Tag Archives: classification

Items of some interest…

Posted on by

These are my recent Pinboard.in links:

  • Progressives and the Ron Paul fallacies – Salon.com

    The fallacy in this reasoning is glaring. The candidate supported by progressives — President Obama — himself holds heinous views on a slew of critical issues and himself has done heinous things with the power he has been vested. He has slaughtered civilians — Muslim children by the dozens — not once or twice, but continuously in numerous nations with drones, cluster bombs and other forms of attack. He has sought to overturn a global ban on cluster bombs. He has institutionalized the power of Presidents — in secret and with no checks — to target American citizens for assassination-by-CIA, far from any battlefield. He has waged an unprecedented war against whistleblowers, the protection of which was once a liberal shibboleth. He rendered permanently irrelevant the War Powers Resolution, a crown jewel in the list of post-Vietnam liberal accomplishments, and thus enshrined the power of Presidents to wage war even in the face of a Congressional vote against it. His obsession with secrecy is so extreme that it has become darkly laughable in its manifestations, and he even worked to amend the Freedom of Information Act (another crown jewel of liberal legislative successes) when compliance became inconvenient.

    politics party-politics-in-particular cognitive-dissonance cultural-assumptions dialog-it-ain't

  • A modest proposal to give Free Software equal legal standing as proprietary. | Carlo Piana :: Law is Freedom ::

    Laws are more often than not an annoyance, despite their aim to improve the legal framework in any given field. Free Software (AKA "Open Source") has thrieved despite the absence of any legal recognition by the law, if not in spite of rules that clearly are shaped around proprietary software. In many jurisdictions it has passed the enforceability test. So, no laws seem necessary to make it work. Yet, can some legal principle be put forward, and included in some laws, to help?

    via:Glyn-Moody licensing law contracts modest-proposals

  • 2011 in Review

    to-read to-keep-in-mind lists movies books comix

  • Best and Worst Science Fiction/Fantasy Movies of 2011

    to-keep-in-mind movies lists

  • [1109.3248] Reconstruction of sequential data with density models

    We introduce the problem of reconstructing a sequence of multidimensional real vectors where some of the data are missing. This problem contains regression and mapping inversion as particular cases where the pattern of missing data is independent of the sequence index. The problem is hard because it involves possibly multivalued mappings at each vector in the sequence, where the missing variables can take more than one value given the present variables; and the set of missing variables can vary from one vector to the next. To solve this problem, we propose an algorithm based on two redundancy assumptions: vector redundancy (the data live in a low-dimensional manifold), so that the present variables constrain the missing ones; and sequence redundancy (e.g. continuity), so that consecutive vectors constrain each other. We capture the low-dimensional nature of the data in a probabilistic way with a joint density model, here the generative topographic mapping, which results in a Gaussian mixture. Candidate reconstructions at each vector are obtained as all the modes of the conditional distribution of missing variables given present variables. The reconstructed sequence is obtained by minimising a global constraint, here the sequence length, by dynamic programming. We present experimental results for a toy problem and for inverse kinematics of a robot arm.

    inverse-problems statistics algorithms learning-from-data nudge-targets

  • [1110.5063] Recovering a Clipped Signal in Sparseland

    In many data acquisition systems it is common to observe signals whose amplitudes have been clipped. We present two new algorithms for recovering a clipped signal by leveraging the model assumption that the underlying signal is sparse in the frequency domain. Both algorithms employ ideas commonly used in the field of Compressive Sensing; the first is a modified version of Reweighted $ell_1$ minimization, and the second is a modification of a simple greedy algorithm known as Trivial Pursuit. An empirical investigation shows that both approaches can recover signals with significant levels of clipping

    signal-processing inference compressive-sensing algorithms nudge-targets

  • [1112.2316] Complexity-entropy causality plane: a useful approach for distinguishing songs

    Nowadays we are often faced with huge databases resulting from the rapid growth of data storage technologies. This is particularly true when dealing with music databases. In this context, it is essential to have techniques and tools able to discriminate properties from these massive sets. In this work, we report on a statistical analysis of more than ten thousand songs aiming to obtain a complexity hierarchy. Our approach is based on the estimation of the permutation entropy combined with an intensive complexity measure, building up the complexity-entropy causality plane. The results obtained indicate that this representation space is very promising to discriminate songs as well as to allow a relative quantitative comparison among songs. Additionally, we believe that the here-reported method may be applied in practical situations since it is simple, robust and has a fast numerical implementation.

    signal-processing classification data-analysis clustering representation music nudge-targets

  • [1112.6178] A general framework for online audio source separation

    We consider the problem of online audio source separation. Existing algorithms adopt either a sliding block approach or a stochastic gradient approach, which is faster but less accurate. Also, they rely either on spatial cues or on spectral cues and cannot separate certain mixtures. In this paper, we design a general online audio source separation framework that combines both approaches and both types of cues. The model parameters are estimated in the Maximum Likelihood (ML) sense using a Generalised Expectation Maximisation (GEM) algorithm with multiplicative updates. The separation performance is evaluated as a function of the block size and the step size and compared to that of an offline algorithm.

    signal-processing audio-segmentation statistics algorithms metaheuristics nudge-targets

Items of some interest…

Posted on by

These are my recent Pinboard.in links:

