The accurate identification of active sites in proteins is essential for the advancement of life sciences and pharmaceutical development, as these sites are of critical importance for enzyme activity and drug design. Recent advancements in protein language models (PLMs), trained on extensive datasets of amino acid sequences, have significantly improved our understanding of proteins. However, compared to the abundant protein sequence data, functional annotations, especially precise per-residue annotations, are scarce, which limits the performance of PLMs. On the other hand, textual descriptions of proteins, which could be annotated by human experts or a pretrained protein sequence-to-text model, provide meaningful context that could assist in the functional annotations, such as the localization of active sites. This motivates us to construct a $\textbf{ProT}$ein-$\textbf{A}$ttribute text $\textbf{D}$ataset ($\textbf{ProTAD}$), comprising over 570,000 pairs of protein sequences and multi-attribute textual descriptions.

Recent advances in prompt optimization have notably enhanced the performance of pre-trained language models (PLMs) on downstream tasks. However, the potential of optimized prompts on domain generalization has been under-explored. To explore the nature of prompt generalization on unknown domains, we conduct pilot experiments and find that (i) Prompts gaining more attention weight from PLMs' deep layers are more generalizable and (ii) Prompts with more stable attention distributions in PLMs' deep layers are more generalizable. Thus, we offer a fresh objective towards domain-generalizable prompts optimization named ''Concentration'', which represents the ''lookback'' attention from the current decoding token to the prompt tokens, to increase the attention strength on prompts and reduce the fluctuation of attention distribution.We adapt this new objective to popular soft prompt and hard prompt optimization methods, respectively. Extensive experiments demonstrate that our idea improves comparison prompt optimization methods by 1.42% for soft prompt generalization and 2.16% for hard prompt generalization in accuracy on the multi-source domain generalization setting, while maintaining satisfying in-domain performance. The promising results validate the effectiveness of our proposed prompt optimization objective and provide key insights into domain-generalizable prompts.

In the field of natural language processing, the prevalent approach involves fine-tuning pretrained language models (PLMs) using local samples.

Accurately modeling weather variation pattern from large amount of meteorological variables sequences is increasingly vital for providing efficient weather analysis support for disaster warning.

By analyzing the intrinsic dimension (ID) and neighbor composition, we find that the representations evolve similarly in transformers trained on protein language tasks and image reconstruction tasks.