冷冻电子显微镜(Cryo-EM)已成为确定蛋白质结构,尤其是近年来大型蛋白质复合物和组件的结构的关键技术。Cryo-EM数据分析中的一个关键挑战是从冷冻EM密度图中自动重建精确的蛋白质结构。在这篇综述中,我们简要概述了从冷冻EM密度图构建蛋白质结构的各种深度学习方法,分析其影响,并讨论准备高质量数据集以培训深度学习模型的挑战。展望未来,需要开发更先进的深度学习模型,以有效地将冷冻EM数据与其他互补数据(例如蛋白质序列和Alphafold预测的结构)相结合,以进一步推进该领域。
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Recent advances in deep learning have enabled us to address the curse of dimensionality (COD) by solving problems in higher dimensions. A subset of such approaches of addressing the COD has led us to solving high-dimensional PDEs. This has resulted in opening doors to solving a variety of real-world problems ranging from mathematical finance to stochastic control for industrial applications. Although feasible, these deep learning methods are still constrained by training time and memory. Tackling these shortcomings, Tensor Neural Networks (TNN) demonstrate that they can provide significant parameter savings while attaining the same accuracy as compared to the classical Dense Neural Network (DNN). In addition, we also show how TNN can be trained faster than DNN for the same accuracy. Besides TNN, we also introduce Tensor Network Initializer (TNN Init), a weight initialization scheme that leads to faster convergence with smaller variance for an equivalent parameter count as compared to a DNN. We benchmark TNN and TNN Init by applying them to solve the parabolic PDE associated with the Heston model, which is widely used in financial pricing theory.
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The findable, accessible, interoperable, and reusable (FAIR) data principles have provided a framework for examining, evaluating, and improving how we share data with the aim of facilitating scientific discovery. Efforts have been made to generalize these principles to research software and other digital products. Artificial intelligence (AI) models -- algorithms that have been trained on data rather than explicitly programmed -- are an important target for this because of the ever-increasing pace with which AI is transforming scientific and engineering domains. In this paper, we propose a practical definition of FAIR principles for AI models and create a FAIR AI project template that promotes adherence to these principles. We demonstrate how to implement these principles using a concrete example from experimental high energy physics: a graph neural network for identifying Higgs bosons decaying to bottom quarks. We study the robustness of these FAIR AI models and their portability across hardware architectures and software frameworks, and report new insights on the interpretability of AI predictions by studying the interplay between FAIR datasets and AI models. Enabled by publishing FAIR AI models, these studies pave the way toward reliable and automated AI-driven scientific discovery.
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Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License.
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Recent developments in the methods of explainable AI (XAI) methods allow researchers to explore the inner workings of deep neural networks (DNNs), revealing crucial information about input-output relationships and realizing how data connects with machine learning models. In this paper we explore interpretability of DNN models designed to identify jets coming from top quark decay in high energy proton-proton collisions at the Large Hadron Collider (LHC). We review a subset