  • [1108.4135] Complex-Valued Autoencoders

    "Autoencoders are unsupervised machine learning circuits whose learning goal is to minimize a distortion measure between inputs and outputs. Linear autoencoders can be defined over any field and only real-valued linear autoencoder have been studied so far. Here we study complex-valued linear autoencoders where the components of the training vectors and adjustable matrices are defined over the complex field with the $L_2$ norm. We provide simpler and more general proofs that unify the real-valued and complex-valued cases, showing that in both cases the landscape of the error function is invariant under certain groups of transformations. The landscape has no local minima, a family of global minima associated with Principal Component Analysis, and many families of saddle points associated with orthogonal projections onto sub-space spanned by sub-optimal subsets of eigenvectors of the covariance matrix. The theory yields several iterative, convergent, learning algorithms, a clear understanding of the generalization properties of the trained autoencoders, and can equally be applied to the hetero-associative case when external targets are provided. Partial results on deep architecture as well as the differential geometry of autoencoders are also presented. The general framework described here is useful to classify autoencoders and identify general common properties that ought to be investigated for each class, illuminating some of the connections between information theory, unsupervised learning, clustering, Hebbian learning, and auto encoders."

    neural-networks machine-learning classification encoding algorithms nudge-targets

  • [1108.5685] Predicting flow reversals in chaotic natural convection using data assimilation

    "A simplified model of natural convection, similar to the Lorenz (1963) system, is compared to computational fluid dynamics simulations in order to test data assimilation methods and better understand the dynamics of convection. The thermosyphon is represented by a long time flow simulation, which serves as a reference "truth". Forecasts are then made using the Lorenz-like model and synchronized to noisy and limited observations of the truth using data assimilation. The resulting analysis is observed to infer dynamics absent from the model when using short assimilation windows.

    Furthermore, chaotic flow reversal occurrence and residency times in each rotational state are forecast using analysis data. Flow reversals have been successfully forecast in the related Lorenz system, as part of a perfect model experiment, but never in the presence of significant model error or unobserved variables. Finally, we provide new details concerning the fluid dynamical processes present in the thermosyphon during these flow reversals."

    chaos dynamical-systems experiment prediction numerical-methods algorithms nudge-targets

  • [1108.1320] Compressed Matrix Multiplication

    "Motivated by the problems of computing sample covariance matrices, and of transforming a collection of vectors to a basis where they are sparse, we present a simple algorithm that computes an approximation of the product of two n-by-n real matrices A and B.…"

    approximation algorithms nudge-targets

  • [1110.5296] Computing a Longest Common Palindromic Subsequence

    "The {em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. Palindrome is a word which reads the same forward as it does backward. The {em longest common palindromic subsequence (LCPS)} problem is an interesting variant of the classic LCS problem which finds the longest common subsequence between two given strings such that the computed subsequence is also a palindrome. In this paper, we study the LCPS problem and give efficient algorithms to solve this problem. To the best of our knowledge, this is the first attempt to study and solve this interesting problem."

    combinatorics strings algorithms nudge-targets

Items of some interest…

Posted on by

These are my recent Pinboard.in links:

  • Classifying Heart Sounds Challenge

    "According to the World Health Organisation, cardiovascular diseases (CVDs) are the number one cause of death globally: more people die annually from CVDs than from any other cause. An estimated 17.1 million people died from CVDs in 2004, representing 29% of all global deaths. Of these deaths, an estimated 7.2 million were due to coronary heart disease. Any method which can help to detect signs of heart disease could therefore have a significant impact on world health. This challenge is to produce methods to do exactly that. Specifically, we are interested in creating the first level of screening of cardiac pathologies both in a Hospital environment by a doctor (using a digital stethoscope) and at home by the patient (using a mobile device).

    The problem is of particular interest to machine learning researchers as it involves classification of audio sample data, where distinguishing between classes of interest is non-trivial. Data is gathered in real-world situations and frequently contains background noise of every conceivable type. The differences between heart sounds corresponding to different heart symptoms can also be extremely subtle and challenging to separate. Success in classifying this form of data requires extremely robust classifiers. Despite its medical significance, to date this is a relatively unexplored application for machine learning."

    machine-learning competition nudge-targets classification segmentation data-analysis supervised-learning

Items of some interest…

Posted on by

These are my recent Pinboard.in links:

  • [1110.1462] Dynamic Clustering of Histogram Data Based on Adaptive Squared Wasserstein Distances

    "…To cluster sets of histogram data, we propose to use Dynamic Clustering Algorithm, (based on adaptive squared Wasserstein distances) that is a k-means-like algorithm for clustering a set of individuals into K classes that are apriori fixed. The main aim of this research is to provide a tool for clustering histograms, emphasizing the different contributions of the histogram variables, and their components, to the definition of the clusters. We demonstrate that this can be achieved using adaptive distances.

    Two kind of adaptive distances are considered: the first takes into account the variability of each component of each descriptor for the whole set of individuals; the second takes into account the variability of each component of each descriptor in each cluster. We furnish interpretative tools of the obtained partition based on an extension of the classical measures (indexes) to the use of adaptive distances in the clustering criterion function. Applications on synthetic and real-world data corroborate the proposed procedure."

    classification statistics histograms metrics clustering

  • [1110.1412] Quantifying loopy network architectures

    "Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture containing closed loops at many different levels. Although a number of methods have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated graphs, such as artificial models and optimal distribution networks, as well as natural graphs extracted from digitized images of dicotyledonous leaves and vasculature of rat cerebral neocortex. We calculate various metrics based on the Asymmetry, the cumulative size distribution and the Strahler bifurcation ratios of the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information (exact location of edges and nodes) from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs."

    complexology biophysics network-theory metrics

  • [1110.1393] High-Precision Tuning of State for Memristive Devices by Adaptable Variation-Tolerant Algorithm

    "Using memristive properties common for the titanium dioxide thin film devices, we designed a simple write algorithm to tune device conductance at a specific bias point to 1% relative accuracy (which is roughly equivalent to 7-bit precision) within its dynamic range even in the presence of large variations in switching behavior. The high precision state is nonvolatile and the results are likely to be sustained for nanoscale memristive devices because of the inherent filamentary nature of the resistive switching. The proposed functionality of memristive devices is especially attractive for analog computing with low precision data. As one representative example we demonstrate hybrid circuitry consisting of CMOS summing amplifier and two memristive devices to perform analog multiply and accumulate computation, which is a typical bottleneck operation in information processing."

    memristors engineering-design simulation control-systems nudge-targets

  • [1110.1521] Nodal domains of a non-separable problem – the right angled isosceles triangle

    "Our result may be generalized to other domains where similar algorithms may apply. Our algorithm is based on the fact that the eigenfunctions are presented as a linear combination of simple plane waves. It is therefore tempting to try and generalize it for other drums with similar property. The equilateral triangle is an immediate candidate (see [29] and references within).

