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.

Embedding models have shown great power in knowledge graph completion (KGC) task. By learning structural constraints for each training triple, these methods implicitly memorize intrinsic relation rules to infer missing links. However, this paper points out that the multi-hop relation rules are hard to be reliably memorized due to the inherent deficiencies of such implicit memorization strategy, making embedding models underperform in predicting links between distant entity pairs. To alleviate this problem, we present Vertical Learning Paradigm (VLP), which extends embedding models by allowing to explicitly copy target information from related factual triples for more accurate prediction. Rather than solely relying on the implicit memory, VLP directly provides additional cues to improve the generalization ability of embedding models, especially making the distant link prediction significantly easier. Moreover, we also propose a novel relative distance based negative sampling technique (ReD) for more effective optimization. Experiments demonstrate the validity and generality of our proposals on two standard benchmarks. Our code is available at https://github.com/rui9812/VLP.