“… As a departure from such traditional trust models, we propose a generic, machine learning approach based trust framework where an agent uses its own previous transactions (with other agents) to build a knowledge base, and utilize this to assess the trustworthiness of a transaction based on associated features, which are capable of distinguishing successful transactions from unsuccessful ones. These features are harnessed using appropriate machine learning algorithms to extract relationships between the potential transaction and previous transactions.…”

“We study the 2-dimensional vector packing problem, which is a generalization of the classical bin packing problem where each item has 2 distinct weights and each bin has 2 corresponding capacities. The goal is to group items into minimum number of bins, without violating the bin capacity constraints.…”

“Thinning of character images is a big challenge. Removal of strokes or deformities in thinning is a difficult problem.…”

“… We examine here how the algorithm of phyllotaxis could contribute to the analysis of the structure of collagen fibrils. Such an algorithm indeed leads to organizations giving to each element of the assembly the most homogeneous and isotropic dense environment in a situation of cylindrical symmetry. The scattered intensity expected from a phyllotactic distribution of triple helices in collagen fibrils well agrees with the major features observed along the equatorial direction of their X ray patterns. Following this approach, the aggregation of triple helices in fibrils should be considered within the frame of soft condensed matter studies rather than that of molecular crystal studies.”

“Even when the numbers of non-zero entries per column/row in the measurement matrices are limited to $O(1)$, numerical experiments indicate that the algorithm can still typically recover the original signal perfectly with an $O(N)$ computational cost per update as well if the density $\rho$ of non-zero entries of the signal is lower than a certain critical value $\rho_{\rm th}(\alpha)$ as $N,M \to \infty$.”

“We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model’s rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm.”

“In this work we introduce a new linear time compression algorithm, called “Re-pair for Trees”, which compresses ranked ordered trees using linear straight-line context-free tree grammars. Such grammars generalize straight-line context-free string grammars and allow basic tree operations, like traversal along edges, to be executed without prior decompression. Our algorithm can be considered as a generalization of the “Re-pair” algorithm developed by N. Jesper Larsson and Alistair Moffat in 2000. The latter algorithm is a dictionary-based compression algorithm for strings. We also introduce a succinct coding which is specialized in further compressing the grammars generated by our algorithm. This is accomplished without loosing the ability do directly execute queries on this compressed representation of the input tree.…”

“Until I started using Specification Workshops as the name for a collaborative meeting about acceptance tests, it was very hard to convince business users to participate. But a simple change in naming made the problem go away.”

“Weather data didn’t come to be because of an Open Government Directive. It wasn’t created because of a White House mandate. Government did not release the data and then enterprising people built companies on top of it. It’s more accurate to make the argument that we have a national weather service because of one man’s deep desire to keep his job and to get promoted to colonel in the Army. It could be a vast network of lobbyists to help that man get promoted, or the vast network of lobbyists from shipping companies trying to get access to data already being created. Or it could be that it was just pretty obvious that access to weather data would save lives.”

“While company filings and regulations may not be the most glamorous parts of your startup, they’re absolutely critical to the success of your business and safety of your personal savings. Here’s a quick rundown of the laws and regulations you need to consider when creating a startup. Of course, depending on your type of business, hiring a tax accountant or good attorney with specific experience in your industry can go a long way to helping you steer clear of trouble.”

“We study, using simulated experiments inspired by thin film magnetic domain patterns, the feasibility of phase retrieval in X-ray diffractive imaging in the presence of intrinsic charge scattering given only photon-shot-noise limited diffraction data. We detail a reconstruction algorithm to recover the sample’s magnetization distribution under such conditions, and compare its performance with that of Fourier transform holography. Concerning the design of future experiments, we also chart out the reconstruction limits of diffractive imaging when photon– shot-noise and the intensity of charge scattering noise are independently varied. This work is directly relevant to the time-resolved imaging of magnetic dynamics using coherent and ultrafast radiation from X-ray free electron lasers and also to broader classes of diffractive imaging experiments which suffer noisy data, missing data or both.”

“We have shown that there exists a large ensemble of minimal Boolean networks that show reliable and robust dynamics. The networks are minimal in the respect that the number of connections of a node is not larger than necessary for obtaining a desired reliable trajectory. A reliable trajectory is an attractor of the dynamics of the network that does not change when the update schedule is changed or randomized. This means that under parallel update, at each time step only one node changes its state. The reliable trajectories were chosen at random, given a fixed average number of flips per node. High robustness was achieved by using an evolutionary algorithm that modifies the update functions and that accepts only those changes that do not decrease robustness.…”

“Our 2.546-approximation is quite simple. The performance guarantee is based on a simple area argument. This gives rise to the following question: what is the smallest square that suffices for packing any set of circles of total area 1? We believe the worst-case may very well be shown in Figure 13, which yields a lower bound of 1.471299… We believe there are relatively easy ways to improve the upper bound.”

