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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 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
Publisher Correction: The curious case of the test set AUROC 出版商更正:测试集 AUROC 的奇特案例
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-12 DOI: 10.1038/s42256-024-00834-6
Michael Roberts, Alon Hazan, Sören Dittmer, James H. F. Rudd, Carola-Bibiane Schönlieb
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引用次数: 0
Equivariant 3D-conditional diffusion model for molecular linker design 用于分子连接体设计的等变三维条件扩散模型
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-11 DOI: 10.1038/s42256-024-00815-9
Ilia Igashov, Hannes Stärk, Clément Vignac, Arne Schneuing, Victor Garcia Satorras, Pascal Frossard, Max Welling, Michael Bronstein, Bruno Correia
Fragment-based drug discovery has been an effective paradigm in early-stage drug development. An open challenge in this area is designing linkers between disconnected molecular fragments of interest to obtain chemically relevant candidate drug molecules. In this work, we propose DiffLinker, an E(3)-equivariant three-dimensional conditional diffusion model for molecular linker design. Given a set of disconnected fragments, our model places missing atoms in between and designs a molecule incorporating all the initial fragments. Unlike previous approaches that are only able to connect pairs of molecular fragments, our method can link an arbitrary number of fragments. Additionally, the model automatically determines the number of atoms in the linker and its attachment points to the input fragments. We demonstrate that DiffLinker outperforms other methods on the standard datasets, generating more diverse and synthetically accessible molecules. We experimentally test our method in real-world applications, showing that it can successfully generate valid linkers conditioned on target protein pockets. Fragment-based molecular design uses chemical motifs and combines them into bio-active compounds. While this approach has grown in capability, molecular linker methods are restricted to linking fragments one by one, which makes the search for effective combinations harder. Igashov and colleagues use a conditional diffusion model to link multiple fragments in a one-shot generative process.
基于片段的药物发现一直是早期药物开发的有效范例。这一领域的一个挑战是如何设计互不相连的分子片段之间的连接物,以获得化学相关的候选药物分子。在这项工作中,我们提出了 DiffLinker--一种用于分子连接体设计的 E(3)- 等价三维条件扩散模型。给定一组断开的片段,我们的模型将缺失的原子放在中间,并设计出一个包含所有初始片段的分子。与以往只能连接成对分子片段的方法不同,我们的方法可以连接任意数量的片段。此外,该模型还能自动确定连接体中原子的数量及其与输入片段的连接点。我们证明,DiffLinker 在标准数据集上的表现优于其他方法,它生成的分子更多样化,更易于合成。我们在实际应用中对我们的方法进行了实验测试,结果表明它能成功生成以目标蛋白质口袋为条件的有效连接体。
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引用次数: 0
A neural speech decoding framework leveraging deep learning and speech synthesis 利用深度学习和语音合成的神经语音解码框架
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-08 DOI: 10.1038/s42256-024-00824-8
Xupeng Chen, Ran Wang, Amirhossein Khalilian-Gourtani, Leyao Yu, Patricia Dugan, Daniel Friedman, Werner Doyle, Orrin Devinsky, Yao Wang, Adeen Flinker
Decoding human speech from neural signals is essential for brain–computer interface (BCI) technologies that aim to restore speech in populations with neurological deficits. However, it remains a highly challenging task, compounded by the scarce availability of neural signals with corresponding speech, data complexity and high dimensionality. Here we present a novel deep learning-based neural speech decoding framework that includes an ECoG decoder that translates electrocorticographic (ECoG) signals from the cortex into interpretable speech parameters and a novel differentiable speech synthesizer that maps speech parameters to spectrograms. We have developed a companion speech-to-speech auto-encoder consisting of a speech encoder and the same speech synthesizer to generate reference speech parameters to facilitate the ECoG decoder training. This framework generates natural-sounding speech and is highly reproducible across a cohort of 48 participants. Our experimental results show that our models can decode speech with high correlation, even when limited to only causal operations, which is necessary for adoption by real-time neural prostheses. Finally, we successfully decode speech in participants with either left or right hemisphere coverage, which could lead to speech prostheses in patients with deficits resulting from left hemisphere damage. Recent research has focused on restoring speech in populations with neurological deficits. Chen, Wang et al. develop a framework for decoding speech from neural signals, which could lead to innovative speech prostheses.