    A further, and quite surprising, result is the recursive formula for the number of nodal loops. To our knowledge this is the first known exact formula for the nodal count of a non-separable planar manifold (for certain eigenfunctions of tori exact formulas have been given in [22]). The formula was found by direct inspection of large tables and has been verified for a large bulk of data computationally. An obvious challenge is to prove this formula. In particular, the recursive part of the formula resembles the famous Euclid algorithm for the greatest common divisor. A further investigation of the mentioned formula might therefore expose some new number theoretical properties of the nodal count."

    physics algorithms analytical-results open-questions geometry acoustics exact-form nudge-targets

  • [1110.1485] A Face Recognition Scheme using Wavelet Based Dominant Features

    "In this paper, a multi-resolution feature extraction algorithm for face recognition is proposed based on two-dimensional discrete wavelet transform (2D-DWT), which efficiently exploits the local spatial variations in a face image. For the purpose of feature extraction, instead of considering the entire face image, an entropy-based local band selection criterion is developed, which selects high-informative horizontal segments from the face image. In order to capture the local spatial variations within these highinformative horizontal bands precisely, the horizontal band is segmented into several small spatial modules. Dominant wavelet coefficients corresponding to each local region residing inside those horizontal bands are selected as features. In the selection of the dominant coefficients, a threshold criterion is proposed, which not only drastically reduces the feature dimension but also provides high within-class compactness and high between-class separability. A principal component analysis is performed to further reduce the dimensionality of the feature space. Extensive experimentation is carried out upon standard face databases and a very high degree of recognition accuracy is achieved by the proposed method in comparison to those obtained by some of the existing methods."

    face-recognition algorithms image-processing wavelets nudge-targets

  • [1110.1553] Hierarchical QR factorization algorithms for multi-core cluster systems

    "This paper describes a new QR factorization algorithm which is especially designed for massively parallel platforms combining parallel distributed multi-core nodes. These platforms make the present and the foreseeable future of high-performance computing. Our new QR factorization algorithm falls in the category of the tile algorithms which naturally enables good data locality for the sequential kernels executed by the cores (high sequential performance), low number of messages in a parallel distributed setting (small latency term), and fine granularity (high parallelism)."

    parallel-computing operations-research factorization algorithms nudge-targets meta-algorithms

  • [1110.1560] On the Coloring of Grid Wireless Sensor Networks: the Vector-Based Coloring Method

    "Graph coloring is used in wireless networks to optimize network resources: bandwidth and energy. Nodes access the medium according to their color. It is the responsibility of the coloring algorithm to ensure that interfering nodes do not have the same color. In this research report, we focus on wireless sensor networks with grid topologies. How does a coloring algorithm take advantage of the regularity of grid topology to provide an optimal periodic coloring, that is a coloring with the minimum number of colors? We propose the Vector-Based Coloring Method, denoted VCM, a new method that is able to provide an optimal periodic coloring for any radio transmission range and for any h-hop coloring, h>=1. This method consists in determining at which grid nodes a color can be reproduced without creating interferences between these nodes while minimizing the number of colors used. We compare the number of colors provided by VCM with the number of colors obtained by a distributed coloring algorithm with line and column priority assignments. We also provide bounds on the number of colors of optimal general colorings of the infinite grid, and show that periodic colorings (and thus VCM) are asymptotically optimal. Finally, we discuss the applicability of this method to a real wireless network."

    graph-theory algorithms operations-research nudge-targets

  • [1110.1580] A Polylogarithmic-Competitive Algorithm for the k-Server Problem

    "We give the first polylogarithmic-competitive randomized online algorithm for the $k$-server problem on an arbitrary finite metric space. In particular, our algorithm achieves a competitive ratio of O(log^3 n log^2 k log log n) for any metric space on n points. Our algorithm improves upon the deterministic (2k-1)-competitive algorithm of Koutsoupias and Papadimitriou [J.ACM'95] whenever n is sub-exponential in k."

    scheduling operations-research algorithms nudge-targets

  • [1110.1590] PSA: The Packet Scheduling Algorithm for Wireless Sensor Networks

    "The main cause of wasted energy consumption in wireless sensor networks is packet collision. The packet scheduling algorithm is therefore introduced to solve this problem. Some packet scheduling algorithms can also influence and delay the data transmitting in the real-time wireless sensor networks. This paper presents the packet scheduling algorithm (PSA) in order to reduce the packet congestion in MAC layer leading to reduce the overall of packet collision in the system The PSA is compared with the simple CSMA/CA and other approaches using network topology benchmarks in mathematical method. The performances of our PSA are better than the standard (CSMA/CA). The PSA produces better throughput than other algorithms. On other hand, the average delay of PSA is higher than previous works. However, the PSA utilizes the channel better than all algorithms."

    sensor-networks distributed-processing scheduling routing operations-research algorithms nudge-targets

  • [1110.0725] A Survey of Distributed Data Aggregation Algorithms

    "Distributed data aggregation has been an active field of research in the last decade, and a huge diverse amount of techniques can be found in the literature. For this reasons, this survey intends to be an important time saving instrument, for those that desire to get a quick and comprehensive overview of the state of the art on distributed data aggregation. Moreover, by carefully highlighting the strength and limitations of the more pertinent approaches, this study can provide a useful assistance to help readers choose which technique to apply in specific settings.

