4,287 results on '"Benner, P."'
Search Results
2. Development of Radar and Optical Tracking of Near-Earth Asteroids at the University of Tasmania
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White, Oliver James, Calvés, Guifré Molera, Horiuchi, Shinji, Giorgini, Jon, Stacy, Nick, Cole, Andrew, Phillips, Chris, Edwards, Phil, Kruzins, Ed, Stevens, Jamie, Benner, Lance, and Peters, Edwin
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Physics - Space Physics - Abstract
We detail the use of the University of Tasmania's (UTAS) optical and radio telescopes to conduct observations of near-Earth asteroids from 2021 to 2024. The Canberra Deep Space Communication Complex transmitted a radio signal at 7159.45 MHz, with the radar echo detected by the UTAS radio telescopes. The method of accounting for the Doppler shift between the stations and the near-Earth object is described so that others can implement a similar program. We present our results, with confirmed detections of 1994 PC1 and 2003 UC20 asteroids using the Hobart and Katherine 12-m antennas, demonstrating the feasibility of using small radio telescopes for these observations. Additionally, the recently upgraded Ceduna 30 m antenna was used to detect 2024 MK. Data collected from other observatories, such as Tidbinbilla, as well as the UTAS radar tracking of the moon are also presented in the context of demonstrating the means of applying these Doppler corrections and the accuracy of each method. Optical observations conducted in this period are also detailed as they complement radar observations and aid in refining the orbit parameters., Comment: 21 pages, 16 figures, published in Remote Sensing
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- 2025
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3. Non-intrusive reduced-order modeling for dynamical systems with spatially localized features
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Gkimisis, Leonidas, Aretz, Nicole, Tezzele, Marco, Richter, Thomas, Benner, Peter, and Willcox, Karen E.
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Mathematics - Dynamical Systems - Abstract
This work presents a non-intrusive reduced-order modeling framework for dynamical systems with spatially localized features characterized by slow singular value decay. The proposed approach builds upon two existing methodologies for reduced and full-order non-intrusive modeling, namely Operator Inference (OpInf) and sparse Full-Order Model (sFOM) inference. We decompose the domain into two complementary subdomains which exhibit fast and slow singular value decay. The dynamics of the subdomain exhibiting slow singular value decay are learned with sFOM while the dynamics with intrinsically low dimensionality on the complementary subdomain are learned with OpInf. The resulting, coupled OpInf-sFOM formulation leverages the computational efficiency of OpInf and the high resolution of sFOM, and thus enables fast non-intrusive predictions for conditions beyond those sampled in the training data set. A novel regularization technique with a closed-form solution based on the Gershgorin disk theorem is introduced to promote stable sFOM and OpInf models. We also provide a data-driven indicator for the subdomain selection and ensure solution smoothness over the interface via a post-processing interpolation step. We evaluate the efficiency of the approach in terms of offline and online speedup through a quantitative, parametric computational cost analysis. We demonstrate the coupled OpInf-sFOM formulation for two test cases: a one-dimensional Burgers' model for which accurate predictions beyond the span of the training snapshots are presented, and a two-dimensional parametric model for the Pine Island Glacier ice thickness dynamics, for which the OpInf-sFOM model achieves an average prediction error on the order of $1 \%$ with an online speedup factor of approximately $8\times$ compared to the numerical simulation.
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- 2025
4. Variable selection via fused sparse-group lasso penalized multi-state models incorporating molecular data
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Miah, Kaya, Goeman, Jelle J., Putter, Hein, Kopp-Schneider, Annette, and Benner, Axel
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Statistics - Methodology ,Statistics - Applications - Abstract
In multi-state models based on high-dimensional data, effective modeling strategies are required to determine an optimal, ideally parsimonious model. In particular, linking covariate effects across transitions is needed to conduct joint variable selection. A useful technique to reduce model complexity is to address homogeneous covariate effects for distinct transitions. We integrate this approach to data-driven variable selection by extended regularization methods within multi-state model building. We propose the fused sparse-group lasso (FSGL) penalized Cox-type regression in the framework of multi-state models combining the penalization concepts of pairwise differences of covariate effects along with transition grouping. For optimization, we adapt the alternating direction method of multipliers (ADMM) algorithm to transition-specific hazards regression in the multi-state setting. In a simulation study and application to acute myeloid leukemia (AML) data, we evaluate the algorithm's ability to select a sparse model incorporating relevant transition-specific effects and similar cross-transition effects. We investigate settings in which the combined penalty is beneficial compared to global lasso regularization.
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- 2024
5. SynCoTrain: A Dual Classifier PU-learning Framework for Synthesizability Prediction
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Amariamir, Sasan, George, Janine, and Benner, Philipp
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Condensed Matter - Materials Science ,Computer Science - Machine Learning - Abstract
Material discovery is a cornerstone of modern science, driving advancements in diverse disciplines from biomedical technology to climate solutions. Predicting synthesizability, a critical factor in realizing novel materials, remains a complex challenge due to the limitations of traditional heuristics and thermodynamic proxies. While stability metrics such as formation energy offer partial insights, they fail to account for kinetic factors and technological constraints that influence synthesis outcomes. These challenges are further compounded by the scarcity of negative data, as failed synthesis attempts are often unpublished or context-specific. We present SynCoTrain, a semi-supervised machine learning model designed to predict the synthesizability of materials. SynCoTrain employs a co-training framework leveraging two complementary graph convolutional neural networks: SchNet and ALIGNN. By iteratively exchanging predictions between classifiers, SynCoTrain mitigates model bias and enhances generalizability. Our approach uses Positive and Unlabeled (PU) Learning to address the absence of explicit negative data, iteratively refining predictions through collaborative learning. The model demonstrates robust performance, achieving high recall on internal and leave-out test sets. By focusing on oxide crystals, a well-characterized material family with extensive experimental data, we establish SynCoTrain as a reliable tool for predicting synthesizability while balancing dataset variability and computational efficiency. This work highlights the potential of co-training to advance high-throughput materials discovery and generative research, offering a scalable solution to the challenge of synthesizability prediction.