从神经信号中解码人类语音对于旨在恢复神经功能障碍人群语音的脑机接口(BCI)技术至关重要。然而,这仍然是一项极具挑战性的任务,而具有相应语音、数据复杂性和高维度的神经信号的稀缺性又加剧了这项任务的难度。在这里,我们提出了一种新颖的基于深度学习的神经语音解码框架,其中包括一个可将大脑皮层的皮质电图(ECoG)信号转化为可解释的语音参数的 ECoG 解码器,以及一个可将语音参数映射到频谱图的新颖的可微分语音合成器。我们开发了一个配套的语音到语音自动编码器,由语音编码器和相同的语音合成器组成,用于生成参考语音参数,以方便 ECoG 解码器的训练。该框架能生成自然的语音,并且在 48 名参与者中具有很高的可重复性。我们的实验结果表明,我们的模型能以高相关性解码语音,即使仅限于因果运算,这对于实时神经义肢的采用是必要的。最后,我们成功地对左半球或右半球覆盖的参与者进行了语音解码,这可能会为左半球受损导致功能障碍的患者提供语音义肢。
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引用次数: 0
Geometry-enhanced pretraining on interatomic potentials 几何增强型原子间电位预训练
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-05 DOI: 10.1038/s42256-024-00818-6
Taoyong Cui, Chenyu Tang, Mao Su, Shufei Zhang, Yuqiang Li, Lei Bai, Yuhan Dong, Xingao Gong, Wanli Ouyang
Machine learning interatomic potentials (MLIPs) describe the interactions between atoms in materials and molecules by learning them from a reference database generated by ab initio calculations. MLIPs can accurately and efficiently predict such interactions and have been applied to various fields of physical science. However, high-performance MLIPs rely on a large amount of labelled data, which are costly to obtain by ab initio calculations. Here we propose a geometric structure learning framework that leverages unlabelled configurations to improve the performance of MLIPs. Our framework consists of two stages: first, using classical molecular dynamics simulations to generate unlabelled configurations of the target molecular system; and second, applying geometry-enhanced self-supervised learning techniques, including masking, denoising and contrastive learning, to capture structural information. We evaluate our framework on various benchmarks ranging from small molecule datasets to complex periodic molecular systems with more types of elements. We show that our method significantly improves the accuracy and generalization of MLIPs with only a few additional computational costs and is compatible with different invariant or equivariant graph neural network architectures. Our method enhances MLIPs and advances the simulations of molecular systems. Using machine learning methods to model interatomic potentials enables molecular dynamics simulations with ab initio level accuracy at a relatively low computational cost, but requires a large number of labelled training data obtained through expensive ab initio computations. Cui and colleagues propose a geometric learning framework that leverages self-supervised learning pretraining to enhance existing machine learning based interatomic potential models at a negligible additional computational cost.
机器学习原子间势(MLIPs)通过学习由 ab initio 计算生成的参考数据库来描述材料和分子中原子间的相互作用。MLIPs 可以准确、高效地预测这种相互作用,已被应用于物理科学的各个领域。然而,高性能的 MLIPs 依赖于大量的标记数据,而通过 ab initio 计算获得这些数据的成本很高。在这里,我们提出了一个几何结构学习框架,利用未标记的构型来提高 MLIPs 的性能。我们的框架包括两个阶段:首先,利用经典分子动力学模拟生成目标分子系统的无标签构型;其次,应用几何增强型自监督学习技术,包括掩蔽、去噪和对比学习,以捕捉结构信息。我们在从小分子数据集到包含更多元素类型的复杂周期分子系统的各种基准上评估了我们的框架。我们的研究表明,我们的方法大大提高了 MLIPs 的准确性和泛化能力,只增加了少量计算成本,而且与不同的不变或等变图神经网络架构兼容。我们的方法增强了 MLIPs,推进了分子系统的模拟。
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引用次数: 0
Tandem mass spectrum prediction for small molecules using graph transformers 利用图变换器进行小分子串联质谱预测
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-05 DOI: 10.1038/s42256-024-00816-8
Adamo Young, Hannes Röst, Bo Wang
Tandem mass spectra capture fragmentation patterns that provide key structural information about molecules. Although mass spectrometry is applied in many areas, the vast majority of small molecules lack experimental reference spectra. For over 70 years, spectrum prediction has remained a key challenge in the field. Existing deep learning methods do not leverage global structure in the molecule, potentially resulting in difficulties when generalizing to new data. In this work we propose the MassFormer model for accurately predicting tandem mass spectra. MassFormer uses a graph transformer architecture to model long-distance relationships between atoms in the molecule. The transformer module is initialized with parameters obtained through a chemical pretraining task, then fine-tuned on spectral data. MassFormer outperforms competing approaches for spectrum prediction on multiple datasets and accurately models the effects of collision energy. Gradient-based attribution methods reveal that MassFormer can identify compositional relationships between peaks in the spectrum. When applied to spectrum identification problems, MassFormer generally surpasses the performance of existing prediction-based methods. Identifying compounds in tandem mass spectrometry requires extensive databases of known compounds or computational methods to simulate spectra for samples not found in databases. Simulating tandem mass spectra is still challenging, and long-range connections in particular are difficult to model for graph neural networks. Young and colleagues use a graph transformer model to learn patterns of long-distance relations between atoms and molecules.