    Currently, there is no ideal general solution to the distributed computation of an aggregation function, all existing techniques have its pitfalls (some more than others). Therefore, more research in this field will be expected in the next few years. In particular, due to the added value of computing complex aggregates, new algorithms might arise to estimate the statistical distribution of values, as the few existing approaches exhibit some limitations in terms of accuracy and resource consumption. Additional research efforts should be made to improve the support to churn, message loss, and continuous estimation of mutable input values."

    statistics reviews distributed-processing communication coordination nudge-targets

  • [0911.3482] Complexity of Networks (reprise)

    "Network or graph structures are ubiquitous in the study of complex systems. Often, we are interested in complexity trends of these system as it evolves under some dynamic. An example might be looking at the complexity of a food web as species enter an ecosystem via migration or speciation, and leave via extinction.

    In a previous paper, a complexity measure of networks was proposed based on the {em complexity is information content} paradigm. To apply this paradigm to any object, one must fix two things: a representation language, in which strings of symbols from some alphabet describe, or stand for the objects being considered; and a means of determining when two such descriptions refer to the same object. With these two things set, the information content of an object can be computed in principle from the number of equivalent descriptions describing a particular object.

    The previously proposed representation language had the deficiency that the fully connected and empty networks were the most complex for a given number of nodes. A variation of this measure, called zcomplexity, applied a compression algorithm to the resulting bitstring representation, to solve this problem. Unfortunately, zcomplexity proved too computationally expensive to be practical.
    In this paper, I propose a new representation language that encodes the number of links along with the number of nodes and a representation of the linklist. This, like zcomplexity, exhibits minimal complexity for fully connected and empty networks, but is as tractable as the original measure."

    network-theory complexology complex-systems measurement perform structure-function-relations discrete-mathematics

  • [1108.4279] Detection and emergence

    "Two different conceptions of emergence are reconciled as two instances of the phenomenon of detection. In the process of comparing these two conceptions, we find that the notions of complexity and detection allow us to form a unified definition of emergence that clearly delineates the role of the observer."

    complexology emergence pragmatism-it-ain't but-soon

  • [1001.4278] Weight Optimization for Distributed Average Consensus Algorithm in Symmetric, CCS & KCS Star Networks

    "This paper addresses weight optimization problem in distributed consensus averaging algorithm over networks with symmetric star topology. We have determined optimal weights and convergence rate of the network in terms of its topological parameters. In addition, two alternative topologies with more rapid convergence rates have been introduced. The new topologies are Complete-Cored Symmetric (CCS) star and K-Cored Symmetric (KCS) star topologies. It has been shown that the optimal weights for the edges of central part in symmetric and CCS star configurations are independent of their branches. By simulation optimality of obtained weights under quantization constraints have been verified."

    operations-research decision-making network-theory nudge-targets

  • [1109.5389] Water drives peptide conformational transitions

    "Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that water is the main driving force of the conformational changes."

    molecular-design systems-biology simulation intracellular-dynamics kinda-knew-this-a-long-time-ago biochemistry

  • [1105.1445] Vehicular traffic flow at an intersection with the possibility of turning

    "We have developed a Nagel-Schreckenberg cellular automata model for describing of vehicular traffic flow at a single intersection. A set of traffic lights operating in fixed-time scheme controls the traffic flow. Open boundary condition is applied to the streets each of which conduct a uni-directional flow. Streets are single-lane and cars can turn upon reaching to the intersection with prescribed probabilities. Extensive Monte Carlo simulations are carried out to find the model flow characteristics. In particular, we investigate the flows dependence on the signalisation parameters, turning probabilities and input rates. It is shown that for each set of parameters, there exist a plateau region inside which the total outflow from the intersection remains almost constant. We also compute total waiting time of vehicles per cycle behind red lights for various control parameters."

    cellular-automata complexology traffic-models agent-based simulation nudge-substrates

  • [1110.1391] A Comparison of Different Machine Transliteration Models

    "Machine transliteration is a method for automatically converting words in one language into phonetically equivalent ones in another language. Machine transliteration plays an important role in natural language applications such as information retrieval and machine translation, especially for handling proper nouns and technical terms. Four machine transliteration models — grapheme-based transliteration model, phoneme-based transliteration model, hybrid transliteration model, and correspondence-based transliteration model — have been proposed by several researchers. To date, however, there has been little research on a framework in which multiple transliteration models can operate simultaneously. Furthermore, there has been no comparison of the four models within the same framework and using the same data. We addressed these problems by 1) modeling the four models within the same framework, 2) comparing them under the same conditions, and 3) developing a way to improve machine transliteration through this comparison. Our comparison showed that the hybrid and correspondence-based models were the most effective and that the four models can be used in a complementary manner to improve machine transliteration performance."

    natural-language-processing machine-learning review nudge-targets

  • [1108.5508] A Pattern Measure

    "In this paper we propose numerical measures for evaluating the aesthetic interest of simple patterns. The patterns consist of elements (symbols, pixels, etc.) in regular square arrays. The measures depend on two characteristics of the patterns: the number of different types of element, and the number of symmetries in their arrangement. We define two complementary composite measures L and C for the degree of pattern in a design, and compute them here for 2×2 and 6×6 arrays. The results distinguish simple from high-variation cases. We suspect that the measure L corresponds to the degree that human beings intuitively feel a design to be "interesting", so this model would aid in quantifying the visual connection of two- dimensional designs with viewers. The other composite measure C based on these numerical properties characterizes the extent of randomness of an array. Combining symbol variety with symmetry calculations allows us to employ hierarchical scaling to count the relative impact of different levels of scale. By identifying substructures we can distinguish between organized patterns and disorganized complexity. The measures described here are related to verbal descriptors derived from work by psychologists on responses to visual environments."

