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“We study several problems related to finding reset words in deterministic finite automata. In particular, we establish that the problem of deciding whether a shortest reset word has length k is complete for the complexity class DP. This result answers a question posed by Volkov. For the search problems of finding a shortest reset word and the length of a shortest reset word, we establish membership in the complexity classes FP^NP and FP^NP[log], respectively. Moreover, we show that both these problems are hard for FP^NP[log]. Finally, we observe that computing a reset word of a given length is FNP-complete.”
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“Here we propose a generic mechanism — networked buffering — for generating robust traits in complex systems that requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role within a system and 2) agents are degenerate, i.e. there exists partial overlap in the functional capabilities of agents. Given these prerequisites, degenerate systems can readily produce a distributed systemic response to local perturbations. Reciprocally, excess resources related to a single function can indirectly support multiple unrelated functions within a degenerate system.…”
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“This paper presents a complex systems overview of a power grid network. In recent years, concerns about the robustness of the power grid have grown because of several cascading outages in different parts of the world. In this paper, cascading effect has been simulated on three different networks, the IEEE 300 bus test system, the IEEE 118 bus test system, and the WSCC 179 bus equivalent model, using the DC Power Flow Model. Power Degradation has been discussed as a measure to estimate the damage to the network, in terms of load loss and node loss. A network generator has been developed to generate graphs with characteristics similar to the IEEE standard networks and the generated graphs are then … have been suggested.”
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“We apply multiple testing procedures to the validation of estimated default probabilities in credit rating systems. The goal is to identify rating classes for which the probability of default is estimated inaccurately, while still maintaining a predefined level of committing type I errors as measured by the familywise error rate (FWER) and the false discovery rate (FDR). For FWER, we also consider procedures that take possible discreteness of the data resp. test statistics into account. The performance of these methods is illustrated in a simulation setting and for empirical default data.”
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“The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. …”
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“I’m not an economist, but we’ve got five applicants for every single job opening. If you tell me that the best response to that situation is to lay off hundreds of thousands of teachers, I will not accept that this means that you’re smarter and more expert than I am. I will instead conclude — regardless of your prestige or position or years of study — that you’re a moral imbecile. And knowing what I know about your inability to make moral judgments I will have no reason to trust you to make complicated macroeconomic ones.”
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“The Lin-Kernighan heuristic is known to be one of the most successful heuristics for the Traveling Salesman Problem (TSP). It has also proven its efficiency in application to some other problems. In this paper we discuss possible adaptations of TSP heuristics for the Generalized Traveling Salesman Problem (GTSP) and focus on the case of the Lin-Kernighan algorithm. At first, we provide an easy-to-understand description of the original Lin-Kernighan heuristic. Then we propose several adaptations, both trivial and complicated. Finally, we conduct a fair competition between all the variations of the Lin-Kernighan adaptation and some other GTSP heuristics. It appears that our adaptation of the Lin-Kernighan algorithm for the GTSP reproduces the success of the original heuristic. Different variations of our adaptation outperform all other heuristics in a wide range of trade-offs between solution quality and running time, making Lin-Kernighan the state-of-the-art GTSP local search.”
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“Each time-series has its own linear trend, the directionality of a timeseries, and removing the linear trend is crucial to get the more intuitive matching results. Supporting the linear detrending in subsequence matching is a challenging problem due to a huge number of possible subsequences. In this paper we define this problem the linear detrending subsequence matching and propose its efficient index-based solution. To this end, we first present a notion of LD-windows (LD means linear detrending), which is obtained as follows: we eliminate the linear trend from a subsequence rather than each window itself and obtain LD-windows by dividing the subsequence into windows. Using the LD-windows we then present a lower bounding theorem for the index-based matching solution and formally prove its correctness.…”
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“In the social sciences, it is useful to understand the relative similarities of concepts that are embedded in a particular text (from a particular group or a particular person). For example, in trying to estimate conservative bias in FoxNews, one might estimate its tendency to associate conservative concepts (conservative, republican) and good concepts (good, positive, etc.), compared to conservative and bad concepts. The output would indicate conservative favoritism. This comparison could be further refined by taking into account important “baseline” information about the valences associated with liberal, namely liberal and good in comparison to liberal and bad.…”
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Sometimes physics is just pretty.