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- 2024
6. Stability and decay rate estimates for a nonlinear dispersed flow reactor model with boundary control
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Yevgenieva, Yevgeniia, Zuyev, Alexander, and Benner, Peter
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Mathematics - Analysis of PDEs ,Mathematics - Optimization and Control ,49K40, 93D23, 47D03, 35G31 - Abstract
We investigate a nonlinear parabolic partial differential equation whose boundary conditions contain a single control input. This model describes a chemical reaction of the type ''$A \to $ product'', occurring in a dispersed flow tubular reactor. The existence and uniqueness of solutions to the nonlinear Cauchy problem under consideration are established by applying the theory of strongly continuous semigroups of operators. Using Lyapunov's direct method, a feedback control design that ensures the exponential stability of the steady state is proposed, and the exponential decay rate of solutions is evaluated., Comment: 10 pages, 4 figures, 1 table
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- 2024
7. Zeitenwenden: Detecting changes in the German political discourse
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Lange, Kai-Robin, Rieger, Jonas, Benner, Niklas, and Jentsch, Carsten
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Computer Science - Computation and Language - Abstract
From a monarchy to a democracy, to a dictatorship and back to a democracy -- the German political landscape has been constantly changing ever since the first German national state was formed in 1871. After World War II, the Federal Republic of Germany was formed in 1949. Since then every plenary session of the German Bundestag was logged and even has been digitized over the course of the last few years. We analyze these texts using a time series variant of the topic model LDA to investigate which events had a lasting effect on the political discourse and how the political topics changed over time. This allows us to detect changes in word frequency (and thus key discussion points) in political discourse., Comment: 7 pages, 6 figures
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- 2024
8. Discrete empirical interpolation in the tensor t-product framework
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Chellappa, Sridhar, Feng, Lihong, and Benner, Peter
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Mathematics - Numerical Analysis ,Computer Science - Computational Engineering, Finance, and Science ,Mathematics - Dynamical Systems - Abstract
The discrete empirical interpolation method (DEIM) is a well-established approach, widely used for state reconstruction using sparse sensor/measurement data, nonlinear model reduction, and interpretable feature selection. We introduce the tensor t-product Q-DEIM (t-Q-DEIM), an extension of the DEIM framework for dealing with tensor-valued data. The proposed approach seeks to overcome one of the key drawbacks of DEIM, viz., the need for matricizing the data, which can distort any structural and/or geometric information. Our method leverages the recently developed tensor t-product algebra to avoid reshaping the data. In analogy with the standard DEIM, we formulate and solve a tensor-valued least-squares problem, whose solution is achieved through an interpolatory projection. We develop a rigorous, computable upper bound for the error resulting from the t-Q-DEIM approximation. Using five different tensor-valued datasets, we numerically illustrate the better approximation properties of t-Q-DEIM and the significant computational cost reduction it offers., Comment: 37 pages, 22 figures, 1 table
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- 2024
9. Data-Augmented Predictive Deep Neural Network: Enhancing the extrapolation capabilities of non-intrusive surrogate models
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Sun, Shuwen, Feng, Lihong, and Benner, Peter
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Computer Science - Machine Learning ,Mathematics - Numerical Analysis - Abstract
Numerically solving a large parametric nonlinear dynamical system is challenging due to its high complexity and the high computational costs. In recent years, machine-learning-aided surrogates are being actively researched. However, many methods fail in accurately generalizing in the entire time interval $[0, T]$, when the training data is available only in a training time interval $[0, T_0]$, with $T_0
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- 2024
10. Accessible Work-Integrated Learning Experiences: An Analysis of the University of Victoria's CanWork Program
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Niels Melis-De Lamper and Allison Benner
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The University of Victoria, Canada, strives to enhance undergraduate students' labor market readiness through work-integrated learning (WIL) experiences. Students with disabilities have historically encountered low participation and success rates in WIL, potentially resulting in their under-representation in the post-graduation labor market. To address this issue, the CanWork program was created, aimed at eliminating participation barriers in co-operative education for students with disabilities. The program offered tailored support, including job development, one-on-one guidance at all stages, and the removal of grade point average (GPA) thresholds. As of its completion in September 2022, the CanWork program facilitated pre-employment training for 107 students with disabilities and 84 co-op work placements. Demographic-specific and personalized support mechanisms boosted participation and success rates for students with disabilities in work-integrated learning. Furthermore, an analysis of program data highlights that GPA requirements in well-resourced programs create unnecessary barriers for students with disabilities.
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- 2024
11. Structure-preserving learning for multi-symplectic PDEs
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Yıldız, Süleyman, Goyal, Pawan, and Benner, Peter
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Computer Science - Machine Learning ,Mathematics - Numerical Analysis - Abstract
This paper presents an energy-preserving machine learning method for inferring reduced-order models (ROMs) by exploiting the multi-symplectic form of partial differential equations (PDEs). The vast majority of energy-preserving reduced-order methods use symplectic Galerkin projection to construct reduced-order Hamiltonian models by projecting the full models onto a symplectic subspace. However, symplectic projection requires the existence of fully discrete operators, and in many cases, such as black-box PDE solvers, these operators are inaccessible. In this work, we propose an energy-preserving machine learning method that can infer the dynamics of the given PDE using data only, so that the proposed framework does not depend on the fully discrete operators. In this context, the proposed method is non-intrusive. The proposed method is grey box in the sense that it requires only some basic knowledge of the multi-symplectic model at the partial differential equation level. We prove that the proposed method satisfies spatially discrete local energy conservation and preserves the multi-symplectic conservation laws. We test our method on the linear wave equation, the Korteweg-de Vries equation, and the Zakharov-Kuznetsov equation. We test the generalization of our learned models by testing them far outside the training time interval.
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- 2024
12. Active Sampling of Interpolation Points to Identify Dominant Subspaces for Model Reduction
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Reddig, Celine, Goyal, Pawan, Duff, Igor Pontes, and Benner, Peter
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Statistics - Machine Learning ,Computer Science - Machine Learning ,Mathematics - Dynamical Systems ,Mathematics - Numerical Analysis ,15A24, 15A23, 34K06, 34K35, 93C05, 93C23, 41A05 - Abstract
Model reduction is an active research field to construct low-dimensional surrogate models of high fidelity to accelerate engineering design cycles. In this work, we investigate model reduction for linear structured systems using dominant reachable and observable subspaces. When the training set $-$ containing all possible interpolation points $-$ is large, then these subspaces can be determined by solving many large-scale linear systems. However, for high-fidelity models, this easily becomes computationally intractable. To circumvent this issue, in this work, we propose an active sampling strategy to sample only a few points from the given training set, which can allow us to estimate those subspaces accurately. To this end, we formulate the identification of the subspaces as the solution of the generalized Sylvester equations, guiding us to select the most relevant samples from the training set to achieve our goals. Consequently, we construct solutions of the matrix equations in low-rank forms, which encode subspace information. We extensively discuss computational aspects and efficient usage of the low-rank factors in the process of obtaining reduced-order models. We illustrate the proposed active sampling scheme to obtain reduced-order models via dominant reachable and observable subspaces and present its comparison with the method where all the points from the training set are taken into account. It is shown that the active sample strategy can provide us $17$x speed-up without sacrificing any noticeable accuracy., Comment: 20 pages, 9 figures
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- 2024
13. A physics-encoded Fourier neural operator approach for surrogate modeling of divergence-free stress fields in solids
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Khorrami, Mohammad S., Goyal, Pawan, Mianroodi, Jaber R., Svendsen, Bob, Benner, Peter, and Raabe, Dierk
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Computer Science - Computational Engineering, Finance, and Science ,Condensed Matter - Materials Science ,Computer Science - Machine Learning ,Mathematics - Analysis of PDEs - Abstract
The purpose of the current work is the development of a so-called physics-encoded Fourier neural operator (PeFNO) for surrogate modeling of the quasi-static equilibrium stress field in solids. Rather than accounting for constraints from physics in the loss function as done in the (now standard) physics-informed approach, the physics-encoded approach incorporates or "encodes" such constraints directly into the network or operator architecture. As a result, in contrast to the physics-informed approach in which only training is physically constrained, both training and output are physically constrained in the physics-encoded approach. For the current constraint of divergence-free stress, a novel encoding approach based on a stress potential is proposed. As a "proof-of-concept" example application of the proposed PeFNO, a heterogeneous polycrystalline material consisting of isotropic elastic grains subject to uniaxial extension is considered. Stress field data for training are obtained from the numerical solution of a corresponding boundary-value problem for quasi-static mechanical equilibrium. This data is also employed to train an analogous physics-guided FNO (PgFNO) and physics-informed FNO (PiFNO) for comparison. As confirmed by this comparison and as expected on the basis of their differences, the output of the trained PeFNO is significantly more accurate in satisfying mechanical equilibrium than the output of either the trained PgFNO or the trained PiFNO., Comment: 17 pages, 11 figures
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- 2024
14. Fine-mapping the CYP2A6 regional association with nicotine metabolism among African American smokers
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Pouget, Jennie G., Giratallah, Haidy, Langlois, Alec W. R., El-Boraie, Ahmed, Lerman, Caryn, Knight, Jo, Cox, Lisa Sanderson, Nollen, Nikki L., Ahluwalia, Jasjit S., Benner, Christian, Chenoweth, Meghan J., and Tyndale, Rachel F.
