Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

Answering logical queries on knowledge graphs (KG) poses a significant challenge for machine reasoning. The primary obstacle in this task stems from the inherent incompleteness of KGs. Existing research has predominantly focused on addressing the issue of missing edges in KGs, thereby neglecting another aspect of incompleteness: the emergence of new entities. Furthermore, most of the existing methods tend to reason over each logical operator separately, rather than comprehensively analyzing the query as a whole during the reasoning process. In this paper, we propose a query-aware prompt-fused framework named Pro-QE, which could incorporate existing query embedding methods and address the embedding of emerging entities through contextual information aggregation. Additionally, a query prompt, which is generated by encoding the symbolic query, is introduced to gather information relevant to the query from a holistic perspective. To evaluate the efficacy of our model in the inductive setting, we introduce two new challenging benchmarks. Experimental results demonstrate that our model successfully handles the issue of unseen entities in logical queries. Furthermore, the ablation study confirms the efficacy of the aggregator and prompt components.

Rule mining is an effective approach for reasoning over knowledge graph (KG). Existing works mainly concentrate on mining rules. However, there might be several rules that could be applied for reasoning for one relation, and how to select appropriate rules for completion of different triples has not been discussed. In this paper, we propose to take the context information into consideration, which helps select suitable rules for the inference tasks. Based on this idea, we propose a transformer-based rule mining approach, Ruleformer. It consists of two blocks: 1) an encoder extracting the context information from subgraph of head entities with modified attention mechanism, and 2) a decoder which aggregates the subgraph information from the encoder output and generates the probability of relations for each step of reasoning. The basic idea behind Ruleformer is regarding rule mining process as a sequence to sequence task. To make the subgraph a sequence input to the encoder and retain the graph structure, we devise a relational attention mechanism in Transformer. The experiment results show the necessity of considering these information in rule mining task and the effectiveness of our model.