    cognition aesthetics experimental-psychology nudge-targets learning-by-watching

  • [1106.5264] Acquiring Correct Knowledge for Natural Language Generation

    "Natural language generation (NLG) systems are computer software systems that produce texts in English and other human languages, often from non-linguistic input data. NLG systems, like most AI systems, need substantial amounts of knowledge. However, our experience in two NLG projects suggests that it is difficult to acquire correct knowledge for NLG systems; indeed, every knowledge acquisition (KA) technique we tried had significant problems. In general terms, these problems were due to the complexity, novelty, and poorly understood nature of the tasks our systems attempted, and were worsened by the fact that people write so differently. This meant in particular that corpus-based KA approaches suffered because it was impossible to assemble a sizable corpus of high-quality consistent manually written texts in our domains; and structured expert-oriented KA techniques suffered because experts disagreed and because we could not get enough information about special and unusual cases to build robust systems. We believe that such problems are likely to affect many other NLG systems as well. In the long term, we hope that new KA techniques may emerge to help NLG system builders. In the shorter term, we believe that understanding how individual KA techniques can fail, and using a mixture of different KA techniques with different strengths and weaknesses, can help developers acquire NLG knowledge that is mostly correct."

    natural-language-processing artificial-intelligence interesting-problems high-hanging-fruit machine-learning nudge-targets

  • [1105.2423] Cytoskeleton and Cell Motility

    "The present article is an invited contribution to the Encyclopedia of Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009). It is a review of the biophysical mechanisms that underly cell motility.…"

    biophysics biology review i-used-to-do-this-stuff lovely

  • [1110.0671] Width Distributions for Convex Regular Polyhedra

    "The mean width is a measure on three-dimensional convex bodies that enjoys equal status with volume and surface area [Rota]. As the phrase suggests, it is the mean of a probability density f. We verify formulas for mean widths of the regular tetrahedron and the cube. Higher-order moments of f_tetra and f_cube have not been examined until now. Assume that each polyhedron has edges of unit length. We deduce that the mean square width of the regular tetrahedron is 1/3+(3+sqrt(3))/(3*pi) and the mean square width of the cube is 1+4/pi."

    geometry mathematical-recreations nudge-targets

  • [cs/0305036] Using Dynamic Simulation in the Development of Construction Machinery

    "As in the car industry for quite some time, dynamic simulation of complete vehicles is being practiced more and more in the development of off-road machinery. However, specific questions arise due not only to company structure and size, but especially to the type of product. Tightly coupled, non-linear subsystems of different domains make prediction and optimisation of the complete system's dynamic behaviour a challenge. Furthermore, the demand for versatile machines leads to sometimes contradictory target requirements and can turn the design process into a hunt for the least painful compromise. This can be avoided by profound system knowledge, assisted by simulation-driven product development. This paper gives an overview of joint research into this issue by Volvo Wheel Loaders and Linkoping University on that matter, lists the results of a related literature review and introduces the term "operateability". Rather than giving detailed answers, the problem space for ongoing and future research is examined and possible solutions are sketched."

    engineering-design design-automation modeling dynamical-systems manufacturing nudge-targets

Items of some interest…

Posted on by

These are my recent Pinboard.in links:

  • [1105.4335] Physical approaches to the dynamics of genetic circuits: A tutorial

    "Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have been studied for decades using the tools of statistical and nonlinear physics. The goal of this review is to show how approaches traditionally used in physics can help in reaching a systems-level understanding of living cells. To that end, we present an overview of the dynamical phenomena exhibited by genetic circuits and their functional significance. We also describe the theoretical and experimental approaches that are being used to unravel the relationship between circuit structure and function in dynamical cellular processes under the influence of noise, both at the single-cell level and in cellular populations, where intercellular coupling plays an important role."

    systems-biology biological-engineering genetic-regulatory-networks emergent-design biochemistry overview

  • [1106.0371] A Novel Image Segmentation Enhancement Technique based on Active Contour and Topological Alignments

    "Topological alignments and snakes are used in image processing, particularly in locating object boundaries. Both of them have their own advantages and limitations. To improve the overall image boundary detection system, we focused on developing a novel algorithm for image processing. The algorithm we propose to develop will based on the active contour method in conjunction with topological alignments method to enhance the image detection approach. The algorithm presents novel technique to incorporate the advantages of both Topological Alignments and snakes. Where the initial segmentation by Topological Alignments is firstly transformed into the input of the snake model and begins its evolvement to the interested object boundary. The results show that the algorithm can deal with low contrast images and shape cells, demonstrate the segmentation accuracy under weak image boundaries, which responsible for lacking accuracy in image detecting techniques. We have achieved better segmentation and boundary detecting for the image, also the ability of the system to improve the low contrast and deal with over and under segmentation."

    image-segmentation algorithms nudge-targets

  • [1106.2508] A Practical Implementation of the Bernoulli Factory

    "…While several practical uses of the method have been proposed in Monte Carlo applications, these require an implementation framework that is flexible, general and efficient. We present such a framework for functions that are either strictly linear, concave, or convex on the unit interval using a series of envelope functions defined through a cascade, and show that this method not only greatly reduces the number of input bits needed in practice compared to other currently proposed solutions for more specific problems, but can easily be coupled to more asymptotically efficient methods to allow for theoretically strong results."

    algorithms numerical-methods Monte-Carlo-simulation probability-theory nudge-targets

  • [1105.1729] Evolutionary search for novel superhard materials

    "We have developed a method for prediction of the hardest crystal structures in a given chemical system. It is based on the evolutionary algorithm USPEX and electronegativity-based hardness model that we have augmented with bond-valence model and graph theory. These extensions enable correct description of the hardness of layered, molecular and low-symmetry crystal structures. Applying this method to C and TiO2, we have (i) obtained a number of low-energy carbon structures with hardness slightly lower than diamond and (ii) proved that TiO2 in any of its possible polymorphs cannot be the hardest oxide, its hardness being below 17 GPa."

