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3,249 Research products

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hao Zhou; Melike Erol-Kantarci; Yuanwei Liu; H. Vincent Poor;

    Reconfigurable intelligent surfaces (RISs) have received considerable attention as a key enabler for envisioned 6G networks, for the purpose of improving the network capacity, coverage, efficiency, and security with low energy consumption and low hardware cost. However, integrating RISs into the existing infrastructure greatly increases the network management complexity, especially for controlling a significant number of RIS elements. To unleash the full potential of RISs, efficient optimization approaches are of great importance. This work provides a comprehensive survey on optimization techniques for RIS-aided wireless communications, including model-based, heuristic, and machine learning (ML) algorithms. In particular, we first summarize the problem formulations in the literature with diverse objectives and constraints, e.g., sum-rate maximization, power minimization, and imperfect channel state information constraints. Then, we introduce model-based algorithms that have been used in the literature, such as alternating optimization, the majorization-minimization method, and successive convex approximation. Next, heuristic optimization is discussed, which applies heuristic rules for obtaining low-complexity solutions. Moreover, we present state-of-the-art ML algorithms and applications towards RISs, i.e., supervised and unsupervised learning, reinforcement learning, federated learning, graph learning, transfer learning, and hierarchical learning-based approaches. Model-based, heuristic, and ML approaches are compared in terms of stability, robustness, optimality and so on, providing a systematic understanding of these techniques. Finally, we highlight RIS-aided applications towards 6G networks and identify future challenges. Comment: This paper has been accepted by IEEE Communications Surveys and Tutorials

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    https://doi.org/10.1109/comst....
    Article . 2023
    License: IEEE Copyright
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    https://doi.org/10.48550/arxiv...
    Article . 2023
    License: CC 0
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      https://doi.org/10.1109/comst....
      Article . 2023
      License: IEEE Copyright
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      https://doi.org/10.48550/arxiv...
      Article . 2023
      License: CC 0
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fasina, Oluwadamilola; Huguet, Guillaume; Tong, Alexander; Zhang, Yanlei; +4 Authors

    Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the underlying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells). Comment: 13 pages, 11 figures, 1 table

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    https://doi.org/10.48550/arxiv...
    Article . 2023
    License: arXiv Non-Exclusive Distribution
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      https://doi.org/10.48550/arxiv...
      Article . 2023
      License: arXiv Non-Exclusive Distribution
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Cai, Yang; Devanur, Nikhil R.; Goldner, Kira; McAfee, R. Preston;

    We study a new model of complementary valuations, which we call "proportional complementarities." In contrast to common models, such as hypergraphic valuations, in our model, we do not assume that the extra value derived from owning a set of items is independent of the buyer's base valuations for the items. Instead, we model the complementarities as proportional to the buyer's base valuations, and these proportionalities are known market parameters. Our goal is to design a simple pricing scheme that, for a single buyer with proportional complementarities, yields approximately optimal revenue. We define a new class of mechanisms where some number of items are given away for free, and the remaining items are sold separately at inflated prices. We find that the better of such a mechanism and selling the grand bundle earns a 12-approximation to the optimal revenue for pairwise proportional complementarities. This confirms the intuition that items should not be sold completely separately in the presence of complementarities. In the more general case, a buyer has a maximum of proportional positive hypergraphic valuations, where a hyperedge in a given hypergraph describes the boost to the buyer's value for item $i$ given by owning any set of items $T$ in addition. The maximum-out-degree of such a hypergraph is $d$, and $k$ is the positive rank of the hypergraph. For valuations given by these parameters, our simple pricing scheme is an $O(\min\{d,k\})$-approximation. Comment: Appeared in the 2019 ACM Conference on Economics and Computation (ACM EC '19)

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ https://dl.acm.org/d...arrow_drop_down
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    https://dl.acm.org/doi/pdf/10....
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    https://doi.org/10.1145/332852...
    Conference object . 2019
    License: ACM Copyright Policies
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    https://doi.org/10.48550/arxiv...
    Article . 2019
    License: arXiv Non-Exclusive Distribution
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ https://dl.acm.org/d...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      https://dl.acm.org/doi/pdf/10....
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      https://doi.org/10.1145/332852...
      Conference object . 2019
      License: ACM Copyright Policies
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      https://doi.org/10.48550/arxiv...
      Article . 2019
      License: arXiv Non-Exclusive Distribution
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Neale, Chris; Herce, Henry D.; Pomès, Régis; García, Angel E.;

