Medical open-domain question answering demands substantial access to specialized knowledge. Recent efforts have sought to decouple knowledge from model parameters, counteracting architectural scaling and allowing for training on common low-resource hardware. The retrieve-then-read paradigm has become ubiquitous, with model predictions grounded on relevant knowledge pieces from external repositories such as PubMed, textbooks, and UMLS. An alternative path, still under-explored but made possible by the advent of domain-specific large language models, entails constructing artificial contexts through prompting. As a result, “to generate or to retrieve” is the modern equivalent of Hamlet’s dilemma. This paper presents MedGENIE, the first generate-then-read framework for multiple-choice question answering in medicine. We conduct extensive experiments on MedQA-USMLE, MedMCQA, and MMLU, incorporating a practical perspective by assuming a maximum of 24GB VRAM. MedGENIE sets a new state-of-the-art in the open-book setting of each testbed, allowing a small-scale reader to outcompete zero-shot closed-book 175B baselines while using up to 706x fewer parameters. Our findings reveal that generated passages are more effective than retrieved ones in attaining higher accuracy.

The latest batch of research has equipped language models with the ability to attend over relevant and factual information from non-parametric external sources, drawing a complementary path to architectural scaling. Besides mastering language, exploiting and contextualizing the latent world knowledge is crucial in complex domains like biomedicine. However, most works in the field rely on general-purpose models supported by databases like Wikipedia and Books. We introduce BioReader, the first retrieval-enhanced text-to-text model for biomedical natural language processing. Our domain-specific T5-based solution augments the input prompt by fetching and assembling relevant scientific literature chunks from a neural database with ≈60 million tokens centered on PubMed. We fine-tune and evaluate BioReader on a broad array of downstream tasks, significantly outperforming several state-of-the-art methods despite using up to 3x fewer parameters. In tandem with extensive ablation studies, we show that domain knowledge can be easily altered or supplemented to make the model generate correct predictions bypassing the retraining step and thus addressing the literature overload issue.

Biomedical events represent complex, graphical, and semantically rich interactions expressed in the scientific literature. Almost all contributions in the event realm orbit around semantic parsing, usually employing discriminative architectures and cumbersome multi-step pipelines limited to a small number of target interaction types. We present the first lightweight framework to solve both event extraction and event verbalization with a unified text-to-text approach, allowing us to fuse all the resources so far designed for different tasks. To this end, we present a new event graph linearization technique and release highly comprehensive event-text paired datasets, covering more than 150 event types from multiple biology subareas (English language). By streamlining parsing and generation to translations, we propose baseline transformer model results according to multiple biomedical text mining benchmarks and NLG metrics. Our extractive models achieve greater state-of-the-art performance than single-task competitors and show promising capabilities for the controlled generation of coherent natural language utterances from structured data.