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High-resolution real-space reconstruction of cryo-EM structures using a neural field network 利用神经场网络对低温电子显微镜结构进行高分辨率实空间重建
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-12 DOI: 10.1038/s42256-024-00870-2
Yue Huang, Chengguang Zhu, Xiaokang Yang, Manhua Liu
The elucidation of three-dimensional (3D) structures is crucial for unravelling the protein function and illuminating mechanisms in structural biology. Cryogenic electron microscopy (cryo-EM) single-particle analysis provides direct measurements to determine the structures of macromolecules. However, the main challenge is reconstructing high-resolution 3D structures from extremely noisy and randomly oriented two-dimensional projection images. Most existing methods involve the optimization of multiple two-dimensional slices in the Fourier domain but ignore the anisotropy among these slices, thereby limiting the reconstruction of high-frequency structures. In this paper, we propose a cryo-EM neural field reconstruction network using 3D spatial-domain optimization that learns a directional isotropic representation of the cryo-EM structure by mapping the spatial coordinates to the corresponding density values. We qualitatively and quantitatively evaluate the cryo-EM neural field reconstruction network on four datasets. The cryo-EM neural field reconstruction network improves the directional isotropy and 3D density resolution beyond the limits of existing algorithms in homogeneous reconstruction and resolves the missing elements of SARS-CoV-2 in heterogeneous reconstruction. Elucidating three-dimensional structures is crucial for unravelling the macromolecule function in structural biology. This study presents a cryogenic electron microscopy neural field reconstruction network using real-space optimization, enhancing the resolution in cryogenic electron microscopy reconstruction.
阐明三维(3D)结构对于揭示蛋白质功能和阐明结构生物学机制至关重要。低温电子显微镜(cryo-EM)单颗粒分析为确定大分子结构提供了直接测量方法。然而,从噪声极高且随机定向的二维投影图像中重建高分辨率三维结构是一大挑战。现有方法大多涉及傅立叶域中多个二维切片的优化,但忽略了这些切片之间的各向异性,从而限制了高频结构的重建。在本文中,我们提出了一种利用三维空间域优化的冷冻电镜神经场重建网络,该网络通过将空间坐标映射到相应的密度值来学习冷冻电镜结构的定向各向同性表示。我们在四个数据集上对低温电磁神经场重建网络进行了定性和定量评估。在同质重建中,冷冻电镜神经场重建网络提高了方向各向同性和三维密度分辨率,超越了现有算法的极限,并在异质重建中解决了 SARS-CoV-2 缺失的元素。
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引用次数: 0
Unsupervised learning of topological non-Abelian braiding in non-Hermitian bands 非ermitian 带中拓扑非阿贝尔辫状结构的无监督学习
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-12 DOI: 10.1038/s42256-024-00871-1
Yang Long, Haoran Xue, Baile Zhang
The topological classification of energy bands has laid the foundation for the discovery of various topological phases of matter in recent decades. While previous work focused on real-energy bands in Hermitian systems, recent studies have shifted attention to the intriguing topology of complex-energy, or non-Hermitian, bands, freeing them from the constraint of energy conservation. For example, the spectral winding of complex-energy bands can give rise to unique topological structures such as braids, holding substantial promise for advancing quantum computing. However, discussions of complex-energy braids have been predominantly limited to the Abelian braid group $${{mathbb{B}}}_{2}$$ owing to its relative simplicity. Identifying topological non-Abelian braiding remains challenging, as it lacks a universally applicable topological invariant for characterization. Here we present a machine learning algorithm for the unsupervised identification of non-Abelian braiding within multiple complex-energy bands. We demonstrate that the results are consistent with Artin’s well-known topological equivalence conditions in braiding. Inspired by these findings, we introduce a winding matrix as a topological invariant for characterizing braiding topology. The winding matrix also reveals the bulk-edge correspondence of non-Hermitian bands with non-Abelian braiding. Finally, we extend our approach to identify non-Abelian braiding topology in two-dimensional and three-dimensional exceptional semimetals and address the unknotting problem in an unsupervised manner. The topological classification of complex-energy bands has uncovered various topological phases beyond Hermitian systems. Long and colleagues exploit unsupervised learning to fully identify the non-Abelian braiding topology of non-Hermitian bands.