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“The Open Enterprise is a new organizational design. Unlike organizations using traditional management structures, Open Enterprises replace the command and control hierarchy with a meritocracy based on collaboration and open participation.
Organizations that adopt this new organizational structure can make decisions faster and respond quicker to their markets. They look more like living dynamic networks, and less like pyramids. People working in these organizations will have (and feel) more ownership. They’re more engaged in their work, and have the freedom to work on what they want, when they want to. Most importantly this model enables people to once again bring their full humanity – values, beliefs and passions – to the workplace, removing disconnect between organizational and personal values”
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Specifically: “Genome-wide association study of hair length in dogs”
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“The human immune system has numerous properties that make it ripe for exploitation in the computational domain, such as robustness and fault tolerance, and many different algorithms, collectively termed Artificial Immune Systems (AIS), have been inspired by it. Two generations of AIS are currently in use, with the first generation relying on simplified immune models and the second generation utilising interdisciplinary collaboration to develop a deeper understanding of the immune system and hence produce more complex models. Both generations of algorithms have been successfully applied to a variety of problems, including anomaly detection, pattern recognition, optimisation and robotics.…”
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“This paper is concerned with designing self-driven fitness functions for Embedded Evolutionary Robotics. The proposed approach considers the entropy of the sensori-motor stream generated by the robot controller. This entropy is computed using unsupervised learning; its maximization, achieved by an on-board evolutionary algorithm, implements a “curiosity instinct”, favouring controllers visiting many diverse sensori-motor states (sms). Further, the set of sms discovered by an individual can be transmitted to its offspring, making a cultural evolution mode possible. Cumulative entropy (computed from ancestors and current individual visits to the sms) defines another self-driven fitness; its optimization implements a “discovery instinct”, as it favours controllers visiting new or rare sensori-motor states. Empirical results on the benchmark problems proposed by Lehman and Stanley (2008) comparatively demonstrate the merits of the approach.”
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“Music composition used to be a pen and paper activity. These these days music is often composed with the aid of computer software, even to the point where the computer compose parts of the score autonomously. The composition of most styles of music is governed by rules. We show that by approaching the automation, analysis and verification of composition as a knowledge representation task and formalising these rules in a suitable logical language, powerful and expressive intelligent composition tools can be easily built. …”
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“… Using wireless sensor network technology, we obtained high-resolution data of CPIs during a typical day at an American high school, permitting the reconstruction of the social network relevant for infectious disease transmission. At a 94% coverage, we collected 762,868 CPIs at a maximal distance of 3 meters among 788 individuals. The data revealed a high density network with typical small world properties and a relatively homogenous distribution of both interaction time and interaction partners among subjects.…”
Monthly Archives: June 2010
links for 2010-06-28
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“We present a novel method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram reweighting procedure a posteriori. Due to the presence of the bias potential, our method can also be used to accelerate rare events. In addition, the calculated free energy landscape is not restricted to the actual choice of collective variables and can in principle be extended to all variables of interest without further numerical effort. We present numerical results for the alanine dipeptide and the Met-Enkephalin in explicit solution to illustrate our approach.”
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“We present a framework for simulating signal propagation in geometric networks (i.e. networks that can be mapped to geometric graphs in some space) and for developing algorithms that estimate (i.e. map) the state and functional topology of complex dynamic geometric net– works. Within the framework we define the key features typically present in such networks and of particular relevance to biological cellular neural networks: Dynamics, signaling, observation, and control. The framework is particularly well-suited for estimating functional connectivity in cellular neural networks from experimentally observable data, and has been implemented using graphics processing unit (GPU) high performance computing. Computationally, the framework can simulate cellular network signaling close to or faster than real time. We further propose a standard test set of networks to measure performance and compare different mapping algorithms.”
