nature

r0:21222df107462b80fde54a74d060bc7e

When silence is safer: a review and decision-theoretic framework for LLM abstention in healthcare

Large language models (LLMs) are designed to generate answers to user prompts, which often drives them to respond even when uncertainty is high, information is incomplete, or a refusal would be more appropriate. In healthcare, this tendency can be dangerous: confidently stated but inaccurate medical advice can cause significant harm, making the ability to abstain especially important. In this paper, we review studies investigating LLM abstention behaviors in healthcare. The literature highlights two main motivations: (1) uncertainty-driven abstention, where the model withholds a response when confidence is low, and (2) safety-driven abstention, where the model declines to provide potentially harmful information. Most existing mechanisms are extrinsic and rely on auxiliary tools to determine when to abstain. We find that state-of-the-art LLMs still struggle to refuse inappropriate prompts, and that few benchmarks evaluate abstention in realistic medical scenarios, where performance lags behind other domains. Building on these findings, we introduce a decision-theoretic formalization of abstention that models the trade-off between answering and withholding responses under uncertainty and potential harm. Based on this formulation, we present MedSAFE, a framework for evaluating abstention in clinical dialogs, and demonstrate its operationalization through a proof-of-concept pilot across clinical scenarios derived from the review.

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r0:e8a2060e33594781594577f87d876bb1

Advancing regulatory variant effect prediction with AlphaGenome

Deep learning models that predict functional genomic measurements from DNA sequences are powerful tools for deciphering the genetic regulatory code. Existing methods involve a trade-off between input sequence length and prediction resolution, thereby limiting their modality scope and performance1,2,3,4,5. We present AlphaGenome, a unified DNA sequence model, which takes as input 1 Mb of DNA sequence and predicts thousands of functional genomic tracks up to single-base-pair resolution across diverse modalities. The modalities include gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chromatin contact maps, splice site usage and splice junction coordinates and strength. Trained on human and mouse genomes, AlphaGenome matches or exceeds the strongest available external models in 25 of 26 evaluations of variant effect prediction. The ability of AlphaGenome to simultaneously score variant effects across all modalities accurately recapitulates the mechanisms of clinically relevant variants near the TAL1 oncogene6. To facilitate broader use, we provide tools for making genome track and variant effect predictions from sequence.

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