Jia Qu

Cheng Ge, Yi Lu, Jia Qu et al.

De novo peptide sequencing from mass spectrometry data is an important method for protein identification. Recently, various deep learning approaches were applied for de novo peptide sequencing and DeepNovoV2 is one of the represetative models. In this study, we proposed an enhanced model, DePS, which can improve the accuracy of de novo peptide sequencing even with missing signal peaks or large number of noisy peaks in tandem mass spectrometry data. It is showed that, for the same test set of DeepNovoV2, the DePS model achieved excellent results of 74.22%, 74.21% and 41.68% for amino acid recall, amino acid precision and peptide recall respectively. Furthermore, the results suggested that DePS outperforms DeepNovoV2 on the cross species dataset.

Ningyuan Xi, Xiaoyu Wang, Yetao Wu et al.

Current research efforts are focused on enhancing the thinking and reasoning capability of large language model (LLM) by prompting, data-driven emergence and inference-time computation. In this study, we consider stimulating language model's thinking and cognitive abilities from a modular perspective, which mimics the human brain architecture. We select a specific intermediate attention layer with newly implemented language heads. We conduct dual-layer fine-tuning by annotated (query, thought, answer) samples and show that the intermediate layer can also learn to decode fluent and reasonable language tokens. A two-pass inference mechanism is designed to generate thoughts then formal responses. The entire framework is called modularized thinking language model (MeTHanol) which can enhance LLM's cognitive behaviors as indicated by Theory of Mind (ToM) and Vignette-based experiments. Case studies also show that MeTHanol can plan and self-reflect and generate human-like thoughts and answers, even on unseen and open-domain tasks. MeTHanol can also adapt to a personalized prompt and behave as the specified character. Our study holds promise for significant cognitive gains from a modular perspective. Our code, model and data are available at https://bachozean.github.io/methanol-page