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arXiv 2025年

作者： Partin, Alexander Vasanthakumari, Priyanka Narykov, Oleksandr Wilke, Andreas Koussa, Natasha Jones, Sara E. Zhu, Yitan Overbeek, Jamie C. Jain, Rajeev Fernando, Gayara Demini Sanchez-Villalobos, Cesar Garcia-Cardona, Cristina Mohd-Yusof, Jamaludin Chia, Nicholas Wozniak, Justin M. Ghosh, Souparno Pal, Ranadip Brettin, Thomas S. Weil, M. Ryan Stevens, Rick L. Division of Data Science and Learning Argonne National Laboratory LemontIL United States Frederick National Laboratory for Cancer Research Cancer Data Science Initiatives Cancer Research Technology Program FrederickMD United States Department of Statistics University of Nebraska–Lincoln LincolnNE United States Department of Electrical & Computer Engineering Texas Tech University LubbockTX United States Division of Computer Computational and Statistical Sciences Los Alamos National Laboratory Los AlamosNM United States Department of Computer Science The University of Chicago ChicagoIL United States

Deep learning (DL) and machine learning (ML) models have shown promise in drug response prediction (DRP), yet their ability to generalize across datasets remains an open question, raising concerns about their real-world applicability. Due to the lack of standardized benchmarking approaches, model evaluations and comparisons often rely on inconsistent datasets and evaluation criteria, making it difficult to assess true predictive capabilities. In this work, we introduce a benchmarking framework for evaluating cross-dataset prediction generalization in DRP models. Our framework incorporates five publicly available drug screening datasets, six standardized DRP models, and a scalable workflow for systematic evaluation. To assess model generalization, we introduce a set of evaluation metrics that quantify both absolute performance (e.g., predictive accuracy across datasets) and relative performance (e.g., performance drop compared to within-dataset results), enabling a more comprehensive assessment of model transferability. Our results reveal substantial performance drops when models are tested on unseen datasets, underscoring the importance of rigorous generalization assessments. While several models demonstrate relatively strong cross-dataset generalization, no single model consistently outperforms across all datasets. Furthermore, we identify CTRPv2 as the most effective source dataset for training, yielding higher generalization scores across target datasets. By sharing this standardized evaluation framework with the community, our study aims to establish a rigorous foundation for model comparison, and accelerate the development of robust DRP models for real-world applications. © 2025, CC BY.

关键词： Prediction models

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Structural properties of hyperuniform Voronoi networks

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Physical Review E 2025年第3期111卷 034123-034123页

作者： Eli Newby Wenlong Shi Yang Jiao Reka Albert Salvatore Torquato Department of Physics Pennsylvania State University University Park Pennsylvania 16802 USA Materials Science and Engineering Arizona State University Tempe Arizona 85287 USA Department of Physics Arizona State University Tempe Arizona 85287 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Institute of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Disordered hyperuniform many-particle systems are recently discovered exotic states of matter, characterized by the complete suppression of normalized infinite-wavelength density fluctuations, as in perfect crystals, while lacking conventional long-range order, as in liquids and glasses. In this work, we begin a program to quantify the structural properties of nonhyperuniform and hyperuniform networks. In particular, large two-dimensional (2D) Voronoi networks (graphs) containing approximately 10,000 nodes are created from a variety of different point configurations, including the antihyperuniform hyperplane intersection process (HIP), nonhyperuniform Poisson process, nonhyperuniform random sequential addition (RSA) saturated packing, and both non-stealthy and stealthy hyperuniform point processes. We carry out an extensive study of the Voronoi-cell area distribution of each of the networks by determining multiple metrics that characterize the distribution, including their average areas and corresponding variances as well as higher-order cumulants (i.e., skewness γ1 and excess kurtosis γ2). We show that the HIP distribution is far from Gaussian, as evidenced by a high skewness (γ1=3.16) and large positive excess kurtosis (γ2=16.2). The Poisson (with γ1=1.07 and γ2=1.79) and non-stealthy hyperuniform (with γ1=0.257 and γ2=0.0217) distributions are Gaussian-like distributions, since they exhibit a small but positive skewness and excess kurtosis. The RSA (with γ1=0.450 and γ2=−0.0384) and the highest stealthy hyperuniform distributions (with γ1=0.0272 and γ2=−0.0626) are also non-Gaussian because of their low skewness and negative excess kurtosis, which is diametrically opposite of the non-Gaussian behavior of the HIP. The fact that the cell-area distributions of large, finite-sized RSA and stealthy hyperuniform networks (e.g., with N≈10,000 nodes) are narrower, have larger peaks, and smaller tails than a Gaussian distribution implies that in the thermodynamic limit th

关键词： Gaussian distribution

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Performance analysis of PDE based parallel algorithms on different computer architectures

Performance analysis of PDE based parallel algorithms on dif...

