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arXiv 2023年

作者： LaBella, Dominic Adewole, Maruf Alonso-Basanta, Michelle Altes, Talissa Anwar, Syed Muhammad Baid, Ujjwal Bergquist, Timothy Bhalerao, Radhika Chen, Sully Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Godfrey, Devon Hilal, Fathi Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kent, Collin Kirkpatrick, John Koer, Florian Van Leemput, Koen Li, Hongwei Bran Liu, Xinyang Mahtabfar, Aria McBurney-Lin, Shan McLean, Ryan Meier, Zeke Moawad, Ahmed W. Mongan, John Nedelec, Pierre Pajot, Maxence Piraud, Marie Rashid, Arif Reitman, Zachary Shinohara, Russell Takeshi Velichko, Yury Wang, Chunhao Warman, Pranav Wiggins, Walter Aboian, Mariam Albrecht, Jake Anazodo, Udunna Bakas, Spyridon Flanders, Adam Janas, Anastasia Khanna, Goldey Linguraru, Marius George Menze, Bjoern Nada, Ayman Rauschecker, Andreas M. Rudie, Jeff Tahon, Nourel Hoda Villanueva-Meyer, Javier Wiestler, Benedikt Calabrese, Evan Department of Radiation Oncology Duke University Medical Center DurhamNC United States Lab Crestview Radiology Lagos Nigeria Department of Radiation Oncology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Missouri University ColumbiaMO United States Children's National Hospital WashingtonDC United States George Washington University WashingtonDC United States University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Sage Bionetworks United States University of California San Francisco CA United States Duke University Medical Center School of Medicine United States Mayo Clinic MN United States Center for Global Health Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Informatics Technical University Munich Germany TranslaTUM Central Institute for Translational Cancer Research Technical University of Munich Germany Children's Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States PrecisionFDA U.S. Food and Drug Administration Silver SpringMD United States Helmholtz Ai Helmholtz Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum Rechts der Isar Technical University of Munich Germany Department of Applied Mathematics and Computer Science Technical University of Denmark Denmark Department of Neuroradiology Technical University of Munich Munich Germany University of Zurich Switzerland Department of Neurosurgery Thomas Jefferson Univer

Meningiomas are the most common primary intracranial tumor in adults and can be associated with significant morbidity and mortality. Radiologists, neurosurgeons, neuro-oncologists, and radiation oncologists rely on multiparametric MRI (mpMRI) for diagnosis, treatment planning, and longitudinal treatment monitoring;yet automated, objective, and quantitative tools for non-invasive assessment of meningiomas on mpMRI are lacking. The BraTS meningioma 2023 challenge will provide a community standard and benchmark for state-of-the-art automated intracranial meningioma segmentation models based on the largest expert annotated multilabel meningioma mpMRI dataset to date. Challenge competitors will develop automated segmentation models to predict three distinct meningioma sub-regions on MRI including enhancing tumor, non-enhancing tumor core, and surrounding nonenhancing T2/FLAIR hyperintensity. Models will be evaluated on separate validation and held-out test datasets using standardized metrics utilized across the BraTS 2023 series of challenges including the Dice similarity coefficient and Hausdorff distance. The models developed during the course of this challenge will aid in incorporation of automated meningioma MRI segmentation into clinical practice, which will ultimately improve care of patients with meningioma. Copyright © 2023, The Authors. All rights reserved.

关键词： Tumors

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Structure learning from time series with false discovery control

arXiv

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arXiv 2018年

作者： Pegueroles, Bernat Guillen Vinzamuri, Bhanukiran Shanmugam, Karthikeyan Hedden, Steve Moyer, Jonathan D. Varshney, Kush R. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States IBM Research Yorktown HeightsNY10598 United States Frederick S. Pardee Center for International Futures Josef Korbel School of International Studies University of Denver DenverCO80210 United States

We consider the Granger causal structure learning problem from time series data. Granger causal algorithms predict a 'Granger causal effect' between two variables by testing if prediction error of one decreases significantly in the absence of the other variable among the predictor covariates. Almost all existing Granger causal algorithms condition on a large number of variables (all but two variables) to test for effects between a pair of variables. We propose a new structure learning algorithm called MMPC-p inspired by the well known MMHC algorithm for non-time series data. We show that under some assumptions, the algorithm provides false discovery rate control. The algorithm is sound and complete when given access to perfect directed information testing oracles. We also outline a novel tester for the linear Gaussian case. We show through our extensive experiments that the MMPC-p algorithm scales to larger problems and has improved statistical power compared to existing state of the art for large sparse graphs. We also apply our algorithm on a global development dataset and validate our findings with subject matter experts. Copyright © 2018, The Authors. All rights reserved.

