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IEEE Conference on Decision and Control

作者： Thomas Beckers Jacob Seidman Paris Perdikaris George J. Pappas Department of Electrical and Systems Engineering University of Pennsylvania Philadelphia PA USA graduate program in Applied Mathematics and Computational Science University of Pennsylvania Philadelphia PA USA Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania Philadelphia PA USA

ISBN: (数字)9781665467612

ISBN: (纸本)9781665467629

Data-driven approaches achieve remarkable results for the modeling of complex dynamics based on collected data. However, these models often neglect basic physical principles which determine the behavior of any real-world system. This omission is unfavorable in two ways: The models are not as data-efficient as they could be by incorporating physical prior knowledge, and the model itself might not be physically correct. We propose Gaussian Process Port-Hamiltonian systems (GPPHS) as a physics-informed Bayesian learning approach with uncertainty quantification. The Bayesian nature of GP-PHS uses collected data to form a distribution over all possible Hamiltonians instead of a single point estimate. Due to the underlying physics model, a GP-PHS generates passive systems with respect to designated inputs and outputs. Further, the proposed approach preserves the compositional nature of Port-Hamiltonian systems.

关键词： Uncertainty Gaussian processes Probabilistic logic Data models Bayes methods Behavioral sciences Kernel

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Diversity and Evolution of RNA Recognition Motifs: A Case Study on the Utility of RdRp in the phylum Duplornaviricota

Diversity and Evolution of RNA Recognition Motifs: A Case St...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Mikyung Je Myeongji Cho Hyeon S. Son Interdisciplinary Graduate Program in Bioinformatics College of Natural Science Seoul National University Seoul Republic of Korea Lab. of Computational Biology & Bioinformatics Graduate School of Public Health Seoul National University Seoul Republic of Korea Institute of Health and Environment Seoul National University Seoul Republic of Korea

Viruses possess specific conserved regions known as RNA recognition motifs, which are shared within taxonomic groups. Applying these to the Baltimore virus classification system, there are genes/proteins that serve as biomarkers for each of the seven groups. Mutations in conserved sequence regions can have a significant impact on the function of a virus, especially if these conserved regions are part of a major protein. In this study, we analyzed the RdRp gene, known to be a representative RRM of RNA viruses, from viruses of five families (Alternaviridae, Chrysoviridae, Totiviridae, Sedoreoviridae, and Spinareoviridae) within the phylum Duplornaviricota. Data were retrieved from the NCBI non-redundant (nr) database (https://***/protein) applying a cut-off of 300 amino acids in length. RdRp protein sequences were aligned using PROMALS3D, and PhyML (v3.0) was used for phylogenetic analysis. In the next step, we utilized the officially provided ICTV taxonomy and bioinformatics tools to assign the phylogenetic position of RdRp. Although this analysis focused solely on RdRp, it can be concluded that using this gene as a marker may be sufficient for taxonomic assignment. Subsequent analyses will target DNA viruses and RT viruses to perform a more comprehensive assessment. This extensive analysis aims to validate the usefulness of marker genes in the overall viral taxonomy.

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multi-kernel and multi-scale learning based deep ensemble model for predicting recurrence of non-small cell lung cancer

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PeerJ Computer science 2023年 9卷

作者： Kim, Gihyeon Park, Young Mi Yoon, Hyun Jung Choi, Jang-Hwan Department of Computational Medicine Graduate Program in System Health Science and Engineering Ewha Womans University Seoul Korea Republic of Department of Molecular Medicine College of Medicine Ewha Womans University Seoul Korea Republic of Department of Radiology Veterans Health Service Medical Center Seoul Korea Republic of Division of Mechanical and Biomedical Engineering Graduate Program in System Health Science and Engineering Ewha Womans University Seoul Korea Republic of Department of Artificial Intelligence Ewha Womans University Seoul Korea Republic of

Predicting recurrence in patients with non-small cell lung cancer (NSCLC) before treatment is vital for guiding personalized medicine. Deep learning techniques have revolutionized the application of cancer informatics, including lung cancer timeto-event prediction. Most existing convolutional neural network (CNN) models are based on a single two-dimensional (2D) computational tomography (CT) image or three-dimensional (3D) CT volume. However, studies have shown that using multiscale input and fusing multiple networks provide promising performance. This study proposes a deep learning-based ensemble network for recurrence prediction using a dataset of 530 patients with NSCLC. This network assembles 2DCNNmodels of various input slices, scales, and convolutional kernels, using a deep learning-based feature fusion model as an ensemble strategy. The proposed framework is uniquely designed to benefit from (i) multiple 2D in-plane slices to provide more information than a single central slice, (ii) multi-scale networks and multi-kernel networks to capture the local and peritumoral features, (iii) ensemble design to integrate features from various inputs and model architectures for final prediction. The ensemble of five 2D-CNN models, three slices, and two multi-kernel networks, using 5×5 and 6×6 convolutional kernels, achieved the best performance with an accuracy of 69.62%, area under the curve (AUC) of 72.5%, F1 score of 70.12%, and recall of 70.81%. Furthermore, the proposed method achieved competitive results compared with the 2D and 3D-CNN models for cancer outcome prediction in the benchmark studies. Our model is also a potential adjuvant treatment tool for identifying NSCLC patients with a high risk of recurrence. © 2023 Kim et al.