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- 2025
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15. Muskelin is a substrate adaptor of the highly regulated Drosophila embryonic CTLH E3 ligase
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Briney, Chloe A, Henriksen, Jesslyn C, Lin, Chenwei, Jones, Lisa A, Benner, Leif, Rains, Addison B, Gutierrez, Roxana, Gafken, Philip R, and Rissland, Olivia S
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- 2025
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16. In vivo hyperphosphorylation of tau is associated with synaptic loss and behavioral abnormalities in the absence of tau seeds
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Watamura, Naoto, Foiani, Martha S., Bez, Sumi, Bourdenx, Mathieu, Santambrogio, Alessia, Frodsham, Claire, Camporesi, Elena, Brinkmalm, Gunnar, Zetterberg, Henrik, Patel, Saisha, Kamano, Naoko, Takahashi, Mika, Rueda-Carrasco, Javier, Katsouri, Loukia, Fowler, Stephanie, Turkes, Emir, Hashimoto, Shoko, Sasaguri, Hiroki, Saito, Takashi, Islam, AFM Saiful, Benner, Seico, Endo, Toshihiro, Kobayashi, Katsuji, Ishida, Chiho, Vendruscolo, Michele, Yamada, Masahito, Duff, Karen E., and Saido, Takaomi C.
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- 2025
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17. An evaporite sequence from ancient brine recorded in Bennu samples
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McCoy, T. J., Russell, S. S., Zega, T. J., Thomas-Keprta, K. L., Singerling, S. A., Brenker, F. E., Timms, N. E., Rickard, W. D. A., Barnes, J. J., Libourel, G., Ray, S., Corrigan, C. M., Haenecour, P., Gainsforth, Z., Dominguez, G., King, A. J., Keller, L. P., Thompson, M. S., Sandford, S. A., Jones, R. H., Yurimoto, H., Righter, K., Eckley, S. A., Bland, P. A., Marcus, M. A., DellaGiustina, D. N., Ireland, T. R., Almeida, N. V., Harrison, C. S., Bates, H. C., Schofield, P. F., Seifert, L. B., Sakamoto, N., Kawasaki, N., Jourdan, F., Reddy, S. M., Saxey, D. W., Ong, I. J., Prince, B. S., Ishimaru, K., Smith, L. R., Benner, M. C., Kerrison, N. A., Portail, M., Guigoz, V., Zanetta, P.-M., Wardell, L. R., Gooding, T., Rose, T. R., Salge, T., Le, L., Tu, V. M., Zeszut, Z., Mayers, C., Sun, X., Hill, D. H., Lunning, N. G., Hamilton, V. E., Glavin, D. P., Dworkin, J. P., Kaplan, H. H., Franchi, I. A., Tait, K. T., Tachibana, S., Connolly, Jr., H. C., and Lauretta, D. S.
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- 2025
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18. Exponential synchronization of bi-directional associative memory neural networks with delay on arbitrary time domains
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Kumar, Vipin, Heiland, Jan, and Benner, Peter
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- 2025
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19. Modelling Gas Networks with Compressors: A port-Hamiltonian Approach
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Bendokat, Thomas, Benner, Peter, Grundel, Sara, and Nayak, Ashwin S.
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Mathematics - Optimization and Control ,93-10 (Primary) 93-04, 76N15 (Secondary) - Abstract
Transient gas network simulations can significantly assist in design and operational aspects of gas networks. Models used in these simulations require a detailed framework integrating various models of the network constituents - pipes and compressor stations among others. In this context, the port-Hamiltonian modelling framework provides an energy-based modelling approach with a port-based coupling mechanism. This study investigates developing compressor models in an integrated isothermal port-Hamiltonian model for gas networks. Four different models of compressors are considered and their inclusion in a larger network model is detailed. A numerical implementation for a simple testcase is provided to confirm the validity of the proposed model and to highlight their differences., Comment: 9 pages, 3 figures. Submitted to Proceedings of the 94 Annual Meeting of GAMM
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- 2024
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20. GN-SINDy: Greedy Sampling Neural Network in Sparse Identification of Nonlinear Partial Differential Equations
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Forootani, Ali and Benner, Peter
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Mathematics - Dynamical Systems ,Computer Science - Machine Learning - Abstract
The sparse identification of nonlinear dynamical systems (SINDy) is a data-driven technique employed for uncovering and representing the fundamental dynamics of intricate systems based on observational data. However, a primary obstacle in the discovery of models for nonlinear partial differential equations (PDEs) lies in addressing the challenges posed by the curse of dimensionality and large datasets. Consequently, the strategic selection of the most informative samples within a given dataset plays a crucial role in reducing computational costs and enhancing the effectiveness of SINDy-based algorithms. To this aim, we employ a greedy sampling approach to the snapshot matrix of a PDE to obtain its valuable samples, which are suitable to train a deep neural network (DNN) in a SINDy framework. SINDy based algorithms often consist of a data collection unit, constructing a dictionary of basis functions, computing the time derivative, and solving a sparse identification problem which ends to regularised least squares minimization. In this paper, we extend the results of a SINDy based deep learning model discovery (DeePyMoD) approach by integrating greedy sampling technique in its data collection unit and new sparsity promoting algorithms in the least squares minimization unit. In this regard we introduce the greedy sampling neural network in sparse identification of nonlinear partial differential equations (GN-SINDy) which blends a greedy sampling method, the DNN, and the SINDy algorithm. In the implementation phase, to show the effectiveness of GN-SINDy, we compare its results with DeePyMoD by using a Python package that is prepared for this purpose on numerous PDE discovery
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- 2024
21. GS-PINN: Greedy Sampling for Parameter Estimation in Partial Differential Equations
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Forootani, Ali, Kapadia, Harshit, Chellappa, Sridhar, Goyal, Pawan, and Benner, Peter
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Mathematics - Dynamical Systems - Abstract
Partial differential equation parameter estimation is a mathematical and computational process used to estimate the unknown parameters in a partial differential equation model from observational data. This paper employs a greedy sampling approach based on the Discrete Empirical Interpolation Method to identify the most informative samples in a dataset associated with a partial differential equation to estimate its parameters. Greedy samples are used to train a physics-informed neural network architecture which maps the nonlinear relation between spatio-temporal data and the measured values. To prove the impact of greedy samples on the training of the physics-informed neural network for parameter estimation of a partial differential equation, their performance is compared with random samples taken from the given dataset. Our simulation results show that for all considered partial differential equations, greedy samples outperform random samples, i.e., we can estimate parameters with a significantly lower number of samples while simultaneously reducing the relative estimation error. A Python package is also prepared to support different phases of the proposed algorithm, including data prepossessing, greedy sampling, neural network training, and comparison.