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5th International Conference on Soft Computing, Computing with Words and Perceptions in System Analysis, Decision and Control, ICSCCW 2009

作者： Kopan, Ilker Çelebi, M. Serdar Informatics Institute Computational Science and Engineering Program ITU Istanbul Turkey

ISBN: (纸本)9781424434282

Performance of an algorithm mainly depends on both computer architecture and software. An Intel Xeon processor based HPC cluster and Intel Itanium2 based symmetric multiprocessing (SMP) architectures are used for performance analysis of PDE based parallel algorithm. Algorithm is parallelized using MPI and performance measurements are done using Tuning and Analysis Utilities (TAU). computational optimization reveals data independency and helps compiler to generate more efficient program for that specific processor. Removing data dependency inside loop is the key in this work. In iterative algorithms, like Gauss-Seidel method, each processor communicates with the same processors at every iteration. This feature makes persistent connection preferable. MPI has different types of communication methods for different communication characteristics. Persistent connection is one of them. Persistent connection removes connection overhead by leaving connection open for further communications. It can be preferred if data is transferred repeatedly between same nodes. In this work source code changed to help compiler to generate more efficient program for the specific processor. Also MPI persistent connection is used for communication at each iteration in Gauss-Seidel method. In some parallel algorithms, communication must be synchronized. Making communication between processors at the same time becomes a bottleneck if communication medium is shared. This fact has been studies and analyzed. ©2009 IEEE.

关键词： Parallel algorithms

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Gravitational effects on global hemodynamics in different postures:A closed-loop multiscale mathematical analysis

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Acta Mechanica Sinica 2017年第3期33卷 595-618页

作者： Xiancheng Zhang Shigeho Noda Ryutaro Himeno Hao Liu Graduate School of Engineering Chiba University Computational Science Research Program RIKEN Shanghai Jiao Tong University and Chiba University International Cooperative Research Center (SJTU-CU ICRC)

We present a novel methodology and strategy to predict pressures and flow rates in the global cardiovascular network in different postures varying from supine to upright. A closed-loop, multiscale mathematical model of the entire cardiovascular system (CVS) is developed through an integration of one-dimensional (1D) modeling of the large systemic arteries and veins, and zero-dimensional (0D) lumped-parameter modeling of the heart, the cardiac-pulmonary circulation, the cardiac and venous valves, as well as the microcirculation. A versatile junction model is proposed and incorporated into the 1D model to cope with splitting and/or merging flows across a multibranched junction, which is validated to be capable of estimating both subcritical and supercritical flows while ensuring the mass conservation and total pressure continuity. To model gravitational effects on global hemodynamics during postural change, a robust venous valve model is further established for the 1D venous flows and distributed throughout the entire venous network with consideration of its anatomically realistic numbers and locations. The present integrated model is proven to enable reasonable prediction of pressure and flow rate waveforms associated with cardiopulmonary circulation, systemic circulation in arteries and veins, as well as microcirculation within normal physiological ranges, particularly in mean venous pressures, which well match the in vivo measurements. Applications of the cardiovascular model at different postures demonstrate that gravity exerts remarkable influence on arterial and venous pressures, venous returns and cardiac outputs whereas venous pressures below the heart level show a specific correlation between central venous and hydrostatic pressures in right atrium and veins.

关键词： Gravitational effects Cardiovascular system (CVS) Postural change Multiscale cardiovascular model Multibranched junction model Venous valve

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Obtaining bulk-like correlated oxide surfaces with protective caps

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Applied Physics Letters 2025年第16期126卷

作者： Cohen, Amit Baskin, Maria Shoham, Lishai Caspi, Shaked Shekhter, Pini Lee, Tien-Lin Chambers, Scott A. Kornblum, Lior Andrew and Erna Viterbi Department of Electrical and Computer Engineering Technion—Israel Institute of Technology Haifa32000-03 Israel The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology Technion—Israel Institute of Technology Haifa32000-03 Israel Wolfson Applied Materials Research Centre Tel Aviv University Tel Aviv Israel Diamond Light Source Ltd Harwell Science & Innovation Campus DidcotOX11 0DE United Kingdom Physical and Computational Sciences Directorate Pacific Northwest National Laboratory RichlandWA99352 United States

