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Diving into deep learning 深入学习
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-05-10 DOI: 10.1038/s42256-024-00840-8
Ge Wang
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引用次数: 0
Predicting equilibrium distributions for molecular systems with deep learning 用深度学习预测分子系统的平衡分布
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-05-08 DOI: 10.1038/s42256-024-00837-3
Shuxin Zheng, Jiyan He, Chang Liu, Yu Shi, Ziheng Lu, Weitao Feng, Fusong Ju, Jiaxi Wang, Jianwei Zhu, Yaosen Min, He Zhang, Shidi Tang, Hongxia Hao, Peiran Jin, Chi Chen, Frank Noé, Haiguang Liu, Tie-Yan Liu
Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure but rather determined from the equilibrium distribution of structures. Conventional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. Here we introduce a deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG uses deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system such as a chemical graph or a protein sequence. This framework enables the efficient generation of diverse conformations and provides estimations of state densities, orders of magnitude faster than conventional methods. We demonstrate applications of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst–adsorbate sampling and property-guided structure generation. DiG presents a substantial advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in the molecular sciences. Methods for predicting molecular structure predictions have so far focused on only the most probable conformation, but molecular structures are dynamic and can change when performing their biological functions, for example. Zheng et al. use a graph transformer approach to learn the equilibrium distribution of molecular systems and show that this can be helpful for a number of downstream tasks, including protein structure prediction, ligand docking and molecular design.
深度学习的进步极大地改进了分子结构预测。然而,对现实世界应用非常重要的许多宏观观测结果并不是单一分子结构的函数,而是由结构的平衡分布决定的。获取这些分布的传统方法(如分子动力学模拟)计算成本高昂,而且往往难以实现。在这里,我们引入了一个深度学习框架,称为分布式图解器(DiG),试图预测分子系统的平衡分布。受热力学退火过程的启发,DiG 利用深度神经网络将简单分布转化为平衡分布,并以分子系统的描述符(如化学图谱或蛋白质序列)为条件。这一框架能高效生成各种构象,并提供状态密度的估计值,其速度比传统方法快了几个数量级。我们展示了 DiG 在多个分子任务中的应用,包括蛋白质构象采样、配体结构采样、催化剂吸附剂采样和属性引导结构生成。DiG 在统计理解分子系统的方法上取得了重大进步,为分子科学开辟了新的研究机会。
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引用次数: 0
Augmenting large language models with chemistry tools 用化学工具增强大型语言模型
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-05-08 DOI: 10.1038/s42256-024-00832-8
Andres M. Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D. White, Philippe Schwaller
Large language models (LLMs) have shown strong performance in tasks across domains but struggle with chemistry-related problems. These models also lack access to external knowledge sources, limiting their usefulness in scientific applications. We introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery and materials design. By integrating 18 expert-designed tools and using GPT-4 as the LLM, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned and executed the syntheses of an insect repellent and three organocatalysts and guided the discovery of a novel chromophore. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow’s effectiveness in automating a diverse set of chemical tasks. Our work not only aids expert chemists and lowers barriers for non-experts but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. Large language models can be queried to perform chain-of-thought reasoning on text descriptions of data or computational tools, which can enable flexible and autonomous workflows. Bran et al. developed ChemCrow, a GPT-4-based agent that has access to computational chemistry tools and a robotic chemistry platform, which can autonomously solve tasks for designing or synthesizing chemicals such as drugs or materials.
