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Deep learning prediction of glycopeptide tandem mass spectra powers glycoproteomics 糖肽串联质谱的深度学习预测为糖蛋白组学提供动力
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-30 DOI: 10.1038/s42256-024-00875-x
Yu Zong, Yuxin Wang, Xipeng Qiu, Xuanjing Huang, Liang Qiao
Protein glycosylation, a post-translational modification of proteins by glycans, plays an important role in numerous physiological and pathological cellular functions. Glycoproteomics, the study of protein glycosylation on a proteome-wide scale, utilizes liquid chromatography coupled with tandem mass spectrometry (MS/MS) to get combinational information on glycosylation site, glycosylation level and glycan structure. However, current database searching methods for glycoproteomics often struggle with glycan structure determination due to the limited occurrence of structure-determining ions. Although spectral searching methods can leverage fragment intensity to facilitate the structure identification of glycopeptides, their application is hindered by difficulties in spectral library construction. In this work, we present DeepGP, a hybrid deep learning framework based on transformer and graph neural networks, for the prediction of MS/MS spectra and retention time of glycopeptides. Two graph neural network modules are employed to capture the branched glycan structure and predict glycan ion intensity, respectively. Additionally, a pretraining strategy is implemented to alleviate the insufficiency of glycoproteomics data. Testing on multiple biological datasets, DeepGP accurately predicts MS/MS spectra and retention time of glycopeptides, closely aligning with the experimental results. Comprehensive benchmarking of DeepGP on synthetic and biological datasets validates its effectiveness in distinguishing similar glycans. Based on various decoy methods, DeepGP in combination with database searching can increase glycopeptide detection sensitivity. We anticipate that DeepGP can inspire extensive future work in glycoproteomics. Glycosylation, a prevalent type of post-translational modification of proteins by glycan molecules, plays a major role in the proteome. Zong et al. present DeepGP, a hybrid deep learning framework based on transformer and graph neural network architectures that accurately predicts tandem mass spectra and retention times of glycopeptides, providing information on glycosylation and glycan structure.
蛋白质糖基化是蛋白质通过聚糖进行的翻译后修饰,在细胞的多种生理和病理功能中发挥着重要作用。糖蛋白组学是在整个蛋白质组范围内研究蛋白质糖基化的方法,它利用液相色谱法和串联质谱法(MS/MS)获得糖基化位点、糖基化水平和聚糖结构的综合信息。然而,目前用于糖蛋白组学的数据库搜索方法往往由于结构决定离子的出现有限而难以确定糖分子结构。虽然光谱搜索方法可以利用片段强度来促进糖肽的结构鉴定,但其应用受到光谱库构建困难的阻碍。在这项工作中,我们提出了基于变换器和图神经网络的混合深度学习框架 DeepGP,用于预测糖肽的 MS/MS 图谱和保留时间。我们采用了两个图神经网络模块,分别用于捕捉支链聚糖结构和预测聚糖离子强度。此外,还采用了预训练策略,以缓解糖蛋白组学数据不足的问题。在多个生物数据集上进行测试后,DeepGP 准确预测了糖肽的 MS/MS 图谱和保留时间,与实验结果非常吻合。在合成和生物数据集上对 DeepGP 进行的全面基准测试验证了它在区分相似聚糖方面的有效性。基于各种诱饵方法,DeepGP 与数据库搜索相结合可以提高糖肽检测灵敏度。我们预计,DeepGP 将激发未来在糖蛋白组学领域的广泛工作。
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引用次数: 0
Advanced AI assistants that act on our behalf may not be ethically or legally feasible 代表我们行事的高级人工智能助手可能在道德或法律上不可行
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-29 DOI: 10.1038/s42256-024-00877-9
Silvia Milano, Sven Nyholm
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引用次数: 0
A question of trust for AI research in medicine 医学人工智能研究的信任问题
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-24 DOI: 10.1038/s42256-024-00880-0
Medical research is one of the most impactful areas for machine learning applications, but access to large and diverse health datasets is needed for models to be useful. Winning trust from patients by demonstrating that data are handled securely and effectively is key.