Functional oxides exhibit a diverse range of correlated electron phenomena, some of which are highly attractive for novel electronic, magnetic, and optical devices. Despite decades of advancement of our fundamental understanding of these materials, they consistently fall short of realizing their promise in functional devices. We identify a significant bottleneck toward device realization to be surface overoxidation. Protective caps can effectively prevent overoxidation, but their interfaces with functional oxides are not well understood. These interfaces are critical for effectively using functional oxides in field-effect devices, where "the interface is the device." This work addresses the chemistry and physics of the interface between protective caps and the correlated metal SrVO3, a model functional oxide. Our comparison of five different cap materials reveals effective protection and similar SrVO3 surface chemistry in all cases. Systematic comparisons of surface and bulk-sensitive photoelectron spectra reveal that negligible interface redox takes place, elucidating the cap-SrVO3 interface chemistry. This work demonstrates a robust and simple solution to the surface overoxidation problem in vanadates, paving the way toward effectively using these materials in field-effect devices. Our conclusions are general and can be applied to numerous other systems, thus moving oxide electronics closer to the realization of functional devices. © 2025 Author(s).

关键词： Redox reactions

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Three-dimensional numerical simulation of flames supported by a spinning porous-plug burner

Three-dimensional numerical simulation of flames supported b...

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Fall Technical Meeting of the Eastern States Section of the Combustion Institute 2007: Chemical and Physical Processes in Combustion

作者： Hossain, K.N. Jackson, T.L. Buckmaster, J. Computational Science and Engineering Program University of Illinois UrbanaIL61801 United States

ISBN: (纸本)9781604239454

A three-dimensional numerical study is undertaken to analyze the characteristics of flames supported by a spinning porous piug methane burner. These flames are characterized by muiti-dimensiona] instabilities at near extinction conditions. The instabilities appear in the form of holes and spirais as observed in experimental studies [1], [2]. The non-uniform flames are simulated numerically for Damkohler numbers on the upper branch of the S-response curve ciose to the extinction point. The flames are analyzed to determine the mechanism of onset of the patterns and to gain an understanding of the dynamics of the system.

关键词： Combustion

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Strategies to Reduce Long-Term Drug Resistance by Considering Effects of Differential Selective Treatments 3rd

Strategies to Reduce Long-Term Drug Resistance by Considerin...

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3rd International Symposium on Mathematical and computational Oncology, ISMCO 2021

作者： Ghodsi Asnaashari, Tina Chang, Young Hwan Department of Biomedical Engineering and Computational Biology Program Oregon Health and Science University Portland United States

ISBN: (纸本)9783030912406

Despite great advances in modeling and cancer therapy using optimal control theory, tumor heterogeneity and drug resistance are major obstacles in cancer treatments. Since recent biological studies demonstrated the evidence of tumor heterogeneity and assessed potential biological and clinical implications, tumor heterogeneity should be taken into account in the optimal control problem to improve treatment strategies. Here, first we study the effects of two different treatment strategies (i.e., symmetric and asymmetric) in a minimal two-population model to examine the long-term effects of these treatment methods on the system. Second, by considering tumor adaptation to treatment as a factor of the cost function, the optimal treatment strategy is derived. Numerical examples show that optimal treatment decreases tumor burden for the long-term by decreasing rate of tumor adaptation over time. © 2021, Springer Nature Switzerland AG.

关键词： Tumors

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Narrowing of the Racial Disparities Gap in Survival of Patients With Mycosis Fungoides: A Longitudinal Analysis of the SEER Database

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Clinical Lymphoma, Myeloma and Leukemia 2025年

作者： Le, Britney Soror, Noha Ismail, Hamid D. Baker, Mohammed Shetayyah, Salman Abu Chung, Catherine G. William, Basem M. Ohio University Heritage College of Osteopathic Medicine Dublin OH The University of Oklahoma College of Medicine Oklahoma City OK United States Department of Computational Data Science and Engineering North Carolina Agricultural and Technical State University Greensboro NC United States Faculty of Medicine Jordan University of Science and Technology Irbid Jordan The Ohio State University Comprehensive Cancer Center: Arthur G. James Cancer Hospital and Richard J. Solove Research Institute Division of Dermatology Columbus OH Ohio Health Blood and Marrow Transplant Program Columbus OH