大型语言模型(LLMs)在各领域的任务中表现出很强的性能,但在处理与化学有关的问题时却举步维艰。这些模型还无法访问外部知识源,限制了它们在科学应用中的实用性。我们介绍的 ChemCrow 是一种 LLM 化学代理,旨在完成有机合成、药物发现和材料设计等任务。通过集成 18 种专家设计的工具并使用 GPT-4 作为 LLM,ChemCrow 增强了 LLM 在化学领域的性能,并产生了新的能力。我们的代理自主规划并执行了一种驱虫剂和三种有机催化剂的合成,并指导发现了一种新型发色团。我们的评估(包括 LLM 和专家评估)证明了 ChemCrow 在自动完成各种化学任务方面的有效性。我们的工作不仅为专家化学家提供了帮助,降低了非专家的门槛,还通过弥合实验化学与计算化学之间的差距促进了科学进步。
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引用次数: 0
Maximum diffusion reinforcement learning 最大扩散强化学习
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-05-02 DOI: 10.1038/s42256-024-00829-3
Thomas A. Berrueta, Allison Pinosky, Todd D. Murphey
Robots and animals both experience the world through their bodies and senses. Their embodiment constrains their experiences, ensuring that they unfold continuously in space and time. As a result, the experiences of embodied agents are intrinsically correlated. Correlations create fundamental challenges for machine learning, as most techniques rely on the assumption that data are independent and identically distributed. In reinforcement learning, where data are directly collected from an agent’s sequential experiences, violations of this assumption are often unavoidable. Here we derive a method that overcomes this issue by exploiting the statistical mechanics of ergodic processes, which we term maximum diffusion reinforcement learning. By decorrelating agent experiences, our approach provably enables single-shot learning in continuous deployments over the course of individual task attempts. Moreover, we prove our approach generalizes well-known maximum entropy techniques and robustly exceeds state-of-the-art performance across popular benchmarks. Our results at the nexus of physics, learning and control form a foundation for transparent and reliable decision-making in embodied reinforcement learning agents. The central assumption in machine learning that data are independent and identically distributed does not hold in many reinforcement learning settings, as experiences of reinforcement learning agents are sequential and intrinsically correlated in time. Berrueta and colleagues use the mathematical theory of ergodic processes to develop a reinforcement framework that can decorrelate agent experiences and is capable of learning in single-shot deployments.
机器人和动物都通过自己的身体和感官来体验世界。它们的身体限制了它们的体验,确保它们在空间和时间上持续展开。因此,具身代理的体验在本质上是相关的。相关性给机器学习带来了根本性的挑战,因为大多数技术都依赖于数据独立且分布相同的假设。在强化学习中,数据是直接从代理的连续经验中收集的,违反这一假设往往是不可避免的。在这里,我们通过利用遍历过程的统计力学,推导出一种克服这一问题的方法,我们称之为最大扩散强化学习。通过对代理经验进行去相关化处理,我们的方法可以在单个任务尝试过程中的连续部署中实现单次学习。此外,我们还证明了我们的方法可以推广众所周知的最大熵技术,并在流行的基准测试中稳健地超越了最先进的性能。我们在物理学、学习和控制领域的研究成果为强化学习代理的透明、可靠决策奠定了基础。
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引用次数: 0
The rewards of reusable machine learning code 可重复使用的机器学习代码的回报
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-04-24 DOI: 10.1038/s42256-024-00835-5
Research papers can make a long-lasting impact when the code and software tools supporting the findings are made readily available and can be reused and built on. Our reusability reports explore and highlight examples of good code sharing practices.
如果能随时提供支持研究成果的代码和软件工具,并能在此基础上重复使用,那么研究论文就能产生长久的影响。我们的可重用性报告探讨并强调了良好的代码共享实践范例。
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引用次数: 0
The benefits, risks and bounds of personalizing the alignment of large language models to individuals 根据个人情况个性化调整大型语言模型的益处、风险和界限
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-04-23 DOI: 10.1038/s42256-024-00820-y
Hannah Rose Kirk, Bertie Vidgen, Paul Röttger, Scott A. Hale
Large language models (LLMs) undergo ‘alignment’ so that they better reflect human values or preferences, and are safer or more useful. However, alignment is intrinsically difficult because the hundreds of millions of people who now interact with LLMs have different preferences for language and conversational norms, operate under disparate value systems and hold diverse political beliefs. Typically, few developers or researchers dictate alignment norms, risking the exclusion or under-representation of various groups. Personalization is a new frontier in LLM development, whereby models are tailored to individuals. In principle, this could minimize cultural hegemony, enhance usefulness and broaden access. However, unbounded personalization poses risks such as large-scale profiling, privacy infringement, bias reinforcement and exploitation of the vulnerable. Defining the bounds of responsible and socially acceptable personalization is a non-trivial task beset with normative challenges. This article explores ‘personalized alignment’, whereby LLMs adapt to user-specific data, and highlights recent shifts in the LLM ecosystem towards a greater degree of personalization. Our main contribution explores the potential impact of personalized LLMs via a taxonomy of risks and benefits for individuals and society at large. We lastly discuss a key open question: what are appropriate bounds of personalization and who decides? Answering this normative question enables users to benefit from personalized alignment while safeguarding against harmful impacts for individuals and society. Tailoring the alignment of large language models (LLMs) to individuals is a new frontier in generative AI, but unbounded personalization can bring potential harm, such as large-scale profiling, privacy infringement and bias reinforcement. Kirk et al. develop a taxonomy for risks and benefits of personalized LLMs and discuss the need for normative decisions on what are acceptable bounds of personalization.
