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Finding motifs in biological, social, technological, and other types of networks has become a widespread method to gain more knowledge about these networks’ structure and function. However, this task is very computationally demanding, because it is highly associated with the graph isomorphism which is an NP problem (not known to belong to P or NP-complete subsets yet). Accordingly, this research is endeavoring to decrease the need to call NAUTY isomorphism detection method, which is the most time-consuming step in many existing algorithms. The work provides an extremely fast motif detection algorithm called QuateXelero, which has a Quaternary Tree data structure in the heart. The proposed algorithm is based on the well-known ESU (FANMOD) motif detection algorithm. The results of experiments on some standard model networks approve the overal superiority of the proposed algorithm, namely QuateXelero, compared with two of the fastest existing algorithms, G-Tries and Kavosh. QuateXelero is especially fastest in constructing the central data structure of the algorithm from scratch based on the input network.
This article shows that there exist two particular linear orders such that first-order logic with these two linear orders has the same expressive power as first-order logic with the Bit-predicate FO(Bit). As a corollary we obtain that there also exists a built-in permutation such that first-order logic with a linear order and this permutation is as expressive as FO(Bit).
Succinctness is a natural measure for comparing the strength of different logics. Intuitively, a logic L_1 is more succinct than another logic L_2 if all properties that can be expressed in L_2 can be expressed in L_1 by formulas of (approximately) the same size, but some properties can be expressed in L_1 by (significantly) smaller formulas.
We study the succinctness of logics on linear orders. Our first theorem is concerned with the finite variable fragments of first-order logic. We prove that:
(i) Up to a polynomial factor, the 2- and the 3-variable fragments of first-order logic on linear orders have the same succinctness. (ii) The 4-variable fragment is exponentially more succinct than the 3-variable fragment. Our second main result compares the succinctness of first-order logic on linear orders with that of monadic second-order logic. We prove that the fragment of monadic second-order logic that has the same expressiveness as first-order logic on linear orders is non-elementarily more succinct than first-order logic.
Effect sizes in experimental pain produced by gender, genetic variants and sensitization procedures
(2011)
Background: Various effects on pain have been reported with respect to their statistical significance, but a standardized measure of effect size has been rarely added. Such a measure would ease comparison of the magnitude of the effects across studies, for example the effect of gender on heat pain with the effect of a genetic variant on pressure pain. Methodology/Principal Findings: Effect sizes on pain thresholds to stimuli consisting of heat, cold, blunt pressure, punctuate pressure and electrical current, administered to 125 subjects, were analyzed for 29 common variants in eight human genes reportedly modulating pain, gender and sensitization procedures using capsaicin or menthol. The genotype explained 0–5.9% of the total interindividual variance in pain thresholds to various stimuli and produced mainly small effects (Cohen's d 0–1.8). The largest effect had the TRPA1 rs13255063T/rs11988795G haplotype explaining >5% of the variance in electrical pain thresholds and conferring lower pain sensitivity to homozygous carriers. Gender produced larger effect sizes than most variant alleles (1–14.8% explained variance, Cohen's d 0.2–0.8), with higher pain sensitivity in women than in men. Sensitization by capsaicin or menthol explained up to 63% of the total variance (4.7–62.8%) and produced largest effects according to Cohen's d (0.4–2.6), especially heat sensitization by capsaicin (Cohen's d = 2.6). Conclusions: Sensitization, gender and genetic variants produce effects on pain in the mentioned order of effect sizes. The present report may provide a basis for comparative discussions of factors influencing pain.
In dyadic communication, both interlocutors adapt to each other linguistically, that is, they align interpersonally. In this article, we develop a framework for modeling interpersonal alignment in terms of the structural similarity of the interlocutors’ dialog lexica. This is done by means of so-called two-layer time-aligned network series, that is, a time-adjusted graph model. The graph model is partitioned into two layers, so that the interlocutors’ lexica are captured as subgraphs of an encompassing dialog graph. Each constituent network of the series is updated utterance-wise. Thus, both the inherent bipartition of dyadic conversations and their gradual development are modeled. The notion of alignment is then operationalized within a quantitative model of structure formation based on the mutual information of the subgraphs that represent the interlocutor’s dialog lexica. By adapting and further developing several models of complex network theory, we show that dialog lexica evolve as a novel class of graphs that have not been considered before in the area of complex (linguistic) networks. Additionally, we show that our framework allows for classifying dialogs according to their alignment status. To the best of our knowledge, this is the first approach to measuring alignment in communication that explores the similarities of graph-like cognitive representations. Keywords: alignment in communication; structural coupling; linguistic networks; graph distance measures; mutual information of graphs; quantitative network analysis
Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. To truly appreciate the myriad of events which relate synaptic function and vesicle dynamics, simulations should be done in a spatially realistic environment. This holds true in particular in order to explain the rather astonishing motor patterns presented here which we observed within in vivo recordings which underlie peristaltic contractions at a well characterized synapse, the neuromuscular junction (NMJ) of the Drosophila larva. To this end, we have employed a reductionist approach and generated three dimensional models of single presynaptic boutons at the Drosophila larval NMJ. Vesicle dynamics are described by diffusion-like partial differential equations which are solved numerically on unstructured grids using the uG platform. In our model we varied parameters such as bouton-size, vesicle output probability (Po), stimulation frequency and number of synapses, to observe how altering these parameters effected bouton function. Hence we demonstrate that the morphologic and physiologic specialization maybe a convergent evolutionary adaptation to regulate the trade off between sustained, low output, and short term, high output, synaptic signals. There seems to be a biologically meaningful explanation for the co-existence of the two different bouton types as previously observed at the NMJ (characterized especially by the relation between size and Po),the assigning of two different tasks with respect to short- and long-time behaviour could allow for an optimized interplay of different synapse types. As a side product, we demonstrate how advanced methods from numerical mathematics could help in future to resolve also other difficult experimental neurobiological issues.
