MolGround: A Benchmark for Molecular Grounding

Current molecular understanding approaches predominantly focus on the descriptive aspect of human perception, providing broad, topic-level insights. However, the referential aspect -- linking molecular concepts to specific structural components -- remains largely unexplored. To address this gap, we propose a molecular grounding benchmark designed to evaluate a model's referential abilities. We align molecular grounding with established conventions in NLP, cheminformatics, and molecular science, showcasing the potential of NLP techniques to advance molecular understanding within the AI for Science movement. Furthermore, we constructed the largest molecular understanding benchmark to date, comprising 79k QA pairs, and developed a multi-agent grounding prototype as proof of concept. This system outperforms existing models, including GPT-4o, and its grounding outputs have been integrated to enhance traditional tasks such as molecular captioning and ATC (Anatomical, Therapeutic, Chemical) classification.

Multi-Level Querying using A Knowledge Pyramid

This paper addresses the need for improved precision in existing Retrieval-Augmented Generation (RAG) methods that primarily focus on enhancing recall. We propose a multi-layer knowledge pyramid approach within the RAG framework to achieve a better balance between precision and recall. The knowledge pyramid consists of three layers: Ontologies, Knowledge Graphs (KGs), and chunk-based raw text. We employ cross-layer augmentation techniques for comprehensive knowledge coverage and dynamic updates of the Ontology schema and instances. To ensure compactness, we utilize cross-layer filtering methods for knowledge condensation in KGs. Our approach, named PolyRAG, follows a waterfall model for retrieval, starting from the top of the pyramid and progressing down until a confident answer is obtained. We introduce two benchmarks for domain-specific knowledge retrieval, one in the academic domain and the other in the financial domain. The effectiveness of the methods has been validated through comprehensive experiments by outperforming 19 SOTA methods. An encouraging observation is that the proposed method has augmented the GPT-4, providing 395\% F1 gain by improving its performance from 0.1636 to 0.8109.