近几十年来,能带的拓扑分类为发现物质的各种拓扑阶段奠定了基础。以前的工作主要集中在赫米特系统中的实能带,而最近的研究则把注意力转移到了复能带或非赫米特能带的奇妙拓扑学上,使它们摆脱了能量守恒的限制。例如,复能带的谱绕组可以产生独特的拓扑结构,如辫状结构,为推进量子计算带来了巨大希望。然而,关于复能辫状结构的讨论主要局限于阿贝尔辫状结构群({{mathbb{B}}}_{2}),因为它相对简单。识别拓扑非阿贝尔辫状结构仍然具有挑战性,因为它缺乏普遍适用的拓扑不变量来表征。在这里,我们提出了一种机器学习算法,用于在多个复能带内无监督地识别非阿贝尔辫状结构。我们证明了这一结果与阿尔廷著名的辫状拓扑等价条件是一致的。受这些发现的启发,我们引入了缠绕矩阵作为表征辫状拓扑的拓扑不变量。缠绕矩阵还揭示了非赫米带与非阿贝尔辫状结构的体边对应关系。最后,我们扩展了我们的方法,以识别二维和三维非凡半金属中的非阿贝尔编织拓扑,并以无监督的方式解决解结问题。
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引用次数: 0
An interpretable deep learning framework for genome-informed precision oncology 用于基因组信息精准肿瘤学的可解释深度学习框架
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-11 DOI: 10.1038/s42256-024-00866-y
Shuangxia Ren, Gregory F. Cooper, Lujia Chen, Xinghua Lu
Cancers result from aberrations in cellular signalling systems, typically resulting from driver somatic genome alterations (SGAs) in individual tumours. Precision oncology requires understanding the cellular state and selecting medications that induce vulnerability in cancer cells under such conditions. To this end, we developed a computational framework consisting of two components: (1) a representation-learning component, which learns a representation of the cellular signalling systems when perturbed by SGAs and uses a biologically motivated and interpretable deep learning model, and (2) a drug-response prediction component, which predicts drug responses by leveraging the information of the cellular state of the cancer cells derived by the first component. Our cell-state-oriented framework notably improves the accuracy of predictions of drug responses compared to models using SGAs directly in cell lines. Moreover, our model performs well with real patient data. Importantly, our framework enables the prediction of responses to chemotherapy agents based on SGAs, thus expanding genome-informed precision oncology beyond molecularly targeted drugs. Precision oncology requires analysis of genomic alterations in cancer cells. Ren et al. develop an interpretable artificial intelligence framework that transforms somatic genomic alterations into representations of cellular signalling systems and accurately predicts cells’ responses to anticancer drugs.
癌症源于细胞信号系统的畸变,通常是由单个肿瘤中的体细胞基因组驱动改变(SGA)引起的。精准肿瘤学需要了解细胞状态,并选择能在这种条件下诱导癌细胞脆弱性的药物。为此,我们开发了一个由两部分组成的计算框架:(1)表征学习组件,学习细胞信号系统在受到 SGAs 干扰时的表征,并使用具有生物学动机和可解释的深度学习模型;(2)药物反应预测组件,利用第一个组件得出的癌细胞状态信息预测药物反应。与直接在细胞系中使用 SGA 的模型相比,我们以细胞状态为导向的框架显著提高了药物反应预测的准确性。此外,我们的模型在实际患者数据中表现良好。重要的是,我们的框架可以根据 SGA 预测化疗药物的反应,从而将基因组信息精准肿瘤学扩展到分子靶向药物之外。
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引用次数: 0
Shielding sensitive medical imaging data 屏蔽敏感的医学成像数据
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-11 DOI: 10.1038/s42256-024-00865-z
Gaoyang Liu, Chen Wang, Tian Xia
Differential privacy offers protection in medical image processing but is traditionally thought to hinder accuracy. A recent study offers a reality check on the relationship between privacy measures and the ability of an artificial intelligence (AI) model to accurately analyse medical images.
