BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs

Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs

Structured Prediction as Translation between Augmented Natural Languages

We propose a new framework, Translation between Augmented Natural Languages (TANL), to solve many structured prediction language tasks including joint entity and relation extraction, nested named entity recognition, relation classification, semantic role labeling, event extraction, coreference resolution, and dialogue state tracking. Instead of tackling the problem by training task-specific discriminative classifiers, we frame it as a translation task between augmented natural languages, from which the task-relevant information can be easily extracted. Our approach can match or outperform task-specific models on all tasks, and in particular, achieves new state-of-the-art results on joint entity and relation extraction (CoNLL04, ADE, NYT, and ACE2005 datasets), relation classification (FewRel and TACRED), and semantic role labeling (CoNLL-2005 and CoNLL-2012). We accomplish this while using the same architecture and hyperparameters for all tasks and even when training a single model to solve all tasks at the same time (multi-task learning). Finally, we show that our framework can also significantly improve the performance in a low-resource regime, thanks to better use of label semantics