    AbstractG-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane’s cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a molecular mechanism for the experimental observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G-protein-coupled receptors suggests that intracellular lipid ingression between receptor helices H6 and H7 may be a general mechanism for active-state stabilization.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Biophysical Journalarrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Biophysical Journal
    Article
    License: Elsevier Non-Commercial
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Biophysical Journal
    Article
    License: Elsevier Non-Commercial
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Europe PubMed Central
    Other literature type . 2015
    Data sources: PubMed Central
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Biophysical Journalarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Biophysical Journal
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      License: Elsevier Non-Commercial
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Biophysical Journal
      Article
      License: Elsevier Non-Commercial
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Europe PubMed Central
      Other literature type . 2015
      Data sources: PubMed Central
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Joe C, Liang; Andrew L, Chang; Andrew B, Kennedy; Christina D, Smolke;

    Recent advances have demonstrated the use of RNA-based control devices to program sophisticated cellular functions; however, the efficiency with which these devices can be quantitatively tailored has limited their broader implementation in cellular networks. Here, we developed a high-efficiency, high-throughput and quantitative two-color fluorescence-activated cell sorting-based screening strategy to support the rapid generation of ribozyme-based control devices with user-specified regulatory activities. The high-efficiency of this screening strategy enabled the isolation of a single functional sequence from a library of over 10(6) variants within two sorting cycles. We demonstrated the versatility of our approach by screening large libraries generated from randomizing individual components within the ribozyme device platform to efficiently isolate new device sequences that exhibit increased in vitro cleavage rates up to 10.5-fold and increased in vivo activation ratios up to 2-fold. We also identified a titratable window within which in vitro cleavage rates and in vivo gene-regulatory activities are correlated, supporting the importance of optimizing RNA device activity directly in the cellular environment. Our two-color fluorescence-activated cell sorting-based screen provides a generalizable strategy for quantitatively tailoring genetic control elements for broader integration within biological networks.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Europe PubMed Central
    Article . 2012
    Data sources: PubMed Central
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    Caltech Authors
    Article . 2012
    Data sources: Caltech Authors
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    Nucleic Acids Research
    Article . 2012
    License: CC BY NC
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      Europe PubMed Central
      Article . 2012
      Data sources: PubMed Central
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      Caltech Authors
      Article . 2012
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      Nucleic Acids Research
      Article . 2012
      License: CC BY NC
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    Authors: Grumbach, Stéphane; Su, Jianwen;

    AbstractIn this paper, we study the expressive power and the complexity of first-order logic with arithmetic, as a query language over relational and constraint databases. We consider constraints over various domains (N, Z, Q, and R), and with various arithmetical operations (⩽, +, ×, etc.).We first consider the data complexity of first-order queries. We prove in particular that linear queries can be evaluated in AC0 over finite integer databases, and in NC1 over linear constraint databases. This improves previously known bounds. We also show that over all domains, enough arithmetic lead to arithmetical queries, therefore, showing the frontiers of constraints for database purposes.We then tackle the problem of the expressive power, with the definability of the parity and the connectivity, which are the most classical examples of queries not expressible in first-order logic over finite structures. We prove that these two queries are first-order definable in the presence of (enough) arithmetic. Nevertheless, we show that they are not definable with constraints of interest for constraint databases such as linear constraints for instance. Finally, we developed reduction techniques for queries over constraint databases, that allow us to draw conclusions with respect to their undefinability in various constraint query languages.

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    Theoretical Computer Science
    Article . 1997
    License: Elsevier Non-Commercial
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      Theoretical Computer Science
      Article . 1997
      License: Elsevier Non-Commercial
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    Authors: Ernazar Abdikamalov; Christian D. Ott; David Radice; Luke F. Roberts; +5 Authors

