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arXiv 2018年

作者： Campelo, Felipe Takahashi, Fernanda Operations Research and Complex Systems Laboratory Universidade Federal de Minas Gerais Belo Horizonte31270-010 Brazil Department of Electrical Engineering Universidade Federal de Minas Gerais Brazil Graduate Program in Electrical Engineering Universidade Federal de Minas Gerais Brazil

Experimental comparisons of performance represent an important aspect of research on optimization algorithms. In this work we present a methodology for defining the required sample sizes for designing experiments with desired statistical properties for the comparison of two methods on a given problem class. The proposed approach allows the experimenter to define desired levels of accuracy for estimates of mean performance differences on individual problem instances, as well as the desired statistical power for comparing mean performances over a problem class of interest. The method calculates the required number of problem instances, and runs the algorithms on each test instance so that the accuracy of the estimated differences in performance is controlled at the predefined level. Two examples illustrate the application of the proposed method, and its ability to achieve the desired statistical properties with a methodologically sound definition of the relevant sample sizes. Copyright © 2018, The Authors. All rights reserved.

关键词： Sampling

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Tuning metaheuristics by sequential optimization of regression models

arXiv

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arXiv 2018年

作者： Trindade, Áthila R. Campelo, Felipe Operations Research and Complex Systems Laboratory Universidade Federal de Minas Gerais Belo Horizonte31270-010 Brazil Graduate Program in Electrical Engineering Universidade Federal de Minas Gerais Brazil Department of Electrical Engineering Universidade Federal de Minas Gerais Brazil

Tuning parameters is an important step for the application of metaheuristics to problem classes of interest. In this work we present a tuning framework based on the sequential optimization of perturbed regression models. Besides providing algorithm configurations with good expected performance, the proposed methodology can also provide insights on the relevance of each parameter and their interactions, as well as models of expected algorithm performance for a given problem class, conditional on the parameter values. A test case is presented for the tuning of six parameters of a decomposition-based multiobjective optimization algorithm, in which an instantiation of the proposed framework is compared against the results obtained by the most recent version the Iterated Racing (Irace) procedure. The results suggest that the proposed approach returns solutions that are as good as those of Irace in terms of mean performance, with the advantage of providing more information on the relevance and effect of each parameter on the expected performance of the algorithm. Copyright © 2018, The Authors. All rights reserved.

关键词： Heuristic algorithms

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Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation

Research Square

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Research Square 2021年

作者： Freedman, Matthew L. Baca, Sylvan C. Singler, Cassandra Zacharia, Soumya Seo, Ji-Heui Morova, Tunc Hach, Faraz Ding, Yi Schwarz, Tommer Huang, Chia-Chi Flora Kalita, Cynthia Groha, Stefan Pomerantz, Mark M. Wang, Victoria Linder, Simon Sweeney, Christopher J. Zwart, Wilbert Lack, Nathan A. Pasaniuc, Bogdan Takeda, David Y. Gusev, Alexander Department of Medical Oncology Dana-Farber Cancer Institute BostonMA United States Center for Functional Cancer Epigenetics Dana-Farber Cancer Institute BostonMA United States The Eli and Edythe L. Broad Institute CambridgeMA United States Laboratory of Genitourinary Cancer Pathogenesis Center for Cancer Research National Cancer Institute BethesdaMD United States Vancouver Prostate Centre University of British Columbia VancouverBC Canada Bioinformatics Interdepartmental Program UCLA Los AngelesCA United States Division of Genetics Brigham & Women’s Hospital BostonMA United States Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute BostonMA United States Department of Biostatistics Harvard School of Public Health BostonMA United States Division of Oncogenomics Oncode Institute The Netherlands Cancer Institute Amsterdam Netherlands Laboratory of Chemical Biology Institute for Complex Molecular Systems Department of Biomedical Engineering Eindhoven University of Technology Eindhoven Netherlands School of Medicine Koç University Istanbul Turkey Department of Computational Medicine David Geffen School of Medicine at UCLA Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine at UCLA Los AngelesCA United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine at UCLA Los AngelesCA United States

Methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs), are widely used to functionally annotate trait-associated variants, but they are limited in identifying context-dependent effects on transcription. To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for nominating variants that impact traits through their effects on chromatin state. CWAS associates the genetic determinants of cistromes (e.g., the genome-wide profiles of transcription factor binding sites or histone modifications) with traits using summary statistics from genome-wide association studies (GWAS). We performed CWASs of prostate cancer and androgen-related traits, using a reference panel of 307 prostate cistromes from 165 individuals. CWAS nominated susceptibility regulatory elements or androgen receptor (AR) binding sites at 52 out of 98 known prostate cancer GWAS loci and implicated an additional 17 novel loci. We functionally validated a subset of our results using CRISPRi and in vitro reporter assays. At 28 of the 52 risk loci, CWAS identified regulatory mechanisms that are not observable via eQTLs, implicating genes with complex or context-specific regulation that are overlooked by current approaches that relying on steady-state transcript measurements. CWAS genes include transcription factors that govern prostate development such as NKX3-1, HOXB13, GATA2, and KLF5. Moreover, CWAS boosts discovery power in modestly sized GWAS, identifying novel genetic associations mediated through AR binding for androgen-related phenotypes, including resistance to prostate cancer therapy. CWAS is a powerful and biologically interpretable paradigm for studying variants that influence traits by affecting context-dependent transcriptional regulation. © 2021, CC BY.

关键词： Transcription

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Dynamical patterns in nematic active matter on a sphere

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Physical Review E 2018年第4期97卷 042605-042605页

作者： Silke Henkes M. Cristina Marchetti Rastko Sknepnek Institute for Complex Systems and Mathematical Biology Department of Physics University of Aberdeen Aberdeen AB24 3UE United Kingdom Department of Physics and Soft Matter Program Syracuse University Syracuse New York 13244 USA School of Sciences and Engineering and School of Life Sciences University of Dundee Dundee DD1 4HN United Kingdom

Using simulations of self-propelled agents with short-range repulsion and nematic alignment, we explore the dynamical phases of a dense active nematic confined to the surface of a sphere. We map the nonequilibrium phase diagram as a function of curvature, alignment strength, and activity. Our model reproduces several phases seen in recent experiments on active microtubule bundles confined the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1/2 defects. As the driving is increased, geodesic forces drive the transition to a polar band wrapping around an equator, with large empty spherical caps corresponding to two +1 defects at the poles. Upon further increasing activity, the bands fold onto themselves, and the system eventually transitions to a turbulent state marked by the proliferation of pairs of topological defects. We highlight the key role of the nematic persistence length in controlling pattern formation in these confined systems with positive Gaussian curvature.

关键词： Biomimetic & bio-inspired materials Collective behavior Confinement Conformation & topology Emergence of patterns

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CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional programs to Drive Prostate Tumorigenesis (vol 35, pg 603, 2019)

引用

CANCER CELL 2019年第5期35卷 817-819页

作者： Augello, Michael A. Liu, Deli Deonarine, Lesa D. Robinson, Brian D. Huang, Dennis Stelloo, Suzan Blattner, Mirjam Doane, Ashley S. Wong, Elissa W. P. Chen, Yu Rubin, Mark A. Beltran, Himisha Elemento, Olivier Bergman, Andries M. Zwart, Wilbert Sboner, Andrea Dephoure, Noah Barbieri, Christopher E. Department of Urology Weill Cornell Medicine New York NY 10065 USA Sandra and Edward Meyer Cancer Center Weill Cornell Medicine New York NY 10065 USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New York NY 10065 USA Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY 10065 USA Caryl and Israel Englander Institute for Precision Medicine Weill Cornell Medicine New York NY 10065 USA Division of Oncogenomics Oncode Institute The Netherlands Cancer Institute Amsterdam the Netherlands Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer Center New York NY 10065 USA Department of Medicine Memorial Sloan Kettering Cancer Center New York NY 10065 USA Department of Medicine Weill Cornell Medicine New York NY 10065 USA Division of Medical Oncology Netherlands Cancer Institute Amsterdam The Netherlands Laboratory of Chemical Biology and Institute for Complex Molecular Systems Department of Biomedical Engineering Eindhoven University of Technology Eindhoven The Netherlands Department of Biochemistry Weill Cornell Medicine New York NY 10065 USA

