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Addendum: Resolving data bias improves generalization in binding affinity prediction 附录:解决数据偏差可以提高绑定亲和力预测的泛化
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2026-01-27 DOI: 10.1038/s42256-025-01174-9
David Graber, Peter Stockinger, Fabian Meyer, Siddhartha Mishra, Claus Horn, Rebecca Buller
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引用次数: 0
Multi-agent AI systems need transparency 多智能体人工智能系统需要透明度
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2026-01-27 DOI: 10.1038/s42256-026-01183-2
Agentic artificial intelligence (AI) frameworks are in vogue. However, implementing such systems in scientific research workflows requires clear motivations and explanations, given the risk of wasting computational as well as human resources.
人工智能(AI)框架正在流行。然而,考虑到浪费计算资源和人力资源的风险,在科学研究工作流程中实施这样的系统需要明确的动机和解释。
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引用次数: 0
Modelling drug-induced cellular perturbation responses with a biologically informed dual-branch transformer 模拟药物诱导的细胞扰动响应与生物知情双支路变压器
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2026-01-26 DOI: 10.1038/s42256-025-01165-w
Yue Guo, Hao Zhang, Haitao Hu, Jialu Wu, Ji Cao, Chang-Yu Hsieh, Bo Yang
Systematic mapping of chemical perturbation responses is revolutionizing polypharmacological drug discovery, yet remains constrained by experimental scalability. Here we introduce XPert, a biologically informed dual-branch transformer model designed to model gene-specific perturbation effects and dose–time dynamics. The dual-branch architecture separately encodes pre-perturbation and post-perturbation cellular states, allowing the model to disentangle intrinsic transcriptional patterns from regulatory shifts triggered by perturbations. By leveraging context-aware gene network modelling, XPert overcomes the over-denoising issues inherent in dominant variational-autoencoder-based approaches, achieving 36.7% higher Pearson’s correlation coefficient and 78.2% lower mean square error in cold-cell generalization under single-dose–single-time scenarios. Through extension to multidose–multitime prediction, XPert precisely resolves pharmacodynamic trajectories and uncovers key molecular events underlying the drug effects. To address real-world data scarcity, we apply knowledge transfer from large-scale preclinical screens to clinical contexts, achieving up to 15.04% improvement in patient-specific response predictions. Furthermore, XPert provides mechanistic interpretability, as evidenced by the identification of clinically validated resistance biomarkers. A dual-branch framework that disentangles cell states from drug-induced regulatory shifts to predict transcriptional responses is presented. It captures nonlinear dose–time dynamics and excels in generalizing to unseen cellular contexts.
化学扰动反应的系统映射是革命性的多药理学药物发现,但仍然受到实验可扩展性的限制。在这里,我们介绍了XPert,一个生物学信息的双分支变压器模型,旨在模拟基因特异性扰动效应和剂量-时间动力学。双分支结构分别编码扰动前和扰动后的细胞状态,使该模型能够从扰动引发的调节变化中分离出固有的转录模式。通过利用上下文感知基因网络建模,XPert克服了基于变分自编码器的主流方法固有的过度去噪问题,在单剂量单时间场景下的冷细胞泛化中,Pearson相关系数提高了36.7%,均方误差降低了78.2%。通过扩展到多剂量多时间预测,XPert精确地解决药效学轨迹和揭示药物作用的关键分子事件。为了解决现实世界的数据稀缺问题,我们将大规模临床前筛选的知识转移到临床环境中,在患者特异性反应预测方面实现了高达15.04%的改进。此外,XPert提供了机制可解释性,临床验证的耐药生物标志物的鉴定证明了这一点。提出了一个双分支框架,从药物诱导的调节转变中解开细胞状态,以预测转录反应。它捕获了非线性剂量-时间动力学,并擅长将其推广到不可见的细胞环境。
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引用次数: 0
Proposing and solving olympiad geometry with guided tree search 用引导树搜索提出并求解奥林匹克几何题
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2026-01-26 DOI: 10.1038/s42256-025-01164-x
Chi Zhang, Jiajun Song, Siyu Li, Yitao Liang, Yuxi Ma, Wei Wang, Yixin Zhu, Song-Chun Zhu
Mathematics olympiads are prestigious competitions in which both proposing and solving problems are highly honoured. Building artificial intelligence systems capable of addressing these olympiad-level challenges remains an open frontier in automated reasoning, particularly in geometry due to its unique blend of numerical precision and spatial intuition. Here we show that TongGeometry, a neuro-symbolic system using guided tree search, both discovers and proves olympiad-level geometry theorems. Within the same computational budget as existing state-of-the-art systems, TongGeometry establishes a larger repository of geometry theorems: 6.7 billion requiring auxiliary constructions, including 4.1 billion exhibiting geometric symmetry. Among these, three of TongGeometry’s discoveries were selected for regional mathematical olympiads, appearing in a national team qualifying exam in China and a top civil olympiad in the USA. Guided by fine-tuned large language models, TongGeometry solved all International Mathematical Olympiad geometry problems in the IMO-AG-30 benchmark, outperforming average top human competitors on this specific dataset. It also surpasses the existing state of the art across a broader spectrum of olympiad-level problems and requires only consumer-grade computing resources. These results demonstrate that TongGeometry operates as both a mathematical discoverer and a solver, becoming an artificial intelligence system to achieve this dual capability. The deployment of a preliminary system based on TongGeometry demonstrates practical applications and opens fresh possibilities for artificial-intelligence-assisted mathematical research and education. TongGeometry both solves and proposes olympiad-level geometry problems. It uses guided tree search to find hard but concise problems, making advanced mathematical reasoning more accessible.