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- 2024
22. Position-dependent function of human sequence-specific transcription factors
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Duttke, Sascha H, Guzman, Carlos, Chang, Max, Delos Santos, Nathaniel P, McDonald, Bayley R, Xie, Jialei, Carlin, Aaron F, Heinz, Sven, and Benner, Christopher
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Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Genetics ,Biological Sciences ,Human Genome ,1.1 Normal biological development and functioning ,Humans ,Binding Sites ,Gene Expression Regulation ,Genome ,Human ,Nucleotide Motifs ,Promoter Regions ,Genetic ,Protein Binding ,Transcription Factors ,Transcription Initiation Site ,Transcription Initiation ,Genetic ,Genetic Variation ,General Science & Technology - Abstract
Patterns of transcriptional activity are encoded in our genome through regulatory elements such as promoters or enhancers that, paradoxically, contain similar assortments of sequence-specific transcription factor (TF) binding sites1-3. Knowledge of how these sequence motifs encode multiple, often overlapping, gene expression programs is central to understanding gene regulation and how mutations in non-coding DNA manifest in disease4,5. Here, by studying gene regulation from the perspective of individual transcription start sites (TSSs), using natural genetic variation, perturbation of endogenous TF protein levels and massively parallel analysis of natural and synthetic regulatory elements, we show that the effect of TF binding on transcription initiation is position dependent. Analysing TF-binding-site occurrences relative to the TSS, we identified several motifs with highly preferential positioning. We show that these patterns are a combination of a TF's distinct functional profiles-many TFs, including canonical activators such as NRF1, NFY and Sp1, activate or repress transcription initiation depending on their precise position relative to the TSS. As such, TFs and their spacing collectively guide the site and frequency of transcription initiation. More broadly, these findings reveal how similar assortments of TF binding sites can generate distinct gene regulatory outcomes depending on their spatial configuration and how DNA sequence polymorphisms may contribute to transcription variation and disease and underscore a critical role for TSS data in decoding the regulatory information of our genome.
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- 2024
23. Electrophysiological Mechanisms and Validation of Ferritin-Based Magnetogenetics for Remote Control of Neurons.
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Hernández-Morales, Miriam, Morales-Weil, Koyam, Han, Sang Min, Han, Victor, Tran, Tiffany, Benner, Eric, Pegram, Kelly, Meanor, Jenna, Miller, Evan, Kramer, Richard, and Liu, Chunlei
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TMEM16A ,TRPV4 ,ferritin ,magnetogenetics ,membrane potential ,neuromodulation ,Animals ,Ferritins ,Rats ,Neurons ,Male ,Female ,TRPV Cation Channels ,Cells ,Cultured ,Magnetic Fields ,Rats ,Sprague-Dawley ,Membrane Potentials ,Patch-Clamp Techniques ,Hippocampus - Abstract
Magnetogenetics was developed to remotely control genetically targeted neurons. A variant of magnetogenetics uses magnetic fields to activate transient receptor potential vanilloid (TRPV) channels when coupled with ferritin. Stimulation with static or RF magnetic fields of neurons expressing these channels induces Ca2+ transients and modulates behavior. However, the validity of ferritin-based magnetogenetics has been questioned due to controversies surrounding the underlying mechanisms and deficits in reproducibility. Here, we validated the magnetogenetic approach Ferritin-iron Redistribution to Ion Channels (FeRIC) using electrophysiological (Ephys) and imaging techniques. Previously, interference from RF stimulation rendered patch-clamp recordings inaccessible for magnetogenetics. We solved this limitation for FeRIC, and we studied the bioelectrical properties of neurons expressing TRPV4 (nonselective cation channel) and transmembrane member 16A (TMEM16A; chloride-permeable channel) coupled to ferritin (FeRIC channels) under RF stimulation. We used cultured neurons obtained from the rat hippocampus of either sex. We show that RF decreases the membrane resistance (Rm) and depolarizes the membrane potential in neurons expressing TRPV4FeRIC RF does not directly trigger action potential firing but increases the neuronal basal spiking frequency. In neurons expressing TMEM16AFeRIC, RF decreases the Rm, hyperpolarizes the membrane potential, and decreases the spiking frequency. Additionally, we corroborated the previously described biochemical mechanism responsible for RF-induced activation of ferritin-coupled ion channels. We solved an enduring problem for ferritin-based magnetogenetics, obtaining direct Ephys evidence of RF-induced activation of ferritin-coupled ion channels. We found that RF does not yield instantaneous changes in neuronal membrane potentials. Instead, RF produces responses that are long-lasting and moderate, but effective in controlling the bioelectrical properties of neurons.
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- 2024
24. Navigating the Challenges of Structured Social and Emotional Programming
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Lee, Erica O., Michael, Elizabeth, and Benner, Gregory J.
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- 2024
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25. Regionale Innovations- und Wirtschaftspolitik in Zeiten transformativen Wandels: Der CORIS-Ansatz als Orientierungsrahmen
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Trippl, Michaela, Benner, Maximilian, and Baumgartinger-Seiringer, Simon
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- 2024
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26. Population-specific putative causal variants shape quantitative traits
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Koyama, Satoshi, Liu, Xiaoxi, Koike, Yoshinao, Hikino, Keiko, Koido, Masaru, Li, Wei, Akaki, Kotaro, Tomizuka, Kohei, Ito, Shuji, Otomo, Nao, Suetsugu, Hiroyuki, Yoshino, Soichiro, Akiyama, Masato, Saito, Kohei, Ishikawa, Yuki, Benner, Christian, Natarajan, Pradeep, Ellinor, Patrick T., Mushiroda, Taisei, Horikoshi, Momoko, Ikeda, Masashi, Iwata, Nakao, Matsuda, Koichi, Niida, Shumpei, Ozaki, Kouichi, Momozawa, Yukihide, Ikegawa, Shiro, Takeuchi, Osamu, Ito, Kaoru, and Terao, Chikashi
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- 2024
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27. A folding motif formed with an expanded genetic alphabet
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Wang, Bang, Rocca, James R., Hoshika, Shuichi, Chen, Cen, Yang, Zunyi, Esmaeeli, Reza, Wang, Jianguo, Pan, Xiaoshu, Lu, Jianrong, Wang, Kevin K., Cao, Y. Charles, Tan, Weihong, and Benner, Steven A.