Summary Deletion of the gene encoding the chromatin remodeler CHD1 is among the most common alterations in prostate cancer (PCa); however, the tumor-suppressive functions of CHD1 and reasons for its tissue-specific loss remain undefined. We demonstrated that CHD1 occupied prostate-specific enhancers enriched for the androgen receptor (AR) and lineage-specific cofactors. Upon CHD1 loss, the AR cistrome was redistributed in patterns consistent with the oncogenic AR cistrome in PCa samples and drove tumor formation in the murine prostate. Notably, this cistrome shift was associated with a unique AR transcriptional signature enriched for pro-oncogenic pathways unique to this tumor subclass. Collectively, these data credential CHD1 as a tumor suppressor in the prostate that constrains AR binding/function to limit tumor progression.

关键词： prostate cancer androgen receptor prostate cancer subclass AR CHD1 epigenetics HOXB13 chromatin remodeling cistrome reprogramming interactome

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Manifold learning for organizing unstructured sets of process observations

arXiv

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arXiv 2018年

作者： Dietrich, Felix Kooshkbaghi, Mahdi Bollt, Erik M. Kevrekidis, Ioannis G. Department of Chemical and Biomolecular Engineering Department of Applied Mathematics and Statistics Johns Hopkins University BaltimoreMD21218 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Mathematics Department of Electrical and Computer Engineering Clarkson Center for Complex Systems Science Clarkson University PotsdamNY13699-5815 United States

Data mining is routinely used to organize ensembles of short temporal observations so as to reconstruct useful, low-dimensional realizations of an underlying dynamical system. In this paper, we use manifold learning to organize unstructured ensembles of observations ("trials") of a system's response surface. We have no control over where every trial starts;and during each trial operating conditions are varied by turning "agnostic" knobs, which change system parameters in a systematic but unknown way. As one (or more) knobs "turn" we record (possibly partial) observations of the system response. We demonstrate how such partial and disorganized observation ensembles can be integrated into coherent response surfaces whose dimension and parametrization can be systematically recovered in a data-driven fashion. The approach can be justified through the Whitney and Takens embedding theorems, allowing reconstruction of manifolds/attractors through different types of observations. We demonstrate our approach by organizing unstructured observations of response surfaces, including the reconstruction of a cusp bifurcation surface for Hydrogen combustion in a Continuous Stirred Tank Reactor. Finally, we demonstrate how this observation-based reconstruction naturally leads to informative transport maps between input parameter space and output/state variable *** codes 37M20 Copyright © 2018, The Authors. All rights reserved.

关键词： Dynamical systems

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Aggregation of two-dimensional composite grains due to self-gravitation

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AIP Conference Proceedings 2020年第1期2219卷

作者： S. Viridi F. F. Florena F. Faizal A. Suroso Nurhasan Y. Bindar 1Nuclear Physics and Biophysics Institut Teknologi Bandung Bandung 40132 Indonesia 2Master Program in Physics Institut Teknologi Bandung Bandung 40132 Indonesia 3Nanotechnology and Graphene Research Center Universitas Padjadjaran Sumedang 45363 Indonesia 4Theoretical High Energy Physics Institut Teknologi Bandung Bandung 40132 Indonesia 5Physics of Earth and Complex Systems Institut Teknologi Bandung Bandung 40132 Indonesia 6Energy and Processing System of Chemical Engineering Institut Teknologi Bandung Bandung 40132 Indonesia

Binding force in the form of spring force binds two adjacent spherical grains and based on this interaction various structures of composite particles can be constructed. In this work only composite particles up to N = 4 are discussed, where N is number of spherical grains in a composite particle, and the forms are limited to the two-dimensional cases only. There is only one structure of composite particle for each value of N for 1 < N ≤ 2. For N = 3 there are five structures and for N = 4 there are fifteen structures. Between spherical grains from different composite particles only two types of force are considered. The first is a long-range attractive force in the form of gravitation force and the last is a short-range repulsion force in the form of normal force. The first type of force will help the aggregation process, while the second will prevent two spherical grains to collapse into a single grain due to the first. It is observed that the time required to produce the compact aggregate or T is dependent on N, where larger N makes larger T.

