Zhonghang Yuan, Zhefan Wang, Fang Hu, Zihong Chen, Jinzhe Li, Gang Li, Jie Ying, Huanjun Kong, Songyang Zhang, Nanqing Dong. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Jie Ying, Zihong Chen, Zhefan Wang, Wanli Jiang, Chenyang Wang, Zhonghang Yuan, Haoyang Su, Huanjun Kong, Fan Yang, Nanqing Dong. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Protein sequence not only determines its structure but also provides important clues of its subcellular localization. Although a series of artificial intelligence models have been reported to predict protein subcellular localization, most of them provide only textual outputs. Here, we present deepGPS, a deep generative model for protein subcellular localization prediction. After training with protein primary sequences and fluorescence images, deepGPS shows the ability to predict cytoplasmic and nuclear localizations by reporting both textual labels and generative images as outputs. In addition, cell-type-specific deepGPS models can be developed by using distinct image datasets from different cell lines for comparative analyses. Moreover, deepGPS shows potential to be further extended for other specific organelles, such as vesicles and endoplasmic reticulum, even with limited volumes of training data. Finally, the openGPS website (https://bits.fudan.edu.cn/opengps) is constructed to provide a publicly accessible and user-friendly platform for studying protein subcellular localization and function.

Large language models (LLMs) have demonstrated remarkable efficacy across knowledge-intensive tasks. Nevertheless, their untapped potential in crop science presents an opportunity for advancement. To narrow this gap, we introduce CROP, which includes a novel instruction tuning dataset specifically designed to enhance LLMs’ professional capabilities in the crop science sector, along with a benchmark that serves as a comprehensive evaluation of LLMs’ understanding of the domain knowledge. The CROP dataset is curated through a task-oriented and LLM-human integrated pipeline, comprising 210,038 single-turn and 1,871 multi-turn dialogues related to crop science scenarios. The CROP benchmark includes 5,045 multiple-choice questions covering three difficulty levels. Our experiments based on the CROP benchmark demonstrate notable enhancements in crop science-related tasks when LLMs are fine-tuned with the CROP dataset. To the best of our knowledge, CROP dataset is the first-ever instruction tuning dataset in the crop science domain. We anticipate that CROP will accelerate the adoption of LLMs in the domain of crop science, ultimately contributing to global food production.