    materials-science genetic-algorithm condensed-matter simulation nudge-targets

  • [1109.0573] Phase Retrieval via Matrix Completion

    "This paper considers the fundamental problem of recovering a general signal, an image for example, from the magnitude of its Fourier transform. This problem, also known as phase retrieval, arises in many applications and has challenged engineers, physicists, and mathematicians for decades. Its origin comes from the fact that detectors can often times only record the squared modulus of the Fresnel or Fraunhofer diffraction pattern of the radiation that is scattered from an object. In such settings, one cannot measure the phase of the optical wave reaching the detector and, therefore, much information about the scattered object or the optical field is lost since, as is well known, the phase encodes a lot of the structural content of the image we wish to form."

    image-processing inverse-problems signal-processing system-identification frequency-space algorithms nudge-targets numerical-methods

  • [1109.0807] Harmonic Analysis of Boolean Networks: Determinative Power and Perturbations

    "Consider a large Boolean network with a feed forward structure. Given a probability distribution for the inputs, can one find-possibly small-collections of input nodes that determine the states of most other nodes in the network?…"

    Boolean-networks Kauffmania complexology discrete-mathematics mathematical-recreations nudge-targets

  • [0801.0830] Evolution of central pattern generators for the control of a five-link bipedal walking mechanism

    "With the aim of producing a stable human-like bipedal gait, a five-link planar walking mechanism is coupled with a central pattern generator (CPG) neural network, consisting of units based on Matsuoka's half-center oscillator model with a firm basis in neurophysiology. As a minimalistic approach to bipedal walking, this type of walking mechanism contains only four actuators, and is lacking feet and ankles. The mechanism is simulated with accurate physics, allowing realistic fitness evaluations for the creation of CPG controllers through evolutionary computation. The oscillatory parameters, internal connectivity structure, and external feedback pathways of the networks are determined through genetic algorithms (GA) optimization. The evolved CPG networks are transferred to a hardware implementation of the mechanism, to test their performance under real-world dynamics. Results confirm that the biologically inspired CPG model is very well suited for controlling legged locomotion, since a diverse manifestation of CPG networks (with and without external feedback) have been observed to succeed during the course of GA evaluations. Observations also imply that while the CPG mechanism is inherently able to sustain a stable gait, the utilization of feedback pathways makes the gait more human-like and is needed to provide a means to adapt to irregularities in the environment."

    robotics engineering-design genetic-algorithm neural-networks cybernetics nudge-targets

  • [1109.3351] Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation

    "Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the quantitative characteristics of protein-DNA interactions, no such principles are known for the cooperative interactions between DNA-binding proteins. We consider a simple theoretical model for two interacting transcription factor (TF) species, searching for and binding to two adjacent target sites hidden in the genomic background. We study the kinetic competition of a dimer search pathway and a monomer search pathway, as well as the steady-state regulation function mediated by the two TFs over a broad range of TF-TF interaction strengths. Using a transcriptional AND-logic as exemplary functional context, we identify the functionally desirable regime for the interaction. We find that both weak and very strong TF-TF interactions are favorable, albeit with different characteristics. However, there is also an unfavorable regime of intermediate interactions where the genetic response is prohibitively slow."

    biological-engineering genetic-regularory-networks systems-biology emergent-design nudge-targets

  • [1109.6874] #h00t: Censorship Resistant Microblogging

    "Microblogging services such as Twitter are an increasingly important way to communicate, both for individuals and for groups through the use of hashtags that denote topics of conversation. However, groups can be easily blocked from communicating through blocking of posts with the given hashtags. We propose #h00t, a system for censorship resistant microblogging. #h00t presents an interface that is much like Twitter, except that hashtags are replaced with very short hashes (e.g., 24 bits) of the group identifier. Naturally, with such short hashes, hashtags from different groups may collide and #h00t users will actually seek to create collisions. By encrypting all posts with keys derived from the group identifiers, #h00t client software can filter out other groups' posts while making such filtering difficult for the adversary. In essence, by leveraging collisions, groups can tunnel their posts in other groups' posts. A censor could not block a given group without also blocking the other groups with colliding hashtags. We evaluate the feasibility of #h00t through traces collected from Twitter, showing that a single modern computer has enough computational throughput to encrypt every tweet sent through Twitter in real time. We also use these traces to analyze the bandwidth and anonymity tradeoffs that would come with different variations on how group identifiers are encoded and hashtags are selected to purposefully collide with one another."

    social-media steganography robustness activism cute

  • [1107.0414] A random walk on image patches

    "In this paper we address the problem of understanding the success of algorithms that organize patches according to graph-based metrics. Algorithms that analyze patches extracted from images or time series have led to state-of-the art techniques for classification, denoising, and the study of nonlinear dynamics. The main contribution of this work is to provide a theoretical explanation for the above experimental observations. Our approach relies on a detailed analysis of the commute time metric on prototypical graph models that epitomize the geometry observed in general patch graphs.…"

    image-segmentation image-analysis algorithms combinatorics nudge-targets

  • [1107.0385] An algorithm for autonomously plotting solution sets in the presence of turning points

    "Plotting solution sets for particular equations may be complicated by the existence of turning points. Here we describe an algorithm which not only overcomes such problematic points, but does so in the most general of settings. Applications of the algorithm are highlighted through two examples: the first provides verification, while the second demonstrates a non-trivial application. The latter is followed by a thorough run-time analysis. While both examples deal with bivariate equations, it is discussed how the algorithm may be generalized for space curves in $R^{3}$."