奥林匹克数学竞赛是久负盛名的竞赛,提出问题和解决问题都受到高度尊重。构建能够解决这些奥林匹克级别挑战的人工智能系统在自动推理领域仍然是一个开放的前沿,特别是在几何领域,因为它独特地融合了数值精度和空间直觉。在这里,我们展示了TongGeometry,一个神经符号系统,使用引导树搜索,发现并证明了奥林匹克级的几何定理。在与现有最先进的系统相同的计算预算内,TongGeometry建立了一个更大的几何定理库:67亿个需要辅助构造,其中41亿个展示几何对称。其中,通几何的三个发现入选了地区数学奥林匹克竞赛,出现在中国国家队资格考试和美国顶级民用奥林匹克竞赛中。在经过微调的大型语言模型的指导下,TongGeometry解决了IMO-AG-30基准测试中的所有国际奥数几何问题,在该特定数据集上的表现超过了平均顶级人类对手。它还在更广泛的奥林匹克级问题范围内超越了现有的技术水平,只需要消费级的计算资源。这些结果表明,TongGeometry既是一个数学发现者,也是一个求解者,成为一个实现这双重能力的人工智能系统。基于TongGeometry的初步系统的部署展示了实际应用,并为人工智能辅助数学研究和教育开辟了新的可能性。同几何解决并提出了奥林匹克水平的几何问题。它使用引导树搜索来查找困难但简洁的问题,使高级数学推理更容易理解。
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引用次数: 0
Jointly modeling cardiovascular biomarkers 联合建模心血管生物标志物
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2026-01-21 DOI: 10.1038/s42256-025-01172-x
Sully F. Chen
Capturing the complexity of cardiovascular dynamics demands multiple monitoring modalities, each with inherent trade-offs. Diffusion-based modeling offers a promising route for synthesizing and generating cross-modal data.
捕捉心血管动力学的复杂性需要多种监测模式,每种模式都有内在的权衡。基于扩散的建模为合成和生成跨模态数据提供了一条很有前途的途径。
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引用次数: 0
Benchmarking large language models on safety risks in scientific laboratories 在科学实验室中对大型语言模型的安全风险进行基准测试
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2026-01-14 DOI: 10.1038/s42256-025-01152-1
Yujun Zhou, Jingdong Yang, Yue Huang, Kehan Guo, Zoe Emory, Bikram Ghosh, Amita Bedar, Sujay Shekar, Zhenwen Liang, Pin-Yu Chen, Tian Gao, Werner Geyer, Nuno Moniz, Nitesh V. Chawla, Xiangliang Zhang
Artificial intelligence is revolutionizing scientific research, yet its growing integration into laboratory environments presents critical safety challenges. Large language models and vision language models now assist in experiment design and procedural guidance, yet their ‘illusion of understanding’ may lead researchers to overtrust unsafe outputs. Here we show that current models remain far from meeting the reliability needed for safe laboratory operation. We introduce LabSafety Bench, a comprehensive benchmark that evaluates models on hazard identification, risk assessment and consequence prediction across 765 multiple-choice questions and 404 realistic laboratory scenarios, encompassing 3,128 open-ended tasks. Evaluations on 19 advanced large language models and vision language models show that no model evaluated on hazard identification surpasses 70% accuracy. While proprietary models perform well on structured assessments, they do not show a clear advantage in open-ended reasoning. These results underscore the urgent need for specialized safety evaluation frameworks before deploying artificial intelligence systems in real laboratory settings. Large language models are starting to be used in safety-critical tasks such as controlling robots. Zhou et al. present LabSafety Bench, a benchmark evaluating the ability of large language models to identify hazards and assess laboratory risks.