医学研究是对机器学习应用影响最大的领域之一,但要使模型发挥作用,就需要获取大量、多样的健康数据集。关键是要证明数据得到了安全有效的处理,从而赢得患者的信任。
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引用次数: 0
DNA language model GROVER learns sequence context in the human genome DNA 语言模型 GROVER 学习人类基因组中的序列上下文
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-23 DOI: 10.1038/s42256-024-00872-0
Melissa Sanabria, Jonas Hirsch, Pierre M. Joubert, Anna R. Poetsch
Deep-learning models that learn a sense of language on DNA have achieved a high level of performance on genome biological tasks. Genome sequences follow rules similar to natural language but are distinct in the absence of a concept of words. We established byte-pair encoding on the human genome and trained a foundation language model called GROVER (Genome Rules Obtained Via Extracted Representations) with the vocabulary selected via a custom task, next-k-mer prediction. The defined dictionary of tokens in the human genome carries best the information content for GROVER. Analysing learned representations, we observed that trained token embeddings primarily encode information related to frequency, sequence content and length. Some tokens are primarily localized in repeats, whereas the majority widely distribute over the genome. GROVER also learns context and lexical ambiguity. Average trained embeddings of genomic regions relate to functional genomics annotation and thus indicate learning of these structures purely from the contextual relationships of tokens. This highlights the extent of information content encoded by the sequence that can be grasped by GROVER. On fine-tuning tasks addressing genome biology with questions of genome element identification and protein–DNA binding, GROVER exceeds other models’ performance. GROVER learns sequence context, a sense for structure and language rules. Extracting this knowledge can be used to compose a grammar book for the code of life. Genomes can be modelled with language approaches by treating nucleotide bases A, C, G and T like text, but there is no natural concept of what the words would be and whether there is even a ‘language’ to be learned this way. Sanabria et al. have developed a language model called GROVER that learns with a ‘vocabulary’ of genome sequences with byte-pair encoding, a method from text compression, and shows good performance on genome biological tasks.
在 DNA 上学习语感的深度学习模型在基因组生物任务上取得了很高的性能。基因组序列遵循与自然语言类似的规则,但由于没有单词概念而与自然语言截然不同。我们在人类基因组上建立了字节对编码,并训练了一个名为 GROVER(通过提取表征获得的基因组规则)的基础语言模型,其词汇量是通过自定义任务--下一个 k-mer 预测--选择的。人类基因组中定义的词库为 GROVER 提供了最好的信息内容。通过分析学习到的表征,我们发现训练有素的标记嵌入主要编码与频率、序列内容和长度相关的信息。有些标记主要集中在重复序列中,而大多数标记则广泛分布在基因组中。GROVER 还能学习上下文和词汇歧义。基因组区域的平均训练嵌入与功能基因组注释有关,因此表明这些结构的学习纯粹来自于标记的上下文关系。这凸显了 GROVER 所能掌握的序列编码信息内容的范围。在针对基因组生物学的微调任务中,GROVER 在基因组元素识别和蛋白质-DNA 结合方面的表现超过了其他模型。GROVER 可以学习序列上下文、结构感和语言规则。提取这些知识可用于编写生命代码语法书。
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引用次数: 0
Partial-convolution-implemented generative adversarial network for global oceanic data assimilation 用于全球海洋数据同化的部分卷积生成对抗网络
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-22 DOI: 10.1038/s42256-024-00867-x
Yoo-Geun Ham, Yong-Sik Joo, Jeong-Hwan Kim, Jeong-Gil Lee
The oceanic data assimilation (DA) system has been developed to optimally combine numerical-model predictions with actual measurements from the ocean to create the best estimates of current ocean conditions and their uncertainties, improving our ability to forecast and understand the global climate variations. We developed DeepDA, a global oceanic DA system using deep learning, by integrating a partial convolutional neural network and a generative adversarial network. Partial convolution serves as an observation operator, mapping irregular observational data onto gridded fields, while generative adversarial network incorporates observational information from previous time frames. Our observing system simulation experiments, using simulated observations for the DA, revealed that DeepDA markedly reduces analysis error of the oceanic temperature, outperforming both background and observed values. DeepDA’s real-case global temperature reanalysis spanning from 1981 to 2020 accurately reconstructs observed global climatological temperature fields, along with their seasonal cycles, major oceanic temperature variabilities and global warming trend. Developed solely with a long-term control simulation, DeepDA lowers technical hurdles in creating global ocean reanalysis datasets using multiple numerical models’ physical constraints, thereby diminishing systematic uncertainties in estimating global oceanic states over decades with these models. Data assimilation (DA) techniques are commonly used to assess global Earth system variability but require considerable computational resources and struggle to handle sparse observational data. Ham and colleagues introduce a partial convolution and generative adversarial network-based global oceanic DA system and successfully reconstruct the observed global temperature in a real case study with smaller computational costs than traditional DA systems.
