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Learning dynamical models from stochastic trajectories 从随机轨迹学习动力学模型
Pub Date : 2024-06-04 DOI: arxiv-2406.02363
Pierre Ronceray
The dynamics of biological systems, from proteins to cells to organisms, iscomplex and stochastic. To decipher their physical laws, we need to bridgebetween experimental observations and theoretical modeling. Thanks to progressin microscopy and tracking, there is today an abundance of experimentaltrajectories reflecting these dynamical laws. Inferring physical models fromnoisy and imperfect experimental data, however, is challenging. Because thereare no inference methods that are robust and efficient, model reconstructionfrom experimental trajectories is a bottleneck to data-driven biophysics. Inthis Thesis, I present a set of tools developed to bridge this gap and permitrobust and universal inference of stochastic dynamical models from experimentaltrajectories. These methods are rooted in an information-theoretical frameworkthat quantifies how much can be inferred from trajectories that are short,partial and noisy. They permit the efficient inference of dynamical models foroverdamped and underdamped Langevin systems, as well as the inference ofentropy production rates. I finally present early applications of thesetechniques, as well as future research directions.
从蛋白质到细胞再到生物体,生物系统的动力学是复杂而随机的。为了破译它们的物理规律,我们需要在实验观察和理论建模之间架起一座桥梁。得益于显微镜和跟踪技术的进步,如今已有大量反映这些动力学规律的实验轨迹。然而,从杂乱无章和不完美的实验数据中推断物理模型是一项挑战。由于没有稳健高效的推理方法,从实验轨迹重建模型成为数据驱动生物物理学的瓶颈。在这篇论文中,我介绍了为弥合这一差距而开发的一系列工具,它们允许从实验轨迹对随机动力学模型进行稳健而通用的推理。这些方法植根于一个信息论框架,该框架量化了从短小、局部和有噪声的轨迹中能推断出多少东西。这些方法允许高效推断过阻尼和欠阻尼朗文系统的动力学模型,以及推断熵产生率。最后,我将介绍这些技术的早期应用以及未来的研究方向。
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引用次数: 0
Inferring interaction potentials from stochastic particle trajectories 从随机粒子轨迹推断相互作用势
Pub Date : 2024-06-03 DOI: arxiv-2406.01522
Ella M. King, Megan C. Engel, Caroline Martin, Alp M. Sunol, Qian-Ze Zhu, Sam S. Schoenholz, Vinothan N. Manoharan, Michael P. Brenner
Accurate interaction potentials between microscopic components such ascolloidal particles or cells are crucial to understanding a range of processes,including colloidal crystallization, bacterial colony formation, and cancermetastasis. Even in systems where the precise interaction mechanisms areunknown, effective interactions can be measured to inform simulation anddesign. However, these measurements are difficult and time-intensive, and oftenrequire conditions that are drastically different from in situ conditions ofthe system of interest. Moreover, existing methods of measuring interparticlepotentials rely on constraining a small number of particles at equilibrium,placing limits on which interactions can be measured. We introduce a method forinferring interaction potentials directly from trajectory data of interactingparticles. We explicitly solve the equations of motion to find a form of thepotential that maximizes the probability of observing a known trajectory. Ourmethod is valid for systems both in and out of equilibrium, is well-suited tolarge numbers of particles interacting in typical system conditions, and doesnot assume a functional form of the interaction potential. We apply our methodto infer the interactions of colloidal spheres from experimental data,successfully extracting the range and strength of a depletion interaction fromthe motion of the particles.
