• Pair bond endurance promotes cooperative food defense and inhibits conflict in coral reef butterflyfishes

      Nowicki, Jessica; Walker, Stefan; Coker, Darren James; Hoey, Andrew; Nicolet, Katia; Pratchett, Morgan (Cold Spring Harbor Laboratory, 2017-11-14)
      Pair bonding is generally linked to monogamous mating systems, where the reproductive benefits of extended mate guarding and/or of bi-parental care are considered key adaptive functions. However, in some species, including coral reef butterflyfishes (f. Chaetodonitidae), pair bonding occurs in sexually immature and homosexual partners, and in the absence of parental care, suggesting there must be non-reproductive adaptive benefits of pair bonding. Here, we examined whether pair bonding butterflyfishes cooperate in defense of food, conferring direct benefits to one or both partners. Pairs of Chaetodon lunulatus and C. baronessa use contrasting cooperative strategies. In C. lunulatus, both partners mutually defend their territory, while in C. baronessa, males prioritize territory defence; conferring improvements in feeding and energy reserves in both sexes relative to solitary counterparts. We further demonstrate that partner fidelity contributes to this function by showing that re-pairing invokes intra-pair conflict and inhibits cooperatively-derived feeding benefits, and that partner endurance is required for these costs to abate. Overall, our results suggest that in butterflyfishes, pair bonding enhances cooperative defense of prey resources, ultimately benefiting both partners by improving food resource acquisition and energy reserves.
    • Parameter-free Network Sparsification and Data Reduction by Minimal Algorithmic Information Loss

      Zenil, Hector; Kiani, Narsis A.; Tegner, Jesper (arXiv, 2018-02-16)
      The study of large and complex datasets, or big data, organized as networks has emerged as one of the central challenges in most areas of science and technology. Cellular and molecular networks in biology is one of the prime examples. Henceforth, a number of techniques for data dimensionality reduction, especially in the context of networks, have been developed. Yet, current techniques require a predefined metric upon which to minimize the data size. Here we introduce a family of parameter-free algorithms based on (algorithmic) information theory that are designed to minimize the loss of any (enumerable computable) property contributing to the object's algorithmic content and thus important to preserve in a process of data dimension reduction when forcing the algorithm to delete first the least important features. Being independent of any particular criterion, they are universal in a fundamental mathematical sense. Using suboptimal approximations of efficient (polynomial) estimations we demonstrate how to preserve network properties outperforming other (leading) algorithms for network dimension reduction. Our method preserves all graph-theoretic indices measured, ranging from degree distribution, clustering-coefficient, edge betweenness, and degree and eigenvector centralities. We conclude and demonstrate numerically that our parameter-free, Minimal Information Loss Sparsification (MILS) method is robust, has the potential to maximize the preservation of all recursively enumerable features in data and networks, and achieves equal to significantly better results than other data reduction and network sparsification methods.
    • Parameters and Fractional Differentiation Orders Estimation for Linear Continuous-Time Non-Commensurate Fractional Order Systems

      Belkhatir, Zehor; Laleg-Kirati, Taous-Meriem (Submitted to Elsevier, 2017-05-31)
      This paper proposes a two-stage estimation algorithm to solve the problem of joint estimation of the parameters and the fractional differentiation orders of a linear continuous-time fractional system with non-commensurate orders. The proposed algorithm combines the modulating functions and the first-order Newton methods. Sufficient conditions ensuring the convergence of the method are provided. An error analysis in the discrete case is performed. Moreover, the method is extended to the joint estimation of smooth unknown input and fractional differentiation orders. The performance of the proposed approach is illustrated with different numerical examples. Furthermore, a potential application of the algorithm is proposed which consists in the estimation of the differentiation orders of a fractional neurovascular model along with the neural activity considered as input for this model.
    • Particle Simulation of Fractional Diffusion Equations

