Biomedical Named Entity Recognition (BioNER) faces significant challenges in real-world applications due to limited annotated data and the constant emergence of new entity types, making zero-shot learning capabilities crucial. While Large Language Models (LLMs) possess extensive domain knowledge necessary for specialized fields like biomedicine, their computational costs often make them impractical. To address these challenges, we introduce OpenBioNER, a lightweight BERT-based cross-encoder architecture that can identify any biomedical entity using only its description, eliminating the need for retraining on new, unseen entity types. Through comprehensive evaluation on established biomedical benchmarks, we demonstrate that OpenBioNER surpasses state-of-the-art baselines, including specialized 7B NER LLMs and GPT-4o, achieving up to 10% higher F1 scores while using 110M parameters only. Moreover, OpenBioNER outperforms existing small-scale models that match textual spans with entity types rather than descriptions, both in terms of accuracy and computational efficiency.

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.