npj Digital Medicine, Published online: 18 November 2025; doi:10.1038/s41746-025-02066-3

Reply to: Utilizing foundation models for developing clinical tools

arXiv:2410.21348v3 Announce Type: replace-cross Abstract: With the increasing application of large language models (LLMs) in the medical domain, evaluating these models' performance using benchmark datasets has become crucial. This paper presents a comprehensive survey of various benchmark datasets employed in medical LLM tasks. These datasets span multiple modalities including text, image, and multimodal benchmarks, focusing on different aspects of medical knowledge such as electronic health records (EHRs), doctor-patient dialogues, medical question-answering, and medical image captioning. The survey categorizes the datasets by modality, discussing their significance, data structure, and impact on the development of LLMs for clinical tasks such as diagnosis, report generation, and predictive decision support. Key benchmarks include MIMIC-III, MIMIC-IV, BioASQ, PubMedQA, and CheXpert, which have facilitated advancements in tasks like medical report generation, clinical summarization, and synthetic data generation. The paper summarizes the challenges and opportunities in leveraging these benchmarks for advancing multimodal medical intelligence, emphasizing the need for datasets with a greater degree of language diversity, structured omics data, and innovative approaches to synthesis. This work also provides a foundation for future research in the application of LLMs in medicine, contributing to the evolving field of medical artificial intelligence.

arXiv:2511.05385v1 Announce Type: cross Abstract: Retrieval-Augmented Generation (RAG) utilizes external knowledge to augment Large Language Models' (LLMs) reliability. For flexibility, agentic RAG employs autonomous, multi-round retrieval and reasoning to resolve queries. Although recent agentic RAG has improved via reinforcement learning, they often incur substantial token overhead from search and reasoning processes. This trade-off prioritizes accuracy over efficiency. To address this issue, this work proposes TeaRAG, a token-efficient agentic RAG framework capable of compressing both retrieval content and reasoning steps. 1) First, the retrieved content is compressed by augmenting chunk-based semantic retrieval with a graph retrieval using concise triplets. A knowledge association graph is then built from semantic similarity and co-occurrence. Finally, Personalized PageRank is leveraged to highlight key knowledge within this graph, reducing the number of tokens per retrieval. 2) Besides, to reduce reasoning steps, Iterative Process-aware Direct Preference Optimization (IP-DPO) is proposed. Specifically, our reward function evaluates the knowledge sufficiency by a knowledge matching mechanism, while penalizing excessive reasoning steps. This design can produce high-quality preference-pair datasets, supporting iterative DPO to improve reasoning conciseness. Across six datasets, TeaRAG improves the average Exact Match by 4% and 2% while reducing output tokens by 61% and 59% on Llama3-8B-Instruct and Qwen2.5-14B-Instruct, respectively. Code is available at https://github.com/Applied-Machine-Learning-Lab/TeaRAG.

arXiv:2412.16378v4 Announce Type: replace-cross Abstract: To mitigate reward hacking from response verbosity, modern preference optimization methods are increasingly adopting length normalization (e.g., SimPO, ORPO, LN-DPO). While effective against this bias, we demonstrate that length normalization itself introduces a failure mode: the URSLA shortcut. Here models learn to satisfy the alignment objective by prematurely truncating low-quality responses rather than learning from their semantic content. To address this, we introduce REFA, a new alignment framework that proposes probabilistic control on a structural token that controls termination. Our core innovation is a new class of regularizers that operate directly on the probability of the End-of-Sequence (EOS) token, a previously unexploited control lever. This token-level intervention provides a principled solution to the URSLA shortcut, ensuring genuine quality improvements. Furthermore, it unlocks a versatile mechanism for managing the alignment-efficiency tradeoff, enabling practitioners to fine-tune models that adhere to specific token budgets. Empirically, REFA achieves a 60.29% win rate and a 52.17% length-controlled win rate on AlpacaEval2 with Llama-3-8B-Instruct, demonstrating the power of our token-level control paradigm.

arXiv:2510.21031v1 Announce Type: cross Abstract: The emergence of foundation models (FMs) has enabled the development of highly capable and autonomous agents, unlocking new application opportunities across a wide range of domains. Evaluating the architecture of agents is particularly important as the architectural decisions significantly impact the quality attributes of agents given their unique characteristics, including compound architecture, autonomous and non-deterministic behaviour, and continuous evolution. However, these traditional methods fall short in addressing the evaluation needs of agent architecture due to the unique characteristics of these agents. Therefore, in this paper, we present AgentArcEval, a novel agent architecture evaluation method designed specially to address the complexities of FM-based agent architecture and its evaluation. Moreover, we present a catalogue of agent-specific general scenarios, which serves as a guide for generating concrete scenarios to design and evaluate the agent architecture. We demonstrate the usefulness of AgentArcEval and the catalogue through a case study on the architecture evaluation of a real-world tax copilot, named Luna.

Oncogene, Published online: 01 March 2025; doi:10.1038/s41388-025-03322-2

Preclinical application of a CD155 targeting chimeric antigen receptor T cell therapy for digestive system cancers

A multiscale drug discovery platform integrating human induced pluripotent stem cells, 3D-engineered heart tissues, and animal models identifies artesunate as a safe and potent antifibrotic compound.

Nature, Published online: 08 May 2024; doi:10.1038/s41586-024-07370-8

Enhanced light–molecule interactions in high-finesse fibre-based Fabry–Pérot microcavities are used to detect and profile individual unlabelled solution-phase biomolecules, leading to potential applications in the life and chemical sciences.

Nature, Published online: 12 July 2023; doi:10.1038/s41586-023-06327-7

Retrotransposons hijack the alternative end-joining DNA repair process of the host for a circularization step to synthesize their second-strand DNA.