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Also: how about an inverse Doomsday algorithm. “We propose a simplification of a key component in the Doomsday Algorithm for calculating the day-of-the-week of any given date.…”
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“A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible, and an explicit solvent is optionally included. …Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered.”
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“We present two novel approaches for the computation of the exact distribution of a pattern in a long sequence. Both approaches take into account the sparse structure of the problem. The first approach relies on a partial recursion computing the largest eigenvalue of the the transition matrix of a Markov chain embedding. The second approach uses fast Taylor expansions of an exact bivariate rational reconstruction of the distribution. We illustrate the interest of both approaches on a simple toy-example and two biological applications: the transcription factors of the Human Chromosome 5 and the PROSITE signatures of functional motifs in proteins. On these examples our methods demonstrate their complementarity and their hability to extend the domain of feasibility for exact computations in pattern problems to a new level.”
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“We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. …”
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“The speed of laser light pulses launched from Earth and returned by a retro-reflector on the Moon was calculated from precision round-trip time-of-flight measurements and modeled distances. The measured speed of light © in the moving observers rest frame was found to exceed the canonical value c = 299,792,458 m/s by 200+/-10 m/s, just the speed of the observatory along the line-of-sight due to the rotation of the Earth during the measurements. This is a first-order violation of local Lorentz invariance; the speed of light seems to depend on the motion of the observer after all, as in classical wave theory, and implies that a preferred reference frame exists for the propagation of light. However, the present experiment cannot identify the physical system to which such a reference frame might be tied.”
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“The main goal of the paper is to introduce methods which compute B\‘ezier curves faster than Casteljau’s method does. These methods are based on the spectral factorization of a $n\times n$ Bernstein matrix, $B^e_n(s)= P_nG_n(s)P_n^{-1}$, where $P_n$ is the $n\times n$ lower triangular Pascal matrix. So we first calculate the exact optimum positive value $t$ in order to transform $P_n$ in a scaled Toeplitz matrix, which is a problem that was partially solved by X. Wang and J. Zhou (2006). Then fast Pascal matrix-vector multiplications and strategies of polynomial evaluation are put together to compute B\‘ezier curves. Nevertheless, when $n$ increases, more precise Pascal matrix-vector multiplications allied to affine transformations of the vectors of coordinates of the control points of the curve are then necessary to stabilize all the computation.”
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“We propose a novel distributed algorithm to cluster graphs. The algorithm recovers the solution obtained from spectral clustering without the need for expensive eigenvalue/vector computations. We prove that, by propagating waves through the graph, a local fast Fourier transform yields the local component of every eigenvector of the Laplacian matrix, which are used to cluster graphs. For large graphs, the proposed algorithm is orders of magnitude faster than random walk based approaches. We prove the equivalence of the proposed algorithm to spectral clustering and derive convergence rates. We also demonstrate the benefit of using this decentralized clustering algorithm to accelerate distributed estimation for sensor networks and for efficient computation of distributed multi-agent search strategies.”
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“Imputation of missing data in large regions of satellite imagery is necessary when the acquired image has been damaged by shadows due to clouds, or information gaps produced by sensor failure.
The general approach for imputation of missing data, that could not be considered missed at random, suggests the use of other available data. Previous work, like local linear histogram matching, take advantage of a co-registered older image obtained by the same sensor, yielding good results in filling homogeneous regions, but poor results if the scenes being combined have radical differences in target radiance due, for example, to the presence of sun glint or snow.…” -
“…In this work, we give a short overview of traditional community roles. We adapt those models and apply them to virtual online communities. We suggest a community membership life cycle model describing roles a user can take during his membership in a community. Our model is systematic and generic; it can be adapted to concrete communities in the web. The knowledge of a community’s life cycle allows influencing the group structure: Stage transitions can be supported or harmed, e.g. to strengthen the binding of a user to a site and keep communities alive.”