    We conduct a series of numerical experiments into the nature of three-dimensional (3D) hydrodynamics in the postbounce stalled-shock phase of core-collapse supernovae using 3D general-relativistic hydrodynamic simulations of a $27$-$M_\odot$ progenitor star with a neutrino leakage/heating scheme. We vary the strength of neutrino heating and find three cases of 3D dynamics: (1) neutrino-driven convection, (2) initially neutrino-driven convection and subsequent development of the standing accretion shock instability (SASI), (3) SASI dominated evolution. This confirms previous 3D results of Hanke et al. 2013, ApJ 770, 66 and Couch & Connor 2014, ApJ 785, 123. We carry out simulations with resolutions differing by up to a factor of $\sim$4 and demonstrate that low resolution is artificially favorable for explosion in the 3D convection-dominated case, since it decreases the efficiency of energy transport to small scales. Low resolution results in higher radial convective fluxes of energy and enthalpy, more fully buoyant mass, and stronger neutrino heating. In the SASI-dominated case, lower resolution damps SASI oscillations. In the convection-dominated case, a quasi-stationary angular kinetic energy spectrum $E(\ell)$ develops in the heating layer. Like other 3D studies, we find $E(\ell) \propto \ell^{-1}$ in the "inertial range," while theory and local simulations argue for $E(\ell) \propto \ell^{-5/3}$. We argue that current 3D simulations do not resolve the inertial range of turbulence and are affected by numerical viscosity up to the energy containing scale, creating a "bottleneck" that prevents an efficient turbulent cascade. 24 pages, 15 figures. Accepted for publication in The Astrophysical Journal. Added one figure and made minor modifications to text according to suggestions from the referee

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    Caltech Authors
    Article . 2015
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    The Astrophysical Journal
    Article . 2015
    License: IOP Copyright Policies
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    MPG.PuRe
    Article . 2015
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    https://doi.org/10.48550/arxiv...
    Article . 2014
    License: arXiv Non-Exclusive Distribution
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      The Astrophysical Journal
      Article . 2015
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      Article . 2015
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      https://doi.org/10.48550/arxiv...
      Article . 2014
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    Authors: Jasmin Coulombe-Huntington; Yu Xia;

    The evolution of transcriptional regulatory networks has thus far mostly been studied at the level of cis-regulatory elements. To gain a complete understanding of regulatory network evolution we must also study the evolutionary role of trans-factors, such as transcription factors (TFs). Here, we systematically assess genomic and network-level determinants of TF evolutionary rate in yeast, and how they compare to those of generic proteins, while carefully controlling for differences of the TF protein set, such as expression level. We found significantly distinct trends relating TF evolutionary rate to mRNA expression level, codon adaptation index, the evolutionary rate of physical interaction partners, and, confirming previous reports, to protein-protein interaction degree and regulatory in-degree. We discovered that for TFs, the dominant determinants of evolutionary rate lie in the structure of the regulatory network, such as the median evolutionary rate of target genes and the fraction of species-specific target genes. Decomposing the regulatory network by edge sign, we found that this modular evolution of TFs and their targets is limited to activating regulatory relationships. We show that fast evolving TFs tend to regulate other TFs and niche-specific processes and that their targets show larger evolutionary expression changes than targets of other TFs. We also show that the positive trend relating TF regulatory in-degree and evolutionary rate is likely related to the species-specificity of the transcriptional regulation modules. Finally, we discuss likely causes for TFs' different evolutionary relationship to the physical interaction network, such as the prevalence of transient interactions in the TF subnetwork. This work suggests that positive and negative regulatory networks follow very different evolutionary rules, and that transcription factor evolution is best understood at a network- or systems-level. Author Summary Transcription factors (TFs) are proteins which regulate the expression of genes by interacting with DNA. Mutations in TF protein sequences can affect the expression levels of regulated genes throughout evolution. In this study, we look into the factors which cause the different TFs in baker's yeast to be more or less tolerant of mutations during recent evolution. This tolerance is measured as the evolutionary rate, defined for each protein as the relative rate of protein-changing DNA mutations over other mutations (Ka/Ks). We found that the typical determinants of protein evolutionary rate, such as expression level and network interactions have a very different influence on TF evolutionary rate. We found that TF evolutionary rate is most highly correlated to the evolutionary properties of the genes which they regulate and specifically genes which they activate. We also show that TF evolutionary rate predicts actual evolutionary expression differences of regulated genes and we discuss some of the features unique to TFs which likely contribute to their different evolutionary trends, such as the types of protein-protein interactions prevalent in the TF subnetwork or TFs' potential role in adaptive evolution.

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    Europe PubMed Central
    Article . 2012
    Data sources: PubMed Central
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    PLoS Computational Biology
    Article . 2012
    License: CC BY
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    PLoS Computational Biology
    Article
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      PLoS Computational Biology
      Article . 2012
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    Authors: Chitambar, Eric; Miller, Carl A.; Shi, Yaoyun;

    In this brief report, we consider the equivalence between two sets of $m+1$ bipartite quantum states under local unitary transformations. For pure states, this problem corresponds to the matrix algebra question of whether two degree $m$ matrix polynomials are unitarily equivalent; i.e. $UA_iV^\dagger=B_i$ for $0\leq i\leq m$ where $U$ and $V$ are unitary and $(A_i, B_i)$ are arbitrary pairs of rectangular matrices. We present a randomized polynomial-time algorithm that solves this problem with an arbitrarily high success probability and outputs transforming matrices $U$ and $V$.