Since the description of sepsis by Schottmüller in 1914, the amount on knowledge available on sepsis and its underlying pathophysiology has substantially increased. Epidemiologic examinations of abdominal septic shock patients show the potential for high risk posed by and the extensive therapy situation in the intensive care unit (ICU) (5). Unfortunately, until now it has not been possible to significantly reduce the mortality rate of septic shock, which is as high as 50-60% worldwide, although PROWESS' results (1) are encouraging. This paper summarizes the main results of the MEDAN project and their medical impacts. Several aspects are already published, see the references. The heterogeneity of patient groups and the variations in therapy strategies is seen as one of the main problems for sepsis trials. In the MEDAN multi-center study of 71 intensive care units in Germany, a group of 382 patients made up exclusively of abdominal septic shock patients who met the consensus criteria for septic shock (3) was analysed. For use within scores or stand-alone experiments variables are often studied as isolated variables, not as a multidimensional whole, e.g. a recent study takes a look at the role thrombocytes play (15). To avoid this limitation, our study compares several established scores (SOFA, APACHE II, SAPS II, MODS) by a multi-dimensional neuronal network analysis. For outcome prediction the data of 382 patients was analysed by using most of the commonly documented vital parameters and doses of medicine (metric variables). Data was collected in German hospitals from 1998 to 2001. The 382 handwritten patient records were transferred to an electronic database giving the amount of 2.5 million data entries. The metric data contained in the database is composed of daily measurements and doses of medicine. We used range and plausibility checks to allow no faulty data in the electronic database. 187 of the 382 patients are deceased (49 %).
Attraction and commercial success of web sites depend heavily on the additional values visitors may find. Here, individual, automatically obtained and maintained user profiles are the key for user satisfaction. This contribution shows for the example of a cooking information site how user profiles might be obtained using category information provided by cooking recipes. It is shown that metrical distance functions and standard clustering procedures lead to erroneous results. Instead, we propose a new mutual information based clustering approach and outline its implications for the example of user profiling.
Data driven automatic model selection and parameter adaptation – a case study for septic shock
(2004)
In bioinformatics, biochemical pathways can be modeled by many differential equations. It is still an open problem how to fit the huge amount of parameters of the equations to the available data. Here, the approach of systematically learning the parameters is necessary. This paper propose as model selection criterion the least complex description of the observed data by the model, the minimum description length. For the small, but important example of inflammation modeling the performance of the approach is evaluated.
In bioinformatics, biochemical signal pathways can be modeled by many differential equations. It is still an open problem how to fit the huge amount of parameters of the equations to the available data. Here, the approach of systematically obtaining the most appropriate model and learning its parameters is extremely interesting. One of the most often used approaches for model selection is to choose the least complex model which “fits the needs”. For noisy measurements, the model which has the smallest mean squared error of the observed data results in a model which fits too accurately to the data – it is overfitting. Such a model will perform good on the training data, but worse on unknown data. This paper propose as model selection criterion the least complex description of the observed data by the model, the minimum description length. For the small, but important example of inflammation modeling the performance of the approach is evaluated. Keywords: biochemical pathways, differential equations, septic shock, parameter estimation, overfitting, minimum description length.