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[1006.2332] Collective beliefs and individual stubbornness in the dynamics of public debates“Since the collective beliefs are not given to modifica– tions within short timescales, the best approach for one opinion to win is to focus on getting as many as pos– sible inflexibles along its side. However this goal could demand to overstate the validity of some arguments to sustain and legitimate that opinion. In contrast, such a behavior could rise ethical questions.…”
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“…We find that a well-defined temporal component exists and accounts for some of the variance in the data. This temporal component arises because active regions with high magnetic field strength evolve, breaking up into small-scale magnetic elements with low field strength, and radiative and magnetic fluxes are sensitive to different active-region components. We generate empirical models that relate radiative flux to magnetic flux, allowing us to predict spectral-irradiance variations from observations of disk-averaged magnetic-flux density. In most cases, the model reconstructions can account for 85–90% of the variability of the radiative flux from the chromosphere and corona. Our results are important for understanding the relationship between magnetic and radiative measures of solar and stellar variability.”
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“The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists {\it ab aeterno}. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. We analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.”
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“We study the acoustic scattering properties of a phononic crystal designed to behave as a gradient index lens in water, both experimentally and theoretically. The gradient index lens is designed using a square lattice of stainless-steel cylinders based on a multiple scattering approach in the homogenization limit. We experimentally demonstrate that the lens follows the graded index equations derived for optics by mapping the pressure intensity generated from a spherical source at 20 kHz. We find good agreement between the experimental result and theoretical modeling based on multiple scattering theory.”
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“Minimization of boundary curvature is a classic regularization technique for image segmentation in the presence of noisy image data. Techniques for minimizing curvature have historically been derived from descent methods which could be trapped in a local minimum and therefore required a good initialization. Recently, combinatorial optimization techniques have been applied to the optimization of curvature which provide a solution that achieves nearly a global optimum. However, when applied to image segmentation these methods required a meaningful data term. Unfortunately, for many images, particularly medical images, it is difficult to find a meaningful data term. Therefore, we propose to remove the data term completely and instead weight the curvature locally, while still achieving a global optimum.”
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“…Even though we cannot present all the algorithms in full detail, we can at least show “in princi– ple”, how a whole variety of important and practical algorithms come out from our refinement process. These include above all the (DLG) algorithm of Doligez, Leroy and Gonthier [9] – which sometimes is considered the culmination of concurrent collector development [1] – and its descendants.”
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“In this work, we study the target detection and tracking problem in mobile sensor networks, where the performance metrics of interest are probability of detection and tracking coverage, when the target can be stationary or mobile and its duration is finite. We propose a physical coverage-based mobility model, where the mobile sensor nodes move such that the overlap between the covered areas by different mobile nodes is small. It is shown that for stationary target scenario the proposed mobility model can achieve a desired detection probability with a significantly lower number of mobile nodes especially when the detection requirements are highly stringent. Similarly, when the target is mobile the coverage-based mobility model produces a consistently higher detection probability compared to other models under investigation.”
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“The prisoner’s dilemma (PD) game is a simple model for understanding cooperative patterns in complex systems consisting of selfish individuals. Here, we study a PD game problem in scale-free networks containing hierarchically organized modules and controllable shortcuts connecting separated hubs. We find that cooperator clusters exhibit a percolation transition in the parameter space (p,b), where p is the occupation probability of shortcuts and b is the temptation payoff in the PD game. The cluster size distribution follows a power law at the transition point. Such a critical behavior, resulting from the combined effect of stochastic processes in the PD game and the heterogeneous structure of complex networks, illustrates the diversity of social relationships and the self-organization of cooperator communities in real-world systems.”