关键词： Time series

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Feature selection using stochastic gates

arXiv

引用

arXiv 2018年

作者： Yamada, Yutaro Lindenbaum, Ofir Negahban, Sahand Kluger, Yuval Statistics Department Yale University New HavenCT United States Applied Mathematics Program Yale University New HavenCT United States Computational Biology and Bioinformatics Yale University New HavenCT United States Department of Pathology Yale University New HavenCT United States

Feature selection problems have been extensively studied for linear estimation, for instance, Lasso, but less emphasis has been placed on feature selection for non-linear functions. In this study, we propose a method for feature selection in high-dimensional non-linear function estimation problems. The new procedure is based on minimizing the `0 norm of the vector of indicator variables that represent if a feature is selected or not. Our approach relies on the continuous relaxation of Bernoulli distributions, which allows our model to learn the parameters of the approximate Bernoulli distributions via gradient descent. This general framework simultaneously minimizes a loss function while selecting relevant features. Furthermore, we provide an information-theoretic justification of incorporating Bernoulli distribution into our approach and demonstrate the potential of the approach on synthetic and real-life applications. Copyright © 2018, The Authors. All rights reserved.

关键词： Feature extraction

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Stable memory with unstable synapses

arXiv

引用

arXiv 2018年

作者： Susman, Lee Brenner, Naama Barak, Omri Interdisciplinary Program in Applied Mathematics Technion Israel Institute of Technology Haifa Israel Network Biology Research Laboratories Technion Israel Institute of Technology Haifa Israel Faculty of Chemical Engineering Technion Israel Institute of Technology Haifa Israel Rappaport Faculty of Medicine Technion Israel Institute of Technology Haifa Israel

What is the physiological basis of long-term memory? The prevailing view in neuroscience attributes changes in synaptic efficacy to memory acquisition. This view implies that stable memories correspond to stable connectivity patterns. However, an increasing body of experimental evidence points to significant, activity-independent dynamics in synaptic strengths. Motivated by these observations, we explore the possibility of memory storage within a global component of network connectivity, while individual connections fluctuate. We find a simple and general principle, stemming from stability arguments, that links eigenvalues in the complex plane to memories. Specifically, imaginary-coded memories are more resilient to noise and homeostatic plasticity than their real-coded counterparts. Memory representations are stored as time-varying attractors in neural state-space and support associative retrieval of learned information. Our results suggest a link between the properties of learning rules and those of network-level memory representations, and point at measurable signatures to be sought in experimental data. Copyright © 2018, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

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Fabrication of ruby by flame fusion technique and their properties

引用

Materials Today: Proceedings 2018年第7期5卷 15010-15013页

作者： Kitipun Boonin Wichaboon Songpakob Nina Siti Aminah Jakrapong Kaewkhao Applied Physics Program Faculty of Sciences and Technology Suan Sunandha Rajabhat University Bangkok 10300 Thailand Center of Excellence in Glass Technology and Materials Science (CEGM) Nakhon Pathom Rajabhat University Nakhon Pathom 73000 Thailand 13 Charansanitwong 8 Thapra Bangkok 10600 Thailand Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung 40132 Indonesia

In this work, ruby (Cr doped Al 2 O 3 bulk crystal) with the size of ∅10×21 mm was grown by the flame fusion technique (FFT). Absorption spectrum was carried out in the range of 300–800 nm by spectrophotometer, It shows 2 absorption peaks of Cr 3+ in ruby near 400 nm and 550 nm . The crystal structure and the lattice parameters were estimated using X-Ray diffraction studies. The density, refractive index and hardness of synthesis ruby were measured and shown the values in the range of natural ruby material.

关键词： Crystal growth Ruby Optical Hardness

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Dynamics of topological solitons, knotted streamlines, and transport of cargo in liquid crystals

引用

Physical Review E 2018年第5期97卷 052701-052701页

作者： Hayley R. O. Sohn Paul J. Ackerman Timothy J. Boyle Ghadah H. Sheetah Bengt Fornberg Ivan I. Smalyukh Soft Materials Research Center and Materials Science and Engineering Program University of Colorado Boulder Colorado 80309 USA Department of Physics and Department of Electrical Computer and Energy Engineering University of Colorado Boulder Colorado 80309 USA Department of Applied Mathematics University of Colorado Boulder Colorado 80309 USA Renewable and Sustainable Energy Institute National Renewable Energy Laboratory and University of Colorado Boulder Colorado 80309 USA