串联质谱捕捉碎片模式,提供分子的关键结构信息。尽管质谱技术应用于许多领域,但绝大多数小分子缺乏实验参考光谱。70 多年来,光谱预测一直是这一领域的关键挑战。现有的深度学习方法无法利用分子中的全局结构,这可能导致在推广新数据时遇到困难。在这项工作中,我们提出了准确预测串联质谱的 MassFormer 模型。MassFormer 使用图转换器架构来模拟分子中原子间的长距离关系。转换器模块使用通过化学预训练任务获得的参数进行初始化,然后根据光谱数据进行微调。在多个数据集的光谱预测方面,MassFormer 的表现优于其他竞争方法,并能准确模拟碰撞能量的影响。基于梯度的归因方法表明,MassFormer 可以识别光谱中峰值之间的成分关系。当应用于光谱识别问题时,MassFormer 的性能普遍超过了现有的基于预测的方法。
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引用次数: 0
A 5′ UTR language model for decoding untranslated regions of mRNA and function predictions 用于 mRNA 非翻译区解码和功能预测的 5′ UTR 语言模型
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-05 DOI: 10.1038/s42256-024-00823-9
Yanyi Chu, Dan Yu, Yupeng Li, Kaixuan Huang, Yue Shen, Le Cong, Jason Zhang, Mengdi Wang
The 5′ untranslated region (UTR), a regulatory region at the beginning of a messenger RNA (mRNA) molecule, plays a crucial role in regulating the translation process and affects the protein expression level. Language models have showcased their effectiveness in decoding the functions of protein and genome sequences. Here, we introduce a language model for 5′ UTR, which we refer to as the UTR-LM. The UTR-LM is pretrained on endogenous 5′ UTRs from multiple species and is further augmented with supervised information including secondary structure and minimum free energy. We fine-tuned the UTR-LM in a variety of downstream tasks. The model outperformed the best known benchmark by up to 5% for predicting the mean ribosome loading, and by up to 8% for predicting the translation efficiency and the mRNA expression level. The model was also applied to identifying unannotated internal ribosome entry sites within the untranslated region and improved the area under the precision–recall curve from 0.37 to 0.52 compared to the best baseline. Further, we designed a library of 211 new 5′ UTRs with high predicted values of translation efficiency and evaluated them via a wet-laboratory assay. Experiment results confirmed that our top designs achieved a 32.5% increase in protein production level relative to well-established 5′ UTRs optimized for therapeutics. The 5′ untranslated region is a critical regulatory region of mRNA, influencing gene expression regulation and translation. Chu, Yu and colleagues develop a language model for analysing untranslated regions of mRNA. The model, pretrained on data from diverse species, enhances the prediction of mRNA translation activities and has implications for new vaccine design.