    visualization mathematics graphics approximation algorithms nudge-targets

  • [1105.1033] Adaptively Learning the Crowd Kernel

    "We introduce an algorithm that, given n objects, learns a similarity matrix over all n^2 pairs, from crowdsourced data alone. The algorithm samples responses to adaptively chosen triplet-based relative-similarity queries. Each query has the form "is object 'a' more similar to 'b' or to 'c'?" and is chosen to be maximally informative given the preceding responses. The output is an embedding of the objects into Euclidean space (like MDS); we refer to this as the "crowd kernel." SVMs reveal that the crowd kernel captures prominent and subtle features across a number of domains, such as "is striped" among neckties and "vowel vs. consonant" among letters."

    classification ontology-discovery crowdsourcing feature-extraction algorithms nudge-targets performance-space-analysis

  • [1109.1030] An Algorithm for Detecting Intrinsically Knotted Graphs

    "We describe an algorithm that recognizes some (perhaps all) intrinsically knotted (IK) graphs, and can help find knotless embeddings for graphs that are not IK. The algorithm, implemented as a Mathematica program, has already been used by Goldberg, Mattman, and Naimi [6] to greatly expand the list of known minor minimal IK graphs, and to find knotless embeddings for some graphs that had previously resisted attempts to classify them as IK or non-IK."

    combinatorics topology algorithms nudge-targets

  • [1109.5635] Approximating Edit Distance in Near-Linear Time

    "We show how to compute the edit distance between two strings of length n up to a factor of 2^{~O(sqrt(log n))} in n^(1+o(1)) time. This is the first sub-polynomial approximation algorithm for this problem that runs in near-linear time, improving on the state-of-the-art n^(1/3+o(1)) approximation. Previously, approximation of 2^{~O(sqrt(log n))} was known only for embedding edit distance into l_1, and it is not known if that embedding can be computed in less than quadratic time."

    algorithms string-editing Levenshtein-distance rewriting-systems bioinformatics nudge-targets

  • [1107.1866] Priority-based task reassignments in hierarchical 2D mesh-connected systems using tableaux

    "Task reassignments in 2D mesh-connected systems (2D-MSs) have been researched and simulated for several decades. We propose a hierarchical 2D mesh-connected system (2D-HMS) in order to exploit the regular nature of a 2D-MS. In our approach priority-based task assignments and reassignments in a 2D-HMS are represented by tableaux and their algorithms. We provide examples of priority-based task reassignments in a 2D-HMS in which task relocations are simply reduced to a jeu de taquin slide."

    scheduling operations-research algorithms grid-computing optimization nudge-targets

  • [1101.4744] Clustering functional data using wavelets

    "We present two methods for detecting patterns and clusters in high dimensional time-dependent functional data. Our methods are based on wavelet-based similarity measures, since wavelets are well suited for identifying highly discriminant local time and scale features. The multiresolution aspect of the wavelet transform provides a time-scale decomposition of the signals allowing to visualize and to cluster the functional data into homogeneous groups. For each input function, through its empirical orthogonal wavelet transform the first method uses the distribution of energy across scales generate a handy number of features that can be sufficient to still make the signals well distinguishable. Our new similarity measure combined with an efficient feature selection technique in the wavelet domain is then used within more or less classical clustering algorithms to effectively differentiate among high dimensional populations. The second method uses dissimilarity measures between the whole time-scale representations and are based on wavelet-coherence tools. The clustering is then performed using a k-centroid algorithm starting from these dissimilarities. Practical performance of these methods that jointly designs both the feature selection in the wavelet domain and the classification distance is demonstrated through simulations as well as daily profiles of the French electricity power demand."

    classification time-series feature-extraction machine-learning multiobjective-optimization ontology-discovery wavelets nudge-targets

  • [1105.3726] Controlling Complex Networks with Compensatory Perturbations

    "The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can affect other nodes, in a process that may cause the entire or substantial part of the system to change behavior and possibly collapse. Recent research in metabolic and food-web networks has demonstrated the concept that network damage caused by external perturbations can often be mitigated or reversed by the application of compensatory perturbations. Compensatory perturbations are constrained to be physically admissible and amenable to implementation on the network. However, the systematic identification of compensatory perturbations that conform to these constraints remains an open problem. Here, we present a method to construct compensatory perturbations that can control the fate of general networks under such constraints. Our approach accounts for the full nonlinear behavior of real complex networks and can bring the system to a desirable target state even when this state is not directly accessible. Applications to genetic networks show that compensatory perturbations are effective even when limited to a small fraction of all nodes in the network and that they are far more effective when limited to the highest-degree nodes. The approach is conceptually simple and computationally efficient, making it suitable for the rescue, control, and reprogramming of large complex networks in various domains."

    emergent-design complexology control biological-engineering nudge-targets

  • [1109.1275] A Formal Verification Approach to the Design of Synthetic Gene Networks

    "The design of genetic networks with specific functions is one of the major goals of synthetic biology. However, constructing biological devices that work "as required" remains challenging, while the cost of uncovering flawed designs experimentally is large. To address this issue, we propose a fully automated framework that allows the correctness of synthetic gene networks to be formally verified in silico from rich, high level functional specifications.
    Given a device, we automatically construct a mathematical model from experimental data characterizing the parts it is composed of. The specific model structure guarantees that all experimental observations are captured and allows us to construct finite abstractions through polyhedral operations. The correctness of the model with respect to temporal logic specifications can then be verified automatically using methods inspired by model checking.
    Overall, our procedure is conservative but it can filter through a large number of potential device designs and select few that satisfy the specification to be implemented and tested further experimentally. Illustrative examples of the application of our methods to the design of simple synthetic gene networks are included."

    genetic-regulatory-networks bioinformatics biological-engineering design-automation emergent-design acceptance-testing performance-measure nudge