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Author Correction: Discrepancy in scientific authority and media visibility of climate change scientists and contrarians

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Nature communications 2019年第1期10卷 3966页

作者： Alexander Michael Petersen Emmanuel M Vincent Anthony LeRoy Westerling Management of Complex Systems Department Ernest and Julio Gallo Management Program School of Engineering University of California Merced CA 95343 USA. apetersen3@ucmerced.edu. Medialab Sciences Po Paris 75007 France. mel.manux@***. Center for Climate Communication University of California Merced CA 95343 USA. mel.manux@***. Management of Complex Systems Department Ernest and Julio Gallo Management Program School of Engineering University of California Merced CA 95343 USA. awesterling@ucmerced.edu. Center for Climate Communication University of California Merced CA 95343 USA. awesterling@ucmerced.edu. Sierra Nevada Research Institute University of California Merced CA 95343 USA. awesterling@ucmerced.edu.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Photon drag of a Bose-Einstein condensate

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Physical Review B 2018年第16期98卷 165405-165405页

作者： V. M. Kovalev A. E. Miroshnichenko I. G. Savenko A.V. Rzhanov Institute of Semiconductor Physics Siberian Branch of Russian Academy of Sciences Novosibirsk 630090 Russia Department of Applied and Theoretical Physics Novosibirsk State Technical University Novosibirsk 630073 Russia School of Engineering and Information Technology University of New South Wales Canberra ACT 2600 Australia Center for Theoretical Physics of Complex Systems Institute for Basic Science (IBS) Daejeon 34126 Korea Basic Science Program Korea University of Science and Technology (UST) Daejeon 34113 Korea

Kepler's observation of comet tails initiated the research on the radiation pressure of celestial objects and 250 years later they found new incarnation after the Maxwell's equations were formulated to describe a plethora of light-matter coupling phenomena. Further, quantum mechanics gave birth to the photon drag effect. Here, we develop a microscopic theory of this effect which can occur in a general system containing Bose-Einstein–condensed particles, which possess an internal structure of quantum states. By analyzing the response of the system to an external electromagnetic field we find that such a drag results in a flux of particles constituting both the condensate and the excited states. We show that in the presence of the condensed phase, the response of the system acquires steplike behavior as a function of the electromagnetic field frequency with the elementary step determined by the internal energy structure of the particles.

关键词： Bose-Einstein condensates Cold atoms & matter waves Electronic transitions Light-matter interaction Mechanical effects of light on material media

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Quantum processor-inspired machine learning in the biomedical sciences

arXiv

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arXiv 2019年

作者： Li, Richard Y. Gujja, Sharvari Bajaj, Sweta R. Gamel, Omar E. Cilfone, Nicholas Gulcher, Jeffrey R. Lidar, Daniel A. Chittenden, Thomas W. Department of Chemistry University of Southern California Los AngelesCA United States Computational Biology and Bioinformatics Program Department of Biological Sciences University of Southern California Los AngelesCA United States Center for Quantum Information Science & Technology University of Southern California Los AngelesCA United States Computational Statistics and Bioinformatics Group Advanced Artificial Intelligence Research Laboratory Genuity Science BostonMA United States Complex Biological Systems Alliance MedfordMA United States Cancer Genetics Group Genuity Science BostonMA United States Department of Electrical Engineering University of Southern California Los AngelesCA United States Department of Physics and Astronomy University of Southern California Los AngelesCA United States Division of Genetics and Genomics Boston Children's Hospital Harvard Medical School BostonMA United States

Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired in part by recent advances in physical quantum processors, we evaluated several unconventional machine learning (ML) strategies on actual human tumor data;namely "Ising-type" methods whose objective function is formulated identically to simulated annealing and quantum annealing, as well as a restricted Boltzmann machine. Here we show for the first time the efficacy of multiple Ising-type ML algorithms for classification of high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas. To assess algorithm performance, we compared these classifiers to a variety of standard ML methods. Our results indicate the feasibility of using Ising-type ML to provide competitive classification of human cancer types and associated molecular subtypes and superior performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing approaches in the biomedical sciences. © 2019, CC BY.

关键词： Machine learning

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