“In this paper we present a technique for fusion of optical and thermal face images based on image pixel fusion approach. Out of several factors, which affect face recognition performance in case of visual images, illumination changes are a significant factor that needs to be addressed. Thermal images are better in handling illumination conditions but not very consistent in capturing texture details of the faces. Other factors like sunglasses, beard, moustache etc also play active role in adding complicacies to the recognition process. Fusion of thermal and visual images is a solution to overcome the drawbacks present in the individual thermal and visual face images.…”

“OpenCV (Open Source Computer Vision) is a library of programming functions for real time computer vision.

OpenCV is released under a BSD license, it is free for both academic and commercial use.
The library has >500 optimized algorithms (see figure below). It is used around the world, has >2M downloads and >40K people in the user group. Uses range from interactive art, to mine inspection, stitching maps on the web on through advanced robotics.”

“We study the dynamics of the Naming Game [Baronchelli et al., (2006) J. Stat. Mech.: Theory Exp. P06014] in empirical social networks. This stylized agent-based model captures essential features of agreement dynamics in a network of autonomous agents, corresponding to the development of shared classification schemes in a network of artificial agents or opinion spreading and social dynamics in social networks. Our study focuses on the impact that communities in the underlying social graphs have on the outcome of the agreement process. We find that networks with strong community structure hinder the system from reaching global agreement; the evolution of the Naming Game in these networks maintains clusters of coexisting opinions indefinitely. Further, we investigate agent-based network strategies to facilitate convergence to global consensus.”

“Neuronal activity arises from an interaction between ongoing firing generated spontaneously by neural circuits and responses driven by external stimuli. Using mean-field analysis, we ask how a neural network that intrinsically generates chaotic patterns of activity can remain sensitive to extrinsic input. We find that inputs not only drive network responses, they also actively suppress ongoing activity, ultimately leading to a phase transition in which chaos is completely eliminated. The critical input intensity at the phase transition is a non-monotonic function of stimulus frequency, revealing a “resonant” frequency at which the input is most effective at suppressing chaos even though the power spectrum of the spontaneous activity peaks at zero and falls exponentially. A prediction of our analysis is that the variance of neural responses should be most strongly suppressed at frequencies matching the range over which many sensory systems operate.”

“Developing large-scale distributed applications can be a daunting task. object-based environments have attempted to alleviate problems by providing distributed objects that look like local objects. We advocate that this approach has actually only made matters worse, as the developer needs to be aware of many intricate internal details in order to adequately handle partial failures. The result is an increase of application complexity. We present an alternative in which distribution transparency is lessened in favor of clearer semantics. In particular, we argue that a developer should always be offered the unambiguous semantics of local objects, and that distribution comes from copying those objects to where they are needed. We claim that it is often sufficient to provide only small, immutable objects, along with facilities to group objects into clusters.”

“The task of image restration is to find the spatial correspondence of two or more given images. In this paper we assume that the correspondence is given either by an Euclidean, or by an affine volume-preserving transformation. Since the registration problem can be seen as an optimization problem on a finite dimensional Lie group, we use a recently developed framework of approximate-Newton methods on manifolds, which leads to locally quadratically convergent algorithms. To reduce numerical costs, we present two strategies: One makes use of the quasi Monte Carlo Method and the other ends up with an algorithm acting on spline function spaces. An extension for multi-modal image registration is given as well.”

“l1-minimization refers to finding the minimum l1-norm solution to an underdetermined linear system b=Ax. It has recently received much attention, mainly motivated by the new compressive sensing theory that shows that under quite general conditions the minimum l1-norm solution is also the sparsest solution to the system of linear equations. Although the underlying problem is a linear program, conventional algorithms such as interior-point methods suffer from poor scalability for large-scale real world problems. A number of accelerated algorithms have been recently proposed that take advantage of the special structure of the l1-minimization problem. In this paper, we provide a comprehensive review of five representative approaches, namely, Gradient Projection, Homotopy, Iterative Shrinkage-Thresholding, Proximal Gradient, and Augmented Lagrange Multiplier. …”

“Sparse data models, where data is assumed to be well represented as a linear combination of a few elements from a dictionary, have gained considerable attention in recent years, and their use has led to state-of-the-art results in many signal and image processing tasks. It is now well understood that the choice of the sparsity regularization term is critical in the success of such models. Based on a codelength minimization interpretation of sparse coding, and using tools from universal coding theory, we propose a framework for designing sparsity regularization terms which have theoretical and practical advantages when compared to the more standard l0 or l1 ones. The presentation of the framework and theoretical foundations is complemented with examples that show its practical advantages in image denoising, zooming and classification.”