  • [1108.1150] Epistasis can lead to fragmented neutral spaces and contingency in evolution

    "Under neutral reciprocal sign epistasis, two genetic changes are jointly neutral, even though their individual effects are deleterious. By using the widely studied mapping from an RNA sequence to secondary structure, we investigate the effect of this kind of epistasis on neutral spaces corresponding to networks of genotypes that fold to the same secondary structure. Neutral networks for RNA structures with n bonds are typically fragmented into at least 2^n different neutral components that cannot be connected by single point mutations. By exhaustive enumeration of all RNA secondary structures of sequences of length 15 we show that most networks are not dominated by one neutral component, but are rather broken up into multiple large components. Although they generate the same phenotype, components of a single neutral network are heterogeneous, showing wide variations in their robustness and their evolvability. Both properties are correlated with component size, rather than with the size of their underlying neutral network. In particular, sets of accessible phenotypes can vary quite strongly between components. Thus, the potential for future innovation is contingent on which neutral component a population occupies. We further argue that neutral reciprocal sign epistasis may have similar consequences for neutral evolution of other biological systems as well."

    combinatorics RNA neutral-networks complexology bioinformatics polymer-models mathematical-recreations nudge-targets

  • OldFonts.com | About Us

    "Willson founded 3IP in 1989 to self-publish a book of pretentious nature essays. Soon after, he found himself tinkering with type design, and 3IP has since become known for its library of authentic-looking handwriting fonts—many of them modeled after historical penmanship—and antique text simulations."

    typography fonts handwriting

  • Collective Wisdom — Crooked Timber

    "More broadly, a simple dictum such as ‘listen to the experts’ isn’t going to work, precisely because our most powerful methods of generating new knowledge (viz. the sciences) are not so much based on listening to individual experts, as on including these experts (and many others) in broader social systems which expose them continually to the ideas of others and vice-versa. Designing (or – perhaps better- nurturing) such systems is hard to think about and hard to do – but it has to be the way forward."

    via:arsyed wisdom-of-crowds complexology innovation cultural-assumptions credentialing problem-solving what-is-true-is-what-gets-said

  • [1109.1146] A Distributed Mincut/Maxflow Algorithm Combining Path Augmentation and Push-Relabel

    "We develop a novel distributed algorithm for the minimum cut problem. We primarily aim at solving large sparse problems. Assuming vertices of the graph are partitioned into several regions, the algorithm performs path augmentations inside the regions and updates of the push-relabel style between the regions. The interaction between regions is considered expensive (regions are loaded into the memory one-by-one or located on separate machines in a network). The algorithm works in sweeps – passes over all regions. Let $B$ be the set of vertices incident to inter-region edges of the graph. We present a sequential and parallel versions of the algorithm which terminate in at most $2|B|^2+1$ sweeps. The competing algorithm by Delong and Boykov uses push-relabel updates inside regions. In the case of a fixed partition we prove that this algorithm has a tight $O(n^2)$ bound on the number of sweeps, where $n$ is the number of vertices. We tested sequential versions of the algorithms on instances of maxflow problems in computer vision. Experimentally, the number of sweeps required by the new algorithm is much lower than for the Delong and Boykov's variant. Large problems (up to $10^8$ vertices and $6cdot 10^8$ edges) are solved using under 1GB of memory in about 10 sweeps."

    algorithms operations-research nudge-targets

  • [1105.4953] A fast nearest neighbor search algorithm based on vector quantization

    "In this article, we propose a new fast nearest neighbor search algorithm, based on vector quantization. Like many other branch and bound search algorithms [1,10], a preprocessing recursively partitions the data set into disjointed subsets until the number of points in each part is small enough. In doing so, a search-tree data structure is built. This preliminary recursive data-set partition is based on the vector quantization of the empirical distribution of the initial data-set. Unlike previously cited methods, this kind of partitions does not a priori allow to eliminate several brother nodes in the search tree with a single test. To overcome this difficulty, we propose an algorithm to reduce the number of tested brother nodes to a minimal list that we call "friend Voronoi cells". The complete description of the method requires a deeper insight into the properties of Delaunay triangulations and Voronoi diagrams"

    algorithms search-algorithms data-analysis nudge-targets

  • [1108.0986] A proximal point algorithm for sequential feature extraction applications

    "We propose a proximal point algorithm to solve LAROS problem, that is the problem of finding a "large approximately rank-one submatrix". This LAROS problem is used to sequentially extract features in data. We also develop a new stopping criterion for the proximal point algorithm, which is based on the duality conditions of eps-optimal solutions of the LAROS problem, with a theoretical guarantee. We test our algorithm with two image databases and show that we can use the LAROS problem to extract appropriate common features from these images."

    algorithms image-segmentation feature-extraction nudge-targets

  • [1011.2348] Ergodic Control and Polyhedral approaches to PageRank Optimization

    "We study a general class of PageRank optimization problems which consist in finding an optimal outlink strategy for a web site subject to design constraints. We consider both a continuous problem, in which one can choose the intensity of a link, and a discrete one, in which in each page, there are obligatory links, facultative links and forbidden links. We show that the continuous problem, as well as its discrete variant when there are no constraints coupling different pages, can both be modeled by constrained Markov decision processes with ergodic reward, in which the webmaster determines the transition probabilities of websurfers. Although the number of actions turns out to be exponential, we show that an associated polytope of transition measures has a concise representation, from which we deduce that the continuous problem is solvable in polynomial time, and that the same is true for the discrete problem when there are no coupling constraints. We also provide efficient algorithms, adapted to very large networks. Then, we investigate the qualitative features of optimal outlink strategies, and identify in particular assumptions under which there exists a "master" page to which all controlled pages should point. We report numerical results on fragments of the real web graph."

    optimization PageRank operations-research algorithms nudge-targets