大型语言模型(LLMs)需要经过 "调整",以便更好地反映人类的价值观或偏好,使其更加安全或有用。然而,对齐本质上是困难的,因为现在与大型语言模型互动的数亿人对语言和对话规范有着不同的偏好,在不同的价值体系下运作,并持有不同的政治信仰。通常情况下,很少有开发人员或研究人员来规定对齐规范,这就有可能导致不同群体被排斥在外或代表性不足。个性化是 LLM 开发的一个新领域,即根据个人情况定制模型。原则上,这可以最大限度地减少文化霸权,提高实用性并扩大使用范围。然而,无限制的个性化也会带来风险,如大规模貌相、侵犯隐私、强化偏见和剥削弱势群体。界定负责任的、社会可接受的个性化界限是一项非同小可的任务,其中充满了规范性挑战。本文探讨了 "个性化对齐",即本地语言工具适应用户特定数据的问题,并重点介绍了本地语言工具生态系统最近向更大程度的个性化转变的情况。我们的主要贡献是通过对个人和整个社会的风险和益处进行分类,探讨了个性化法律信息的潜在影响。最后,我们讨论了一个关键的开放性问题:个性化的适当界限是什么,由谁来决定?回答这个规范性问题可以让用户从个性化调整中受益,同时避免对个人和社会造成有害影响。
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引用次数: 0
Dangers of speech technology for workplace diversity 语音技术对工作场所多样性的危害
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-04-22 DOI: 10.1038/s42256-024-00827-5
Mike Horia Mihail Teodorescu, Mingang K. Geiger, Lily Morse
Speech technology offers many applications to enhance employee productivity and efficiency. Yet new dangers arise for marginalized groups, potentially jeopardizing organizational efforts to promote workplace diversity. Our analysis delves into three critical risks of speech technology and offers guidance for mitigating these risks responsibly.
语音技术为提高员工的生产力和效率提供了许多应用。然而,边缘化群体也面临着新的危险,有可能危及组织为促进工作场所多样性所做的努力。我们的分析深入探讨了语音技术的三个关键风险,并为负责任地降低这些风险提供了指导。
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引用次数: 0
Artificial intelligence tackles the nature–nurture debate 人工智能解决 "自然-养育 "之争
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-04-19 DOI: 10.1038/s42256-024-00828-4
Justin N. Wood
A classic question in cognitive science is whether learning requires innate, domain-specific inductive biases to solve visual tasks. A recent study trained machine-learning systems on the first-person visual experiences of children to show that visual knowledge can be learned in the absence of innate inductive biases about objects or space.
认知科学中的一个经典问题是,学习是否需要先天的、特定领域的归纳偏差来解决视觉任务。最近的一项研究根据儿童的第一人称视觉经验对机器学习系统进行了训练,结果表明,在没有关于物体或空间的先天归纳偏差的情况下,也可以学习视觉知识。
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引用次数: 0
The synergy complement control approach for seamless limb-driven prostheses 无缝肢体驱动假肢的协同互补控制方法
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-04-19 DOI: 10.1038/s42256-024-00825-7
Johannes Kühn, Tingli Hu, Alexander Tödtheide, Edmundo Pozo Fortunić, Elisabeth Jensen, Sami Haddadin
Limb-driven control allows for direct control by using residual limb movements rather than unnatural and complex muscle activation. Existing limb-driven methods simultaneously learn a variety of possible motions, ranging from a residual limb to entire arm motions, from human templates by relying on linear or nonlinear regression techniques. However, the map between a low-dimensional residual limb movement and high-dimensional total limb movement is highly underdetermined. Therefore, this complex, high-dimensional coordination problem cannot be accurately solved by treating it as a data-driven black box problem. Here we address this challenge by introducing the residual limb-driven control framework synergy complement control. Firstly, the residual limb drives a one-dimensional phase variable to simultaneously control the multiple joints of the prosthesis. Secondly, the resulting prosthesis motion naturally complements the movement of the residual limb by its synergy components. Furthermore, our framework adds information on contextual tasks and goals and allows for seamless transitions between these. Experimental validation was conducted using subjects with preserved arms employing an exo-prosthesis setup, and studies involving participants with and without limb differences in a virtual reality setup. The findings affirm that the restoration of lost coordinated synergy capabilities is reliably achieved through the utilization of synergy complement control with the prosthesis. Current limb-driven methods often result in suboptimal prosthetic motions. Kühn and colleagues develop a framework called synergy complement control (SCC) that advances prosthetics by learning ‘cyborg’ limb-driven control, ensuring natural coordination. Validated in diverse trials, SCC offers reliable and intuitive enhancement for limb functionality.