In bioinformatics, biochemical pathways can be modeled by many differential equations. It is still an open problem how to fit the huge amount of parameters of the equations to the available data. Here, the approach of systematically learning the parameters is necessary. In this paper, for the small, important example of inflammation modeling a network is constructed and different learning algorithms are proposed. It turned out that due to the nonlinear dynamics evolutionary approaches are necessary to fit the parameters for sparse, given data. Proceedings of the 15th IEEE International Conference on Tools with Artificial Intelligence - ICTAI 2003
In bioinformatics, biochemical pathways can be modeled by many differential equations. It is still an open problem how to fit the huge amount of parameters of the equations to the available data. Here, the approach of systematically learning the parameters is necessary. In this paper, for the small, important example of inflammation modeling a network is constructed and different learning algorithms are proposed. It turned out that due to the nonlinear dynamics evolutionary approaches are necessary to fit the parameters for sparse, given data. Keywords: model parameter adaption, septic shock. coupled differential equations, genetic algorithm.
In contrast to the symbolic approach, neural networks seldom are designed to explain what they have learned. This is a major obstacle for its use in everyday life. With the appearance of neuro-fuzzy systems which use vague, human-like categories the situation has changed. Based on the well-known mechanisms of learning for RBF networks, a special neuro-fuzzy interface is proposed in this paper. It is especially useful in medical applications, using the notation and habits of physicians and other medically trained people. As an example, a liver disease diagnosis system is presented.
The prevention of credit card fraud is an important application for prediction techniques. One major obstacle for using neural network training techniques is the high necessary diagnostic quality: Since only one financial transaction of a thousand is invalid no prediction success less than 99.9% is acceptable. Due to these credit card transaction proportions complete new concepts had to be developed and tested on real credit card data. This paper shows how advanced data mining techniques and neural network algorithm can be combined successfully to obtain a high fraud coverage combined with a low false alarm rate.
This paper describes the use of a Radial Basis Function (RBF) neural network in the approximation of process parameters for the extrusion of a rubber profile in tyre production. After introducing the rubber industry problem, the RBF network model and the RBF net learning algorithm are developed, which uses a growing number of RBF units to compensate the approximation error up to the desired error limit. Its performance is shown for simple analytic examples. Then the paper describes the modelling of the industrial problem. Simulations show good results, even when using only a few training samples. The paper is concluded by a discussion of possible systematic error influences, improvements and potential generalisation benefits. Keywords: Adaptive process control; Parameter estimation; RBF-nets; Rubber extrusion
In this paper we regard first the situation where parallel channels are disturbed by noise. With the goal of maximal information conservation we deduce the conditions for a transform which "immunizes" the channels against noise influence before the signals are used in later operations. It shows up that the signals have to be decorrelated and normalized by the filter which corresponds for the case of one channel to the classical result of Shannon. Additional simulations for image encoding and decoding show that this constitutes an efficient approach for noise suppression. Furthermore, by a corresponding objective function we deduce the stochastic and deterministic learning rules for a neural network that implements the data orthonormalization. In comparison with other already existing normalization networks our network shows approximately the same in the stochastic case but, by its generic deduction ensures the convergence and enables the use as independent building block in other contexts, e.g. whitening for independent component analysis. Keywords: information conservation, whitening filter, data orthonormalization network, image encoding, noise suppression.
This paper describes the use of a radial basis function (RBF) neural network. It approximates the process parameters for the extrusion of a rubber profile used in tyre production. After introducing the problem, we describe the RBF net algorithm and the modeling of the industrial problem. The algorithm shows good results even using only a few training samples. It turns out that the „curse of dimensions“ plays an important role in the model. The paper concludes by a discussion of possible systematic error influences and improvements.
The paper focuses on the division of the sensor field into subsets of sensor events and proposes the linear transformation with the smallest achievable error for reproduction: the transform coding approach using the principal component analysis (PCA). For the implementation of the PCA, this paper introduces a new symmetrical, lateral inhibited neural network model, proposes an objective function for it and deduces the corresponding learning rules. The necessary conditions for the learning rate and the inhibition parameter for balancing the crosscorrelations vs. the autocorrelations are computed. The simulation reveals that an increasing inhibition can speed up the convergence process in the beginning slightly. In the remaining paper, the application of the network in picture encoding is discussed. Here, the use of non-completely connected networks for the self-organized formation of templates in cellular neural networks is shown. It turns out that the self-organizing Kohonen map is just the non-linear, first order approximation of a general self-organizing scheme. Hereby, the classical transform picture coding is changed to a parallel, local model of linear transformation by locally changing sets of self-organized eigenvector projections with overlapping input receptive fields. This approach favors an effective, cheap implementation of sensor encoding directly on the sensor chip. Keywords: Transform coding, Principal component analysis, Lateral inhibited network, Cellular neural network, Kohonen map, Self-organized eigenvector jets.
After a short introduction into traditional image transform coding, multirate systems and multiscale signal coding the paper focuses on the subject of image encoding by a neural network. Taking also noise into account a network model is proposed which not only learns the optimal localized basis functions for the transform but also learns to implement a whitening filter by multi-resolution encoding. A simulation showing the multi-resolution capabilitys concludes the contribution.