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A nonlinear dimension for machine learning in optical disordered media 光学无序介质中机器学习的非线性维度
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-14 DOI: 10.1038/s43588-024-00648-x
Tianyu Wang
A recent study shows that, by leveraging nonlinear optical processes in disordered media, photonic processors can transform high-dimensional machine-learning data, using nonlinear functions that are otherwise challenging for digital electronic processors to compute.
最近的一项研究表明,通过利用无序介质中的非线性光学过程,光子处理器可以利用非线性函数转换高维机器学习数据,否则数字电子处理器很难计算这些数据。
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引用次数: 0
Large-scale photonic computing with nonlinear disordered media 利用非线性无序介质进行大规模光子计算。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-14 DOI: 10.1038/s43588-024-00644-1
Hao Wang, Jianqi Hu, Andrea Morandi, Alfonso Nardi, Fei Xia, Xuanchen Li, Romolo Savo, Qiang Liu, Rachel Grange, Sylvain Gigan
Neural networks find widespread use in scientific and technological applications, yet their implementations in conventional computers have encountered bottlenecks due to ever-expanding computational needs. Photonic computing is a promising neuromorphic platform with potential advantages of massive parallelism, ultralow latency and reduced energy consumption but mostly for computing linear operations. Here we demonstrate a large-scale, high-performance nonlinear photonic neural system based on a disordered polycrystalline slab composed of lithium niobate nanocrystals. Mediated by random quasi-phase-matching and multiple scattering, linear and nonlinear optical speckle features are generated as the interplay between the simultaneous linear random scattering and the second-harmonic generation, defining a complex neural network in which the second-order nonlinearity acts as internal nonlinear activation functions. Benchmarked against linear random projection, such nonlinear mapping embedded with rich physical computational operations shows improved performance across a large collection of machine learning tasks in image classification, regression and graph classification. Demonstrating up to 27,648 input and 3,500 nonlinear output nodes, the combination of optical nonlinearity and random scattering serves as a scalable computing engine for diverse applications. Nonlinear optical computations have been essential yet challenging for developing optical neural networks with appreciable expressivity. In this paper, light scattering is combined with optical nonlinearity to empower a high-performance, large-scale nonlinear photonic neural system.
神经网络广泛应用于科学和技术领域,但由于计算需求不断扩大,在传统计算机中实现神经网络遇到了瓶颈。光子计算是一种前景广阔的神经形态平台,具有大规模并行、超低延迟和降低能耗等潜在优势,但主要用于计算线性运算。在这里,我们展示了一种基于由铌酸锂纳米晶体组成的无序多晶板的大规模、高性能非线性光子神经系统。在随机准相位匹配和多重散射的介导下,线性和非线性光学斑点特征在同时发生的线性随机散射和二次谐波生成的相互作用下产生,定义了一个复杂的神经网络,其中二阶非线性作为内部非线性激活函数。以线性随机投影为基准,这种嵌入了丰富物理计算操作的非线性映射在图像分类、回归和图分类等大量机器学习任务中显示出更高的性能。光学非线性与随机散射的结合可作为可扩展的计算引擎,适用于各种不同的应用,最多可显示 27648 个输入节点和 3500 个非线性输出节点。
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引用次数: 0
Linguistics-based formalization of the antibody language as a basis for antibody language models 基于语言学的抗体语言形式化是抗体语言模型的基础。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-14 DOI: 10.1038/s43588-024-00642-3
Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug, Victor Greiff
Apparent parallels between natural language and antibody sequences have led to a surge in deep language models applied to antibody sequences for predicting cognate antigen recognition. However, a linguistic formal definition of antibody language does not exist, and insight into how antibody language models capture antibody-specific binding features remains largely uninterpretable. Here we describe how a linguistic formalization of the antibody language, by characterizing its tokens and grammar, could address current challenges in antibody language model rule mining. The parallels between natural language and antibody sequences could serve as a stepping stone to using deep language models for analyzing antibody sequences. This Perspective discusses how issues in antibody language model rule mining could be addressed by linguistically formalizing the antibody language.
自然语言与抗体序列之间的明显相似性导致了将深度语言模型应用于抗体序列以预测同源抗原识别的热潮。然而,抗体语言的语言学形式定义并不存在,而且对抗体语言模型如何捕捉抗体特异性结合特征的深入了解在很大程度上仍无法解读。在此,我们将介绍如何通过表征抗体语言的词块和语法,对抗体语言进行语言形式化,从而解决目前在抗体语言模型规则挖掘方面所面临的挑战。
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引用次数: 0
Data as the next challenge in atomistic machine learning 数据是原子机器学习的下一个挑战。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-12 DOI: 10.1038/s43588-024-00636-1
Chiheb Ben Mahmoud, John L. A. Gardner, Volker L. Deringer
As machine learning models are becoming mainstream tools for molecular and materials research, there is an urgent need to improve the nature, quality, and accessibility of atomistic data. In turn, there are opportunities for a new generation of generally applicable datasets and distillable models.