“In the present article we emphasize the importance of modeling time in the context of agent-based models. To this end, we present a (selective) survey of the Cellular Automata-literature on updating and draw parallels to the issue of agent activation in agent-based models. By means of two simple models, Schelling’s segregation model and Epstein’s demographic prisoner’s dilemma we investigate the influence of choosing different regimes of agent activation. Our experiments indicate that timing is not a critical issue for very simple models but bears huge influence on model behavior and results as soon as the degree of complexity increases only so slightly. After a brief review of the way commonly used ABM simulation environments handle the issue of timing, we draw some tentative conclusions about the importance of timing and the need for more research towards that direction, similar to the concerted effort on updating in cellular automata.”

“Transient algebra is a multi-valued algebra for hazard detection in gate circuits. Sequences of alternating 0’s and 1’s, called transients, represent signal values, and gates are modeled by extensions of boolean functions to transients. Formulas for computing the output transient of a gate from the input transients are known for NOT, AND, OR} and XOR gates and their complements, but, in general, even the problem of deciding whether the length of the output transient exceeds a given bound is NP-complete. We propose a method of evaluating extensions of general boolean functions. We introduce and study a class of functions with the following property: Instead of evaluating an extension of a boolean function on a given set of transients, it is possible to get the same value by using transients derived from the given ones, but having length at most 3. We prove that all functions of three variables, as well as certain other functions, have this property, and can be efficiently evaluated.”

“We define a two-step learner for RFSAs based on an observation table by using an algorithm for minimal DFAs to build a table for the reversal of the language in question and showing that we can derive the minimal RFSA from it after some simple modifications. We compare the algorithm to two other table-based ones of which one (by Bollig et al. 2009) infers a RFSA directly, and the other is another two-step learner proposed by the author. We focus on the criterion of query complexity.”

“…The model is based on the emergent properties of generic genetic networks, it does not refer to specific control circuits and it can therefore hold for a wide class of lineages. The model points to a peculiar role of cellular noise in differentiation, which has never been hypothesized so far, and leads to non trivial predictions which could be subject to experimental testing.”

“This paper presents a novel type-2 Fuzzy logic System to define the Shape of a facial component with the crisp output. This work is the part of our main research effort to design a system (called FASY) which offers a novel face construction approach based on the textual description and also extracts and analyzes the facial components from a face image by an efficient technique. The Fuzzy model, designed in this paper, takes crisp value of width and height of a facial component and produces the crisp value of Shape for different facial components. This method is designed using Matlab 6.5 and Visual Basic 6.0 and tested with the facial components extracted from 200 male and female face images of different ages from different face databases.”

“We consider a generalization of the Gabriel graph, the witness Gabriel graph. Given a set of vertices P and a set of witnesses W in the plane, there is an edge ab between two points of P in the witness Gabriel graph GG-(P,W) if and only if the closed disk with diameter ab does not contain any witness point (besides possibly a and/or b). We study several properties of the witness Gabriel graph, both as a proximity graph and as a new tool in graph drawing.”

“We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths of these interactions. When the nonspecific interaction is strong, liquidlike clustering can precede crystallization; when it is weak, growth can proceed via ordered nuclei. Crystal yields are in certain parameter regimes enhanced by the nonspecific interaction, even though it promotes association without local crystalline order. Our results suggest that equipping nanoscale components with weak nonspecific interactions (such as depletion attractions) can alter both their dynamical pathway of assembly and optimize the yield of the resulting material.”

“Many complex systems present an intrinsic bipartite nature and are often described and modeled in terms of networks [1–5]. Examples include movies and actors [1, 2, 4], authors and scientific papers [6–9], email accounts and emails [10], plants and animals that pollinate them [11, 12]. Bipartite networks are often very heterogeneous in the number of relationships that the elements of one set establish with the elements of the other set. … Here we introduce an unsupervised method to statistically validate each link of the projected network against a null hypothesis taking into account the heterogeneity of the system. We apply our method to three different systems…. In all these systems, both different in size and level of heterogeneity, we find that our method is able to detect network structures which are informative about the system…”

“Work out which bits of the system you know least about. Create the scenarios and have conversations around those bits of the system. You don’t have to grow the system from the beginning – you can pick any point you like! Which bits of the system make you most uncomfortable? Which bits make your stakeholders most uncomfortable?”

“So where does this gulf of experiences come from, why is cucumber loved by some and hated by others. At the risk of over-generalisation and mischaracterisation I recently came up with a theory: the cucumber detractors are not using cuke the way it was intended.”

“We tried a variant of this program starting in 2002 with a more solid economy and we are still trying to recover from how that movie ended. Einstein defined insanity as doing the same thing over and over again and expecting different results. And since the financial sector profited so handsomely from this exercise the last time around, they have every reason to encourage this insanity.”