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“We review recent efforts to detect small numbers of nuclear spins using magnetic resonance force microscopy.…”
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“Recovery of the sparsity pattern (or support) of a sparse vector from a small number of noisy linear samples is a common problem that arises in signal processing and statistics. In the high dimensional setting, it is known that recovery with a vanishing fraction of errors is impossible if the sampling rate and per-sample signal-to-noise ratio (SNR) are finite constants independent of the length of the vector. In this paper, it is shown that recovery with an arbitrarily small but constant fraction of errors is, however, possible, and that in some cases a computationally simple thresholding estimator is near-optimal.…”
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“Isolated, atomically thin conducting membranes of graphite, called graphene, have recently been the subject of intense research with the hope that practical applications in fields ranging from electronics to energy science will emerge. Here, we show that when immersed in ionic solution, a layer of graphene takes on new electrochemical properties that make it a trans-electrode. The trans-electrode’s properties are the consequence of the atomic scale proximity of its two opposing liquid-solid interfaces together with graphene’s well known in-plane conductivity. We show that several trans-electrode properties are revealed by ionic conductivity measurements on a CVD grown graphene membrane that separates two aqueous ionic solutions. Despite this membrane being only one to two atomic layers thick, we find it is a remarkable ionic insulator with a very small stable conductivity that depends on the ion species in solution.…”
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“Evolutionary game dynamics in finite populations is typically subject to noise, inducing effects which are not present in deterministic systems, including fixation and extinction. In the first part of this paper we investigate the phenomenon of drift reversal in finite populations, taking into account that drift is a local quantity in strategy space. Secondly, we study a simple imitation dynamics, and show that it can lead to fixation at internal mixed-strategy fixed points even in finite populations. Imitation in infinite populations is adequately described by conventional replicator dynamics, and these equations are known to have internal fixed points. Internal absorption in finite populations on the other hand is a novel dynamic phenomenon. Due to an outward drift in finite populations this type of dynamic arrest is not found in other commonly studied microscopic dynamics, not even in those with the same deterministic replicator limit as imitation.”
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wondering if there are suitable strategies for autonomous vehicles in traffic which would postpone the transition to jamming, but not increase danger of collision…
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“To our knowledge, the two most prominent aspects of our setting, the presence of asymmetric information and the stationarity requirement (stemming from unknown start times) have not been considered in the literature. For example, the Anderson-Weber strategy for the telephone problem is not stationary — it has a period of n − 1. It would be interesting to see what can be said about the optimal stationary strategies for this and other rendezvous problems. The interested reader is referred to [2,3] and the references therein for more information on rendezvous search games.”
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“Distributed medium access control (MAC) protocols are essential for the proliferation of low cost, decentralized wireless local area networks (WLANs). … In this work, we propose a class of protocols that limit the performance gain which nodes can obtain through selfish manipulation while incurring only a small efficiency loss. The proposed protocols are based on the idea of a review strategy, with which nodes collect signals about the actions of other nodes over a period of time, use a statistical test to infer whether or not other nodes are following the prescribed protocol, and trigger a punishment if a departure from the protocol is perceived. We consider the cases of private and public signals and provide analytical and numerical results to demonstrate the properties of the proposed protocols.”
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“We have shown that a multi-scale optical system can be used to dramatically improve the collection efficiency of light from multiple point sources simultaneously. The micromirror could be integrated with ion traps to achieve a factor of 5 enhancement in light collection over the current state-of-the-art of 5%….”
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ME: what would ‘well-designed’ biochemical nets look like, if you evolved them in silico?