肢体驱动控制可通过使用残肢运动而非不自然和复杂的肌肉激活来实现直接控制。现有的肢体驱动方法通过线性或非线性回归技术,同时从人体模板中学习从残肢到整个手臂的各种可能运动。然而,低维残肢运动与高维全肢运动之间的映射高度不确定。因此,这种复杂的高维协调问题无法通过将其视为数据驱动的黑箱问题来准确解决。在此,我们通过引入残肢驱动控制框架协同互补控制来解决这一难题。首先,残肢驱动一个一维相位变量来同时控制假肢的多个关节。其次,由此产生的假肢运动通过其协同成分自然地补充了残肢的运动。此外,我们的框架还增加了有关情境任务和目标的信息,并允许在这些任务和目标之间进行无缝转换。我们使用外置假肢装置对保留手臂的受试者进行了实验验证,并在虚拟现实装置中对有肢体差异和无肢体差异的受试者进行了研究。研究结果证实,通过使用假肢进行协同互补控制,可以可靠地恢复失去的协调协同能力。
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引用次数: 0
Synthetic Lagrangian turbulence by generative diffusion models 通过生成扩散模型合成拉格朗日湍流
IF 23.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-04-17 DOI: 10.1038/s42256-024-00810-0
T. Li, L. Biferale, F. Bonaccorso, M. A. Scarpolini, M. Buzzicotti
Lagrangian turbulence lies at the core of numerous applied and fundamental problems related to the physics of dispersion and mixing in engineering, biofluids, the atmosphere, oceans and astrophysics. Despite exceptional theoretical, numerical and experimental efforts conducted over the past 30 years, no existing models are capable of faithfully reproducing statistical and topological properties exhibited by particle trajectories in turbulence. We propose a machine learning approach, based on a state-of-the-art diffusion model, to generate single-particle trajectories in three-dimensional turbulence at high Reynolds numbers, thereby bypassing the need for direct numerical simulations or experiments to obtain reliable Lagrangian data. Our model demonstrates the ability to reproduce most statistical benchmarks across time scales, including the fat-tail distribution for velocity increments, the anomalous power law and the increased intermittency around the dissipative scale. Slight deviations are observed below the dissipative scale, particularly in the acceleration and flatness statistics. Surprisingly, the model exhibits strong generalizability for extreme events, producing events of higher intensity and rarity that still match the realistic statistics. This paves the way for producing synthetic high-quality datasets for pretraining various downstream applications of Lagrangian turbulence. Modelling the statistical and geometrical properties of particle trajectories in turbulent flows is key to many scientific and technological applications. Li and colleagues introduce a data-driven diffusion model that can generate high-Reynolds-number Lagrangian turbulence trajectories with statistical properties consistent with those of the training set and even generalize to rare, intense events unseen during training.
拉格朗日湍流是工程、生物流体、大气、海洋和天体物理学中与分散和混合物理学有关的众多应用和基础问题的核心。尽管在过去 30 年中进行了卓越的理论、数值和实验研究,但没有任何现有模型能够忠实地再现湍流中粒子轨迹所表现出的统计和拓扑特性。我们提出了一种基于最先进扩散模型的机器学习方法,用于生成高雷诺数三维湍流中的单粒子轨迹,从而避免了直接通过数值模拟或实验获取可靠拉格朗日数据的需要。我们的模型展示了在时间尺度上再现大多数统计基准的能力,包括速度增量的胖尾分布、反常幂律和耗散尺度附近增加的间歇性。在耗散尺度以下观察到轻微偏差,特别是加速度和平坦度统计。令人惊讶的是,该模型对极端事件表现出很强的普适性,产生的事件强度更高、更罕见,但仍与现实的统计数据相吻合。这为合成高质量数据集以预训练拉格朗日湍流的各种下游应用铺平了道路。
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引用次数: 0
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Nature Machine Intelligence
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