BiCA: Effective Biomedical Dense Retrieval with Citation-Aware Hard Negatives

Hard negatives are essential for training effective retrieval models. Hard-negative mining typically relies on ranking documents using cross-encoders or static embedding models based on similarity metrics such as cosine distance. Hard negative mining becomes challenging for biomedical and scientific domains due to the difficulty in distinguishing between source and hard negative documents. However, referenced documents naturally share contextual relevance with the source document but are not duplicates, making them well-suited as hard negatives. In this work, we propose BiCA: Biomedical Dense Retrieval with Citation-Aware Hard Negatives, an approach for hard-negative mining by utilizing citation links in 20,000 PubMed articles for improving a domain-specific small dense retriever. We fine-tune the GTE_small and GTE_Base models using these citation-informed negatives and observe consistent improvements in zero-shot dense retrieval using nDCG@10 for both in-domain and out-of-domain tasks on BEIR and outperform baselines on long-tailed topics in LoTTE using Success@5. Our findings highlight the potential of leveraging document link structure to generate highly informative negatives, enabling state-of-the-art performance with minimal fine-tuning and demonstrating a path towards highly data-efficient domain adaptation.

Functional Groups are All you Need for Chemically Interpretable Molecular Property Prediction

Molecular property prediction using deep learning (DL) models has accelerated drug and materials discovery, but the resulting DL models often lack interpretability, hindering their adoption by chemists. This work proposes developing molecule representations using the concept of Functional Groups (FG) in chemistry. We introduce the Functional Group Representation (FGR) framework, a novel approach to encoding molecules based on their fundamental chemical substructures. Our method integrates two types of functional groups: those curated from established chemical knowledge (FG), and those mined from a large molecular corpus using sequential pattern mining (MFG). The resulting FGR framework encodes molecules into a lower-dimensional latent space by leveraging pre-training on a large dataset of unlabeled molecules. Furthermore, the proposed framework allows the inclusion of 2D structure-based descriptors of molecules. We demonstrate that the FGR framework achieves state-of-the-art performance on a diverse range of 33 benchmark datasets spanning physical chemistry, biophysics, quantum mechanics, biological activity, and pharmacokinetics while enabling chemical interpretability. Crucially, the model's representations are intrinsically aligned with established chemical principles, allowing chemists to directly link predicted properties to specific functional groups and facilitating novel insights into structure-property relationships. Our work presents a significant step toward developing high-performing, chemically interpretable DL models for molecular discovery.