      Allouch, Samer; Lucchesi, Marco; Maître, O. P. Le; Mustapha, K. A.; Knio, Omar (arXiv, 2017-07-12)
      This work explores different particle-based approaches to the simulation of one-dimensional fractional subdiffusion equations in unbounded domains. We rely on smooth particle approximations, and consider four methods for estimating the fractional diffusion term. The first method is based on direct differentiation of the particle representation, it follows the Riesz definition of the fractional derivative and results in a non-conservative scheme. The other three methods follow the particle strength exchange (PSE) methodology and are by construction conservative, in the sense that the total particle strength is time invariant. The first PSE algorithm is based on using direct differentiation to estimate the fractional diffusion flux, and exploiting the resulting estimates in an integral representation of the divergence operator. Meanwhile, the second one relies on the regularized Riesz representation of the fractional diffusion term to derive a suitable interaction formula acting directly on the particle representation of the diffusing field. A third PSE construction is considered that exploits the Green's function of the fractional diffusion equation. The performance of all four approaches is assessed for the case of a one-dimensional diffusion equation with constant diffusivity. This enables us to take advantage of known analytical solutions, and consequently conduct a detailed analysis of the performance of the methods. This includes a quantitative study of the various sources of error, namely filtering, quadrature, domain truncation, and time integration, as well as a space and time self-convergence analysis. These analyses are conducted for different values of the order of the fractional derivatives, and computational experiences are used to gain insight that can be used for generalization of the present constructions.
    • Passivity and Evolutionary Game Dynamics

      Park, Shinkyu; Shamma, Jeff S.; Martins, Nuno C. (arXiv, 2018-03-21)
      This paper investigates an energy conservation and dissipation -- passivity -- aspect of dynamic models in evolutionary game theory. We define a notion of passivity using the state-space representation of the models, and we devise systematic methods to examine passivity and to identify properties of passive dynamic models. Based on the methods, we describe how passivity is connected to stability in population games and illustrate stability of passive dynamic models using numerical simulations.
    • Path to Stochastic Stability: Comparative Analysis of Stochastic Learning Dynamics in Games

      Jaleel, Hassan; Shamma, Jeff S. (arXiv, 2018-04-08)
      Stochastic stability is a popular solution concept for stochastic learning dynamics in games. However, a critical limitation of this solution concept is its inability to distinguish between different learning rules that lead to the same steady-state behavior. We address this limitation for the first time and develop a framework for the comparative analysis of stochastic learning dynamics with different update rules but same steady-state behavior. We present the framework in the context of two learning dynamics: Log-Linear Learning (LLL) and Metropolis Learning (ML). Although both of these dynamics have the same stochastically stable states, LLL and ML correspond to different behavioral models for decision making. Moreover, we demonstrate through an example setup of sensor coverage game that for each of these dynamics, the paths to stochastically stable states exhibit distinctive behaviors. Therefore, we propose multiple criteria to analyze and quantify the differences in the short and medium run behavior of stochastic learning dynamics. We derive and compare upper bounds on the expected hitting time to the set of Nash equilibria for both LLL and ML. For the medium to long-run behavior, we identify a set of tools from the theory of perturbed Markov chains that result in a hierarchical decomposition of the state space into collections of states called cycles. We compare LLL and ML based on the proposed criteria and develop invaluable insights into the comparative behavior of the two dynamics.
    • Penultimate modeling of spatial extremes: statistical inference for max-infinitely divisible processes

      Huser, Raphaël; Opitz, Thomas; Thibaud, Emeric (arXiv, 2018-01-09)
      Extreme-value theory for stochastic processes has motivated the statistical use of max-stable models for spatial extremes. However, fitting such asymptotic models to maxima observed over finite blocks is problematic when the asymptotic stability of the dependence does not prevail in finite samples. This issue is particularly serious when data are asymptotically independent, such that the dependence strength weakens and eventually vanishes as events become more extreme. We here aim to provide flexible sub-asymptotic models for spatially indexed block maxima, which more realistically account for discrepancies between data and asymptotic theory. We develop models pertaining to the wider class of max-infinitely divisible processes, extending the class of max-stable processes while retaining dependence properties that are natural for maxima: max-id models are positively associated, and they yield a self-consistent family of models for block maxima defined over any time unit. We propose two parametric construction principles for max-id models, emphasizing a point process-based generalized spectral representation, that allows for asymptotic independence while keeping the max-stable extremal-$t$ model as a special case. Parameter estimation is efficiently performed by pairwise likelihood, and we illustrate our new modeling framework with an application to Dutch wind gust maxima calculated over different time units.
    • Perturbation-Based Regularization for Signal Estimation in Linear Discrete Ill-posed Problems