Background: Mycosis fungoides (MF) is the commonest subtype of cutaneous T-cell lymphoma. In the United States, prior studies reported that African Americans (AA) with MF had poor outcomes. Data characterizing differences in racial disparity outcomes over time are limited. Patients and Methods: We collected data from the United States Surveillance, Epidemiology, and End Results (SEER) database to investigate the survival patterns of patients with MF from 1988 to 2011. Cases were divided into 3 cohorts based on the year of diagnosis. Univariable and multivariable analysis were conducted to assess for factors associated with overall survival (OS). Results: 2896 cases of MF were detected, with a median follow-up duration of 60 months. The disparity in survival between the years 1988-1995 and 2004-2011 was significant (P =.05). The parameter estimates of the Cox proportional hazards model for the 1988-1995 period (using the 2004-2011 period as a reference) was also significant (P =.024). Patients diagnosed between 1988 and 1995 were 1.4 times more likely to die from the disease than those diagnosed between 2004 and 2011. The survival gap between AA and white patients narrowed in 1996-2003 and 2004-2011 in comparison to 1988-1995. This indicates improvements in the survival of AA patients over time. Conversely, the survival rates of white patients remained relatively stable over time. Conclusions: Our study demonstrates that AA with MF have reduced survival. Despite the persistent pattern of lower survival across all periods, the gap in survival between white and AA seems to be narrowing over time. © 2025 Elsevier Inc.

关键词： Cutaneous lymphoma Mycosis fungoides Outcome research Racial disparity SEER database

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Diffraction by one-dimensional paracrystals and perturbed lattices

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Acta Crystallographica Section A: Foundations of Crystallography 2000年第5期56卷 497-506页

作者： Millane, R.P. Eads, J.L. Whistler Center for Carbohydrate Research Computational Science and Engineering Program Purdue University West Lafayette IN 47907-1160 United States

A detailed comparison of the one-dimensional paracrystalline and perturbed lattice models of disordered crystals, and their diffraction, is made. If noncumulative (thermal) disorder is added to the paracrystalline model, then the two models and their diffraction patterns are similar but not identical because of their different intersite statistics. However, they are identical in the limiting cases of either strong or weak correlations. Calculation of diffraction patterns shows that, with an appropriate choice of parameters, the two models give essentially identical diffraction for small crystallites and very similar diffraction for larger crystallites. An empirical relationship is derived between parameters of the two models such that they give similar diffraction patterns.

关键词： paracrystals perturbed lattices disorder diffraction.

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Anomalous suppression of large-scale density fluctuations in classical and quantum spin liquids

arXiv

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arXiv 2025年

作者： Chen, Duyu Samajdar, Rhine Jiao, Yang Torquato, Salvatore Materials Research Laboratory University of California Santa BarbaraCA93106 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Center for Theoretical Science Princeton University PrincetonNJ08544 United States Materials Science and Engineering Arizona State University TempeAZ85287 United States Department of Physics Arizona State University TempeAZ85287 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Materials Institute Princeton University PrincetonNJ08540 United States Program in Applied and Computational Mathematics PrincetonNJ08544 United States

Classical spin liquids (CSLs) are intriguing states of matter that do not exhibit long-range magnetic order and are characterized by an extensive ground-state degeneracy. Adding quantum fluctuations, which induce dynamics between these different classical ground states, can give rise to quantum spin liquids (QSLs). QSLs are highly entangled quantum phases of matter characterized by fascinating emergent properties, such as fractionalized excitations and topological order. One such exotic quantum liquid is the Z2 QSL, which can be regarded as a resonating valence bond (RVB) state formed from superpositions of dimer coverings of an underlying lattice. In this work, we unveil a hidden large-scale structural property of archetypal CSLs and QSLs known as hyperuniformity, i.e., normalized infinite-wavelength density fluctuations are completely suppressed in these systems. In particular, we first demonstrate that classical ensembles of close-packed dimers and their corresponding quantum RVB states are perfectly hyperuniform in general. Subsequently, we focus on a ruby-lattice spin liquid that was recently realized in a Rydberg-atom quantum simulator, and show that the QSL remains effectively hyperuniform even in the presence of a finite density of spinon and vison excitations, as long as the dimer constraint is still largely preserved. Moreover, we demonstrate that metrics based on the framework of hyperuniformity can be used to distinguish the QSL from other proximate quantum phases. These metrics can help identify potential QSL candidates, which can then be further analyzed using more advanced, computationally-intensive quantum numerics to confirm their status as true QSLs. © 2025, CC BY-NC-ND.

关键词： Quantum entanglement

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