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- 2024
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28. Estimates of the Kolmogorov n-width for nonlinear transformations with application to distributed-parameter control systems
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Zuyev, Alexander, Feng, Lihong, and Benner, Peter
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Mathematics - Optimization and Control ,93C20, 93C25, 41A25, 41A46, 81Q93, 74K10 - Abstract
This paper aims at characterizing the approximability of bounded sets in the range of nonlinear operators in Banach spaces by finite-dimensional linear varieties. In particular, the class of operators we consider includes the endpoint maps of nonlinear distributed-parameter control systems. We describe the relationship between the Kolmogorov n-width of a bounded subset and the width of its image under an essentially nonlinear transformation. We propose explicit estimates of the n-width in the space of images in terms of the affine part of the corresponding operator and the width of its nonlinear perturbation. These $n$-width estimates enable us to describe the reachable sets for infinite-dimensional bilinear control systems, with applications to controlling the Euler-Bernoulli beam using a contraction force and to a single-input Schr\"odinger equation., Comment: This is a preprint version of the paper submitted to the IEEE L-CSS and CDC 2024
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- 2024
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29. Stability-Certified Learning of Control Systems with Quadratic Nonlinearities
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Duff, Igor Pontes, Goyal, Pawan, and Benner, Peter
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Computer Science - Machine Learning ,Mathematics - Dynamical Systems ,Mathematics - Optimization and Control - Abstract
This work primarily focuses on an operator inference methodology aimed at constructing low-dimensional dynamical models based on a priori hypotheses about their structure, often informed by established physics or expert insights. Stability is a fundamental attribute of dynamical systems, yet it is not always assured in models derived through inference. Our main objective is to develop a method that facilitates the inference of quadratic control dynamical systems with inherent stability guarantees. To this aim, we investigate the stability characteristics of control systems with energy-preserving nonlinearities, thereby identifying conditions under which such systems are bounded-input bounded-state stable. These insights are subsequently applied to the learning process, yielding inferred models that are inherently stable by design. The efficacy of our proposed framework is demonstrated through a couple of numerical examples., Comment: 12 pages, 4 figures
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- 2024
30. MaRDIFlow: A CSE workflow framework for abstracting meta-data from FAIR computational experiments
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Veluvali, Pavan L., Heiland, Jan, and Benner, Peter
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Computer Science - Distributed, Parallel, and Cluster Computing ,68V30 - Abstract
Numerical algorithms and computational tools are instrumental in navigating and addressing complex simulation and data processing tasks. The exponential growth of metadata and parameter-driven simulations has led to an increasing demand for automated workflows that can replicate computational experiments across platforms. In general, a computational workflow is defined as a sequential description for accomplishing a scientific objective, often described by tasks and their associated data dependencies. If characterized through input-output relation, workflow components can be structured to allow interchangeable utilization of individual tasks and their accompanying metadata. In the present work, we develop a novel computational framework, namely, MaRDIFlow, that focuses on the automation of abstracting meta-data embedded in an ontology of mathematical objects. This framework also effectively addresses the inherent execution and environmental dependencies by incorporating them into multi-layered descriptions. Additionally, we demonstrate a working prototype with example use cases and methodically integrate them into our workflow tool and data provenance framework. Furthermore, we show how to best apply the FAIR principles to computational workflows, such that abstracted components are Findable, Accessible, Interoperable, and Reusable in nature., Comment: 13 pages, 7 figures
- Published
- 2024
31. Learning reduced-order Quadratic-Linear models in Process Engineering using Operator Inference
- Author
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Gosea, Ion Victor, Peterson, Luisa, Goyal, Pawan, Bremer, Jens, Sundmacher, Kai, and Benner, Peter
- Subjects
Mathematics - Numerical Analysis ,Computer Science - Machine Learning - Abstract
In this work, we address the challenge of efficiently modeling dynamical systems in process engineering. We use reduced-order model learning, specifically operator inference. This is a non-intrusive, data-driven method for learning dynamical systems from time-domain data. The application in our study is carbon dioxide methanation, an important reaction within the Power-to-X framework, to demonstrate its potential. The numerical results show the ability of the reduced-order models constructed with operator inference to provide a reduced yet accurate surrogate solution. This represents an important milestone towards the implementation of fast and reliable digital twin architectures., Comment: 10 pages, 3 figures
- Published
- 2024
32. Balanced Truncation of Descriptor Systems with a Quadratic Output
- Author
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Przybilla, Jennifer, Duff, Igor Pontes, Goyal, Pawan, and Benner, Peter
- Subjects
Mathematics - Dynamical Systems - Abstract
This work discusses model reduction for differential-algebraic systems with quadratic output equations. Under mild conditions, these systems can be transformed into a Weierstra{\ss} canonical form and, thus, be decoupled into differential equations and algebraic equations. The corresponding decoupled states are referred to as proper and improper states. Due to the quadratic function of the state as an output, the proper and improper states are coupled in the output equation, which imposes a challenge from a model reduction viewpoint. Keeping the coupling in mind, our goal in this work is to find important subspaces of the proper and improper states and to reduce the system accordingly. To that end, we first propose the system's matrices, the so-called Gramians, to characterize the system's dominant subspaces. We pay particular attention to the computation of the observability Gramians that take into account the nonlinear coupling between the proper and the improper states. We furthermore show that the proposed Gramians are related to certain kernel functions, which are used to identify important subspaces. This allows us to propose a reduction algorithm to obtain reduced-order systems by removing the subspaces that are difficult to reach, as well as, difficult to observe. Moreover, we quantify the error between the full-order and reduced-order models and demonstrate the proposed methodology using three numerical experiments.
- Published
- 2024
33. Numerical methods for closed-loop systems with non-autonomous data
- Author
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Baran, B., Benner, P., Saak, J., and Stillfjord, T.
- Subjects
Mathematics - Numerical Analysis ,65F45, 93A15, 93B52, 93C10 - Abstract
By computing a feedback control via the linear quadratic regulator (LQR) approach and simulating a non-linear non-autonomous closed-loop system using this feedback, we combine two numerically challenging tasks. For the first task, the computation of the feedback control, we use the non-autonomous generalized differential Riccati equation (DRE), whose solution determines the time-varying feedback gain matrix. Regarding the second task, we want to be able to simulate non-linear closed-loop systems for which it is known that the regulator is only valid for sufficiently small perturbations. Thus, one easily runs into numerical issues in the integrators when the closed-loop control varies greatly. For these systems, e.g., the A-stable implicit Euler methods fails.\newline On the one hand, we implement non-autonomous versions of splitting schemes and BDF methods for the solution of our non-autonomous DREs. These are well-established DRE solvers in the autonomous case. On the other hand, to tackle the numerical issues in the simulation of the non-linear closed-loop system, we apply a fractional-step-theta scheme with time-adaptivity tuned specifically to this kind of challenge. That is, we additionally base the time-adaptivity on the activity of the control. We compare this approach to the more classical error-based time-adaptivity.\newline We describe techniques to make these two tasks computable in a reasonable amount of time and are able to simulate closed-loop systems with strongly varying controls, while avoiding numerical issues. Our time-adaptivity approach requires fewer time steps than the error-based alternative and is more reliable.
