We propose ProtLLM, a versatile cross-modal large language model (LLM) for both protein-centric and protein-language tasks. ProtLLM features a unique dynamic protein mounting mechanism, enabling it to handle complex inputs where the natural language text is interspersed with an arbitrary number of proteins. Besides, we propose the protein-as-word language modeling approach to train ProtLLM. By developing a specialized protein vocabulary, we equip the model with the capability to predict not just natural language but also proteins from a vast pool of candidates. Additionally, we construct a large-scale interleaved protein-text dataset, named InterPT, for pre-training. This dataset comprehensively encompasses both (1) structured data sources like protein annotations and (2) unstructured data sources like biological research papers, thereby endowing ProtLLM with crucial knowledge for understanding proteins. We evaluate ProtLLM on classic supervised protein-centric tasks and explore its novel protein-language applications. Experimental results demonstrate that ProtLLM not only achieves superior performance against protein-specialized baselines on protein-centric tasks but also induces zero-shot and in-context learning capabilities on protein-language tasks.

We introduce CHARM, the first benchmark for comprehensively and in-depth evaluating the commonsense reasoning ability of large language models (LLMs) in Chinese, which covers both globally known and Chinese-specific commonsense. We evaluated 7 English and 12 Chinese-oriented LLMs on CHARM, employing 5 representative prompt strategies for improving LLMs’ reasoning ability, such as Chain-of-Thought. Our findings indicated that the LLM’s language orientation and the task’s domain influence the effectiveness of the prompt strategy, which enriches previous research findings. We built closely-interconnected reasoning and memorization tasks, and found that some LLMs struggle with memorizing Chinese commonsense, affecting their reasoning ability, while others show differences in reasoning despite similar memorization performance. We also evaluated the LLMs’ memorization-independent reasoning abilities and analyzed the typical errors. Our study precisely identified the LLMs’ strengths and weaknesses, providing the clear direction for optimization. It can also serve as a reference for studies in other fields. We will release CHARM at https://github.com/opendatalab/CHARM.