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Zero-shot transfer of protein sequence likelihood models to thermostability prediction 蛋白质序列似然模型在热稳定性预测中的零点转移
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-20 DOI: 10.1038/s42256-024-00887-7
Shawn Reeves, Subha Kalyaanamoorthy
Protein sequence likelihood models (PSLMs) are an emerging class of self-supervised deep learning algorithms that learn probability distributions over amino acid identities conditioned on structural or evolutionary context. Recently, PSLMs have demonstrated impressive performance in predicting the relative fitness of variant sequences without any task-specific training, but their potential to address a central goal of protein engineering—enhancing stability—remains underexplored. Here we comprehensively analyse the capacity for zero-shot transfer of eight PSLMs towards prediction of relative thermostability for variants of hundreds of heterogeneous proteins across several quantitative datasets. PSLMs are compared with popular task-specific stability models, and we show that some PSLMs have competitive performance when the appropriate statistics are considered. We highlight relative strengths and weaknesses of PSLMs and examine their complementarity with task-specific models, specifically focusing our analyses on stability-engineering applications. Our results indicate that all PSLMs can appreciably augment the predictions of existing methods by integrating insights from their disparate training objectives, suggesting a path forward in the stagnating field of computational stability prediction. Stabilization of proteins is a key task in protein engineering; however, current methods to predict mutant stability face a number of limitations. Reeves and Kalyaanamoorthy study the performance of self-supervised protein sequence likelihood models for stability prediction and find that combining them with task-specific supervised models can lead to appreciable practical gains.
蛋白质序列似然模型(PSLM)是一类新兴的自我监督深度学习算法,它以结构或进化背景为条件学习氨基酸同一性的概率分布。最近,PSLMs 在预测变异序列的相对适合度方面表现出了令人印象深刻的性能,而无需任何特定任务的训练,但它们在实现蛋白质工程的核心目标--增强稳定性--方面的潜力仍未得到充分开发。在这里,我们全面分析了八种 PSLMs 在多个定量数据集上预测数百种异质蛋白质变体相对热稳定性的零点转移能力。我们将 PSLM 与流行的特定任务稳定性模型进行了比较,结果表明,如果考虑到适当的统计数据,一些 PSLM 的性能具有竞争力。我们强调了 PSLM 的相对优缺点,并研究了它们与特定任务模型的互补性,特别是将分析重点放在稳定性工程应用上。我们的研究结果表明,所有 PSLM 都能通过整合不同训练目标的见解,显著增强现有方法的预测能力,为停滞不前的计算稳定性预测领域指明了前进的道路。蛋白质的稳定性是蛋白质工程中的一项关键任务;然而,目前预测突变体稳定性的方法面临着许多限制。Reeves 和 Kalyaanamoorthy 研究了用于稳定性预测的自监督蛋白质序列似然模型的性能,发现将它们与特定任务的监督模型相结合可以带来显著的实际收益。
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引用次数: 0
An end-to-end recurrent compressed sensing method to denoise, detect and demix calcium imaging data 用于钙成像数据去噪、检测和去混合的端到端循环压缩传感方法
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-19 DOI: 10.1038/s42256-024-00892-w
Kangning Zhang, Sean Tang, Vivian Zhu, Majd Barchini, Weijian Yang
Two-photon calcium imaging provides large-scale recordings of neuronal activities at cellular resolution. A robust, automated and high-speed pipeline to simultaneously segment the spatial footprints of neurons and extract their temporal activity traces while decontaminating them from background, noise and overlapping neurons is highly desirable to analyse calcium imaging data. Here we demonstrate DeepCaImX, an end-to-end deep learning method based on an iterative shrinkage-thresholding algorithm and a long short-term memory neural network to achieve the above goals altogether at a very high speed and without any manually tuned hyperparameter. DeepCaImX is a multi-task, multi-class and multi-label segmentation method composed of a compressed sensing-inspired neural network with a recurrent layer and fully connected layers. The neural network can simultaneously generate accurate neuronal footprints and extract clean neuronal activity traces from calcium imaging data. We trained the neural network with simulated datasets and benchmarked it against existing state-of-the-art methods with in vivo experimental data. DeepCaImX outperforms existing methods in the quality of segmentation and temporal trace extraction as well as processing speed. DeepCaImX is highly scalable and will benefit the analysis of mesoscale calcium imaging. Extracting time traces and spatial footprints of single neurons from population calcium imaging data presents challenges. Zhang et al. introduce a deep learning method that efficiently segments neuronal footprints and extracts activity traces from these data. The method surpasses existing approaches in both quality and speed, providing a robust tool for large-scale neuronal circuit analysis.