- Published
- 2024
34. Roadmap on Data-Centric Materials Science
- Author
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Bauer, Stefan, Benner, Peter, Bereau, Tristan, Blum, Volker, Boley, Mario, Carbogno, Christian, Catlow, C. Richard A., Dehm, Gerhard, Eibl, Sebastian, Ernstorfer, Ralph, Fekete, Ádám, Foppa, Lucas, Fratzl, Peter, Freysoldt, Christoph, Gault, Baptiste, Ghiringhelli, Luca M., Giri, Sajal K., Gladyshev, Anton, Goyal, Pawan, Hattrick-Simpers, Jason, Kabalan, Lara, Karpov, Petr, Khorrami, Mohammad S., Koch, Christoph, Kokott, Sebastian, Kosch, Thomas, Kowalec, Igor, Kremer, Kurt, Leitherer, Andreas, Li, Yue, Liebscher, Christian H., Logsdail, Andrew J., Lu, Zhongwei, Luong, Felix, Marek, Andreas, Merz, Florian, Mianroodi, Jaber R., Neugebauer, Jörg, Pei, Zongrui, Purcell, Thomas A. R., Raabe, Dierk, Rampp, Markus, Rossi, Mariana, Rost, Jan-Michael, Saal, James, Saalmann, Ulf, Sasidhar, Kasturi Narasimha, Saxena, Alaukik, Sbailò, Luigi, Scheidgen, Markus, Schloz, Marcel, Schmidt, Daniel F., Teshuva, Simon, Trunschke, Annette, Wei, Ye, Weikum, Gerhard, Xian, R. Patrick, Yao, Yi, Yin, Junqi, Zhao, Meng, and Scheffler, Matthias
- Subjects
Condensed Matter - Materials Science ,Physics - Data Analysis, Statistics and Probability - Abstract
Science is and always has been based on data, but the terms "data-centric" and the "4th paradigm of" materials research indicate a radical change in how information is retrieved, handled and research is performed. It signifies a transformative shift towards managing vast data collections, digital repositories, and innovative data analytics methods. The integration of Artificial Intelligence (AI) and its subset Machine Learning (ML), has become pivotal in addressing all these challenges. This Roadmap on Data-Centric Materials Science explores fundamental concepts and methodologies, illustrating diverse applications in electronic-structure theory, soft matter theory, microstructure research, and experimental techniques like photoemission, atom probe tomography, and electron microscopy. While the roadmap delves into specific areas within the broad interdisciplinary field of materials science, the provided examples elucidate key concepts applicable to a wider range of topics. The discussed instances offer insights into addressing the multifaceted challenges encountered in contemporary materials research., Comment: Review, outlook, roadmap, perspective
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- 2024
35. Interpolatory Necessary Optimality Conditions for Reduced-order Modeling of Parametric Linear Time-invariant Systems
- Author
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Mlinarić, Petar, Benner, Peter, and Gugercin, Serkan
- Subjects
Mathematics - Optimization and Control ,Electrical Engineering and Systems Science - Systems and Control ,Mathematics - Numerical Analysis - Abstract
Interpolatory necessary optimality conditions for $\mathcal{H}_2$-optimal reduced-order modeling of non-parametric linear time-invariant (LTI) systems are known and well-investigated. In this work, using the general framework of $\mathcal{L}_2$-optimal reduced-order modeling of parametric stationary problems, we derive interpolatory $\mathcal{H}_2 \otimes \mathcal{L}_2$-optimality conditions for parametric LTI systems with a general pole-residue form. We then specialize this result to recover known conditions for systems with parameter-independent poles and develop new conditions for a certain class of systems with parameter-dependent poles., Comment: 9 pages
- Published
- 2024
36. TRIF-IFN-I pathway in Helicobacter-induced gastric cancer in an accelerated murine disease model and patient biopsies
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Bali, Prerna, Lozano-Pope, Ivonne, Hernandez, Jonathan, Estrada, Monica V, Corr, Maripat, Turner, Michael A, Bouvet, Michael, Benner, Christopher, and Obonyo, Marygorret
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Infectious Diseases ,Digestive Diseases ,Emerging Infectious Diseases ,Digestive Diseases - (Peptic Ulcer) ,Cancer ,Rare Diseases ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Biological sciences ,Clinical microbiology ,Microbiology - Abstract
Helicobacter pylori (H. pylori) infection is a known cause of many digestive diseases, including gastritis, peptic ulcers, and gastric cancer. However, the underlying mechanisms by which H. pylori infection triggers these disorders are still not clearly understood. Gastric cancer is a slow progressing disease, which makes it difficult to study. We have developed an accelerated disease progression mouse model, which leverages mice deficient in the myeloid differentiation primary response 88 gene (Myd88-/-) infected with Helicobacter felis (H. felis). Using this model and gastric biopsy samples from patients, we report that activation of the Toll/interleukin-1 receptor (TIR)-domain-containing adaptor inducing interferon-β (TRIF)-type I interferon (IFN-I) signaling pathway promotes Helicobacter-induced disease progression toward severe gastric pathology and gastric cancer development. Further, results implicated downstream targets of this pathway in disease pathogenesis. These findings may facilitate stratification of Helicobacter-infected patients and thus enable treatment prioritization of patients.
- Published
- 2024
37. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats
- Author
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de Jong, Tristan V, Pan, Yanchao, Rastas, Pasi, Munro, Daniel, Tutaj, Monika, Akil, Huda, Benner, Chris, Chen, Denghui, Chitre, Apurva S, Chow, William, Colonna, Vincenza, Dalgard, Clifton L, Demos, Wendy M, Doris, Peter A, Garrison, Erik, Geurts, Aron M, Gunturkun, Hakan M, Guryev, Victor, Hourlier, Thibaut, Howe, Kerstin, Huang, Jun, Kalbfleisch, Ted, Kim, Panjun, Li, Ling, Mahaffey, Spencer, Martin, Fergal J, Mohammadi, Pejman, Ozel, Ayse Bilge, Polesskaya, Oksana, Pravenec, Michal, Prins, Pjotr, Sebat, Jonathan, Smith, Jennifer R, Woods, Leah C Solberg, Tabakoff, Boris, Tracey, Alan, Uliano-Silva, Marcela, Villani, Flavia, Wang, Hongyang, Sharp, Burt M, Telese, Francesca, Jiang, Zhihua, Saba, Laura, Wang, Xusheng, Murphy, Terence D, Palmer, Abraham A, Kwitek, Anne E, Dwinell, Melinda R, Williams, Robert W, Li, Jun Z, and Chen, Hao
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Good Health and Well Being ,Rats ,Animals ,Genome ,Molecular Sequence Annotation ,Genomics ,Whole Genome Sequencing ,Genetic Variation ,Rnor_6.0 ,genetic map ,heterogeneous stock ,hybrid rat diversity panel ,inbred strains ,mRatBN7.2 ,phylogenetic tree ,rat ,recombinant inbred ,reference genome - Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
- Published
- 2024
38. Education [Bildung]-Literality-Competence: On Competing Tasks of Public Schools and the Need for New Links between Teaching and Educational Research
- Author
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Benner, Dietrich
- Abstract
Purpose: The article distinguishes between the three concepts of standardization of the tasks of pedagogical action in modern educational systems: the traditional concept of standardizing educational goals through curricula, the literacy concept of psychometric standardization, and the concept of competence, which can be developed in different ways. Design/Approach/Methods: I examine these concepts and show that traditional curricular orientations suffer from the fact that they have not developed controls over the achievement of objectives, that literacy concept allows for psychometric measurement, but this is not coordinated with the actual teaching and its goals, and that competence models only offer further possibilities if their subject-specific requirements are aligned with the educational theoretical and didactic teaching objectives. Findings: Instead of replacing traditional input control with output measurements, it is important to link teaching and educational research in such a way that competence measurements not only measure the levels of demands achieved by learners but also the quality and effectiveness of teaching. Originality/Value: The train of thought overcomes the juxtaposition of philosophy of education and empirical research and shows how the two can cooperate theoretically and empirically.
- Published
- 2023
39. The Potential for Using a Shortened Version of the Everyday Discrimination Scale in Population Research with Young Adults: A Construct Validation Investigation
- Author
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Aprile D. Benner, Shanting Chen, Celeste C. Fernandez, and Mark D. Hayward
- Abstract
Discrimination is associated with numerous psychological health outcomes over the life course. The nine-item Everyday Discrimination Scale (EDS) is one of the most widely used measures of discrimination; however, this nine-item measure may not be feasible in large-scale population health surveys where a shortened discrimination measure would be advantageous. The current study examined the construct validity of a combined two-item discrimination measure adapted from the EDS by Add Health (N = 14,839) as compared to the full nine-item EDS and a two-item EDS scale (parallel to the adapted combined measure) used in the National Survey of American Life (NSAL; N = 1,111) and National Latino and Asian American Study (NLAAS) studies (N = 1,055). Results identified convergence among the EDS scales, with high item-total correlations, convergent validity, and criterion validity for psychological outcomes, thus providing evidence for the construct validity of the two-item combined scale. Taken together, the findings provide support for using this reduced scale in studies where the full EDS scale is not available.