“In this work we investigate a novel approach to handle the challenges of face recognition, which includes rotation, scale, occlusion, illumination etc. Here, we have used thermal face images as those are capable to minimize the affect of illumination changes and occlusion due to moustache, beards, adornments etc. The proposed approach registers the training and testing thermal face images in polar coordinate, which is capable to handle complicacies introduced by scaling and rotation. Line features are extracted from thermal polar images and feature vectors are constructed using these line. Feature vectors thus obtained passes through principal component analysis (PCA) for the dimensionality reduction of feature vectors.…”

“In 1961 Herbert Simon and Albert Ando published the theory behind the long-term behavior of a dynamical system that can be described by a nearly completely decomposable matrix. Over the past fifty years this theory has been used in a variety of contexts, including queueing theory, computer performance, and ecology. In all these applications, the structure of the system is known and the point of interest is the various states the system passes through on its way to some long-term equilibrium. This paper looks at this problem from the other direction. That is, we develop a technique for using the evolution of the system to tell us about its initial structure, and we use this technique to develop a new algorithm for data clustering.”

“Smoothie Charts is a really small chartling library designed for live streaming data. I built it to reduce the headaches I was getting from watching charts jerkily updating every second. What you’re looking up now is pretty much all it does. If you like that, then read on.”

“We discuss the complex dynamics of a non-linear random networks model, as a function of the connectivity k between the elements of the network. We show that this class of networks exhibit an order-chaos phase transition for a critical connectivity k = 2. Also, we show that both, pairwise correlation and complexity measures are maximized in dynamically critical networks. These results are in good agreement with the previously reported studies on random Boolean networks and random threshold networks, and show once again that critical networks provide an optimal coordination of diverse behavior.”

“The new algorithm by Yadava and his colleagues goes one step further. It uses a more realistic physics model of the x-ray source, the detectors, and the x-ray beam. Each of these three is assumed to have specific diameters instead of being considered a point or a line, Yadava says. Depending on the type of scan, the technique is better than ASIR at cutting image noise, and thus the x-rays can be even less intense. The researchers got high-quality abdomen scans of a human model using an eighth of the radiation dose of a conventional scan.”

“Because sharing data resulted in a citation, I wonder how long will it take for Open Data advocates to start using this “open data citation advantage” as an argument for sharing data?”

“As we continue to monitor the markets for evidence of Quote Stuffing and Strange Sequences (Crop Circles), we find that there are dozens if not hundreds of examples to choose from on any given day. As such, this page will be updated often with charts demonstrating this activity.

The common theme with the charts shown on this page is they are obviously all generated in code and are algorithmic. Some demonstrate bizarre price or size cycling, some demonstrate large burst of quotes in extremely short time frames and some will demonstrate both. In most cases these sequences are from a single exchange with no other exchange quoting in the same time frame.”

“While analyzing HFT (High Frequency Trading) quote counts, we were shocked to find cases where one exchange was sending an extremely high number of quotes for one stock in a single second: as high as 5,000 quotes in 1 second! During May 6, there were hundreds of times that a single stock had over 1,000 quotes from one exchange in a single second. Even more disturbing, there doesn’t seem to be any economic justification for this. In many of the cases, the bid/offer is well outside the National Best Bid/Offer (NBBO). We decided to analyze a handful of these cases in detail and graphed the sequential bid/offers to better understand them. What we discovered was a manipulative device with destabilizing effect.”

“…We tested our algorithm on a small benchmark graph and on a network of about 500 papers in information science (weighted with the Salton index of bibliographic coupling). In our tests, this approach results in characteristic ranges of resolution where a large resolution change does not lead to a growth of the natural community. Such stable modules were also obtained by applying the LFK algorithm but since we determine communities for all resolution values in one run, our approach is faster than the LFK reference. And our algorithm reveals the hierarchical structure of the graph more easily.”

can I have some of these particles, please?

“The possibility of microscopic swimming by extraction of energy from an external flow is discussed, focusing on the migration of a simple trimer across a linear shear flow. The geometric properties of swimming, together with the possible generalization to the case of a vesicle, are analyzed.The mechanism of energy extraction from the flow appears to be the generalization to a discrete swimmer of the tank-treading regime of a vesicle. The swimmer takes advantage of the external flow by both extracting energy for swimming and “sailing” through it. The migration velocity is found to scale linearly in the stroke amplitude, and not quadratically as in a quiescent fluid. This effect turns out to be connected with the non-applicability of the scallop theorem in the presence of external flow fields.”

“A particle that moves along a smooth track in a vertical plane is influenced by two forces: gravity and normal force. The force experienced by roller coaster riders is the normal force, so a natural question to ask is: what shape of the track gives a normal force of constant magnitude? Here we solve this problem. It turns out that the solution is related to the Kepler problem; the trajectories in velocity space are conic sections.”