人工智能正在彻底改变科学研究,但它越来越多地融入实验室环境,带来了严峻的安全挑战。大型语言模型和视觉语言模型现在有助于实验设计和程序指导,但它们的“理解错觉”可能导致研究人员过度信任不安全的输出。在这里,我们表明,目前的模型仍然远远不能满足安全实验室操作所需的可靠性。我们介绍了LabSafety Bench,这是一个综合基准,评估了765个选择题和404个现实实验室场景的危害识别、风险评估和后果预测模型,包括3128个开放式任务。对19种先进的大型语言模型和视觉语言模型的评价表明,没有一种模型的危害识别准确率超过70%。虽然专有模型在结构化评估中表现良好,但它们在开放式推理中并没有显示出明显的优势。这些结果强调了在实际实验室环境中部署人工智能系统之前,迫切需要专门的安全评估框架。
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引用次数: 0
Current-diffusion model for metasurface structure discoveries with spatial-frequency dynamics 空间-频率动力学超表面结构发现的电流扩散模型
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2025-12-31 DOI: 10.1038/s42256-025-01162-z
Erji Li, Yusong Wang, Lei Jin, Zheng Zong, Enze Zhu, Bao Wang, Qian Wang, Zongyin Yang, Wen-Yan Yin, Zhun Wei
In AI-driven metamaterials discovery, designing metasurfaces requires extrapolation to unexplored performance regimes to discover new structures. Here we introduce MetaAI, a physics-aware current-diffusion framework that synergizes spatial topologies and frequency-domain responses to discover non-intuitive metasurface architectures. Unlike conventional inverse design constrained by predefined specifications, MetaAI operates as a performance synthesizer by generating electrical current distributions that bridge electromagnetic performance and metasurface structures. This enables both in-distribution and out-of-distribution targets with diverse topologies. The core innovation of the proposed framework lies in its dual-domain diffusion module, which directly correlates meta-atom current mechanisms with electromagnetic behaviours to enable the discovery of structures with 17.2% wider operational bandwidths. We validate MetaAI across single-layer, multilayer and dynamically tunable metasurfaces, demonstrating out-of-distribution generalization across full-wave simulations and experimental prototypes. Metasurface design driven by AI faces challenges, such as extrapolation to unexplored performance regimes. MetaAI, a physics-aware current-diffusion framework, is introduced to advance metamaterial discovery from interpolation to extrapolation.
在人工智能驱动的超材料发现中,设计超表面需要外推到未探索的性能机制,以发现新的结构。在这里,我们介绍了MetaAI,这是一个物理感知的电流扩散框架,可以协同空间拓扑和频域响应来发现非直观的元表面架构。与传统的受预定义规格限制的逆向设计不同,MetaAI通过产生电流分布来桥接电磁性能和超表面结构,从而作为性能合成器运行。这使得分布内和分布外的目标具有不同的拓扑结构。该框架的核心创新在于其双域扩散模块,该模块直接将元原子电流机制与电磁行为联系起来,从而能够发现具有17.2%更宽操作带宽的结构。我们在单层、多层和动态可调的元表面上验证了MetaAI,展示了在全波模拟和实验原型中的分布外泛化。
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引用次数: 0
Inferring spatial single-cell-level interactions through interpreting cell state and niche correlations learned by self-supervised graph transformer 通过解释由自监督图转换器学习的细胞状态和生态位相关性来推断空间单细胞水平的相互作用
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2025-12-31 DOI: 10.1038/s42256-025-01161-0
Xiao Xiao, Le Zhang, Hongyu Zhao, Zuoheng Wang
Cell–cell interactions (CCI), driven by distance-dependent signalling, are important for tissue development and organ function. While imaging-based spatial transcriptomics offers unprecedented opportunities to unravel CCI at single-cell resolution, current analyses face challenges such as limited ligand–receptor pairs measured, insufficient spatial encoding and low interpretability. We present GITIII (graph inductive bias transformer for intercellular interaction investigation), a lightweight, interpretable, self-supervised graph transformer-based model that conceptualizes cells as words and their surrounding cellular neighbourhood as context that shapes the meaning or state of the central cell. GITIII infers CCI by examining the correlation between a cell’s state and its niche, enabling us to understand how sender cells influence the gene expression of receiver cells, visualize spatial CCI patterns, perform CCI-informed cell clustering and construct CCI networks. Applied to four spatial transcriptomics datasets across multiple species, organs and platforms, GITIII effectively identified and statistically interpreted CCI patterns in the brain and tumour microenvironments. Xiao et al. present GITIII, a lightweight and interpretable graph transformer for inferring spatial single-cell-level interactions and quantifying the influence of neighbouring cells on the gene expression of receiver cells in spatial transcriptomics.