关键词： Neural network models

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DLM: A distributed Large Memory System using remote memory swapping over cluster nodes

DLM: A distributed Large Memory System using remote memory s...

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IEEE International Conference on Cluster Computing

作者： Hiroko Midorikawa Motoyoshi Kurokawa Ryutaro Himeno Mitsuhisa Sato Department of Computer and Information Science Seikei University Musashino Tokyo Japan Graduate School of Systems and Information Engineering University of Tsukuba Tennodai Tsukuba Ibaraki Japan Advanced Center of Computing and Communication Wako Saitama Japan Research Program for Computational Science RIKEN Wako Saitama Japan

Emerging 64 bitOSpsilas supply a huge amount of memory address space that is essential for new applications using very large data. It is expected that the memory in connected nodes can be used to store swapped pages efficiently, especially in a dedicated cluster which has a high-speed network such as 10 GbE and Infiniband. In this paper, we propose the distributed large memory system (DLM), which provides very large virtual memory by using remote memory distributed over the nodes in a cluster. The performance of DLM programs using remote memory is compared to ordinary programs using local memory. The results of STREAM, NPB and Himeno benchmarks show that the DLM achieves better performance than other remote paging schemes using a block swap device to access remote memory. In addition to performance, DLM offers the advantages of easy availability and high portability, because it is a user-level software without the need for special hardware. To obtain high performance, the DLM can tune its parameters independently from kernel swap parameters. We also found that DLMpsilas independence of kernel swapping provides more stable behavior.

关键词： Kernel Arrays Memory management Servers Bandwidth Performance evaluation Benchmark testing

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CVIT: CONTINUOUS VISION TRANSFORMER FOR OPERATOR LEARNING

arXiv

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arXiv 2024年

作者： Wang, Sifan Seidman, Jacob H. Sankaran, Shyam Wang, Hanwen Pappas, George J. Perdikaris, Paris Institution for Foundation of Data Science Yale University United States Graduate Program in Applied Mathematics and Computational Science University of Pennsylvania United States Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania United States Department of Electrical and Systems Engineering University of Pennsylvania United States

Operator learning, which aims to approximate maps between infinite-dimensional function spaces, is an important area in scientific machine learning with applications across various physical domains. Here we introduce the Continuous Vision Transformer (CViT), a novel neural operator architecture that leverages advances in computer vision to address challenges in learning complex physical systems. CViT combines a vision transformer encoder, a novel grid-based coordinate embedding, and a query-wise cross-attention mechanism to effectively capture multi-scale dependencies. This design allows for flexible output representations and consistent evaluation at arbitrary resolutions. We demonstrate CViT’s effectiveness across a diverse range of partial differential equation (PDE) systems, including fluid dynamics, climate modeling, and reaction-diffusion processes. Our comprehensive experiments show that CViT achieves state-of-the-art performance on multiple benchmarks, often surpassing larger foundation models, even without extensive pretraining and roll-out fine-tuning. Taken together, CViT exhibits robust handling of discontinuous solutions, multi-scale features, and intricate spatio-temporal dynamics. Our contributions can be viewed as a significant step towards adapting advanced computer vision architectures for building more flexible and accurate machine learning models in the physical sciences. All data and code are publicly available at https://***/PredictiveIntelligenceLab/cvit. © 2024, CC BY-NC-SA.

关键词： Computer vision

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Molecular thermodynamics of trifluoroethanol-induced helix formation:Analyses of the solvation structure and free energy by the 3D-RISM theory

Molecular thermodynamics of trifluoroethanol-induced helix f...

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The International Conference on Theory and Applications of computational Chemistry 2008(2008理论与计算机化学国际会议)

作者： Takashi Imai Andriy Kovalenko Fumio Hirata Akinori Kidera International Graduate School of Arts and Sciences Yokohama City UniversityTsurumiYokohama 230-0045Japan Research Program for Computational Science RIKENWakoSaitama 351-0112Japan National Institute for NanotechnologyNational Research Council of CanadaEdmontonAlberta T6G 2M9Canada Department of Theoretical StudiesInstitute for Molecular ScienceOkazakiAichi 444-8585Japan Research Program for Computational ScienceRIKENWakoSaitama 351-0112Japan

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Atomic photoabsorption process controlled by static and oscillating magnetic fields

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Physical Review A 2009年第4期80卷 043414-043414页

作者： Takeshi Shirahama Xiao-Min Tong Ken-ichi Hino Nobuyuki Toshima Institute of Materials Science University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8573 Japan Center for Computational Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan Doctoral Program in Frontier Science Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8573 Japan

We present a theoretical method to study atomic photoabsorption processes in a temporally periodic external field. The time development of the atomic dipole moment is propagated by numerical time propagation, and the photoabsorption cross sections is obtained directly from the Fourier transform of the autocorrelation function without summing up over the Floquet-Fourier components. As an example, we study the photoabsorption spectra of hydrogen atoms exposed in a mixture of static and periodically oscillating magnetic fields for the transition from 1s→2p. The atomic energy structure and photoabsorption spectra show interesting dependence on the strength of the oscillating magnetic field. Tuning the combination of the magnetic field strengths, we can control the photoabsorption process. The proposed method is general and can be applied to processes in which the number of relevant high harmonic components of the Fourier expansion is so large that the conventional Floquet method is intractable.