“Recently popularized randomized methods for principal component analysis (PCA) efficiently and reliably produce nearly optimal accuracy — even on parallel processors — unlike the classical (deterministic) alternatives. We adapt one of these randomized methods for use with data sets that are too large to be stored in random-access memory (RAM). (The traditional terminology is that our procedure works efficiently “out-of-core.”) We illustrate the performance of the algorithm via several numerical examples. For example, we report on the PCA of a data set stored on disk that is so large that less than a hundredth of it can fit in our computer’s RAM.”

“A story isn’t done until it is being used by real users in production and has been validated to be a useful part of a product.”

“Although Laposky, a draftsman by profession, had received a proper recognition as a pioneer of electronic art, at no time his name has emerged in the context of dynamical chaos theory. The circuits he had implemented for generation of “oscillons” on the screen of a cathode ray tube oscilloscope, remain a mystery. It is known that some of his thirty-seven circuits [2] had “as many as 70 different setting of controls”[3] and that ac-voltage has been used for the circuit feeding. Our analysis is based on the vanity press booklet with the still photos of the fifty-six oscillons, which were exhibited at the Sanford Museum (Cherokee, Iowa) in 1953 [2].”

“It wasn’t all that long ago that the media and banking industry commentators would worry about the coming train wreck in commercial real estate. But peculiarly, that topic has more or less receded from view. It appears the public has only so much interest in banking stories, and the frenzied coverage of financial services non-reform plus eurozone sovereign debt woes, which are really eurozone bank woes, took center stage.”

“It is my opinion, that anybody should be able to use Couch in Rails or Sinatra or plain Ruby application as easily as using ActiveRecord, or, maybe more importantly, the highly faved MongoDB. Please share your opinion in the comments.”

“Is it any wonder that the value of a college education is now being questioned more than it used to be? Perhaps a basic education in personal finance would help more people make informed decisions about college and how to handle the financing of that endeavor.”

“… In particular, the fetishization of autonomy, self-reliance, and progress through mechanical engineering — echoing the desire to escape the suffocating social conditions back east by simply running away — utterly undermine the program itself and are incompatible with life in a space colony (which is likely to be at a minimum somewhat more constrained than life in one of the more bureaucratically obsessive-compulsive European social democracies, and at worst will tend towards the state of North Korea in Space).”

“Look no one wants to see violence in the streets, but history shows that it is not only the capitalists that have 2nd amendment remedies. Joe Hill may have more life in him than they like.”

“Strategy changes are an essential part of evolutionary games. Here we introduce a simple rule that, depending on the value of a single parameter $w$, influences the selection of players that are considered as potential sources of the new strategy. For positive $w$ players with high payoffs will be considered more likely, while for negative $w$ the opposite holds. Setting $w$ equal to zero returns the frequently adopted random selection of the opponent. We find that increasing the probability of adopting the strategy from the fittest player within reach, i.e. setting $w$ positive, promotes the evolution of cooperation. The robustness of this observation is tested against different levels of uncertainty in the strategy adoption process and for different interaction network. Since the evolution to widespread defection is tightly associated with cooperators having a lower fitness than defectors, the fact that positive values of $w$ facilitate cooperation is quite surprising. …”

“In this work we study a weak Prisoner’s Dilemma game in which both strategies and update rules are subjected to evolutionary pressure. Interactions among agents are specified by complex topologies, and we consider both homogeneous and heterogeneous situations. We consider deterministic and stochastic update rules for the strategies, which in turn may consider single links or full context when selecting agents to copy from. Our results indicate that the co-evolutionary process preserves heterogeneous networks as a suitable framework for the emergence of cooperation. Furthermore, on those networks, the update rule leading to a larger fraction of cooperation, replicator dynamics, is selected during co-evolution.…We conclude that for a variety of topologies, the fact that the dynamics coevolves with the strategies leads in general to more cooperation in the weak Prisoner’s Dilemma game.”

“Dynamics of evolutionary games strongly depend on underlying networks. We study the coevolutionary prisoner’s dilemma in which players change their local networks as well as strategies (i.e., cooperate or defect). This topic has been increasingly explored by many researchers. On the basis of active linking dynamics [J. M. Pacheco et al., J. Theor. Biol. 243, 437 (2006), J. M. Pacheco et al., Phys. Rev. Lett. 97, 258103 (2006)], we show that cooperation is enhanced fairly robustly. In particular, cooperation evolves when the payoff of the player is normalized by the number of neighbors; this is not the case in the evolutionary prisoner’s dilemma on static networks.”

“Biological networks of interacting agents exhibit similar topological properties for a wide range of scales, from cellular to ecological levels, suggesting the existence of a common evolutionary origin. A general evolutionary mechanism based on global stability has been proposed recently [J I Perotti, O V Billoni, F A Tamarit, D R Chialvo, S A Cannas, Phys. Rev. Lett. 103, 108701 (2009)]. This mechanism is incorporated into a model of a growing network of interacting agents in which each new agent’s membership in the network is determined by the agent’s effect on the network’s global stability. We show that, out of this stability constraint, several topological properties observed in biological networks emerge in a self organized manner. The influence of the stability selection mechanism on the dynamics associated to the resulting network is analyzed as well.”