微观成分(如胶体粒子或细胞)之间精确的相互作用势对于理解一系列过程至关重要,这些过程包括胶体结晶、细菌菌落形成和癌症转移。即使在精确的相互作用机制未知的系统中,也可以测量有效的相互作用,为模拟和设计提供信息。然而,这些测量既困难又耗时,而且所需的条件往往与相关系统的原位条件大相径庭。此外,现有的粒子间势能测量方法依赖于对少量处于平衡状态的粒子进行约束,这就对可以测量的相互作用施加了限制。我们介绍了一种直接从相互作用粒子的轨迹数据推断相互作用势的方法。我们明确地求解运动方程,以找到一种最大化观测已知轨迹概率的相互作用势形式。我们的方法对处于平衡和非平衡状态的系统都有效,非常适合在典型系统条件下相互作用的大量粒子,而且不假定相互作用势的函数形式。我们应用我们的方法从实验数据中推断胶体球的相互作用,成功地从粒子的运动中提取了耗竭相互作用的范围和强度。
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引用次数: 0
Accelerator system parameter estimation using variational autoencoded latent regression 利用变异自动编码潜回归进行加速器系统参数估计
Pub Date : 2024-06-03 DOI: arxiv-2406.01532
Mahindra Rautela, Alan Williams, Alexander Scheinker
Particle accelerators are time-varying systems whose components are perturbedby external disturbances. Tuning accelerators can be a time-consuming processinvolving manual adjustment of multiple components, such as RF cavities, tominimize beam loss due to time-varying drifts. The high dimensionality of thesystem ($sim$100 amplitude and phase RF settings in the LANSCE accelerator)makes it difficult to achieve optimal operation. The time-varying drifts andthe dimensionality make system parameter estimation a challenging optimizationproblem. In this work, we propose a Variational Autoencoded Latent Regression(VALeR) model for robust estimation of system parameters using 2D uniqueprojections of a charged particle beam's 6D phase space. In VALeR, VAE projectsthe phase space projections into a lower-dimensional latent space, and a denseneural network maps the latent space onto the space of system parameters. Thetrained network can predict system parameters for unseen phase spaceprojections. Furthermore, VALeR can generate new projections by randomlysampling the latent space of VAE and also estimate the corresponding systemparameters.
粒子加速器是一种时变系统,其组件会受到外部干扰的扰动。调谐加速器可能是一个耗时的过程,需要手动调整射频腔等多个组件,以尽量减少时变漂移造成的光束损失。系统的高维度(LANSCE 加速器中的 100 美元振幅和相位射频设置)使其难以实现最佳运行。时变漂移和维度使得系统参数估计成为一个具有挑战性的优化问题。在这项工作中,我们提出了一种变异自动编码潜回归(VALeR)模型,利用带电粒子束 6D 相空间的 2D 唯一投影对系统参数进行稳健估计。在 VALeR 模型中,VAE 将相空间投影投射到低维潜在空间中,而密度神经网络则将潜在空间映射到系统参数空间中。经过训练的网络可以预测未知相空间投影的系统参数。此外,VALeR 还能通过对 VAE 的潜空间进行随机抽样生成新的投影,并估算相应的系统参数。
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引用次数: 0
Towards latent space evolution of spatiotemporal dynamics of six-dimensional phase space of charged particle beams 实现带电粒子束六维相空间时空动态的潜空间演化
Pub Date : 2024-06-03 DOI: arxiv-2406.01535
Mahindra Rautela, Alan Williams, Alexander Scheinker
Addressing the charged particle beam diagnostics in accelerators poses aformidable challenge, demanding high-fidelity simulations in limitedcomputational time. Machine learning (ML) based surrogate models have emergedas a promising tool for non-invasive charged particle beam diagnostics. TrainedML models can make predictions much faster than computationally expensivephysics simulations. In this work, we have proposed a temporally structuredvariational autoencoder model to autoregressively forecast the spatiotemporaldynamics of the 15 unique 2D projections of 6D phase space of charged particlebeam as it travels through the LANSCE linear accelerator. In the model, VAEembeds the phase space projections into a lower dimensional latent space. Along-short-term memory network then learns the temporal correlations in thelatent space. The trained network can evolve the phase space projections acrossfurther modules provided the first few modules as inputs. The model predictsall the projections across different modules with low mean squared error andhigh structural similarity index.
解决加速器中的带电粒子束诊断问题是一项艰巨的挑战,需要在有限的计算时间内进行高保真模拟。基于机器学习(ML)的代用模型已成为非侵入式带电粒子束诊断的一种有前途的工具。训练有素的 ML 模型可以比计算昂贵的物理模拟更快地做出预测。在这项工作中,我们提出了一种时间结构变异自动编码器模型,用于自回归预测带电粒子束穿过 LANSCE 直线加速器时 6D 相空间的 15 个独特 2D 投影的时空动态。在该模型中,VAE 将相空间投影嵌入低维潜在空间。然后,沿短期记忆网络学习潜空间中的时间相关性。训练有素的网络可以将前几个模块作为输入,在更多模块中演化出相空间投影。该模型能预测不同模块间的所有投影,且均方误差小,结构相似度指数高。
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引用次数: 0
Predicting the fatigue life of asphalt concrete using neural networks 利用神经网络预测沥青混凝土的疲劳寿命
Pub Date : 2024-06-03 DOI: arxiv-2406.01523
Jakub Houlík, Jan Valentin, Václav Nežerka
Asphalt concrete's (AC) durability and maintenance demands are stronglyinfluenced by its fatigue life. Traditional methods for determining thischaracteristic are both resource-intensive and time-consuming. This studyemploys artificial neural networks (ANNs) to predict AC fatigue life, focusingon the impact of strain level, binder content, and air-void content. Leveraginga substantial dataset, we tailored our models to effectively handle the widerange of fatigue life data, typically represented on a logarithmic scale. Themean square logarithmic error was utilized as the loss function to enhanceprediction accuracy across all levels of fatigue life. Through comparativeanalysis of various hyperparameters, we developed a machine-learning model thatcaptures the complex relationships within the data. Our findings demonstratethat higher binder content significantly enhances fatigue life, while theinfluence of air-void content is more variable, depending on binder levels.Most importantly, this study provides insights into the intricacies of usingANNs for modeling, showcasing their potential utility with larger datasets. Thecodes developed and the data used in this study are provided as open source ona GitHub repository, with a link included in the paper for full access.