- Published
- 2024
- Full Text
- View/download PDF
40. Iterative approximations of periodic trajectories for nonlinear systems with discontinuous inputs
- Author
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Zuyev, Alexander and Benner, Peter
- Subjects
Mathematics - Optimization and Control ,93C15, 34B15, 34A36, 47J25, 65L10, 92E20 - Abstract
Nonlinear control-affine systems described by ordinary differential equations with bounded measurable input functions are considered. The problem of the existence of periodic trajectories for these systems is formulated in the sense of Carath\'eodory solutions. It is shown that, under the dominant linearization assumption, the periodic boundary value problem admits a unique solution for any admissible control. This solution can be obtained as the limit of the proposed simple iterative scheme and a Newton-type method. Under additional technical assumptions, sufficient contraction conditions of the corresponding generating operators are derived analytically. The proposed iterative approach is applied for the computation of periodic solutions of a realistic chemical reaction model with discontinuous control inputs., Comment: 15 pages, 3 figures
- Published
- 2023
41. A foundation model for atomistic materials chemistry
- Author
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Batatia, Ilyes, Benner, Philipp, Chiang, Yuan, Elena, Alin M., Kovács, Dávid P., Riebesell, Janosh, Advincula, Xavier R., Asta, Mark, Avaylon, Matthew, Baldwin, William J., Berger, Fabian, Bernstein, Noam, Bhowmik, Arghya, Blau, Samuel M., Cărare, Vlad, Darby, James P., De, Sandip, Della Pia, Flaviano, Deringer, Volker L., Elijošius, Rokas, El-Machachi, Zakariya, Falcioni, Fabio, Fako, Edvin, Ferrari, Andrea C., Genreith-Schriever, Annalena, George, Janine, Goodall, Rhys E. A., Grey, Clare P., Grigorev, Petr, Han, Shuang, Handley, Will, Heenen, Hendrik H., Hermansson, Kersti, Holm, Christian, Jaafar, Jad, Hofmann, Stephan, Jakob, Konstantin S., Jung, Hyunwook, Kapil, Venkat, Kaplan, Aaron D., Karimitari, Nima, Kermode, James R., Kroupa, Namu, Kullgren, Jolla, Kuner, Matthew C., Kuryla, Domantas, Liepuoniute, Guoda, Margraf, Johannes T., Magdău, Ioan-Bogdan, Michaelides, Angelos, Moore, J. Harry, Naik, Aakash A., Niblett, Samuel P., Norwood, Sam Walton, O'Neill, Niamh, Ortner, Christoph, Persson, Kristin A., Reuter, Karsten, Rosen, Andrew S., Schaaf, Lars L., Schran, Christoph, Shi, Benjamin X., Sivonxay, Eric, Stenczel, Tamás K., Svahn, Viktor, Sutton, Christopher, Swinburne, Thomas D., Tilly, Jules, van der Oord, Cas, Varga-Umbrich, Eszter, Vegge, Tejs, Vondrák, Martin, Wang, Yangshuai, Witt, William C., Zills, Fabian, and Csányi, Gábor
- Subjects
Physics - Chemical Physics ,Condensed Matter - Materials Science - Abstract
Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model - and its qualitative and at times quantitative accuracy - on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, chemical reactions, interfaces and even the dynamics of a small protein. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry., Comment: 119 pages, 63 figures, 37MB PDF
- Published
- 2023
42. Simulation study to evaluate when Plasmode simulation is superior to parametric simulation in estimating the mean squared error of the least squares estimator in linear regression
- Author
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Stolte, Marieke, Schreck, Nicholas, Slynko, Alla, Saadati, Maral, Benner, Axel, Rahnenführer, Jörg, and Bommert, Andrea
- Subjects
Statistics - Methodology ,Statistics - Computation - Abstract
Simulation is a crucial tool for the evaluation and comparison of statistical methods. How to design fair and neutral simulation studies is therefore of great interest for researchers developing new methods and practitioners confronted with the choice of the most suitable method. The term simulation usually refers to parametric simulation, that is, computer experiments using artificial data made up of pseudo-random numbers. Plasmode simulation, that is, computer experiments using the combination of resampling feature data from a real-life dataset and generating the target variable with a known user-selected outcome-generating model (OGM), is an alternative that is often claimed to produce more realistic data. We compare parametric and Plasmode simulation for the example of estimating the mean squared error (MSE) of the least squares estimator (LSE) in linear regression. If the true underlying data-generating process (DGP) and the OGM were known, parametric simulation would obviously be the best choice in terms of estimating the MSE well. However, in reality, both are usually unknown, so researchers have to make assumptions: in Plasmode simulation for the OGM, in parametric simulation for both DGP and OGM. Most likely, these assumptions do not exactly reflect the truth. Here, we aim to find out how assumptions deviating from the true DGP and the true OGM affect the performance of parametric and Plasmode simulations in the context of MSE estimation for the LSE and in which situations which simulation type is preferable. Our results suggest that the preferable simulation method depends on many factors, including the number of features, and on how and to what extent the assumptions of a parametric simulation differ from the true DGP. Also, the resampling strategy used for Plasmode influences the results. In particular, subsampling with a small sampling proportion can be recommended.
- Published
- 2023
- Full Text
- View/download PDF
43. An Actuator with Magnetic Restoration, Part II: Drive Circuit and Control Loops
- Author
-
Mohammadi, Sajjad, Benner, William R., Kirtley, James L., and Lang, Jeffrey H.
- Subjects
Electrical Engineering and Systems Science - Systems and Control - Abstract
In part II, an op-amp-based drive is proposed and designed. Subsequently, a very accurate model for the drive circuit and the current loop is developed as a simulation platform, while its simplified version is derived, tailored for efficient design purposes. Through a comprehensive evaluation, the accuracy and efficacy of both the actuator and drive circuit modeling is scrutinized, showcasing their superiorities over existing approaches. The importance of eddy current modeling is underscored. Also, the effectiveness of the designed current loop and its practical trade-offs are engineered and discussed. Then, three DSP-based position control techniques are implemented: pole placement with voltage drive, pole placement with current drive, and nonlinear control with feed linearization. Both full-order and reduced-order observers are leveraged to estimate the unmeasured states. The performance of control designs across various applications are evaluated through indices such as rise time, overshoot, steady-state error, and large-signal tracking in the step response as well as bandwidth, robustness, phase margin, sensitivity, disturbance rejection, and noise rejection in the frequency domain. The distinctive features of implemented control strategy are compared, offering a nuanced discussion of their respective advantages and drawbacks, shedding light on their potential applications.
- Published
- 2023
44. An Actuator with Magnetic Restoration, Part I: Electromechanical Model and Identification
- Author
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Mohammadi, Sajjad, Benner, William R., Kirtley, James L., and Lang, Jeffrey H.