“How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions between their proteins? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in crowded cellular environment. The model cell includes three independent pathways, whose topologies of PPI subnetworks are different, but whose functional concentrations equally contribute to cell’s fitness. The model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical-chemical properties of protein interactions and their abundances due to a “frustration” effect: strengthening of functional interactions brings about hydrophobic surfaces, which make proteins prone to promiscuous binding.…”

“We introduce the heterogeneous voter model (HVM), in which each agent has its own intrinsic rate to change state, reflective of the heterogeneity of real people, and the partisan voter model (PVM), in which each agent has an innate and fixed preference for one of two possible opinion states. For the HVM, the time until consensus is reached is much longer than in the classic voter model. For the PVM in the mean-field limit, a population evolves to a “selfish” state, where each agent tends to be aligned with its internal preference. For finite populations, discrete fluctuations ultimately lead to consensus being reached in a time that scales exponentially with population size.”

“In this paper we have considered a spherical envelope model (so-called squirmer) to investigate energetics in cilia dynamics and locomotion. Allowing only tangential but time-periodic deformations, we have used an optimization method based on a variational approach to derive computationally the stroke leading to the largest swimming efficiency. The optimal stroke was shown to display weak Lagrangian asymmetry, but strong Eulerian asymmetry, indicative of symmetry-breaking at the whole-organism level, but not at the level of individual cilia.…”

“Linux package managers have to deal with dependencies and conflicts of packages required to be installed by the user. As an NP-complete problem, this is a hard task to solve. In this context, several approaches have been pursued. Apt-pbo is a package manager based on the apt project that encodes the dependency solving problem as a pseudo-Boolean optimization (PBO) problem. This paper compares different PBO solvers and their effectiveness on solving the dependency solving problem.”

“The problem the pattern attempts to solve: identify the URLs in an arbitrary string of text, where by “arbitrary” let’s agree we mean something unstructured such as an email message or a tweet.”

“We have embarked on a research program designed to develop universal models that can recreate empiri– cally observed phenomena in dynamic complex networks. We have shown that, using a suitable reinforced random walk on a “long-term” underlay network, one is able to produce instantaneous networks which reproduce qualitatively characteristic features of real world dynamic networks. This includes, in particular, the construc– tion of scale-free sub-networks of a scale-free “underlay” network, whose local hubs substantially differ from sub– network to sub-network and from those of the underlay.…”

“…For cyclic games with two players and three strategies, we show that the resulting deterministic dynamics crucially depends on the initial condition in a non–trivial way.”

“The transition of the flow in a duct of square cross-section is studied. Like in the similar case of the pipe flow, the motion is linearly stable for all Reynolds numbers; this flow is thus a good candidate to investigate the ‘bypass’ path to turbulence. Initially the so-called ‘linear optimal perturbation problem’ is formulated and solved, yielding optimal disturbances in the form of longitudinal vortices. Such optimals, however, fail to elicit a significant response from the system in the nonlinear regime. Thus, streamwise-inhomogeneous, sub-optimal disturbances are focussed upon; nonlinear quadratic interactions are immediately evoked by such initial perturbations and an unstable streamwise-homogeneous large amplitude mode rapidly emerges. The subsequent evolution of the flow, at a value of the Reynolds number at the edge between fully developed turbulence and relaminarization, shows the alternance of patterns with two pairs of large scale vortices near opposing parallel walls.…”

“The modeling of complex systems such as ecological or socio-economic systems can be very challenging. Although various modeling approaches exist, they are generally not compatible and mutually consistent, and empirical data often do not allow one to decide what model is the right one, the best one, or most appropriate one. Moreover, as the recent financial and economic crisis shows, relying on a single, idealized model can be very costly. This contribution tries to shed new light on problems that arise when complex systems are modeled. While the arguments can be transferred to many different systems, the related scientific challenges are illustrated for social, economic, and traffic systems. The contribution discusses issues that are sometimes overlooked and tries to overcome some frequent misunderstandings and controversies of the past.…”

“We address the problem of estimating unknown model parameters and state variables in stochastic reaction processes when only sparse and noisy measurements are available. Using an asymptotic system size expansion for the backward equation we derive an efficient approximation for this problem. We demonstrate the validity of our approach on model systems and generalize our method to the case when some state variables are not observed.”