随着机器学习模型逐渐成为分子和材料研究的主流工具,迫切需要改进原子数据的性质、质量和可获取性。反过来,新一代普遍适用的数据集和可提炼模型也有了机会。
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引用次数: 0
Scalable design of orthogonal DNA barcode libraries 可扩展的正交 DNA 条形码库设计。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-07 DOI: 10.1038/s43588-024-00646-z
Gokul Gowri, Kuanwei Sheng, Peng Yin
Orthogonal DNA barcode library design is an essential task in bioengineering. Here we present seqwalk, an efficient method for designing barcode libraries that satisfy a sequence symmetry minimization (SSM) heuristic for orthogonality, with theoretical guarantees of maximal or near-maximal library size under certain design constraints. Seqwalk encodes SSM constraints in a de Bruijn graph representation of sequence space, enabling the application of recent advances in discrete mathematics1 to the problem of orthogonal sequence design. We demonstrate the scalability of seqwalk by designing a library of >106 SSM-satisfying barcode sequences in less than 20 s on a standard laptop. Seqwalk is a scalable method for designing orthogonal DNA barcode libraries, producing one million barcodes in 20 s on a standard laptop.
正交 DNA 条形码文库设计是生物工程中的一项重要任务。在此,我们介绍一种高效的条形码文库设计方法 Seqwalk,该方法满足序列对称性最小化(SSM)启发式正交性要求,理论上保证了在特定设计约束条件下最大或接近最大的文库规模。Seqwalk 将 SSM 约束条件编码为序列空间的 de Bruijn 图表示法,从而将离散数学1 的最新进展应用于正交序列设计问题。我们在一台标准笔记本电脑上用不到 20 秒的时间就设计出了大于 106 个满足 SSM 的条形码序列库,证明了 seqwalk 的可扩展性。
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引用次数: 0
Computational morphology and morphogenesis for empowering soft-matter engineering 通过计算形态学和形态发生学实现软物质工程。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-07 DOI: 10.1038/s43588-024-00647-y
Yifan Yang, Fan Xu
Morphing soft matter, which is capable of changing its shape and function in response to stimuli, has wide-ranging applications in robotics, medicine and biology. Recently, computational models have accelerated its development. Here, we highlight advances and challenges in developing computational techniques, and explore the potential applications enabled by such models.
变形软物质能够根据刺激改变形状和功能,在机器人、医学和生物学领域有着广泛的应用。最近,计算模型加速了它的发展。在此,我们将重点介绍在开发计算技术方面取得的进展和面临的挑战,并探讨此类模型的潜在应用。
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引用次数: 0
Advancing computational sustainability in higher education 推进高等教育的计算可持续性。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-07 DOI: 10.1038/s43588-024-00638-z
Mayank Kejriwal, Victoria Petryshyn
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引用次数: 0
Computing the committor with the committor to study the transition state ensemble 计算承诺器与承诺器,研究过渡态集合
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-05 DOI: 10.1038/s43588-024-00645-0
Peilin Kang, Enrico Trizio, Michele Parrinello
The study of the kinetic bottlenecks that hinder the rare transitions between long-lived metastable states is a major challenge in atomistic simulations. Here we propose a method to explore the transition state ensemble, which is the distribution of configurations that the system passes through as it translocates from one metastable basin to another. We base our method on the committor function and the variational principle that it obeys. We find its minimum through a self-consistent procedure that starts from information limited to the initial and final states. Right from the start, our procedure allows the sampling of very many transition state configurations. With the help of the variational principle, we perform a detailed analysis of the transition state ensemble, ranking quantitatively the degrees of freedom mostly involved in the transition and enabling a systematic approach for the interpretation of simulation results and the construction of efficient physics-informed collective variables. A self-consistent iterative procedure is proposed to compute the committor function for rare events, via a variational principle, and extensively sample the transition state ensemble, allowing for the identification of the relevant variables in the process.
研究阻碍长寿命态之间罕见转变的动力学瓶颈是原子模拟的一大挑战。在这里,我们提出了一种探索过渡态集合的方法,过渡态集合是系统从一个态转移到另一个态时所经过的构型分布。我们的方法基于委托函数及其遵循的变分原理。我们从仅限于初始和最终状态的信息出发,通过自洽程序找到其最小值。从一开始,我们的程序就允许对非常多的过渡状态配置进行采样。在变分原理的帮助下,我们对过渡态集合进行了详细分析,定量排序了过渡过程中主要涉及的自由度,并为解释模拟结果和构建高效的物理集合变量提供了系统方法。
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引用次数: 0
Systematic simulations and analysis of transition states using committor functions 使用委托函数对过渡状态进行系统模拟和分析。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-05 DOI: 10.1038/s43588-024-00652-1
Data about the transition states of rare transitions between long-lived states are needed to simulate physical and chemical processes; however, existing computational approaches often gather little information about these states. A machine-learning technique resolves this challenge by exploiting the century-old theory of committor functions.
模拟物理和化学过程需要有关长寿命状态之间罕见转换的过渡状态的数据;然而,现有的计算方法往往收集不到有关这些状态的信息。一种机器学习技术利用具有百年历史的承诺函数理论解决了这一难题。
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引用次数: 0
Integrating computational and experimental worlds 将计算和实验世界融为一体。
IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2024-06-03 DOI: 10.1038/s43588-024-00649-w
Ananya Rastogi
Dr Kelly Ruggles, associate professor at New York University Langone Health, discusses with Nature Computational Science how she uses computational approaches to gain insights into cancer, inflammation and cardiovascular disease, as well as the importance of mentorship.
纽约大学朗贡卫生学院副教授凯利-鲁格尔斯博士与《自然-计算科学》杂志讨论了她如何利用计算方法深入了解癌症、炎症和心血管疾病,以及导师的重要性。
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引用次数: 0
期刊
Nature computational science
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