基于合成数据训练的晶体学深度残差网络。

IF 2.6 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-01-01 DOI:10.1107/S2059798323010586
Derek Mendez, James M Holton, Artem Y Lyubimov, Sabine Hollatz, Irimpan I Mathews, Aleksander Cichosz, Vardan Martirosyan, Teo Zeng, Ryan Stofer, Ruobin Liu, Jinhu Song, Scott McPhillips, Mike Soltis, Aina E Cohen
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引用次数: 0

摘要

使用人工智能处理衍射图像面临的挑战是,需要收集大量精确设计的训练数据集。为了解决这个问题,我们开发了一个名为 Resonet 的代码库,用于合成衍射数据并在这些数据上训练残差神经网络。本文展示了 Resonet 的两种按图案划分的功能:(i) 解析晶体分辨率和 (ii) 识别重叠晶格。Resonet 在同步加速器实验和 X 射线自由电子激光实验的衍射图像汇编中进行了测试。最重要的是,这些模型可在图形处理单元上轻松执行,因此大大优于传统算法。虽然 Resonet 目前用于为斯坦福同步辐射光源的大分子晶体学用户提供实时反馈,但其基于 Python 的简单界面使其很容易嵌入到其他处理框架中。这项工作凸显了基于物理的模拟在训练深度神经网络方面的实用性,并为开发其他模型以增强衍射收集和分析奠定了基础。
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Deep residual networks for crystallography trained on synthetic data.

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

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来源期刊
Acta Crystallographica. Section D, Structural Biology
Acta Crystallographica. Section D, Structural Biology BIOCHEMICAL RESEARCH METHODSBIOCHEMISTRY &-BIOCHEMISTRY & MOLECULAR BIOLOGY
CiteScore
4.50
自引率
13.60%
发文量
216
期刊介绍: Acta Crystallographica Section D welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules or the methods used to determine them. Reports on new structures of biological importance may address the smallest macromolecules to the largest complex molecular machines. These structures may have been determined using any structural biology technique including crystallography, NMR, cryoEM and/or other techniques. The key criterion is that such articles must present significant new insights into biological, chemical or medical sciences. The inclusion of complementary data that support the conclusions drawn from the structural studies (such as binding studies, mass spectrometry, enzyme assays, or analysis of mutants or other modified forms of biological macromolecule) is encouraged. Methods articles may include new approaches to any aspect of biological structure determination or structure analysis but will only be accepted where they focus on new methods that are demonstrated to be of general applicability and importance to structural biology. Articles describing particularly difficult problems in structural biology are also welcomed, if the analysis would provide useful insights to others facing similar problems.
期刊最新文献
Reconsideration of the P-clusters in VFe proteins using the bond-valence method: towards their electron transfer and protonation. Making the most of an abundance of data. AlphaFold-guided molecular replacement for solving challenging crystal structures. Useful experimental aspects of small-wedge synchrotron crystallography for accurate structure analysis of protein molecules. Peter Main (1939-2024).
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