“While the concept of clusters arises when viewing quasicrystalline surfaces at close range, long range quasiperiodic order as seen in diffraction studies is perhaps more naturally described in terms of quasiperiodic tilings. These are the analogs of the “Bravais lattices” for periodic systems, and give a good description of the orientational order and positional long range order seen in quasicrystal diffraction patterns. Tilings are constructed from a small num– ber of tiles arranged so as to avoid overlapping or holes. Quasiperiodic tilings usually possess a hierarchically organised structure, where tilings can be ”in– flated”(”deflated”) so as to obtain a similar tiling on a larger(smaller) length scale.”

“Much recent interest has focused on “open” dynamical systems, in which a classical map or flow is considered only until the trajectory reaches a “hole”, at which the dynamics is no longer considered. Here we consider questions pertaining to the survival probability as a function of time, given an initial measure on phase space. We focus on the case of billiard dynamics, namely that of a point particle moving with constant velocity except for mirror-like reflections at the boundary, and give a number of recent results, physical applications and open problems.”

“Storage optimization in distributed environments is a major concern when talking about reliability in this kind of schemes. Although replication is the most used option, erasure coding is a more optimized one.
However, erasure coding uses a lot of bandwidth to replace one node. In a dynamic scheme, where nodes enter and leave the system frequently, bandwidth use could be an important drawback.
Regenerating Codes introduced by Dimakis et al. minimize the code repair problem by applying Network Coding to the distributed storage scheme. However finding the coefficients for the linear combinations used to replace a node is not easy, specially for the systematic case, and must be calculated for each new node fail.…”

“In this paper, we perform a minimalistic quantization of the classical game of tic-tac-toe, by allowing superpositions of classical moves. In order for the quantum game to reduce properly to the classical game, we require legal quantum moves to be orthogonal to all previous moves. We also admit interference effects, by squaring the sum of amplitudes over all moves by a player to compute his or her occupation level of a given site. A player wins when the sums of occupations along any of the eight straight lines we can draw in the $3 \times 3$ grid is greater than three.…”

“Actual accounting systems are based on transactions. But in the current, knowledge-based economy much of the value creation precedes, sometimes by years, the occurrence of transactions. Until then, the accounting system does not register any value created in contrast to the investments made into R&D, which are fully expensed. This difference, between how the accounting system is handling value created and is handling investments into value creation, is the major reason for the growing disconnect between market values and financial information.”

Makes me want to write a simple agent-based model in which a few people have almost all the money and most everybody else are allowed to move a bit around, for a fee.

“This is a short commentary piece that discusses how the methods used in the natural sciences can apply to economics in general and financial markets specifically.”

“In real communication and transportation networks, the geographical positions of nodes are very important for the efficiency and the tolerance of connectivity. Considering spatially inhomogeneous positions of nodes according to a population, we introduce a multi-scale quartered (MSQ) network that is stochastically constructed by recursive subdivision of polygonal faces as a self-similar tiling. It has several advantages: the robustness of connectivity, the bounded short path lengths, and the shortest distance routing algorithm in a distributive manner. Furthermore, we show that the MSQ network is more efficient with shorter link lengths and more suitable with lower load for avoiding traffic congestion than other geographical networks which have various topologies ranging from river to scale-free networks. These results will be useful for providing an insight into the future design of ad hoc network infrastructures.”

“We describe computer algorithms that produce the complete set of isohedral tilings by n-omino or n-iamond tiles in which the tiles are fundamental domains and the tilings have 3-, 4-, or 6-fold rotational symmetry. The symmetry groups of such tilings are of types p3, p31m, p4, p4g, and p6. There are no isohedral tilings with symmetry groups p3m1, p4m, or p6m that have polyominoes or polyiamonds as fundamental domains. We display the algorithms’ output and give enumeration tables for small values of n.…”

I ♡ pragmatic physics. “We propose a simple rubber friction law, which can be used, e.g., in models of tire (and vehicle) dynamics.”

“It features generic data abstraction through Collections, a Visualization API allowing the creation of pluggable visualizations, and a Scene Graph implementation on top of HTML 5 Canvas. See the GitHub project, the documentation, and an example.”

“For a set of n points in the plane, we consider the axis–aligned (p,k)-Box Covering problem: Find p axis-aligned, pairwise-disjoint boxes that together contain n-k points. In this paper, we consider the boxes to be either squares or rectangles, and we want to minimize the area of the largest box. For general p we show that the problem is NP-hard for both squares and rectangles. For a small, fixed number p, we give algorithms that find the solution in the following running times:
For squares we have O(n+k log k) time for p=1, and O(n log n+k^p log^p k time for p = 2,3. For rectangles we get O(n + k^3) for p = 1 and O(n log n+k^{2+p} log^{p-1} k) time for p = 2,3. In all cases, our algorithms use O(n) space.”

