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Biomedical knowledge graphs (KGs) encode rich, structured information critical for drug discovery tasks, but extracting meaningful insights from large-scale KGs remains challenging due to their complex structure. Existing biomedical subgraph retrieval methods are tailored for graph neural networks (GNNs), limiting compatibility with other paradigms, including large language models (LLMs). We introduce K-Paths, a model-agnostic retrieval framework that extracts structured, diverse, and biologically meaningful multi-hop paths from dense biomedical KGs. These paths enable prediction of unobserved drug-drug and drug-disease interactions, including those involving entities not seen during training, thus supporting inductive reasoning. K-Paths is training-free and employs a diversity-aware adaptation of Yen's algorithm to extract the K shortest loopless paths between entities in a query, prioritizing biologically relevant and relationally diverse connections. These paths serve as concise, interpretable reasoning chains that can be directly integrated with LLMs or GNNs to improve generalization, accuracy, and enable explainable inference. Experiments on benchmark datasets show that K-Paths improves zero-shot reasoning across state-of-the-art LLMs. For instance, Tx-Gemma 27B improves by 19.8 and 4.0 F1 points on interaction severity prediction and drug repurposing tasks, respectively. Llama 70B achieves gains of 8.5 and 6.2 points on the same tasks. K-Paths also boosts the training efficiency of EmerGNN, a state-of-the-art GNN, by reducing the KG size by 90% while maintaining predictive performance. Beyond efficiency, K-Paths bridges the gap between KGs and LLMs, enabling scalable and explainable LLM-augmented scientific discovery. We release our code and the retrieved paths as a benchmark for inductive reasoning. 

Large-scale neural network models combining text and images have made incredible progress in recent years. However, it remains an open question to what extent such models encode compositional representations of the concepts over which they operate, such as correctly identifying red cube by reasoning over the constituents red and cube. In this work, we focus on the ability of a large pretrained vision and language model (CLIP) to encode compositional concepts and to bind variables in a structure-sensitive way (e.g., differentiating cube behind sphere from sphere behind cube). To inspect the performance of CLIP, we compare several architectures from research on compositional distributional semantics models (CDSMs), a line of research that attempts to implement traditional compositional linguistic structures within embedding spaces. We benchmark them on three synthetic datasets– singleobject, two-object, and relational– designed to test concept binding. We find that CLIP can compose concepts in a single-object setting, but in situations where concept binding is needed, performance drops dramatically. At the same time, CDSMs also perform poorly, with best performance at chance level.