沥青混凝土(AC)的耐久性和维护需求受其疲劳寿命的影响很大。确定这一特性的传统方法既耗费资源又耗费时间。本研究利用人工神经网络(ANN)预测混凝土的疲劳寿命,重点关注应变水平、粘结剂含量和空隙含量的影响。利用大量数据集,我们对模型进行了调整,以有效处理通常以对数标度表示的更广泛的疲劳寿命数据。我们使用主题平方对数误差作为损失函数,以提高所有疲劳寿命水平的预测精度。通过对各种超参数的比较分析,我们开发出了一种机器学习模型,可以捕捉数据中的复杂关系。我们的研究结果表明,粘结剂含量越高,疲劳寿命就越长,而空隙含量的影响则因粘结剂含量的不同而变化较大。最重要的是,这项研究深入揭示了使用ANNs建模的复杂性,展示了其在更大数据集中的潜在用途。本研究中开发的代码和使用的数据在 GitHub 存储库中以开放源代码的形式提供,论文中包含了一个链接,供全文访问。
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引用次数: 0
Towards Universal Unfolding of Detector Effects in High-Energy Physics using Denoising Diffusion Probabilistic Models 利用去噪扩散概率模型实现高能物理中探测器效应的普遍展开
Pub Date : 2024-06-03 DOI: arxiv-2406.01507
Camila Pazos, Shuchin Aeron, Pierre-Hugues Beauchemin, Vincent Croft, Martin Klassen, Taritree Wongjirad
The unfolding of detector effects in experimental data is critical forenabling precision measurements in high-energy physics. However, traditionalunfolding methods face challenges in scalability, flexibility, and dependenceon simulations. We introduce a novel unfolding approach using conditionalDenoising Diffusion Probabilistic Models (cDDPM). Our method utilizes the cDDPMfor a non-iterative, flexible posterior sampling approach, which exhibits astrong inductive bias that allows it to generalize to unseen physics processeswithout explicitly assuming the underlying distribution. We test our approachby training a single cDDPM to perform multidimensional particle-wise unfoldingfor a variety of physics processes, including those not seen during training.Our results highlight the potential of this method as a step towards a"universal" unfolding tool that reduces dependence on truth-level assumptions.
在实验数据中展开探测器效应对于实现高能物理的精确测量至关重要。然而,传统的展开方法在可扩展性、灵活性和对模拟的依赖性方面面临挑战。我们介绍了一种使用条件失真扩散概率模型(cDDPM)的新型展开方法。我们的方法利用 cDDPM 作为一种非迭代、灵活的后验采样方法,它表现出强烈的归纳偏差,使其能够泛化到未见的物理过程,而无需明确假设底层分布。我们通过训练单个 cDDPM 来对各种物理过程(包括训练过程中未见的物理过程)执行多维粒子式展开来测试我们的方法。我们的结果凸显了这种方法的潜力,它是向 "通用 "展开工具迈出的一步,减少了对真理级假设的依赖。
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引用次数: 0
SwdFold:A Reweighting and Unfolding method based on Optimal Transport Theory SwdFold:基于最优传输理论的重权重和展开方法
Pub Date : 2024-06-02 DOI: arxiv-2406.01635
Chu-Cheng Pan, Xiang Dong, Yu-Chang Sun, Ao-Yan Cheng, Ao-Bo Wang, Yu-Xuan Hu, Hao Cai
High-energy physics experiments rely heavily on precise measurements ofenergy and momentum, yet face significant challenges due to detectorlimitations, calibration errors, and the intrinsic nature of particleinteractions. Traditional unfolding techniques have been employed to correctfor these distortions, yet they often suffer from model dependency andstability issues. We present a novel method, SwdFold, which utilizes theprinciples of optimal transport to provide a robust, model-independentframework to estimate the probability density ratio for data unfolding. It notonly unfold the toy experimental event by reweighted simulated datadistributions closely with true distributions but also maintains the integrityof physical features across various observables. We can expect it can enablemore reliable predictions and comprehensive analyses as a high precisionreweighting and unfolding tool in high-energy physics.