5′ 非翻译区(UTR)是信使 RNA(mRNA)分子开头的一个调节区,在调节翻译过程和影响蛋白质表达水平方面起着至关重要的作用。语言模型在解码蛋白质和基因组序列的功能方面展示了其有效性。在这里,我们介绍一种针对 5′ UTR 的语言模型,我们称之为 UTR-LM。UTR-LM 在多个物种的内源 5′ UTR 上进行了预训练,并利用二级结构和最小自由能等监督信息进一步增强。我们在各种下游任务中对 UTR-LM 进行了微调。在预测平均核糖体负载量方面,该模型优于已知最佳基准模型达 5%;在预测翻译效率和 mRNA 表达水平方面,优于已知最佳基准模型达 8%。该模型还被用于识别非翻译区内未注释的内部核糖体进入位点,与最佳基准相比,精确度-召回曲线下的面积从 0.37 提高到了 0.52。此外,我们还设计了一个由 211 个具有较高翻译效率预测值的新 5′ UTR 组成的文库,并通过湿实验室实验对其进行了评估。实验结果证实,与经过优化的成熟 5′ UTR 相比,我们的顶级设计使蛋白质生产水平提高了 32.5%。
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引用次数: 0
The curious case of the test set AUROC 测试集 AUROC 的奇特情况
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-04 DOI: 10.1038/s42256-024-00817-7
Michael Roberts, Alon Hazan, Sören Dittmer, James H. F. Rudd, Carola-Bibiane Schönlieb
The area under the receiver operating characteristic curve (AUROC) of the test set is used throughout machine learning (ML) for assessing a model’s performance. However, when concordance is not the only ambition, this gives only a partial insight into performance, masking distribution shifts of model outputs and model instability.
在整个机器学习(ML)过程中,测试集的接收者工作特征曲线下面积(AUROC)被用来评估模型的性能。然而,当一致性不是唯一的目标时,这只能部分反映模型的性能,掩盖模型输出的分布偏移和模型的不稳定性。
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引用次数: 0
Reusability report: Uncovering associations in biomedical bipartite networks via a bilinear attention network with domain adaptation 可重用性报告:通过具有领域适应性的双线性注意力网络揭示生物医学双方位网络中的关联性
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-04 DOI: 10.1038/s42256-024-00822-w
Tao Xu, Haoyuan Shi, Wanling Gao, Xiaosong Wang, Zhenyu Yue
Conditional domain adversarial learning presents a promising approach for enhancing the generalizability of deep learning-based methods. Inspired by the efficacy of conditional domain adversarial networks, Bai and colleagues introduced DrugBAN, a methodology designed to explicitly learn pairwise local interactions between drugs and targets. DrugBAN leverages drug molecular graphs and target protein sequences, employing conditional domain adversarial networks to improve the ability to adapt to out-of-distribution data and thereby ensuring superior prediction accuracy for new drug–target pairs. Here we examine the reusability of DrugBAN and extend the evaluation of its generalizability across a wider range of biomedical contexts beyond the original datasets. Various clustering-based strategies are implemented to resplit the source and target domains to assess the robustness of DrugBAN. We also apply this cross-domain adaptation technique to the prediction of cell line–drug responses and mutation–drug associations. The analysis serves as a stepping-off point to better understand and establish a general template applicable to link prediction tasks in biomedical bipartite networks. In early 2023, Bai and colleagues presented DrugBAN, an interpretable method for drug–target prediction. In this Reusability Report, Xu and colleagues reproduce the original findings and provide a careful exploration of cross-domain adaptability.
条件域对抗学习为提高基于深度学习的方法的普适性提供了一种前景广阔的方法。受条件域对抗网络功效的启发,Bai及其同事推出了DrugBAN,这是一种旨在明确学习药物与靶标之间成对局部相互作用的方法。DrugBAN 利用药物分子图和靶标蛋白质序列,采用条件域对抗网络来提高适应分布外数据的能力,从而确保新药-靶标配对的预测准确性。在此,我们研究了 DrugBAN 的可重用性,并在原始数据集之外的更广泛的生物医学环境中扩展了对其通用性的评估。我们采用了各种基于聚类的策略来重新分割源域和目标域,以评估 DrugBAN 的鲁棒性。我们还将这种跨域适应技术应用于细胞系-药物反应和突变-药物关联的预测。这项分析为更好地理解和建立适用于生物医学双元网络中链接预测任务的通用模板提供了一个起点。
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引用次数: 0
Author Correction: A soft robot that adapts to environments through shape change 作者更正:通过形状变化适应环境的软体机器人
IF 23.8 1区 计算机科学 Q1 Computer Science Pub Date : 2024-04-01 DOI: 10.1038/s42256-024-00814-w
Dylan S. Shah, Joshua P. Powers, Liana G. Tilton, Sam Kriegman, Josh Bongard, Rebecca Kramer-Bottiglio
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引用次数: 0
期刊
Nature Machine Intelligence
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