双光子钙成像技术能以细胞分辨率对神经元活动进行大规模记录。在分析钙成像数据时,我们非常需要一种稳健、自动化和高速的管道来同时分割神经元的空间足迹并提取其时间活动轨迹,同时消除背景、噪声和重叠神经元的污染。在这里,我们展示了 DeepCaImX,一种基于迭代收缩阈值算法和长短期记忆神经网络的端到端深度学习方法,它能以极高的速度实现上述目标,而且无需手动调整超参数。DeepCaImX 是一种多任务、多类和多标签分割方法,由一个包含递归层和全连接层的压缩传感启发神经网络组成。该神经网络可同时生成精确的神经元足迹,并从钙成像数据中提取干净的神经元活动轨迹。我们用模拟数据集训练了神经网络,并用体内实验数据将其与现有的最先进方法进行了比较。DeepCaImX 在分割和时间轨迹提取质量以及处理速度方面都优于现有方法。DeepCaImX 具有很强的可扩展性,对中尺度钙成像分析大有裨益。
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引用次数: 0
Pre-training with fractional denoising to enhance molecular property prediction 利用分数去噪进行预训练,提高分子特性预测能力
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-18 DOI: 10.1038/s42256-024-00900-z
Yuyan Ni, Shikun Feng, Xin Hong, Yuancheng Sun, Wei-Ying Ma, Zhi-Ming Ma, Qiwei Ye, Yanyan Lan
Deep learning methods have been considered promising for accelerating molecular screening in drug discovery and material design. Due to the limited availability of labelled data, various self-supervised molecular pre-training methods have been presented. Although many existing methods utilize common pre-training tasks in computer vision and natural language processing, they often overlook the fundamental physical principles governing molecules. In contrast, applying denoising in pre-training can be interpreted as an equivalent force learning, but the limited noise distribution introduces bias into the molecular distribution. To address this issue, we introduce a molecular pre-training framework called fractional denoising, which decouples noise design from the constraints imposed by force learning equivalence. In this way, the noise becomes customizable, allowing for incorporating chemical priors to substantially improve the molecular distribution modelling. Experiments demonstrate that our framework consistently outperforms existing methods, establishing state-of-the-art results across force prediction, quantum chemical properties and binding affinity tasks. The refined noise design enhances force accuracy and sampling coverage, which contribute to the creation of physically consistent molecular representations, ultimately leading to superior predictive performance. Denoising methods introduce useful priors in pre-training methods for molecular property prediction, but chemically unaware noise can lead to inaccurate predictions in downstream tasks. A molecular pre-training framework that uses fractional denoising to improve molecular distribution modelling is proposed, resulting in better predictions in various property prediction tasks.