高能物理实验在很大程度上依赖于能量和动量的精确测量,但由于探测器的限制、校准误差以及粒子相互作用的内在性质,这些实验面临着巨大的挑战。传统的展开技术被用来校正这些扭曲,但它们往往存在模型依赖性和稳定性问题。我们提出了一种新方法--SwdFold,它利用最优传输原理提供了一个稳健的、与模型无关的框架,用于估计数据展开的概率密度比。它不仅通过重新加权模拟数据分布来展开玩具实验事件,使之与真实分布接近,而且还保持了各种观测指标物理特征的完整性。我们可以期待它作为高能物理中的高精度再加权和展开工具,能够实现更可靠的预测和更全面的分析。
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引用次数: 0
Kolmogorov-Arnold Network for Satellite Image Classification in Remote Sensing 用于遥感卫星图像分类的 Kolmogorov-Arnold 网络
Pub Date : 2024-06-02 DOI: arxiv-2406.00600
Minjong Cheon
In this research, we propose the first approach for integrating theKolmogorov-Arnold Network (KAN) with various pre-trained Convolutional NeuralNetwork (CNN) models for remote sensing (RS) scene classification tasks usingthe EuroSAT dataset. Our novel methodology, named KCN, aims to replacetraditional Multi-Layer Perceptrons (MLPs) with KAN to enhance classificationperformance. We employed multiple CNN-based models, including VGG16,MobileNetV2, EfficientNet, ConvNeXt, ResNet101, and Vision Transformer (ViT),and evaluated their performance when paired with KAN. Our experimentsdemonstrated that KAN achieved high accuracy with fewer training epochs andparameters. Specifically, ConvNeXt paired with KAN showed the best performance,achieving 94% accuracy in the first epoch, which increased to 96% and remainedconsistent across subsequent epochs. The results indicated that KAN and MLPboth achieved similar accuracy, with KAN performing slightly better in laterepochs. By utilizing the EuroSAT dataset, we provided a robust testbed toinvestigate whether KAN is suitable for remote sensing classification tasks.Given that KAN is a novel algorithm, there is substantial capacity for furtherdevelopment and optimization, suggesting that KCN offers a promisingalternative for efficient image analysis in the RS field.
在这项研究中,我们利用 EuroSAT 数据集,首次提出了将 Kolmogorov-Arnold 网络(KAN)与各种预先训练好的卷积神经网络(CNN)模型相结合的方法,用于遥感(RS)场景分类任务。我们的新方法被命名为 KCN,旨在用 KAN 替代传统的多层感知器(MLP),以提高分类性能。我们采用了多种基于 CNN 的模型,包括 VGG16、MobileNetV2、EfficientNet、ConvNeXt、ResNet101 和 Vision Transformer (ViT),并评估了它们与 KAN 配对后的性能。我们的实验证明,KAN 可以用较少的训练历时和参数实现较高的准确率。具体来说,与 KAN 配对的 ConvNeXt 表现最佳,在第一个训练周期中达到 94% 的准确率,在随后的训练周期中准确率提高到 96%,并且保持一致。结果表明,KAN 和 MLP 的准确率相近,KAN 在后期的表现略好。通过利用 EuroSAT 数据集,我们为研究 KAN 是否适用于遥感分类任务提供了一个稳健的测试平台。鉴于 KAN 是一种新型算法,有很大的进一步开发和优化空间,这表明 KCN 为遥感领域的高效图像分析提供了一种很有前途的替代方法。
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引用次数: 0
Non-destructive Degradation Pattern Decoupling for Ultra-early Battery Prototype Verification Using Physics-informed Machine Learning 利用物理信息机器学习对超早期电池原型进行非破坏性降解模式解耦验证
Pub Date : 2024-06-01 DOI: arxiv-2406.00276
Shengyu Tao, Mengtian Zhang, Zixi Zhao, Haoyang Li, Ruifei Ma, Yunhong Che, Xin Sun, Lin Su, Xiangyu Chen, Zihao Zhou, Heng Chang, Tingwei Cao, Xiao Xiao, Yaojun Liu, Wenjun Yu, Zhongling Xu, Yang Li, Han Hao, Xuan Zhang, Xiaosong Hu, Guangmin ZHou
Manufacturing complexities and uncertainties have impeded the transition frommaterial prototypes to commercial batteries, making prototype verificationcritical to quality assessment. A fundamental challenge involves decipheringintertwined chemical processes to characterize degradation patterns and theirquantitative relationship with battery performance. Here we show that aphysics-informed machine learning approach can quantify and visualizetemporally resolved losses concerning thermodynamics and kinetics only usingelectric signals. Our method enables non-destructive degradation patterncharacterization, expediting temperature-adaptable predictions of entirelifetime trajectories, rather than end-of-life points. The verification speedis 25 times faster yet maintaining 95.1% accuracy across temperatures. Suchadvances facilitate more sustainable management of defective prototypes beforemassive production, establishing a 19.76 billion USD scrap material recyclingmarket by 2060 in China. By incorporating stepwise charge acceptance as ameasure of the initial manufacturing variability of normally identicalbatteries, we can immediately identify long-term degradation variations. Weattribute the predictive power to interpreting machine learning insights usingmaterial-agnostic featurization taxonomy for degradation pattern decoupling.Our findings offer new possibilities for dynamic system analysis, such asbattery prototype degradation, demonstrating that complex pattern evolutionscan be accurately predicted in a non-destructive and data-driven fashion byintegrating physics-informed machine learning.