- Subjects
Electrical Engineering and Systems Science - Systems and Control - Abstract
Electromechanical models are crucial in the design and control of motors and actuators. Modeling, identification, drive, and current control loop of a limited-rotation actuator with magnetic restoration is presented. New nonlinear and linearized electromechanical models are developed for the design of the drive as well as small and large signal controls of the actuator. To attain a higher accuracy and an efficient design, and the eddy-currents in the laminations and magnet are modeled. This involves analytically solving 1-D and 2-D diffusion equations, leading to the derivation of a lumped-element circuit for system-level analyses, such as control system design. Additionally, the study analyzes and incorporates the impact of pre-sliding friction. The actuator is prototyped, and the paper delves into the identification of the model, presenting a procedure for parameter extraction. A close agreement is observed between the results obtained from the model, finite element analysis, and experimental results. The superiority of the proposed model over previous approaches is highlighted. Part II of the paper is dedicated to the drive circuit, the current control, as well as linear and nonlinear position control system designs.
- Published
- 2023
45. Fast and Reliable Reduced-Order Models for Cardiac Electrophysiology
- Author
-
Chellappa, Sridhar, Cansız, Barış, Feng, Lihong, Benner, Peter, and Kaliske, Michael
- Subjects
Mathematics - Numerical Analysis - Abstract
Mathematical models of the human heart are increasingly playing a vital role in understanding the working mechanisms of the heart, both under healthy functioning and during disease. The aim is to aid medical practitioners diagnose and treat the many ailments affecting the heart. Towards this, modelling cardiac electrophysiology is crucial as the heart's electrical activity underlies the contraction mechanism and the resulting pumping action. The governing equations and the constitutive laws describing the electrical activity in the heart are coupled, nonlinear, and involve a fast moving wave front, which is generally solved by the finite element method. The simulation of this complex system as part of a virtual heart model is challenging due to the necessity of fine spatial and temporal resolution of the domain. Therefore, efficient surrogate models are needed to predict the dynamics under varying parameters and inputs. In this work, we develop an adaptive, projection-based surrogate model for cardiac electrophysiology. We introduce an a posteriori error estimator that can accurately and efficiently quantify the accuracy of the surrogate model. Using the error estimator, we systematically update our surrogate model through a greedy search of the parameter space. Furthermore, using the error estimator, the parameter search space is dynamically updated such that the most relevant samples get chosen at every iteration. The proposed adaptive surrogate modelling technique is tested on three benchmark models to illustrate its efficiency, accuracy, and ability of generalization., Comment: 28 pages, 17 figures, 1 table
- Published
- 2023
46. Interpolatory $\mathcal{H}_2$-optimality Conditions for Structured Linear Time-invariant Systems
- Author
-
Mlinarić, Petar, Benner, Peter, and Gugercin, Serkan
- Subjects
Mathematics - Numerical Analysis ,Electrical Engineering and Systems Science - Systems and Control ,Mathematics - Optimization and Control - Abstract
Interpolatory necessary optimality conditions for $\mathcal{H}_2$-optimal reduced-order modeling of unstructured linear time-invariant (LTI) systems are well-known. Based on previous work on $\mathcal{L}_2$-optimal reduced-order modeling of stationary parametric problems, in this paper we develop and investigate optimality conditions for $\mathcal{H}_2$-optimal reduced-order modeling of structured LTI systems, in particular, for second-order, port-Hamiltonian, and time-delay systems. Under certain diagonalizability assumptions, we show that across all these different structured settings, bitangential Hermite interpolation is the common form for optimality, thus proving a unifying optimality framework for structured reduced-order modeling., Comment: 23 pages
- Published
- 2023
47. Do Teacher Beliefs Mediate the Relationship between Professional Development and Reading Outcomes of Students with Emotional and Behavioral Disorders? An Exploration of Effects from a Randomized Controlled Trial
- Author
-
Filderman, Marissa J., Barnard-Brak, Lucy, and Benner, Gregory J.
- Abstract
Teachers of students with emotional and behavioral disorders face unique challenges in the classroom that are often not addressed in teacher preparation, which may result in diminished outcomes for teachers and students. The Integrated Literacy Study Groups professional development was designed to support the needs of teachers of students with or at-risk for emotional and behavioral disorders by integrating components of social-emotional learning and literacy instruction. The present study uses structural equation modeling to evaluate how and to what extent teacher beliefs, targeted in training through collaborative work groups and coaching experiences, mediate the relationship between the Integrated Literacy Study Groups and student reading achievement. Among a sample of 74 elementary school teachers, we found a directional relationship such that training influenced: (1) beliefs pertaining to action; (2) beliefs pertaining to self; and (3) student reading outcomes. Beliefs pertaining to self was a significantly stronger mediator of the relationship between professional development and student reading outcomes. We discuss potential reasons for these findings as well as their implications for the design of training of teachers of students with or at-risk for emotional and behavioral disorders. [This is the online version of an article published in "Social Psychology of Education."]
- Published
- 2022
- Full Text
- View/download PDF
48. Drug target prediction through deep learning functional representation of gene signatures.
- Author
-
Chen, Hao, King, Frederick, Zhou, Bin, Wang, Yu, Canedy, Carter, Hayashi, Joel, Zhong, Yang, Chang, Max, Pache, Lars, Wong, Julian, Jia, Yong, Joslin, John, Chanda, Sumit, Zhou, Yingyao, Jiang, Tao, and Benner, Christopher
- Subjects
Humans ,Deep Learning ,Machine Learning ,Computational Biology ,Drug Development - Abstract
Many machine learning applications in bioinformatics currently rely on matching gene identities when analyzing input gene signatures and fail to take advantage of preexisting knowledge about gene functions. To further enable comparative analysis of OMICS datasets, including target deconvolution and mechanism of action studies, we develop an approach that represents gene signatures projected onto their biological functions, instead of their identities, similar to how the word2vec technique works in natural language processing. We develop the Functional Representation of Gene Signatures (FRoGS) approach by training a deep learning model and demonstrate that its application to the Broad Institutes L1000 datasets results in more effective compound-target predictions than models based on gene identities alone. By integrating additional pharmacological activity data sources, FRoGS significantly increases the number of high-quality compound-target predictions relative to existing approaches, many of which are supported by in silico and/or experimental evidence. These results underscore the general utility of FRoGS in machine learning-based bioinformatics applications. Prediction networks pre-equipped with the knowledge of gene functions may help uncover new relationships among gene signatures acquired by large-scale OMICs studies on compounds, cell types, disease models, and patient cohorts.
- Published
- 2024
49. Overcoming resolution attenuation during tilted cryo-EM data collection.
- Author
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Aiyer, Sriram, Baldwin, Philip, Tan, Shi, Shan, Zelin, Oh, Juntaek, Mehrani, Atousa, Bowman, Marianne, Louie, Gordon, Passos, Dario, Đorđević-Marquardt, Selena, Mietzsch, Mario, Hull, Joshua, Hoshika, Shuichi, Barad, Benjamin, Grotjahn, Danielle, McKenna, Robert, Agbandje-McKenna, Mavis, Benner, Steven, Noel, Joseph, Wang, Dong, Tan, Yong, and Lyumkis, Dmitry
- Subjects
Cryoelectron Microscopy ,Anisotropy ,Benchmarking ,Computer Systems ,Data Collection - Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting preferred orientations on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
- Published
- 2024
50. Sustainable and inclusive development in left-behind places
- Author
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Benner, Maximilian, Trippl, Michaela, and Hassink, Robert
- Published
- 2024
- Full Text
- View/download PDF
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