“The reliability with which a network can transmit a particular frequency component of the input signal tra– jectory is determined by the gain-to-noise ratio of the net– work as a function of frequency. For systems that obey the spectral addition rule [32], that is those for which downstream reactions do not affect the input signal, the gain-to-noise ratio is an intrinsic property of the processing network. For networks that do not obey the spectral addition rule the gain-to-noise ratio will be dependent on the statistics of the input signal. The mutual information between input and output signals, which quantifies the information which can be transmitted about a particular input ensemble, also depends on the particular choice of the input signal.…”
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“When I started learning Ruby, managing gems was a huge problem to the point I would make fun of it. Now I use RVM which helps you install multiple versions of ruby on one computer. Not only does it do that, but it makes gem management a breeze as well! Beyond RVM, Rails 3 provides us with bundler, which allows you to install gems based on a list of dependancies automatically. Very slick.
Here I will outline how to install and configure RVM as well as manage your gems with RVM and the Rails 3 bundler.”
links for 2010-06-27
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“But here’s the wonderful revelation. If you’re a well-adjusted person, once you’ve discarded the unhealthy fictitious relationship with a phantasm, you can look around and notice all those other people who are likewise alone, and you’ll realize that we’re all alone together. And that means you aren’t alone at all — you’re among friends. That’s the next step in human progress, is getting away from the notion of minions living under a trail boss, and onwards to working as a cooperative community, with no gods and no masters, only autonomous agents free to think and act.”
links for 2010-06-25
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“We consider the problem of doing fast and reliable estimation of the number of non-zero entries in a sparse boolean matrix product. This problem has applications in databases and computer algebra. Let n denote the total number of non-zero entries in the input matrices. We show how to compute a 1 +- epsilon approximation (with small probability of error) in expected time O(n) for any epsilon > 4/\sqrt[4]{n}. The previously best estimation algorithm, due to Cohen (JCSS 1997), uses time O(n/epsilon^2). We also present a variant using O(sort(n)) I/Os in expectation in the cache-oblivious model. In contrast to these results, the currently best algorithms for computing a sparse boolean matrix product use time omega(n^{4/3}) (resp. omega(n^{4/3}/B) I/Os), even if the result matrix has only z=O(n) nonzero entries.…”
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“Spatially confined rigid membranes reorganize their morphology in response to the imposed constraints. A crumpled elastic sheet presents a complex pattern of random folds focusing the deformation energy while compressing a membrane resting on a soft foundation creates a regular pattern of sinusoidal wrinkles with a broad distribution of energy. … The physical model, exhibiting an analogy with parametric resonance in nonlinear oscillator, is a new theoretical toolkit to understand the morphology of various confined systems, such as coated materials or living tissues, e.g., wrinkled skin, internal structure of lungs, internal elastica of an artery, brain convolutions or formation of fingerprints. Moreover, it opens the way to new kind of microfabrication design of multiperiodic or chaotic (aperiodic) surface topography via self-organization.”
links for 2010-06-24
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“The goal of this work is to provide an empirical basis for research on image segmentation and boundary detection. To this end, we have collected 12,000 hand-labeled segmentations of 1,000 Corel dataset images from 30 human subjects. Half of the segmentations were obtained from presenting the subject with a color image; the other half from presenting a grayscale image. The public benchmark based on this data consists of all of the grayscale and color segmentations for 300 images. The images are divided into a training set of 200 images, and a test set of 100 images.”
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“We present a novel algorithm for segmentation of natural images that harnesses the principle of minimum description length (MDL). Our method is based on observations that a homogeneously textured region of a natural image can be well modeled by a Gaussian distribution and the region boundary can be effectively coded by an adaptive chain code. The optimal segmentation of an image is the one that gives the shortest coding length for encoding all textures and boundaries in the image, and is obtained via an agglomerative clustering process applied to a hierarchy of decreasing window sizes as multi-scale texture features. The optimal segmentation also provides an accurate estimate of the overall coding length and hence the true entropy of the image. We test our algorithm on the publicly available Berkeley Segmentation Dataset. It achieves state-of-the-art segmentation results compared to other existing methods.”
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I wonder to what extent this sort of thing might be useful in heuristics for Pareto-ranking