深度学习方法被认为有望加速药物发现和材料设计中的分子筛选。由于标记数据的可用性有限,人们提出了各种自监督分子预训练方法。虽然许多现有方法利用了计算机视觉和自然语言处理中常见的预训练任务,但它们往往忽略了分子的基本物理原理。相比之下,在预训练中应用去噪可以解释为等效的力学习,但有限的噪声分布会给分子分布带来偏差。为了解决这个问题,我们引入了一种称为分数去噪的分子预训练框架,它将噪声设计与力学习等效性所施加的约束分离开来。通过这种方式,噪声变得可定制,从而可以结合化学先验,大幅改进分子分布建模。实验证明,我们的框架始终优于现有方法,在力预测、量子化学特性和结合亲和力任务方面取得了最先进的结果。经过改进的噪声设计提高了力的准确性和采样覆盖率,有助于创建物理上一致的分子表征,最终实现卓越的预测性能。
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引用次数: 0
Sparse learned kernels for interpretable and efficient medical time series processing 用于可解释和高效医学时间序列处理的稀疏学习核
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-18 DOI: 10.1038/s42256-024-00898-4
Sully F. Chen, Zhicheng Guo, Cheng Ding, Xiao Hu, Cynthia Rudin
Rapid, reliable and accurate interpretation of medical time series signals is crucial for high-stakes clinical decision-making. Deep learning methods offered unprecedented performance in medical signal processing but at a cost: they were compute intensive and lacked interpretability. We propose sparse mixture of learned kernels (SMoLK), an interpretable architecture for medical time series processing. SMoLK learns a set of lightweight flexible kernels that form a single-layer sparse neural network, providing not only interpretability but also efficiency, robustness and generalization to unseen data distributions. We introduce parameter reduction techniques to reduce the size of SMoLK networks and maintain performance. We test SMoLK on two important tasks common to many consumer wearables: photoplethysmography artefact detection and atrial fibrillation detection from single-lead electrocardiograms. We find that SMoLK matches the performance of models orders of magnitude larger. It is particularly suited for real-time applications using low-power devices, and its interpretability benefits high-stakes situations. Deep learning excels in medical signal processing but lacks interpretability. An efficient, interpretable architecture that matches the performance of larger models at orders of magnitude fewer parameters in tasks common to wearable devices has been proposed.
对医学时间序列信号进行快速、可靠和准确的解读,对于事关重大的临床决策至关重要。深度学习方法为医学信号处理提供了前所未有的性能,但也付出了代价:计算密集且缺乏可解释性。我们提出了稀疏混合学习核(SMoLK),这是一种用于医学时间序列处理的可解释架构。SMoLK 学习一组轻量级的灵活内核,形成单层稀疏神经网络,不仅提供可解释性,还提供效率、鲁棒性和对未知数据分布的泛化。我们引入了参数缩减技术,以缩小 SMoLK 网络的规模并保持性能。我们在许多消费类可穿戴设备常见的两个重要任务上测试了 SMoLK:光电血压计伪影检测和单导联心电图的心房颤动检测。我们发现,SMoLK 的性能可媲美更大数量级的模型。它特别适用于使用低功耗设备的实时应用,其可解释性有利于高风险情况。
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引用次数: 0
Realizing full-body control of humanoid robots 实现仿人机器人的全身控制
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-11 DOI: 10.1038/s42256-024-00891-x
Guangliang Li, Randy Gomez
Using deep reinforcement learning, flexible skills and behaviours emerge in humanoid robots, as demonstrated in two recent reports.
正如最近的两篇报告所展示的那样,利用深度强化学习,仿人机器人可以具备灵活的技能和行为。
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引用次数: 0
Author Correction: Integrated structure prediction of protein–protein docking with experimental restraints using ColabDock 作者更正:利用 ColabDock 对带有实验约束的蛋白质-蛋白质对接进行综合结构预测
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-10 DOI: 10.1038/s42256-024-00905-8
Shihao Feng, Zhenyu Chen, Chengwei Zhang, Yuhao Xie, Sergey Ovchinnikov, Yi Qin Gao, Sirui Liu
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引用次数: 0
Accelerating histopathology workflows with generative AI-based virtually multiplexed tumour profiling 利用基于生成式人工智能的虚拟多重肿瘤特征分析加速组织病理学工作流程
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-09 DOI: 10.1038/s42256-024-00889-5
Pushpak Pati, Sofia Karkampouna, Francesco Bonollo, Eva Compérat, Martina Radić, Martin Spahn, Adriano Martinelli, Martin Wartenberg, Marianna Kruithof-de Julio, Marianna Rapsomaniki
Understanding the spatial heterogeneity of tumours and its links to disease initiation and progression is a cornerstone of cancer biology. Presently, histopathology workflows heavily rely on hematoxylin and eosin and serial immunohistochemistry staining, a cumbersome, tissue-exhaustive process that results in non-aligned tissue images. We propose the VirtualMultiplexer, a generative artificial intelligence toolkit that effectively synthesizes multiplexed immunohistochemistry images for several antibody markers (namely AR, NKX3.1, CD44, CD146, p53 and ERG) from only an input hematoxylin and eosin image. The VirtualMultiplexer captures biologically relevant staining patterns across tissue scales without requiring consecutive tissue sections, image registration or extensive expert annotations. Thorough qualitative and quantitative assessment indicates that the VirtualMultiplexer achieves rapid, robust and precise generation of virtually multiplexed imaging datasets of high staining quality that are indistinguishable from the real ones. The VirtualMultiplexer is successfully transferred across tissue scales and patient cohorts with no need for model fine-tuning. Crucially, the virtually multiplexed images enabled training a graph transformer that simultaneously learns from the joint spatial distribution of several proteins to predict clinically relevant endpoints. We observe that this multiplexed learning scheme was able to greatly improve clinical prediction, as corroborated across several downstream tasks, independent patient cohorts and cancer types. Our results showcase the clinical relevance of artificial intelligence-assisted multiplexed tumour imaging, accelerating histopathology workflows and cancer biology. VirtualMultiplexer is a generative AI tool that produces realistic multiplexed immunohistochemistry images from tissue biopsies. The generated images could be used to improve clinical predictions, enhancing histopathology workflows and accelerating cancer research.