      Suliman, Mohamed Abdalla Elhag; Ballal, Tarig; Al-Naffouri, Tareq Y. (arXiv, 2016-11-29)
      Estimating the values of unknown parameters from corrupted measured data faces a lot of challenges in ill-posed problems. In such problems, many fundamental estimation methods fail to provide a meaningful stabilized solution. In this work, we propose a new regularization approach and a new regularization parameter selection approach for linear least-squares discrete ill-posed problems. The proposed approach is based on enhancing the singular-value structure of the ill-posed model matrix to acquire a better solution. Unlike many other regularization algorithms that seek to minimize the estimated data error, the proposed approach is developed to minimize the mean-squared error of the estimator which is the objective in many typical estimation scenarios. The performance of the proposed approach is demonstrated by applying it to a large set of real-world discrete ill-posed problems. Simulation results demonstrate that the proposed approach outperforms a set of benchmark regularization methods in most cases. In addition, the approach also enjoys the lowest runtime and offers the highest level of robustness amongst all the tested benchmark regularization methods.
    • Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire

      Steuernagel, Burkhard; Witek, Kamil; Krattinger, Simon G.; Ramirez-Gonzalez, Ricardo H.; Schoonbeek, Henk-jan; Yu, Guotai; Baggs, Erin; Witek, Agnieszka; Yadav, Inderjit; Krasileva, Ksenia V.; Jones, Jonathan D. G.; Uauy, Cristobal; Keller, Beat; Ridout, Christopher J.; Wulff, Brande; The International Wheat Genome Sequencing Consortium (Cold Spring Harbor Laboratory, 2018-06-05)
      Disease resistance genes encoding intracellular immune receptors of the nucleotide-binding and leucine-rich repeat (NLR) class of proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR encoding genes. The availability of the hexaploid wheat cultivar Chinese Spring reference genome now allows a detailed study of its NLR complement. However, low NLR expression as well as high intra-family sequence homology hinders their accurate gene annotation. Here we developed NLR-Annotator for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. Applying our tool to wheat and combining it with a transcript-validated subset of genes from the reference gene annotation, we characterized the structure, phylogeny and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci of which 1,540 were confirmed as complete genes. NLRs with integrated domains mostly group in specific sub-clades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains suggesting a paired helper-function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts), which may be tissue-specific and/or induced by biotic stress. As a case study for applying our tool to the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease resistant varieties.
    • Possible evidence for spin-transfer torque induced by spin-triplet supercurrent

      Li, Lailai; Zhao, Yuelei; Zhang, Xixiang; Sun, Young (arXiv, 2017-10-04)
      Cooper pairs in superconductors are normally spin singlet. Nevertheless, recent studies suggest that spin-triplet Cooper pairs can be created at carefully engineered superconductor-ferromagnet interfaces. If Cooper pairs are spin-polarized they would transport not only charge but also a net spin component, but without dissipation, and therefore minimize the heating effects associated with spintronic devices. Although it is now established that triplet supercurrents exist, their most interesting property - spin - is only inferred indirectly from transport measurements. In conventional spintronics, it is well known that spin currents generate spin-transfer torques that alter magnetization dynamics and switch magnetic moments. The observation of similar effects due to spin-triplet supercurrents would not only confirm the net spin of triplet pairs but also pave the way for applications of superconducting spintronics. Here, we present a possible evidence for spin-transfer torques induced by triplet supercurrents in superconductor/ferromagnet/superconductor (S/F/S) Josephson junctions. Below the superconducting transition temperature T_c, the ferromagnetic resonance (FMR) field at X-band (~ 9.0 GHz) shifts rapidly to a lower field with decreasing temperature due to the spin-transfer torques induced by triplet supercurrents. In contrast, this phenomenon is absent in ferromagnet/superconductor (F/S) bilayers and superconductor/insulator/ferromagnet/superconductor (S/I/F/S) multilayers where no supercurrents pass through the ferromagnetic layer. These experimental observations are discussed with theoretical predictions for ferromagnetic Josephson junctions with precessing magnetization.
    • Predictive Systems Toxicology