Active colloids and liquid crystals are capable of locally converting the macroscopically supplied energy into directional motion and promise a host of new applications, ranging from drug delivery to cargo transport at the mesoscale. Here we uncover how topological solitons in liquid crystals can locally transform electric energy to translational motion and allow for the transport of cargo along directions dependent on frequency of the applied electric field. By combining polarized optical video microscopy and numerical modeling that reproduces both the equilibrium structures of solitons and their temporal evolution in applied fields, we uncover the physical underpinnings behind this reconfigurable motion and study how it depends on the structure and topology of solitons. We show that, unexpectedly, the directional motion of solitons with and without the cargo arises mainly from the asymmetry in rotational dynamics of molecular ordering in liquid crystal rather than from the asymmetry of fluid flows, as in conventional active soft matter systems.

关键词： Chirality Topological defects Active nematics Cholesteric liquid crystals Nanoparticles Nematic liquid crystals Soft colloids Solitons

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Mapping Multiple Wild Pig Species’ Population Dynamics in Southeast Asia During the African Swine Fever Outbreak (2018–2024)

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Conservation Letters 2025年第3期18卷

作者： Zoë E. Lieb Erik Meijaard Jedediah F. Brodie Adi Shabrani Jayasilan Mohd-Azlan Jatna Supriatna Matthew John Struebig Nicolas J. Deere Katie L. Spencer Suipeng Heon Lok-Jinn Wong Suzika Juiling Andrew Hearn Camille N. Z. Coudrat Agus Sudibyo Jati Matthew Linkie Dusit Ngoprasert Dhritiman Das Oliver R. Wearn Russell J. Gray Al John C. Cabanas Andaman Chankhao Apinya Saisamorn Badrul Azhar Benjamin P. Y.-H. Lee Benoit Goossens Carl Traeholt David W. MacDonald Emilia A. Lastica-Ternura Fernando Garcia-Gil Freddy Pattiselanno Gabriella Fredriksson Glyn Davies Harry Hilser Jamiee Wheelhouse Jan van der Ploeg John Carlo Redeña-Santos Jonathan M. Moore Karmila Parakkasi Laura Marie Berman Samuel Xin Tham Lee Liam J. Hughes Lukemann Haqeem Alen Marc Ancrenaz Marcus A. H. Chua Markus Handschuh Matthew Ward Mohamad Arif Rifqi Mohammad Aliyuddin Bin Jaini Muhammad Syazwan Bin Omar Nantachai Pongpattananurak NayMyo Shwe Olivia Z. Daniel Pablo Sinovas Parag Deka Radinal Ret Thaung Robert M. Ewers Romain Legrand Ronglarp Sukmasuang Sally Soo Kaicheen Salwa Khalid Saw Soe Aung Sheherazade Sheherazade Stuart J. Davies Thiemo Braasch Thomas N. E. Gray Tim Redford Ulmar Grafe Xiaoyang Song Matthew Scott Luskin School of the Environment University of Queensland Brisbane QLD Australia Borneo Futures Bandar Seri Begawan Brunei Durrell Institute of Conservation and Ecology (DICE) University of Kent Canterbury UK Division of Biological Sciences and Wildlife Biology Program University of Montana Missoula Montana USA World Wildlife Fund Malaysia Sabah Office Kota Kinabalu Malaysia Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan Malaysia Department of Biology Faculty of Mathematics and Natural Sciences University of Indonesia University of Indonesia Depok Indonesia Southeast Asia Rainforest Research Partnership (SEARPP) Kota Kinabalu Malaysia Wildlife Conservation Research Unit Department of Biology University of Oxford Oxford UK Association Anoulak Luang Prabang Lao PDR SSC Wild Pig Specialist Group IUCN Heidelberg Germany Wildlife Conservation Society Indonesia Program Jakarta Indonesia Conservation Ecology Program School of Bioresources and Technology King Mongkut's University of Technology Thonburi Bangkok Thailand Pygmy Hog Conservation Programme Durrell Wildlife Conservation Trust Jersey UK Fauna & Flora International Vietnam Program Hanoi Vietnam Save Vietnam's Wildlife Hoa Lư Vietnam Global Initiative Against Transnational Organized Crime (GI-TOC) Geneva Switzerland Mathematics and Natural Sciences Southern Luzon State University Lucban Philippines Department of Forest Biology Kasetsart University Bangkok Thailand Universiti Putra Malaysia Serdang Malaysia Wildlife & Natural Heritage Royal Commission for AlUla Riyadh Saudi Arabia Danau Girang Field Centre Kota Kinabalu Malaysia Organisms and Environment Division Cardiff School of Biosciences Cardiff University Cardiff UK Research and Conservation Division Copenhagen Zoo Copenhagen Denmark University of the Philippines Los Baños Philippines D'ABOVILLE Foundation and Demo Farm Inc. San Jose Philippines Universitas Papua Manokwari West Papua In

