Papers by Pedro Miramontes
The paper "Critical Truths About Power Laws" (Science, 335, pp665-666) by MPH Stumpf MP... more The paper "Critical Truths About Power Laws" (Science, 335, pp665-666) by MPH Stumpf MPH and MA Porter is commented
Royal Society Open Science, 2014
Predator-prey relationships are one of the most studied interactions in population ecology. Howev... more Predator-prey relationships are one of the most studied interactions in population ecology. However, little attention has been paid to the possibility of role exchange between species, despite firm field evidence of such phenomena in nature. In this paper, we build a mathematical model capable of reproducing the main phenomenological features of role reversal in a classical system and present results for both the temporal and spatio-temporal cases. We show that, depending on the choice of parameters, our role-reversal dynamical system exhibits excitable-like behaviour, generating waves of species' concentrations that propagate through space. Our findings fill a long-standing gap in modelling ecological interactions and can be applicable to better understanding ecological niche shifts and planning of sustainable ecosystems.
Lecture Notes in Computer Science, 2006
In the traditional self-organizing map (SOM) the best matching unit (BMU) affects other neurons, ... more In the traditional self-organizing map (SOM) the best matching unit (BMU) affects other neurons, through the learning rule, as a function of distance. Here, we propose a new parameter in the learning rule so neurons are not only affected by BMU as a function of distance, but as a function of the frequency of activation from both, the BMU and
Lecture Notes in Computer Science, 2005
Self-organizing maps (SOM) have been obtained mainly on regular lattices, embedded in euclidean o... more Self-organizing maps (SOM) have been obtained mainly on regular lattices, embedded in euclidean or non-euclidean spaces [1]. We present preliminar results that show SOM can be formed on non-regular lattices by giving evidence that topographic error (TE) is influenced by a few statistical parameters of the neuron lattice, such as the characteristic path length (L), the cluster coefficient (C) and
Lecture Notes in Computer Science, 2005
There are three domains in living nature: archaea, bacteria and eukarya. It has been shown, troug... more There are three domains in living nature: archaea, bacteria and eukarya. It has been shown, trough a number of multivariate tools, that codon usage, a 64 dimensional vector that stablishes how often a given organism makes use of each codon, is related to domain. Another method is proposed here based in rule and tree induction from codon usage of several
Computational Biology and Chemistry, 2014
Markov model Second largest eigenvalue Hexamer Periodicity of 10-11 bases Heterogeneity Codon pos... more Markov model Second largest eigenvalue Hexamer Periodicity of 10-11 bases Heterogeneity Codon positions a
Genome Research, 2000
Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive... more Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif
Rivista di biologia
We present a theoretical framework for biological evolution with the intention of giving precise ... more We present a theoretical framework for biological evolution with the intention of giving precise mathematical definitions of some concepts in evolutionary biology such as fitness, evolutionary pressure, specialization and natural selection. In this framework, such concepts are identified with well-known mathematical terms within the theory of dynamical systems. We also discuss some more general implications in evolution; for instance, the fact that our model naturally exhibits a frequency spectrum of the type 1/f for low frequencies of evolutionary events.
Page 1. Revista Mexicana de Fisica 43, No. 3 (1997) 421-428 Approximations to the configurational... more Page 1. Revista Mexicana de Fisica 43, No. 3 (1997) 421-428 Approximations to the configurational energy of dipolar particles on a 2D lattice HUMIlERTO ARCE, ALEJANDRO LÓPEZ, ANO VICENTA SÁNCHEZ Departamento ...
ABSTRACT Decreasing neighborhood with distance has been identified as one of a few conditions to ... more ABSTRACT Decreasing neighborhood with distance has been identified as one of a few conditions to achieve final states in the self-organizing map (SOM) that resemble the distribution of high-dimensional input data. In the classic SOM model, best matching units (BMU) decrease their influence area as a function of distance. We introduce a modification to the SOM algorithm in which neighborhood is contemplated from the point of view of affected units, not from the view of BMUs. In our proposal, neighborhood for BMUs is not reduced, instead the rest of the units exclude some BMUs from affecting them. Each neuron identifies, from the set of BMUs that influenced it in previous epochs, those to whom it becomes refractory to for the rest of the process. Despite that the condition of decreasing neighborhood over distance is not maintained, self-organization still persists, as shown by several experiments. The maps achieved by the proposed modification have, in many cases, a lower error measure than the maps formed by SOM. Also, the model is able to remove discontinuities (kinks) from the map in a very small number of epochs, which contrasts with the original SOM model.
Abstract and Applied Analysis, 2015
We formulate a susceptible-vaccinated-infected-recovered (SVIR) model by incorporating the vaccin... more We formulate a susceptible-vaccinated-infected-recovered (SVIR) model by incorporating the vaccination of newborns, vaccineage, and mortality induced by the disease into the SIR epidemic model. It is assumed that the period of immunity induced by vaccines varies depending on the vaccine-age. Using the direct Lyapunov method with Volterra-type Lyapunov function, we show the global asymptotic stability of the infection-free and endemic steady states.
International Journal of Genomics, 2013
Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-stand... more Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequencebased nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.
PLoS ONE, 2009
Searching for generic behaviors has been one of the driving forces leading to a deep understandin... more Searching for generic behaviors has been one of the driving forces leading to a deep understanding and classification of diverse phenomena. Usually a starting point is the development of a phenomenology based on observations. Such is the case for power law distributions encountered in a wealth of situations coming from physics, geophysics, biology, lexicography as well as social and financial networks. This finding is however restricted to a range of values outside of which finite size corrections are often invoked. Here we uncover a universal behavior of the way in which elements of a system are distributed according to their rank with respect to a given property, valid for the full range of values, regardless of whether or not a power law has previously been suggested. We propose a two parameter functional form for these rank-ordered distributions that gives excellent fits to an impressive amount of very diverse phenomena, coming from the arts, social and natural sciences. It is a discrete version of a generalized beta distribution, given by f(r) = A(N+1-r) b /r a , where r is the rank, N its maximum value, A the normalization constant and (a, b) two fitting exponents. Prompted by our genetic sequence observations we present a growth probabilistic model incorporating mutation-duplication features that generates data complying with this distribution. The competition between permanence and change appears to be a relevant, though not necessary feature. Additionally, our observations mainly of social phenomena suggest that a multifactorial quality resulting from the convergence of several heterogeneous underlying processes is an important feature. We also explore the significance of the distribution parameters and their classifying potential. The ubiquity of our findings suggests that there must be a fundamental underlying explanation, most probably of a statistical nature, such as an appropriate central limit theorem formulation.
2008 Seventh Mexican International Conference on Artificial Intelligence, 2008
Learning how to count in different bases has been seen as a trivial task in almost all introducto... more Learning how to count in different bases has been seen as a trivial task in almost all introductory mathematics courses. However, the low performance shown by many students, while performing this task, is appalling. This situation has motivated serious research in this matter. In order to study a model of count learning, we analyze the performance of a multilayer perceptron
Uploads
Papers by Pedro Miramontes