“We study the problem of reconstructing a sparse signal from a limited number of its linear projections when a part of its support is known, although the known part may contain some errors. The “known” part of the support, denoted T, may be available from prior knowledge. Alternatively, in a problem of recursively reconstructing time sequences of sparse spatial signals, one may use the support estimate from the previous time instant as the “known” part. The idea of our proposed solution (modified-CS) is to solve a convex relaxation of the following problem: find the signal that satisfies the data constraint and is sparsest outside of T.…”

“We present a form of algebraic reasoning for computational objects which are expressed as graphs. Edges describe the flow of data between primitive operations which are represented by vertices. These graphs have an interface made of half-edges (edges which are drawn with an unconnected end) and enjoy rich compositional principles by connecting graphs along these half-edges. In particular, this allows equations and rewrite rules to be specified between graphs. Particular computational models can then be encoded as an axiomatic set of such rules. Further rules can be derived graphically and rewriting can be used to simulate the dynamics of a computational system, e.g. evaluating a program on an input. Examples of models which can be formalised in this way include traditional electronic circuits as well as recent categorical accounts of quantum information.”

“This expository review is devoted to fish swimming and bird/insect flight.…”

“We analyze over 500 million Twitter messages from an eight month period and find that tracking a small number of flu-related keywords allows us to forecast future influenza rates with high accuracy, obtaining a 95% correlation with national health statistics. We then analyze the robustness of this approach to spurious keyword matches, and we propose a document classification component to filter these misleading messages. We find that this document classifier can reduce error rates by over half in simulated false alarm experiments, though more research is needed to develop methods that are robust in cases of extremely high noise.”

“We propose a degree-based coarse graining approach that not just accelerates the evaluation of dynamics on complex networks, but also satisfies the consistency conditions for both equilibrium statistical distributions and nonequilibrium dynamical flows. For the Ising model and susceptible-infected-susceptible epidemic model, we introduce these required conditions explicitly and further prove that they are satisfied by our coarse-grained network construction within the annealed network approximation. Finally, we numerically show that the phase transitions and fluctuations on the coarse-grained network are all in good agreements with those on the original one.”

“Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. While current methods enable in-depth study of a small number of communities, a simple tool for breadth studies of bacterial population composition in a large number of samples is lacking. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. This method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of the known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture.…”

“The Fermi Paradox is the apparent contradiction between the high probability extraterrestrial civilizations’ existence and the lack of contact with such civilizations. In general, solutions to Fermi’s paradox come down to either estimation of Drake equation parameters i.e. our guesses about the potential number of extraterrestrial civilizations or simulation of civilizations development in the universe. We consider a new type of cellular automata, that allows to analyze Fermi paradox. We introduce bonus stimulation model (BS-model) of development in cellular space (Universe) of objects (Civilizations). When civilizations get in touch they stimulate development each other, increasing their life time. We discovered nonlinear threshold behaviour of total volume of civilizations in universe and on the basis of our model we built analogue of Drake equation.”

“In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particular (DNA) alignment necessarily has subtrees of all possible sizes which are most parsimonious for the corresponding subalignments. We answer the conjecture affirmatively for binary alignments on five taxa but also show how to construct examples for which Maximum Parsimony trees are not hereditary. …we also show that compatible most parsimonious quartets do not have to provide a most parsimonious supertree. Last, we show that our results can be generalized to Maximum Likelihood for certain nucleotide substitution models.”

“Laboratory investigations have shown that a formal theory of fault-tolerance will be essential to harness nanoscale self-assembly as a medium of computation. Several researchers have voiced an intuition that self-assembly phenomena are related to the field of distributed computing. This paper formalizes some of that intuition. We construct tile assembly systems that are able to simulate the solution of the wait-free consensus problem in some distributed systems. (For potential future work, this may allow binding errors in tile assembly to be analyzed, and managed, with positive results in distributed computing, as a “blockage” in our tile assembly model is analogous to a crash failure in a distributed computing model.) …We show that solution of this strengthened consensus problem can be simulated by a two-dimensional tile assembly model only for two processes, whereas a three-dimensional tile assembly model can simulate its solution in a distributed system with any number of processes

“Genetic oscillators are a major theme of interest in the emerging field of synthetic biology. Until recently, most work has been carried out using intra-cellular oscillators, but this approach restricts the broader applicability of such systems. Motivated by a desire to develop large-scale, spatially-distributed cell-based computational systems, we present an initial design for a population-level oscillator which uses three different bacterial strains. Our system is based on the client-server model familiar to computer science, and uses quorum sensing for communication between nodes. We present the results of extensive in silico simulation tests, which confirm that our design is both feasible and robust.”

Frankly, I’ve alway thought this, especially after some early “confusing” experiments that never got published because they were part of my first Ph.D. thesis research: “…We argue that the presence of only the frozen phase in the work of Kauffman et al. was due simply to the specific parametrization used, and is not an inherent feature of this class of functions. However, these networks are significantly more stable than the variants where all possible Boolean functions are allowed.”