差异化隐私在医学图像处理中提供了保护,但传统上被认为会妨碍准确性。最近的一项研究对隐私措施与人工智能(AI)模型准确分析医学图像的能力之间的关系进行了现实检验。
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引用次数: 0
Lifelike agility and play in quadrupedal robots using reinforcement learning and generative pre-trained models 利用强化学习和生成预训练模型实现四足机器人逼真的敏捷性和游戏性
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-05 DOI: 10.1038/s42256-024-00861-3
Lei Han, Qingxu Zhu, Jiapeng Sheng, Chong Zhang, Tingguang Li, Yizheng Zhang, He Zhang, Yuzhen Liu, Cheng Zhou, Rui Zhao, Jie Li, Yufeng Zhang, Rui Wang, Wanchao Chi, Xiong Li, Yonghui Zhu, Lingzhu Xiang, Xiao Teng, Zhengyou Zhang
Knowledge from animals and humans inspires robotic innovations. Numerous efforts have been made to achieve agile locomotion in quadrupedal robots through classical controllers or reinforcement learning approaches. These methods usually rely on physical models or handcrafted rewards to accurately describe the specific system, rather than on a generalized understanding like animals do. Here we propose a hierarchical framework to construct primitive-, environmental- and strategic-level knowledge that are all pre-trainable, reusable and enrichable for legged robots. The primitive module summarizes knowledge from animal motion data, where, inspired by large pre-trained models in language and image understanding, we introduce deep generative models to produce motor control signals stimulating legged robots to act like real animals. Then, we shape various traversing capabilities at a higher level to align with the environment by reusing the primitive module. Finally, a strategic module is trained focusing on complex downstream tasks by reusing the knowledge from previous levels. We apply the trained hierarchical controllers to the MAX robot, a quadrupedal robot developed in-house, to mimic animals, traverse complex obstacles and play in a designed challenging multi-agent chase tag game, where lifelike agility and strategy emerge in the robots. A key challenge in robotics is leveraging pre-training as a form of knowledge to generate movements. The authors propose a general learning framework for reusing pre-trained knowledge across different perception and task levels. The deployed robots exhibit lifelike agility and sophisticated game-playing strategies.
来自动物和人类的知识激发了机器人的创新。为了通过经典控制器或强化学习方法实现四足机器人的敏捷运动,人们做出了许多努力。这些方法通常依赖物理模型或手工制作的奖励来准确描述特定系统,而不是像动物那样依赖广义的理解。在这里,我们提出了一个分层框架,用于构建原始、环境和策略层面的知识,这些知识都是可预先训练、可重复使用和可丰富的,适用于有腿机器人。原始模块总结了来自动物运动数据的知识,受语言和图像理解方面的大型预训练模型的启发,我们引入了深度生成模型,以产生运动控制信号,刺激有腿机器人像真实动物一样行动。然后,我们在更高层次上塑造各种穿越能力,通过重复使用原始模块与环境保持一致。最后,通过重复使用前几级的知识,训练出一个战略模块,专注于复杂的下游任务。我们将训练好的分层控制器应用于 MAX 机器人(一种自主开发的四足机器人),让它模仿动物,穿越复杂的障碍物,并参与设计好的具有挑战性的多代理追逐游戏,在游戏中,机器人表现出栩栩如生的敏捷性和策略性。
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引用次数: 0
Molecular set representation learning 分子集表示学习
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-05 DOI: 10.1038/s42256-024-00856-0
Maria Boulougouri, Pierre Vandergheynst, Daniel Probst
Computational representation of molecules can take many forms, including graphs, string encodings of graphs, binary vectors or learned embeddings in the form of real-valued vectors. These representations are then used in downstream classification and regression tasks using a wide range of machine learning models. However, existing models come with limitations, such as the requirement for clearly defined chemical bonds, which often do not represent the true underlying nature of a molecule. Here we propose a framework for molecular machine learning tasks based on set representation learning. We show that learning on sets of atom invariants alone reaches the performance of state-of-the-art graph-based models on the most-used chemical benchmark datasets and that introducing a set representation layer into graph neural networks can surpass the performance of established methods in the domains of chemistry, biology and material science. We introduce specialized set representation-based neural network architectures for reaction-yield and protein–ligand binding-affinity prediction. Overall, we show that the technique we denote molecular set representation learning is both an alternative and an extension to graph neural network architectures for machine learning tasks on molecules, molecule complexes and chemical reactions. Machine learning methods for molecule predictions use various representations of molecules such as in the form of strings or graphs. As an extension of graph representation learning, Probst and colleagues propose to represent a molecule as a set of atoms, to better capture the underlying chemical nature, and demonstrate improved performance in a range of machine learning tasks.
