Large language models (LLMs) offer a new paradigm for molecular property prediction (MPP), yet a semantic gap between natural language and molecular representations limits LLMs’ ability to capture structure–activity relationships (SAR). Recent approaches have explored injecting structure-level information into LLMs, primarily modeling associations based on statistical regularities. However, these methods are prone to misinterpreting coincidental associations as general principles, imposing a bottleneck on predictive performance. To tackle the challenges above, we propose MCLE-Mol, an ML–LLM–Rule collaborative framework for MPP. It bridges the semantic gap by injecting ML-derived substructure attribution values into LLMs, utilizing Context-Calibrated Substructure Attribution Rules (CCSAR) to calibrate these attributions under specific chemical contexts to mitigate such misinterpretation. In addition, MCLE-Mol introduces a low-cost continual evolution strategy that updates CCSAR with frozen model parameters to adapt to dynamic chemical spaces. Experiments on multiple benchmark datasets demonstrate that MCLE-Mol outperforms all baselines, successfully resolving the trade-off between predictive performance and interpretability.

Elasticsearch (ES) is a distributed RESTful search engine optimized for large-scale and long-text search scenarios. Recent research on text-to-Query has explored using large language models (LLMs) to convert user query intent to executable code, making it an increasingly popular research topic. To our knowledge, we are the first to introduce the novel semantic parsing task text-to-ES. To bridge the gap between LLM and ES, in detail, we leverage LLMs and employ domain experts to generate ES query bodies, which are Domain-Specific Language (DSL), along with the corresponding post-processing code to support multi-index ES queries. Consequently, we propose the text-to-ES benchmark that consists of two datasets: Large Elasticsearch Dataset (LED), containing 26,207 text-ES pairs derived from a 224.9GB schema-free database, and ElasticSearch (BirdES)with 10,926 pairs sourced from the Bird dataset on a 33.4GB schema-fixed database. Compared with fourteen advanced LLMs and six code-based LLMs, the model we trained outperformed DeepSeek-R1 by 15.64% on the LED dataset, setting a new state-of-the-art, and achieved 78% of DeepSeek-R1’s performance on the BirdES dataset. Additionally, we provide in-depth experimental analyses and suggest future research directions for this task. Our datasets are available at https://huggingface.co/datasets/Barry1915/Text-to-ES.