开发海洋数据同化(DA)系统的目的是将数值模式预测与海洋实际测量结果进行优化组合,从而对当前海洋状况及其不确定性做出最佳估计,从而提高我们预测和了解全球气候变异的能力。我们通过整合部分卷积神经网络和生成对抗网络,开发了使用深度学习的全球海洋数据分析系统 DeepDA。部分卷积作为观测算子,将不规则的观测数据映射到网格场上,而生成对抗网络则结合了之前时间段的观测信息。我们利用模拟观测数据进行了观测系统模拟实验,结果表明,DeepDA 显著降低了海洋温度的分析误差,优于背景值和观测值。DeepDA的实况全球温度再分析从1981年一直持续到2020年,准确地重建了观测到的全球气候学温度场及其季节周期、主要海洋温度变率和全球变暖趋势。DeepDA 完全是通过长期控制模拟开发的,它降低了利用多种数值模式物理约束条件创建全球海洋再分析数据集的技术障碍,从而减少了利用这些模式估计几十年全球海洋状态的系统不确定性。
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引用次数: 0
A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas 基于变换器的弱监督计算病理学方法,用于胶质瘤的临床分级诊断和分子标记物发现
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-18 DOI: 10.1038/s42256-024-00868-w
Rui Jiang, Xiaoxu Yin, Pengshuai Yang, Lingchao Cheng, Juan Hu, Jiao Yang, Ying Wang, Xiaodan Fu, Li Shang, Liling Li, Wei Lin, Huan Zhou, Fufeng Chen, Xuegong Zhang, Zhongliang Hu, Hairong Lv
The complex diagnostic criteria for gliomas pose great challenges for making accurate diagnoses with computational pathology methods. There are no in-depth analyses of the accuracy, reliability and auxiliary capability of present approaches from a clinical perspective. Previous studies have overlooked the exploration of molecular and morphological correlations. To overcome these limitations, we propose ROAM, a multiple-instance learning model based on large regions of interest and a pyramid transformer. ROAM enlarges regions of interest to facilitate the consideration of tissue contexts. It utilizes the pyramid transformer to model both intrascale and interscale correlations of morphological features and leverages class-specific multiple-instance learning based on attention to extract slide-level visual representations that can be used to diagnose gliomas. Through comprehensive experiments on both in-house and external glioma datasets, we demonstrate that ROAM can automatically capture key morphological features consistent with the experience of pathologists and thus provide accurate, reliable and adaptable clinical-grade diagnoses of gliomas. Moreover, ROAM has clinical value for auxiliary diagnoses and could pave the way for the study of molecular and morphological correlations. ROAM, based on large regions of interest and a pyramid transformer, can automatically capture key morphological features consistent with the experience of pathologists to provide accurate, reliable and adaptable clinical-grade diagnoses of gliomas while advancing the discovery of molecular and morphological markers related to glioma diagnosis.
神经胶质瘤的诊断标准十分复杂,这给利用计算病理学方法做出准确诊断带来了巨大挑战。目前还没有从临床角度对现有方法的准确性、可靠性和辅助能力进行深入分析。以往的研究忽略了对分子和形态学相关性的探讨。为了克服这些局限性,我们提出了基于大兴趣区域和金字塔转换器的多实例学习模型 ROAM。ROAM 扩大了感兴趣区域,便于考虑组织背景。它利用金字塔变换器对形态特征的级内和级间相关性进行建模,并利用基于注意力的特定类别多实例学习来提取可用于诊断胶质瘤的幻灯片级视觉表征。通过对内部和外部胶质瘤数据集的全面实验,我们证明 ROAM 可以自动捕捉与病理学家经验一致的关键形态特征,从而提供准确、可靠和适应性强的胶质瘤临床级诊断。此外,ROAM 还具有辅助诊断的临床价值,可为分子和形态学相关性研究铺平道路。
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引用次数: 0
Automated construction of cognitive maps with visual predictive coding 利用视觉预测编码自动构建认知地图
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-18 DOI: 10.1038/s42256-024-00863-1
James Gornet, Matt Thomson
Humans construct internal cognitive maps of their environment directly from sensory inputs without access to a system of explicit coordinates or distance measurements. Although machine learning algorithms like simultaneous localization and mapping utilize specialized inference procedures to identify visual features and construct spatial maps from visual and odometry data, the general nature of cognitive maps in the brain suggests a unified mapping algorithmic strategy that can generalize to auditory, tactile and linguistic inputs. Here we demonstrate that predictive coding provides a natural and versatile neural network algorithm for constructing spatial maps using sensory data. We introduce a framework in which an agent navigates a virtual environment while engaging in visual predictive coding using a self-attention-equipped convolutional neural network. While learning a next-image prediction task, the agent automatically constructs an internal representation of the environment that quantitatively reflects spatial distances. The internal map enables the agent to pinpoint its location relative to landmarks using only visual information.The predictive coding network generates a vectorized encoding of the environment that supports vector navigation, where individual latent space units delineate localized, overlapping neighbourhoods in the environment. Broadly, our work introduces predictive coding as a unified algorithmic framework for constructing cognitive maps that can naturally extend to the mapping of auditory, sensorimotor and linguistic inputs. Constructing spatial maps from sensory inputs is challenging in both neuroscience and artificial intelligence. Gornet and Thomson show that as an agent navigates an environment, a self-attention neural network using predictive coding can recover the environment’s map in its latent space.