了解肿瘤的空间异质性及其与疾病发生和发展的关系是癌症生物学的基石。目前,组织病理学工作流程严重依赖苏木精、伊红和连续免疫组化染色,这是一个繁琐的组织排查过程,会导致组织图像不对齐。我们提出的 VirtualMultiplexer 是一种生成式人工智能工具包,它能从输入的苏木精和伊红图像中有效合成多个抗体标记物(即 AR、NKX3.1、CD44、CD146、p53 和 ERG)的多重免疫组化图像。VirtualMultiplexer 可捕捉跨组织尺度的生物相关染色模式,而无需连续的组织切片、图像注册或大量的专家注释。全面的定性和定量评估表明,VirtualMultiplexer 能够快速、稳健、精确地生成染色质量高且与真实染色无异的虚拟多重成像数据集。虚拟多路复用器可成功跨组织尺度和患者群组转移,无需对模型进行微调。最重要的是,虚拟多路复用图像能够训练图转换器,该转换器可同时从多个蛋白质的联合空间分布中学习,以预测临床相关终点。我们观察到,这种多重学习方案能够大大提高临床预测能力,这一点在多个下游任务、独立患者群和癌症类型中都得到了证实。我们的研究结果展示了人工智能辅助多路复用肿瘤成像的临床意义,加快了组织病理学工作流程和癌症生物学的发展。
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引用次数: 0
Efficient and scalable reinforcement learning for large-scale network control 用于大规模网络控制的高效可扩展强化学习
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-09-03 DOI: 10.1038/s42256-024-00879-7
Chengdong Ma, Aming Li, Yali Du, Hao Dong, Yaodong Yang
The primary challenge in the development of large-scale artificial intelligence (AI) systems lies in achieving scalable decision-making—extending the AI models while maintaining sufficient performance. Existing research indicates that distributed AI can improve scalability by decomposing complex tasks and distributing them across collaborative nodes. However, previous technologies suffered from compromised real-world applicability and scalability due to the massive requirement of communication and sampled data. Here we develop a model-based decentralized policy optimization framework, which can be efficiently deployed in multi-agent systems. By leveraging local observation through the agent-level topological decoupling of global dynamics, we prove that this decentralized mechanism achieves accurate estimations of global information. Importantly, we further introduce model learning to reinforce the optimal policy for monotonic improvement with a limited amount of sampled data. Empirical results on diverse scenarios show the superior scalability of our approach, particularly in real-world systems with hundreds of agents, thereby paving the way for scaling up AI systems. Applying large-scale AI systems to multi-agent scenarios in real-world settings is challenging. The authors propose a decentralized model-based policy optimization framework to enable scalable decision-making.