      Kiani, Narsis A.; Shang, Ming-Mei; Zenil, Hector; Tegner, Jesper (arXiv, 2018-01-15)
      In this review we address to what extent computational techniques can augment our ability to predict toxicity. The first section provides a brief history of empirical observations on toxicity dating back to the dawn of Sumerian civilization. Interestingly, the concept of dose emerged very early on, leading up to the modern emphasis on kinetic properties, which in turn encodes the insight that toxicity is not solely a property of a compound but instead depends on the interaction with the host organism. The next logical step is the current conception of evaluating drugs from a personalized medicine point-of-view. We review recent work on integrating what could be referred to as classical pharmacokinetic analysis with emerging systems biology approaches incorporating multiple omics data. These systems approaches employ advanced statistical analytical data processing complemented with machine learning techniques and use both pharmacokinetic and omics data. We find that such integrated approaches not only provide improved predictions of toxicity but also enable mechanistic interpretations of the molecular mechanisms underpinning toxicity and drug resistance. We conclude the chapter by discussing some of the main challenges, such as how to balance the inherent tension between the predictive capacity of models, which in practice amounts to constraining the number of features in the models versus allowing for rich mechanistic interpretability, i.e. equipping models with numerous molecular features. This challenge also requires patient-specific predictions on toxicity, which in turn requires proper stratification of patients as regards how they respond, with or without adverse toxic effects. In summary, the transformation of the ancient concept of dose is currently successfully operationalized using rich integrative data encoded in patient-specific models.
    • Privacy preserving randomized gossip algorithms

      Hanzely, Filip; Konečný, Jakub; Loizou, Nicolas; Richtarik, Peter; Grishchenko, Dmitry (arXiv, 2017-06-23)
      In this work we present three different randomized gossip algorithms for solving the average consensus problem while at the same time protecting the information about the initial private values stored at the nodes. We give iteration complexity bounds for all methods, and perform extensive numerical experiments.
    • Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

      Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian; Huser, Raphaël; Ali, Amal J.; Merzaban, Jasmeen; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T. (Cold Spring Harbor Laboratory, 2018-03-11)
      Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.
    • Quantitative Seq-LGS: Genome-Wide Identification of Genetic Drivers of Multiple Phenotypes in Malaria Parasites

      Abkallo, Hussein M.; Martinelli, Axel; Inoue, Megumi; Ramaprasad, Abhinay; Xangsayarath, Phonepadith; Gitaka, Jesse; Tang, Jianxia; Yahata, Kazuhide; Zoungrana, Augustin; Mitaka, Hayato; Hunt, Paul; Carter, Richard; Kaneko, Osamu; Mustonen, Ville; Illingworth, Christopher J.R.; Pain, Arnab; Culleton, Richard (Cold Spring Harbor Laboratory Press, 2016-10-01)
      Identifying the genetic determinants of phenotypes that impact on disease severity is of fundamental importance for the design of new interventions against malaria. Traditionally, such discovery has relied on labor-intensive approaches that require significant investments of time and resources. By combining Linkage Group Selection (LGS), quantitative whole genome population sequencing and a novel mathematical modeling approach (qSeq-LGS), we simultaneously identified multiple genes underlying two distinct phenotypes, identifying novel alleles for growth rate and strain specific immunity (SSI), while removing the need for traditionally required steps such as cloning, individual progeny phenotyping and marker generation. The detection of novel variants, verified by experimental phenotyping methods, demonstrates the remarkable potential of this approach for the identification of genes controlling selectable phenotypes in malaria and other apicomplexan parasites for which experimental genetic crosses are amenable.
    • Randomized Block Cubic Newton Method

      Doikov, Nikita; Richtarik, Peter (arXiv, 2018-02-12)
      We study the problem of minimizing the sum of three convex functions: a differentiable, twice-differentiable and a non-smooth term in a high dimensional setting. To this effect we propose and analyze a randomized block cubic Newton (RBCN) method, which in each iteration builds a model of the objective function formed as the sum of the natural models of its three components: a linear model with a quadratic regularizer for the differentiable term, a quadratic model with a cubic regularizer for the twice differentiable term, and perfect (proximal) model for the nonsmooth term. Our method in each iteration minimizes the model over a random subset of blocks of the search variable. RBCN is the first algorithm with these properties, generalizing several existing methods, matching the best known bounds in all special cases. We establish ${\cal O}(1/\epsilon)$, ${\cal O}(1/\sqrt{\epsilon})$ and ${\cal O}(\log (1/\epsilon))$ rates under different assumptions on the component functions. Lastly, we show numerically that our method outperforms the state-of-the-art on a variety of machine learning problems, including cubically regularized least-squares, logistic regression with constraints, and Poisson regression.
    • A Randomized Exchange Algorithm for Computing Optimal Approximate Designs of Experiments