由距离依赖信号驱动的细胞-细胞相互作用(CCI)对组织发育和器官功能至关重要。虽然基于成像的空间转录组学为在单细胞分辨率上解开CCI提供了前所未有的机会,但目前的分析面临着诸如测量的配体-受体对有限、空间编码不足和可解释性低等挑战。我们提出了GITIII(用于细胞间相互作用研究的图感应偏置变压器),这是一种轻量级、可解释、自监督的基于图转换器的模型,它将细胞概念化为单词,将其周围的细胞邻居概念化为塑造中心细胞的意义或状态的上下文。GITIII通过检查细胞状态与其生态位之间的相关性来推断CCI,使我们能够了解发送细胞如何影响接收细胞的基因表达,可视化空间CCI模式,执行CCI信息细胞聚类并构建CCI网络。应用于跨多个物种、器官和平台的四个空间转录组学数据集,GITIII有效地识别并统计解释了脑和肿瘤微环境中的CCI模式。
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引用次数: 0
Assessing the potential of deep learning for protein–ligand docking 评估深度学习在蛋白质配体对接中的潜力
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2025-12-31 DOI: 10.1038/s42256-025-01160-1
Alex Morehead, Nabin Giri, Jian Liu, Pawan Neupane, Jianlin Cheng
The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets. Morehead et al. introduce the benchmark PoseBench and evaluate the strengths and limitations of current AI-based protein–ligand docking and structure prediction methods.
配体结合对蛋白质结构及其体内功能的影响对现代生物医学研究和生物技术开发工作(如药物发现)具有许多意义。虽然最近已经引入了几种为蛋白质-配体对接设计的深度学习(DL)方法和基准,但到目前为止,还没有以前的工作系统地研究了最新对接和结构预测方法在广泛适用的背景下的行为:(1)使用预测的(载脂蛋白)蛋白质结构进行对接(例如,适用于新蛋白质);(2)将多个(辅因子)配体同时结合到给定的靶蛋白上(例如,用于酶设计);(3)以前没有绑定口袋的知识(例如,为了推广到未知口袋)。为了更深入地了解对接方法在现实世界中的效用,我们引入了PoseBench,这是一个广泛适用的蛋白质-配体对接的综合基准。PoseBench使研究人员能够使用初级配体和多配体基准数据集,严格和系统地评估载脂蛋白到全息蛋白配体对接和蛋白质配体结构预测的DL方法,我们将后者介绍给DL社区。利用PoseBench,我们发现:(1)深度学习共折叠方法总体上优于传统和深度学习对接基线算法,但流行的方法(如AlphaFold 3)仍然面临着用新的蛋白质-配体结合姿态预测目标的挑战;(2)某些DL编码方法对输入序列比对高度敏感,而其他DL编码方法对输入序列比对不敏感;(3) DL方法在预测新的或多配体蛋白靶点时难以在结构准确性和化学特异性之间取得平衡。
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引用次数: 0
Learning intermediate physical states for inverse metasurface design 学习中间物理状态用于逆超表面设计
IF 23.9 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2025-12-31 DOI: 10.1038/s42256-025-01167-8
Chun-Teh Chen
Deep generative models that learn intermediate surface-current maps, rather than layouts directly, offer a more stable route to inverse design of tunable and stacked metasurfaces.
深度生成模型学习中间表面电流图,而不是直接布局,为可调和堆叠元表面的反向设计提供了更稳定的途径。
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引用次数: 0
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Nature Machine Intelligence
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