The 2018 arrival of African swine fever (ASF) in China was followed by reports of wild pig deaths across most countries in Southeast Asia. However, the magnitude and duration of population-level impacts of ASF on wild pig species remain unclear. To elucidate the spatiotemporal spread of ASF in the region for native pig species, we gathered qualitative information on wild pig population dynamics in Southeast Asia between 2018 and 2024 from 88 expert elicitation questionnaires representing sites in 11 countries. Peak reported population declines occurred in 2021 and 2022, with more than half of respondents reporting declining wild pig populations, far higher than in earlier years. The reported declines waned to 44.23% in 2024, whereas simultaneously, the number of populations reported to be “increasing” increased from 11.3%–13.2% in 2019–2022 to 28.9% in 2024. These reports suggest that the ASF outbreak may have peaked for wild boars and bearded pigs in mainland Southeast Asia, Borneo, and Sumatra, with some subsequent recovery. However, the disease is still expanding into the ranges of island endemic species, such as new reports for the Sulawesi warty pig ( Sus celebensis ) in September of 2024. Island endemics remain particularly vulnerable to extinction from ASF and require urgent monitoring and conservation action.

关键词： bearded pig (Sus barbatus) biodiversity monitoring expert elicitation survey predator-prey depletion Suidaeisland endemics threatened and endangered species wildlife disease ecology wild boar (Sus scrofa) zoonotic virus

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Numerical equivalence between sph and probabilistic mass transfer methods for lagrangian simulation of dispersioni

arXiv

引用

arXiv 2018年

作者： Sole-Mari, Guillem Schmidt, Michael J. Pankavich, Stephen D. Benson, David A. Universitat Politècnica de Catalunya Barcelona Spain UPC-CSIC Barcelona Spain Department of Applied Mathematics and Statistics Colorado School of Mines GoldenCO80401 United States Hydrologic Science and Engineering Program Department of Geology and Geological Engineering Colorado School of Mines GoldenCO80401 United States

Several Lagrangian methodologies have been proposed in recent years to simulate advection-dispersion of solutes in fluids as a mass exchange between numerical particles carrying the fluid. In this paper, we unify these methodologies, showing that mass transfer particle tracking (MTPT) algorithms can be framed within the context of smoothed particle hydrodynamics (SPH), provided the choice of a Gaussian smoothing kernel whose bandwidth depends on the dispersion and the time discretization. Numerical simulations are performed for a simple dispersion problem, and they are compared to an analytical solution. Based on the results, we advocate for the use of a kernel bandwidth of the size of the characteristic dispersion length ` = √2D∆t, at least given a "dense enough" distribution of particles, for in this case the mass transfer operation is not just an approximation, but in fact the exact solution, of the solute’s displacement Copyright © 2018, The Authors. All rights reserved.

关键词： Mass transfer

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Reinforced dynamics for enhanced sampling in large atomic and molecular systems

arXiv

引用

arXiv 2017年

作者： Zhang, Linfeng Wang, Han Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China CAEP Software Center for High Performance Numerical Simulation Huayuan Road 6 Beijing100088 China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China

A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. The method is illustrated by studying the full-atom, explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables. Copyright © 2017, The Authors. All rights reserved.

关键词： Wave functions

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Light Localization in Local Isomorphism Classes of Quasicrystals

引用

Physical Review Letters 2018年第24期120卷 247401-247401页

作者： Chaney Lin Paul J. Steinhardt Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program of Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

We study a continuum of photonic quasicrystal heterostructures derived from local isomorphism (LI) classes of pentagonal quasicrystal tilings. These tilings are obtained by direct projection from a five-dimensional hypercubic lattice. We demonstrate that, with the sole exception of the Penrose LI class, all other LI classes result in degenerate, effectively localized states, with precisely predictable and tunable properties (frequencies, frequency splittings, and densities). We show that localization and tunability are related to a mathematical property of the pattern known as “restorability,” i.e., whether the tiling can be uniquely specified given only a set of rules that fix all allowed clusters smaller than some bound.

关键词： Photonic crystals Photonics Quasicrystals

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