分子的计算表示有多种形式,包括图、图的字符串编码、二进制向量或实值向量形式的学习嵌入。然后,这些表征可通过各种机器学习模型用于下游分类和回归任务。然而,现有的模型有其局限性,例如需要明确定义的化学键,而这些化学键往往不能代表分子的真实基本性质。在此,我们提出了一个基于集合表示学习的分子机器学习任务框架。我们的研究表明,在最常用的化学基准数据集上,仅原子不变式集学习就能达到最先进的基于图的模型的性能,而在图神经网络中引入集合表示层,就能在化学、生物学和材料科学领域超越已有方法的性能。我们为反应产率和蛋白质配体结合亲和力预测引入了基于集合表示的专门神经网络架构。总之,我们表明,我们称之为分子集表示学习的技术既是图神经网络架构的一种替代方法,也是对分子、分子复合物和化学反应机器学习任务的一种扩展。
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引用次数: 0
Visual odometry with neuromorphic resonator networks 利用神经形态共振网络进行视觉里程测量
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-06-27 DOI: 10.1038/s42256-024-00846-2
Alpha Renner, Lazar Supic, Andreea Danielescu, Giacomo Indiveri, E. Paxon Frady, Friedrich T. Sommer, Yulia Sandamirskaya
Visual odometry (VO) is a method used to estimate self-motion of a mobile robot using visual sensors. Unlike odometry based on integrating differential measurements that can accumulate errors, such as inertial sensors or wheel encoders, VO is not compromised by drift. However, image-based VO is computationally demanding, limiting its application in use cases with low-latency, low-memory and low-energy requirements. Neuromorphic hardware offers low-power solutions to many vision and artificial intelligence problems, but designing such solutions is complicated and often has to be assembled from scratch. Here we propose the use of vector symbolic architecture (VSA) as an abstraction layer to design algorithms compatible with neuromorphic hardware. Building from a VSA model for scene analysis, described in our companion paper, we present a modular neuromorphic algorithm that achieves state-of-the-art performance on two-dimensional VO tasks. Specifically, the proposed algorithm stores and updates a working memory of the presented visual environment. Based on this working memory, a resonator network estimates the changing location and orientation of the camera. We experimentally validate the neuromorphic VSA-based approach to VO with two benchmarks: one based on an event-camera dataset and the other in a dynamic scene with a robotic task. Visual odometry, or self-motion estimation, is a fundamental task in robotics. Renner, Supic and colleagues introduce a neuromorphic algorithm for visual odometry that leverages hyperdimensional computing and hierarchical resonators. The approach estimates a robot’s motion from event-based vision, a step towards low-power machine vision for robotics.
视觉里程计(VO)是一种利用视觉传感器估算移动机器人自我运动的方法。不同于惯性传感器或轮子编码器等基于积分差分测量的里程测量法,视觉里程测量法不会受到漂移的影响。然而,基于图像的 VO 对计算要求很高,这限制了它在低延迟、低内存和低能耗要求的使用案例中的应用。神经形态硬件为许多视觉和人工智能问题提供了低功耗解决方案,但设计这种解决方案非常复杂,通常需要从头开始组装。在此,我们建议使用矢量符号架构(VSA)作为抽象层,设计与神经形态硬件兼容的算法。在我们的配套论文中描述的用于场景分析的 VSA 模型的基础上,我们提出了一种模块化神经形态算法,该算法在二维 VO 任务上实现了最先进的性能。具体来说,所提出的算法存储并更新呈现视觉环境的工作记忆。在此工作记忆的基础上,谐振器网络会估算出摄像头不断变化的位置和方向。我们通过两个基准实验验证了基于神经形态 VSA 的虚拟现实方法:一个基于事件摄像机数据集,另一个基于机器人任务的动态场景。
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引用次数: 0
Machine learning for micro- and nanorobots 微型和纳米机器人的机器学习
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-06-27 DOI: 10.1038/s42256-024-00859-x
Lidong Yang, Jialin Jiang, Fengtong Ji, Yangmin Li, Kai-Leung Yung, Antoine Ferreira, Li Zhang
Machine learning (ML) has revolutionized robotics by enhancing perception, adaptability, decision-making and more, enabling robots to work in complex scenarios beyond the capabilities of traditional approaches. However, the downsizing of robots to micro- and nanoscales introduces new challenges. For example, complexities in the actuation and locomotion of micro- and nanorobots defy traditional modelling methods, while control and navigation are complicated by strong environmental disruptions, and tracking in vivo encounters substantial noise interference. Recently, ML has also been shown to offer a promising avenue to tackle these complexities. Here we discuss how ML advances many crucial aspects of micro- and nanorobots, that is, in their design, actuation, locomotion, planning, tracking and navigation. Any application that can benefit from these fundamental advancements will be a potential beneficiary of this field, including micromanipulation, targeted delivery and therapy, bio-sensing, diagnosis and so on. This Review aims to provide an accessible and comprehensive survey for readers to quickly appreciate recent exciting accomplishments in ML for micro- and nanorobots. We also discuss potential issues and prospects of this burgeoning research direction. We hope this Review can foster interdisciplinary collaborations across robotics, computer science, material science and allied disciplines, to develop ML techniques that surmount fundamental challenges and further expand the application horizons of micro- and nanorobotics in biomedicine. Machine learning approaches in micro- and nanorobotics promise to overcome challenges encountered by applying traditional control methods at the microscopic scale. Lidong Yang et al. review this emerging area in robotics and discuss machine learning developments in design, actuation, locomotion, planning, tracking and navigation of microrobots.