人类直接从感官输入构建内部环境认知地图,而无需使用明确的坐标或距离测量系统。虽然机器学习算法(如同步定位和映射)利用专门的推理程序来识别视觉特征,并从视觉和里程数据中构建空间地图,但大脑中认知地图的普遍性表明,一种统一的映射算法策略可以推广到听觉、触觉和语言输入。在这里,我们证明了预测编码为利用感官数据构建空间地图提供了一种自然、通用的神经网络算法。我们介绍了一个框架,在这个框架中,一个代理在虚拟环境中进行导航,同时利用一个配备自我注意力的卷积神经网络进行视觉预测编码。在学习下一个图像预测任务时,代理会自动构建一个定量反映空间距离的内部环境表征。预测编码网络可生成支持矢量导航的环境矢量化编码,其中单个潜在空间单元可划定环境中局部重叠的邻域。从广义上讲,我们的工作将预测编码引入了构建认知地图的统一算法框架,该框架可自然扩展到听觉、感觉运动和语言输入的映射。
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引用次数: 0
The need for reproducible research in soft robotics 软机器人技术领域需要可重复的研究
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-17 DOI: 10.1038/s42256-024-00869-9
Robert Baines, Dylan Shah, Jeremy Marvel, Jennifer Case, Andrew Spielberg
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引用次数: 0
Realistic morphology-preserving generative modelling of the brain 逼真的大脑形态保存生成模型
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-07-15 DOI: 10.1038/s42256-024-00864-0
Petru-Daniel Tudosiu, Walter H. L. Pinaya, Pedro Ferreira Da Costa, Jessica Dafflon, Ashay Patel, Pedro Borges, Virginia Fernandez, Mark S. Graham, Robert J. Gray, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso
Medical imaging research is often limited by data scarcity and availability. Governance, privacy concerns and the cost of acquisition all restrict access to medical imaging data, which, compounded by the data-hungry nature of deep learning algorithms, limits progress in the field of healthcare AI. Generative models have recently been used to synthesize photorealistic natural images, presenting a potential solution to the data scarcity problem. But are current generative models synthesizing morphologically correct samples? In this work we present a three-dimensional generative model of the human brain that is trained at the necessary scale to generate diverse, realistic-looking, high-resolution and morphologically preserving samples and conditioned on patient characteristics (for example, age and pathology). We show that the synthetic samples generated by the model preserve biological and disease phenotypes and are realistic enough to permit use downstream in well-established image analysis tools. While the proposed model has broad future applicability, such as anomaly detection and learning under limited data, its generative capabilities can be used to directly mitigate data scarcity, limited data availability and algorithmic fairness. Medical imaging research is limited by data availability. To address this challenge, Tudosiu and colleagues develop a 3D generative model of the human brain that can generate high-resolution morphologically correct brains conditioned on patient characteristics.
医学影像研究往往受限于数据的稀缺性和可用性。管理、隐私问题和获取成本都限制了医学影像数据的获取,再加上深度学习算法对数据的渴求,限制了医疗人工智能领域的进展。最近,生成模型被用于合成逼真的自然图像,为数据稀缺问题提供了潜在的解决方案。但目前的生成模型是否能合成形态正确的样本呢?在这项工作中,我们提出了一个人脑三维生成模型,该模型经过必要的训练,可生成多样化、逼真、高分辨率和形态保持良好的样本,并以患者特征(如年龄和病理)为条件。我们的研究表明,该模型生成的合成样本保留了生物和疾病表型,而且足够逼真,可用于成熟的图像分析工具的下游。所提出的模型在未来具有广泛的适用性,如异常检测和有限数据下的学习,其生成能力可用于直接缓解数据稀缺、有限数据可用性和算法公平性等问题。
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引用次数: 0
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
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Nature Machine Intelligence
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