of existing top tagger models and explore different quantitative methods to identify which features play the most important roles in identifying the top jets. We also investigate how and why feature importance varies across different XAI metrics, how feature correlations impact their explainability, and how latent space representations encode information as well as correlate with physically meaningful quantities. Our studies uncover some major pitfalls of existing XAI methods and illustrate how they can be overcome to obtain consistent and meaningful interpretation of these models. We additionally illustrate the activity of hidden layers as Neural Activation Pattern (NAP) diagrams and demonstrate how they can be used to understand how DNNs relay information across the layers and how this understanding can help to make such models significantly simpler by allowing effective model reoptimization and hyperparameter tuning. By incorporating observations from the interpretability studies, we obtain state-of-the-art top tagging performance from augmented implementation of existing network
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上下文:大数据的有效处理是SQL和NOSQL数据库的一项具有挑战性的任务,在这种数据库中,有效的软件体系结构起着至关重要的作用。 SQL数据库设计用于构建数据和支持垂直可扩展性。相反,水平可伸缩性由NOSQL数据库支持,并且可以有效地处理较大的非结构化数据。可以根据组织的需求选择正确的范式;但是,做出正确的选择通常可能具有挑战性。 SQL和NOSQL数据库遵循不同的体系结构。同样,混合模型之后是NOSQL数据库的每个类别。因此,对于多个云服务提供商(CSP)的云消费者来说,数据移动变得困难。此外,每个云平台IAAS,PAAS,SaaS和DBAAS还监视各种范式。目的:该系统文献综述(SLR)旨在研究与SQL和NOSQL数据库软件体系结构相关的相关文章,并解决各种云平台之间的数据可移植性和互操作性。最新的状态通过观察缩放,性能,可用性,一致性和分片特性,介绍了SQL和NOSQL数据库的许多性能比较研究。根据研究研究,NOSQL数据库设计的结构可以是大数据分析的正确选择,而SQL数据库适合OLTP数据库。研究人员提出了许多与云中数据流动相关的方法。开发了基于平台的API,这使用户的数据移动变得困难。因此,在跨多个CSP的数据移动期间发现了数据可移植性和互操作性问题。为了最大程度地减少开发人员的努力和互操作性,要求统一的API使数据移动在各种云平台之间相对易于访问。
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现实世界的面部表达识别(FER)数据集遭受吵闹的注释,由于众包,表达式的歧义,注释者的主观性和类间的相似性。但是,最近的深层网络具有强大的能力,可以记住嘈杂的注释导致腐蚀功能嵌入和泛化不良的能力。为了处理嘈杂的注释,我们提出了一个动态FER学习框架(DNFER),其中根据训练过程中的动态类特定阈值选择了干净的样品。具体而言,DNFER基于使用选定的干净样品和使用所有样品的无监督培训的监督培训。在训练过程中,每个微型批次的平均后类概率被用作动态类特异性阈值,以选择干净的样品进行监督训练。该阈值与噪声率无关,与其他方法不同,不需要任何干净的数据。此外,要从所有样品中学习,使用无监督的一致性损失对齐弱调节图像和强大图像之间的后验分布。我们证明了DNFER在合成和实际噪声注释的FER数据集(如RaFDB,Ferplus,Sfew和altimpnet)上的鲁棒性。
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部分微分方程(PDE)用于对科学和工程中的各种动力系统进行建模。深度学习的最新进展使我们能够以新的方式解决维度的诅咒,从而在更高的维度中解决它们。但是,深度学习方法受到训练时间和记忆的约束。为了解决这些缺点,我们实施了张量神经网络(TNN),这是一种量子启发的神经网络体系结构,利用张量网络的想法来改进深度学习方法。我们证明,与经典密集神经网络(DNN)相比,TNN提供了明显的参数节省,同时获得了与经典密集的神经网络相同的准确性。此外,我们还展示了如何以相同的精度来比DNN更快地训练TNN。我们通过将它们应用于求解抛物线PDE,特别是Black-Scholes-Barenblatt方程,该方程广泛用于金融定价理论,基于基准测试。还讨论了进一步的例子,例如汉密尔顿 - 雅各比 - 贝尔曼方程。
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鉴于HEP研究的核心,数据科学(DS)和机器学习(ML)在高能量物理学(HEP)中的作用增长良好和相关。此外,利用物理数据固有的对称性激发了物理信息的ML作为计算机科学研究的充满活力的子场。 HEP研究人员从广泛使用的材料中受益匪浅,可用于教育,培训和劳动力开发。他们还为这些材料做出了贡献,并为DS/ML相关的字段提供软件。物理部门越来越多地在DS,ML和物理学的交集上提供课程,通常使用HEP研究人员开发的课程,并涉及HEP中使用的开放软件和数据。在这份白皮书中,我们探讨了HEP研究与DS/ML教育之间的协同作用,讨论了此交叉路口的机会和挑战,并提出了将是互惠互利的社区活动。
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自动情感识别在许多领域都有应用,例如教育,游戏,软件开发,汽车,医疗保健等。但是,在野外数据集上实现可观的绩效是无琐的任务。野外数据集虽然比合成数据集更好地代表了现实世界中的情况,但前者遇到了不完整标签的问题。受到半监督学习的启发,在本文中,我们在第四次情感行为分析(ABAW)2022竞赛中介绍了提交的多任务学习挑战。在这项挑战中考虑的三个任务是价估计(VA)估计,表达式分为6个基本(愤怒,厌恶,恐惧,幸福,悲伤,惊喜),中立和“其他”类别和12个行动单位(au)编号au - \ {1,2,4,6,7,10,12,15,15,23,24,25,26 \}。我们的方法半监督的多任务面部情感情感识别标题为\ textbf {ss-mfar}使用一个深层残留网络,每个任务都具有特定任务分类器以及每个表达式类别的自适应阈值,每个表达式类别和半监督学习。源代码可从https://github.com/1980x/abaw202​​22dmacs获得。
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