      Harman, Radoslav; Filová, Lenka; Richtarik, Peter (arXiv, 2018-01-17)
      We propose a class of subspace ascent methods for computing optimal approximate designs that covers both existing as well as new and more efficient algorithms. Within this class of methods, we construct a simple, randomized exchange algorithm (REX). Numerical comparisons suggest that the performance of REX is comparable or superior to the performance of state-of-the-art methods across a broad range of problem structures and sizes. We focus on the most commonly used criterion of D-optimality that also has applications beyond experimental design, such as the construction of the minimum volume ellipsoid containing a given set of data-points. For D-optimality, we prove that the proposed algorithm converges to the optimum. We also provide formulas for the optimal exchange of weights in the case of the criterion of A-optimality. These formulas enable one to use REX for computing A-optimal and I-optimal designs.
    • Robustness Analysis of Visual QA Models by Basic Questions

      Huang, Jia-Hong; Alfadly, Modar; Ghanem, Bernard (arXiv, 2017-09-14)
      Visual Question Answering (VQA) models should have both high robustness and accuracy. Unfortunately, most of the current VQA research only focuses on accuracy because there is a lack of proper methods to measure the robustness of VQA models. There are two main modules in our algorithm. Given a natural language question about an image, the first module takes the question as input and then outputs the ranked basic questions, with similarity scores, of the main given question. The second module takes the main question, image and these basic questions as input and then outputs the text-based answer of the main question about the given image. We claim that a robust VQA model is one, whose performance is not changed much when related basic questions as also made available to it as input. We formulate the basic questions generation problem as a LASSO optimization, and also propose a large scale Basic Question Dataset (BQD) and Rscore (novel robustness measure), for analyzing the robustness of VQA models. We hope our BQD will be used as a benchmark for to evaluate the robustness of VQA models, so as to help the community build more robust and accurate VQA models.
    • A salt water battery with high stability and charging rates made from solution processed conjugated polymers with polar side chains

      Moia, Davide; Giovannitti, Alexander; Szumska, Anna A.; Schnurr, Martin; Rezasoltani, Elham; Maria, Iuliana P.; Barnes, Piers R. F.; McCulloch, Iain; Nelson, Jenny (arXiv, 2017-11-28)
      We report a neutral salt water based battery which uses p-type and n-type solution processed polymer films as the cathode and the anode of the cell. The specific capacity of the electrodes (approximately 30 mAh cm-3) is achieved via formation of bipolarons in both the p-type and n-type polymers. By engineering ethylene glycol and zwitterion based side chains attached to the polymer backbone we facilitate rapid ion transport through the non-porous polymer films. This, combined with efficient transport of electronic charge via the conjugated polymer backbones, allowed the films to maintain constant capacity at high charge and discharge rates (>1000 C-rate). The electrodes also show good stability during electrochemical cycling (less than 30% decrease in capacity over >1000 cycles) and an output voltage up to 1.4 V. The performance of these semiconducting polymers with polar side-chains demonstrates the potential of this material class for fast-charging, water based electrochemical energy storage devices.
    • SBP-SAT finite difference discretization of acoustic wave equations on staggered block-wise uniform grids

      Gao, Longfei; Fernandez, David C. Del Rey; Carpenter, Mark; Keyes, David E. (arXiv, 2018-02-16)
      We consider the numerical simulation of the acoustic wave equations arising from seismic applications, for which staggered grid finite difference methods are popular choices due to their simplicity and efficiency. We relax the uniform grid restriction on finite difference methods and allow the grids to be block-wise uniform with nonconforming interfaces. In doing so, variations in the wave speeds of the subterranean media can be accounted for more efficiently. Staggered grid finite difference operators satisfying the summation-by-parts (SBP) property are devised to approximate the spatial derivatives appearing in the acoustic wave equation. These operators are applied within each block independently. The coupling between blocks is achieved through simultaneous approximation terms (SATs), which impose the interface condition weakly, i.e., by penalty. Ratio of the grid spacing of neighboring blocks is allowed to be rational number, for which specially designed interpolation formulas are presented. These interpolation formulas constitute key pieces of the simultaneous approximation terms. The overall discretization is shown to be energy-conserving and examined on test cases of both theoretical and practical interests, delivering accurate and stable simulation results.
    • Seasonal variations of aerosols in Middle East: Contributions of natural and anthropogenic sources and impact of their cross boundary transport

      Shahid, Muhammad Zeeshaan; Stenchikov, Georgiy L.; Ukhov, Alexander; Anisimov, Anatolii; Mostamandi, Suleiman (2017-12)