开发大规模人工智能(AI)系统的主要挑战在于实现可扩展决策--在扩展人工智能模型的同时保持足够的性能。现有研究表明,分布式人工智能可以通过分解复杂任务并将其分配到协作节点来提高可扩展性。然而,由于需要大量的通信和采样数据,以前的技术在现实世界中的适用性和可扩展性大打折扣。在这里,我们开发了一种基于模型的分散式策略优化框架,可以高效地部署在多代理系统中。通过全局动态的代理级拓扑解耦利用局部观察,我们证明了这种分散机制可以实现对全局信息的精确估计。重要的是,我们进一步引入了模型学习,以强化最优策略,从而在采样数据量有限的情况下实现单调改进。在不同场景下的实证结果表明,我们的方法具有卓越的可扩展性,尤其是在拥有数百个代理的真实世界系统中,从而为人工智能系统的扩展铺平了道路。
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引用次数: 0
A large-scale audit of dataset licensing and attribution in AI 对人工智能中的数据集许可和归属进行大规模审计
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-08-30 DOI: 10.1038/s42256-024-00878-8
Shayne Longpre, Robert Mahari, Anthony Chen, Naana Obeng-Marnu, Damien Sileo, William Brannon, Niklas Muennighoff, Nathan Khazam, Jad Kabbara, Kartik Perisetla, Xinyi (Alexis) Wu, Enrico Shippole, Kurt Bollacker, Tongshuang Wu, Luis Villa, Sandy Pentland, Sara Hooker
The race to train language models on vast, diverse and inconsistently documented datasets raises pressing legal and ethical concerns. To improve data transparency and understanding, we convene a multi-disciplinary effort between legal and machine learning experts to systematically audit and trace more than 1,800 text datasets. We develop tools and standards to trace the lineage of these datasets, including their source, creators, licences and subsequent use. Our landscape analysis highlights sharp divides in the composition and focus of data licenced for commercial use. Important categories including low-resource languages, creative tasks and new synthetic data all tend to be restrictively licenced. We observe frequent miscategorization of licences on popular dataset hosting sites, with licence omission rates of more than 70% and error rates of more than 50%. This highlights a crisis in misattribution and informed use of popular datasets driving many recent breakthroughs. Our analysis of data sources also explains the application of copyright law and fair use to finetuning data. As a contribution to continuing improvements in dataset transparency and responsible use, we release our audit, with an interactive user interface, the Data Provenance Explorer, to enable practitioners to trace and filter on data provenance for the most popular finetuning data collections: www.dataprovenance.org . The Data Provenance Initiative audits over 1,800 text artificial intelligence (AI) datasets, analysing trends, permissions of use and global representation. It exposes frequent errors on several major data hosting sites and offers tools for transparent and informed use of AI training data.
在庞大、多样且记录不一致的数据集上训练语言模型的竞赛引发了紧迫的法律和道德问题。为了提高数据的透明度和理解度,我们召集了法律和机器学习专家开展多学科合作,对 1800 多个文本数据集进行系统审核和追踪。我们开发了各种工具和标准来追踪这些数据集的源流,包括它们的来源、创建者、许可证和后续使用情况。我们的分析结果表明,获得商业使用许可的数据在构成和重点方面存在明显差异。包括低资源语言、创造性任务和新合成数据在内的重要类别都倾向于采用限制性许可。我们观察到,在流行的数据集托管网站上,许可证经常被错误归类,许可证遗漏率超过 70%,错误率超过 50%。这凸显了在错误归类和知情使用流行数据集方面存在的危机,而这正是近期许多突破性进展的驱动力。我们对数据源的分析还解释了版权法和合理使用在数据微调中的应用。作为对持续提高数据集透明度和负责任使用的贡献,我们发布了带有交互式用户界面的数据出处资源管理器(Data Provenance Explorer)的审计报告,使从业人员能够追踪和过滤最流行的微调数据集的数据出处:www.dataprovenance.org 。数据出处倡议 "对1800多个人工智能(AI)文本数据集进行审计,分析趋势、使用权限和全球代表性。它揭露了几个主要数据托管网站上经常出现的错误,并为透明、知情地使用人工智能训练数据提供了工具。
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引用次数: 0
What is in your LLM-based framework? 您的基于 LLM 的框架中有哪些内容?
IF 18.8 1区 计算机科学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-08-30 DOI: 10.1038/s42256-024-00896-6
To maintain high standards in clarity and reproducibility, authors need to clearly mention and describe the use of GPT-4 and other large language models in their work.
为了保持高标准的清晰度和可重复性,作者需要清楚地提及并描述 GPT-4 和其他大型语言模型在其工作中的使用情况。
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引用次数: 0
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Nature Machine Intelligence
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