制造的复杂性和不确定性阻碍了从材料原型到商用电池的过渡,因此原型验证对于质量评估至关重要。一个根本性的挑战是破解相互交织的化学过程,以描述降解模式及其与电池性能的定量关系。在这里,我们展示了一种物理信息机器学习方法,该方法仅使用电信号就能量化和可视化有关热力学和动力学的时间分辨损失。我们的方法实现了非破坏性降解模式识别,加快了对整个寿命轨迹而不是寿命终点的温度适应性预测。验证速度提高了 25 倍,同时在不同温度下保持 95.1% 的准确率。这种进步有助于在大规模生产前对有缺陷的原型进行更可持续的管理,到 2060 年,中国将形成 197.6 亿美元的废旧材料回收市场。通过将逐步充电接受度作为衡量正常相同电池初始制造变异性的指标,我们可以立即识别长期降解变异。我们的研究结果为电池原型降解等动态系统分析提供了新的可能性,证明了通过整合物理信息机器学习,可以以非破坏性和数据驱动的方式准确预测复杂的模式演变。
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引用次数: 0
Error evaluation of partial scattering functions obtained from contrast variation small-angle neutron scattering 从对比变化小角中子散射中获得的部分散射函数的误差评估
Pub Date : 2024-06-01 DOI: arxiv-2406.00311
Koichi Mayumi, Shinya Miyajima, Ippei Obayashi, Kazuaki Tanaka
Contrast variation small-angle neutron scattering (CV-SANS) is a powerfultool to evaluate the structure of multi-component systems by decomposingscattering intensities $I$ measured with different scattering contrasts intopartial scattering functions $S$ of self- and cross-correlations betweencomponents. The measured $I$ contains a measurement error, $Delta I$, and$Delta I$ results in an uncertainty of partial scattering functions, $DeltaS$. However, the error propagation from $Delta I$ to $Delta S$ has not beenquantitatively clarified. In this work, we have established deterministic andstatistical approaches to determine $Delta S$ from $Delta I$. We have appliedthe two methods to experimental SANS data of polyrotaxane solutions withdifferent contrasts, and have successfully estimated the errors of $S$. Thequantitative error estimation of $S$ offers us a strategy to optimize thecombination of scattering contrasts to minimize error propagation.
对比度变化小角中子散射(CV-SANS)是一种评估多组分系统结构的强大工具,它将不同散射对比度下测得的散射强度 $I$ 分解为各组分间自相关和交叉相关的部分散射函数 $S$。测得的 $I$ 包含测量误差,即 $Delta I$,而 $Delta I$ 则导致部分散射函数的不确定性,即 $/DeltaS$。然而,从 $Delta I$ 到 $Delta S$ 的误差传播尚未定量阐明。在这项工作中,我们建立了从 $Delta I$ 确定 $Delta S$ 的确定性方法和统计方法。我们将这两种方法应用于不同对比度的聚氧乙烯溶液的 SANS 实验数据,并成功地估算出了 $S$的误差。对 $S$ 的定量误差估计为我们提供了优化散射对比度组合的策略,使误差传播最小化。
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引用次数: 0
期刊
arXiv - PHYS - Data Analysis, Statistics and Probability
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