method that bridges LLMs and VLMs to facilitate the transfer of medical knowledge into VLM prompts. CILMP extracts disease-specific representations from LLMs, intervenes within a low-rank linear subspace and utilizes them to create disease-specific prompts. Additionally, a conditional mechanism is incorporated to condition the intervention process on each individual medical image, generating instance-adaptive prompts and thus enhancing adaptability. Extensive experiments across diverse medical image datasets demonstrate that CILMP consistently outperforms state-of-the-art prompt tuning methods, demonstrating its effectiveness. Code is available at https://usr922.github.io/cilmp.