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    https://doi.org/10.48550/arxiv...
    Article . 2010
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      https://doi.org/10.48550/arxiv...
      Article . 2010
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    Authors: Sabrina J. Abram; Katherine L. Poggensee; Natalia Sánchez; Surabhi N. Simha; +3 Authors

    Our nervous systems can learn optimal control policies in response to changes to our bodies, tasks, and movement contexts. For example, humans can learn to adapt their control policy in walking contexts where the energy-optimal policy is shifted along variables such as step frequency or step width. However, it is unclear how the nervous system determines which ways to adapt its control policy. Here, we asked how human participants explore through variations in their control policy to identify more optimal policies in new contexts. We created new contexts using exoskeletons that apply assistive torques to each ankle at each walking step. We analyzed four variables that spanned the levels of the whole movement, the joint, and the muscle: step frequency, ankle angle range, total soleus activity, and total medial gastrocnemius activity. We found that, across all of these analyzed variables, variability increased upon initial exposure to new contexts and then decreased with experience. This led to adaptive changes in the magnitude of specific variables, and these changes were correlated with reduced energetic cost. The timescales by which adaptive changes progressed and variability decreased were faster for some variables than others, suggesting a reduced search space within which the nervous system continues to optimize its policy. These collective findings support the principle that exploration through general variability leads to specific adaptation toward optimal movement policies.

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    Europe PubMed Central
    Other literature type . 2022
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    Current Biology
    Article . 2022
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    Current Biology
    Article . 2022
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      Current Biology
      Article . 2022
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      Current Biology
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hao Zhou; Melike Erol-Kantarci; Yuanwei Liu; H. Vincent Poor;

    Reconfigurable intelligent surfaces (RISs) have received considerable attention as a key enabler for envisioned 6G networks, for the purpose of improving the network capacity, coverage, efficiency, and security with low energy consumption and low hardware cost. However, integrating RISs into the existing infrastructure greatly increases the network management complexity, especially for controlling a significant number of RIS elements. To unleash the full potential of RISs, efficient optimization approaches are of great importance. This work provides a comprehensive survey on optimization techniques for RIS-aided wireless communications, including model-based, heuristic, and machine learning (ML) algorithms. In particular, we first summarize the problem formulations in the literature with diverse objectives and constraints, e.g., sum-rate maximization, power minimization, and imperfect channel state information constraints. Then, we introduce model-based algorithms that have been used in the literature, such as alternating optimization, the majorization-minimization method, and successive convex approximation. Next, heuristic optimization is discussed, which applies heuristic rules for obtaining low-complexity solutions. Moreover, we present state-of-the-art ML algorithms and applications towards RISs, i.e., supervised and unsupervised learning, reinforcement learning, federated learning, graph learning, transfer learning, and hierarchical learning-based approaches. Model-based, heuristic, and ML approaches are compared in terms of stability, robustness, optimality and so on, providing a systematic understanding of these techniques. Finally, we highlight RIS-aided applications towards 6G networks and identify future challenges. Comment: This paper has been accepted by IEEE Communications Surveys and Tutorials

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    https://doi.org/10.1109/comst....
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      https://doi.org/10.1109/comst....
      Article . 2023
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      https://doi.org/10.48550/arxiv...
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fasina, Oluwadamilola; Huguet, Guillaume; Tong, Alexander; Zhang, Yanlei; +4 Authors

    Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the underlying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells). Comment: 13 pages, 11 figures, 1 table

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    https://doi.org/10.48550/arxiv...
    Article . 2023
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      https://doi.org/10.48550/arxiv...
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Cai, Yang; Devanur, Nikhil R.; Goldner, Kira; McAfee, R. Preston;

    We study a new model of complementary valuations, which we call "proportional complementarities." In contrast to common models, such as hypergraphic valuations, in our model, we do not assume that the extra value derived from owning a set of items is independent of the buyer's base valuations for the items. Instead, we model the complementarities as proportional to the buyer's base valuations, and these proportionalities are known market parameters. Our goal is to design a simple pricing scheme that, for a single buyer with proportional complementarities, yields approximately optimal rev