关键词： Atoms

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CONVERGENCE SPEED AND APPROXIMATION ACCURACY OF NUMERICAL MCMC

arXiv

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arXiv 2022年

作者： Cui, Tiangang Dong, Jing Jasra, Ajay Tong, Xin T. School of Mathematics Monash University Australia Graduate School of Business Columbia University United States Applied Mathematics and Computational Science Program Computer Electrical Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Saudi Arabia Department of Mathematics National University of Singapore Singapore

When implementing Markov Chain Monte Carlo (MCMC) algorithms, perturbation caused by numerical errors is sometimes inevitable. This paper studies how perturbation of MCMC affects the convergence speed and Monte Carlo estimation accuracy. Our results show that when the original Markov chain converges to stationarity fast enough and the perturbed transition kernel is a good approximation to the original transition kernel, the corresponding perturbed sampler has similar convergence speed and high approximation accuracy as well. We discuss two different analysis frameworks: ergodicity and spectral gap, both are widely used in the literature. Our results can be easily extended to obtain non-asymptotic error bounds for MCMC estimators. We also demonstrate how to apply our convergence and approximation results to the analysis of specific sampling algorithms, including Random walk Metropolis and Metropolis adjusted Langevin algorithm with perturbed target densities, and parallel tempering Monte Carlo with perturbed densities. Finally we present some simple numerical examples to verify our theoretical claims. Copyright © 2022, The Authors. All rights reserved.

关键词： Inverse problems

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Functional annotation of chemical libraries across diverse biological processes (vol 13, pg 982, 2017)

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NATURE CHEMICAL BIOLOGY 2017年第12期13卷 1286-1286页

作者： Piotrowski, Jeff S. Li, Sheena C. Deshpande, Raamesh Simpkins, Scott W. Nelson, Justin Yashiroda, Yoko Barber, Jacqueline M. Safizadeh, Hamid Wilson, Erin Okada, Hiroki Gebre, Abraham A. Kubo, Karen Torres, Nikko P. LeBlanc, Marissa A. Andrusiak, Kerry Okamoto, Reika Yoshimura, Mami DeRango-Adem, Eva van Leeuwen, Jolanda Shirahige, Katsuhiko Baryshnikova, Anastasia Brown, Grant W. Hirano, Hiroyuki Costanzo, Michael Andrews, Brenda Ohya, Yoshikazu Osada, Hiroyuki Yoshida, Minoru Myers, Chad L. Boone, Charles RIKEN Center for Sustainable Resource Science Wako Saitama Japan Department of Computer Science and Engineering University of Minnesota-Twin Cities Minneapolis Minnesota USA Bioinformatics and Computational Biology Program University of Minnesota-Twin Cities Minneapolis Minnesota USA Department of Electrical and Computer Engineering University of Minnesota-Twin Cities Minneapolis Minnesota USA Department of Integrated Biosciences Graduate School of Frontier Sciences University of Tokyo Kashiwa Chiba Japan Donnelly Centre University of Toronto Toronto Ontario Canada Institute of Molecular and Cellular Biosciences Center for Epigenetic Disease University of Tokyo Bunkyo-ku Tokyo Japan Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton New Jersey USA Department of Biochemistry University of Toronto Toronto Ontario Canada.

Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound’s mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

关键词： Chemical genetics High-throughput screening Networks and systems biology Target identification

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Opportunities and Challenges from Using Animal Videos in Reinforcement Learning for Navigation

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IFAC-PapersOnLine 2023年第2期56卷 9056-9061页

作者： Vittorio Giammarino James Queeney Lucas C. Carstensen Michael E. Hasselmo Ioannis Ch Paschalidis Division of Systems Engineering Boston University Boston MA 02215 USA Center for Systems Neuroscience Department of Psychological and Brain Sciences and Graduate Program for Neuroscience Boston University Boston MA 02215 USA College of Engineering and Hariri Institute for Computing & Computational Science & Engineering Boston University Boston MA 02215 USA

We investigate the use of animal videos (observations) to improve Reinforcement Learning (RL) efficiency and performance in navigation tasks with sparse rewards. Motivated by theoretical considerations, we make use of weighted policy optimization for off-policy RL and describe the main challenges when learning from animal videos. We propose solutions and test our ideas on a 2D navigation task. We show how the use of animal videos improves performance over RL algorithms that do not leverage such observations.

关键词： Learning for Control Reinforcement Learning Deep Learning RL with demonstrations Imitation Learning Bio-inspired Control

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