机器学习(ML)通过增强感知能力、适应能力、决策能力等,使机器人能够在复杂场景中工作,超越了传统方法的能力范围,从而彻底改变了机器人技术。然而,将机器人缩小到微米级和纳米级带来了新的挑战。例如,微型和纳米机器人的驱动和运动的复杂性使传统的建模方法望而却步,而控制和导航因强烈的环境干扰而变得复杂,体内跟踪也会遇到大量噪声干扰。最近的研究表明,ML 为解决这些复杂问题提供了一条很有前景的途径。在此,我们将讨论 ML 如何在微型和纳米机器人的设计、驱动、运动、规划、跟踪和导航等许多关键方面取得进展。任何能从这些基本进步中获益的应用都将是这一领域的潜在受益者,包括微操纵、定向输送和治疗、生物传感、诊断等。本综述旨在为读者提供一份通俗易懂的综合调查报告,以便读者快速了解微机器人和纳米机器人在智能语言方面最近取得的令人振奋的成就。我们还讨论了这一新兴研究方向的潜在问题和前景。我们希望这篇综述能促进机器人学、计算机科学、材料科学和相关学科之间的跨学科合作,以开发克服基本挑战的 ML 技术,并进一步拓展微纳机器人在生物医学中的应用范围。
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引用次数: 0
Will generative AI transform robotics? 生成式人工智能会改变机器人技术吗?
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-06-27 DOI: 10.1038/s42256-024-00862-2
In the current wave of excitement about applying large vision–language models and generative AI to robotics, expectations are running high, but conquering real-world complexities remains challenging for robots.
目前,将大型视觉语言模型和生成式人工智能应用于机器人技术的热潮正在兴起,人们对此期望很高,但对于机器人来说,征服现实世界的复杂性仍然是一项挑战。
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引用次数: 0
Direct conformational sampling from peptide energy landscapes through hypernetwork-conditioned diffusion 通过超网络条件扩散从多肽能谱中直接进行构象采样
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-06-27 DOI: 10.1038/s42256-024-00860-4
Osama Abdin, Philip M. Kim
Deep learning approaches have spurred substantial advances in the single-state prediction of biomolecular structures. The function of biomolecules is, however, dependent on the range of conformations they can assume. This is especially true for peptides, a highly flexible class of molecules that are involved in numerous biological processes and are of high interest as therapeutics. Here we introduce PepFlow, a transferable generative model that enables direct all-atom sampling from the allowable conformational space of input peptides. We train the model in a diffusion framework and subsequently use an equivalent flow to perform conformational sampling. To overcome the prohibitive cost of generalized all-atom modelling, we modularize the generation process and integrate a hypernetwork to predict sequence-specific network parameters. PepFlow accurately predicts peptide structures and effectively recapitulates experimental peptide ensembles at a fraction of the running time of traditional approaches. PepFlow can also be used to sample conformations that satisfy constraints such as macrocyclization. Modelling the different structures a peptide can assume is integral to understanding their function. The authors introduce PepFlow, a sequence-conditioned deep learning model that is shown to accurately and efficiently generate peptide conformations.
深度学习方法在生物分子结构的单态预测方面取得了长足进步。然而,生物分子的功能取决于它们所能呈现的构象范围。肽是一类高度灵活的分子,参与多种生物过程,作为治疗药物备受关注。在这里,我们介绍一种可转移的生成模型 PepFlow,它可以从输入肽的可构象空间中直接进行全原子采样。我们在扩散框架中训练模型,随后使用等效流进行构象采样。为了克服通用全原子建模成本过高的问题,我们将生成过程模块化,并整合了超网络来预测特定序列的网络参数。PepFlow 能准确预测多肽结构,并有效再现实验中的多肽组合,而运行时间仅为传统方法的一小部分。PepFlow 还可用于采样满足大环化等约束条件的构象。
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引用次数: 0
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Nature Machine Intelligence
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