arXiv subjects

Jose F. Fontanari

Publications and source records attributed to Jose F. Fontanari.

17 recordsLinked to original sources

arXiv2014

Effect of migration in a diffusion model for template coexistence in protocells

The compartmentalization of distinct templates in protocells and the exchange of templates between them (migration) are key elements of a modern scenario for prebiotic evolution. Here we use the diffusion approximation of population genetics to study analytically the steady-state properties of such prebiotic scenario. The coexistence of distinct template types inside a protocell is achieved by a selective pressure at the protocell level (group selection) favoring protocells with a mixed template composition. In the degenerate case, where the templates have the same replication rate, we find that a vanishingly small migration rate suffices to eliminate the segregation effect of random drift and so to promote coexistence. In the non-degenerate case, a small migration rate greatly boosts coexistence as compared with the situation where there is no migration. However, increase of the migration rate beyond a critical value leads to the complete dominance of the more efficient template type (homogeneous regime). In this case, we find a continuous phase transition separating the homogeneous and the coexistence regimes, with the order parameter vanishing linearly with the distance to the transition point.

q-bio.PE↗

arXiv2014

Nonlinear group survival in Kimura's model for the evolution of altruism

Establishing the conditions that guarantee the spreading or the sustenance of altruistic traits in a population is the main goal of intergroup selection models. Of particular interest is the balance of the parameters associated to group size, migration and group survival against the selective advantage of the non-altruistic individuals. Here we use Kimura's diffusion model of intergroup selection to determine those conditions in the case the group survival probability is a nonlinear non-decreasing function of the proportion of altruists in a group. In the case this function is linear, there are two possible steady states which correspond to the non-altruistic and the altruistic phases. At the discontinuous transition line separating these phases there is a non-ergodic coexistence phase. For a continuous concave survival function, we find an ergodic coexistence phase that occupies a finite region of the parameter space in between the altruistic and the non-altruistic phases, and is separated from these phases by continuous transition lines. For a convex survival function, the coexistence phase disappears altogether but a bistable phase appears for which the choice of the initial condition determines whether the evolutionary dynamics leads to the altruistic or the non-altruistic steady state.

q-bio.PE↗

arXiv2013

Reinforcement and inference in cross-situational word learning

Cross-situational word learning is based on the notion that a learner can determine the referent of a word by finding something in common across many observed uses of that word. Here we propose an adaptive learning algorithm that contains a parameter that controls the strength of the reinforcement applied to associations between concurrent words and referents, and a parameter that regulates inference, which includes built-in biases, such as mutual exclusivity, and information of past learning events. By adjusting these parameters so that the model predictions agree with data from representative experiments on cross-situational word learning, we were able to explain the learning strategies adopted by the participants of those experiments in terms of a trade-off between reinforcement and inference. These strategies can vary wildly depending on the conditions of the experiments. For instance, for fast mapping experiments (i.e., the correct referent could, in principle, be inferred in a single observation) inference is prevalent, whereas for segregated contextual diversity experiments (i.e., the referents are separated in groups and are exhibited with members of their groups only) reinforcement is predominant. Other experiments are explained with more balanced doses of reinforcement and inference.

q-bio.NC↗

arXiv2012

Minimal model of associative learning for cross-situational lexicon acquisition

An explanation for the acquisition of word-object mappings is the associative learning in a cross-situational scenario. Here we present analytical results of the performance of a simple associative learning algorithm for acquiring a one-to-one mapping between $N$ objects and $N$ words based solely on the co-occurrence between objects and words. In particular, a learning trial in our learning scenario consists of the presentation of $C + 1 < N$ objects together with a target word, which refers to one of the objects in the context. We find that the learning times are distributed exponentially and the learning rates are given by $\ln{[\frac{N(N-1)}{C + (N-1)^{2}}]}$ in the case the $N$ target words are sampled randomly and by $\frac{1}{N} \ln [\frac{N-1}{C}] $ in the case they follow a deterministic presentation sequence. This learning performance is much superior to those exhibited by humans and more realistic learning algorithms in cross-situational experiments. We show that introduction of discrimination limitations using Weber's law and forgetting reduce the performance of the associative algorithm to the human level.

q-bio.NC↗

arXiv2012

Revisiting the effect of external fields in Axelrod's model of social dynamics

The study of the effects of spatially uniform fields on the steady-state properties of Axelrod's model has yielded plenty of controversial results. Here we re-examine the impact of this type of field for a selection of parameters such that the field-free steady state of the model is heterogeneous or multicultural. Analyses of both one and two-dimensional versions of Axelrod's model indicate that, contrary to previous claims in the literature, the steady state remains heterogeneous regardless of the value of the field strength. Turning on the field leads to a discontinuous decrease on the number of cultural domains, which we argue is due to the instability of zero-field heterogeneous absorbing configurations. We find, however, that spatially nonuniform fields that implement a consensus rule among the neighborhood of the agents enforces homogenization. Although the overall effects of the fields are essentially the same irrespective of the dimensionality of the model, we argue that the dimensionality has a significant impact on the stability of the field-free homogeneous steady state.

physics.soc-ph↗

arXiv2012

Mean-field analysis of the majority-vote model broken-ergodicity steady state

We study analytically a variant of the one-dimensional majority-vote model in which the individual retains its opinion in case there is a tie among the neighbors' opinions. The individuals are fixed in the sites of a ring of size $L$ and can interact with their nearest neighbors only. The interesting feature of this model is that it exhibits an infinity of spatially heterogeneous absorbing configurations for $L \to \infty$ whose statistical properties we probe analytically using a mean-field framework based on the decomposition of the $L$-site joint probability distribution into the $n$-contiguous-site joint distributions, the so-called $n$-site approximation. To describe the broken-ergodicity steady state of the model we solve analytically the mean-field dynamic equations for arbitrary time $t$ in the cases n=3 and 4. The asymptotic limit $t \to \infty$ reveals the mapping between the statistical properties of the random initial configurations and those of the final absorbing configurations. For the pair approximation ($n=2$) we derive that mapping using a trick that avoids solving the full dynamics. Most remarkably, we find that the predictions of the 4-site approximation reduce to those of the 3-site in the case of expectations involving three contiguous sites. In addition, those expectations fit the Monte Carlo data perfectly and so we conjecture that they are in fact the exact expectations for the one-dimensional majority-vote model.

cond-mat.stat-mech↗

arXiv2012

Categories of Emotion names in Web retrieved texts

The categorization of emotion names, i.e., the grouping of emotion words that have similar emotional connotations together, is a key tool of Social Psychology used to explore people's knowledge about emotions. Without exception, the studies following that research line were based on the gauging of the perceived similarity between emotion names by the participants of the experiments. Here we propose and examine a new approach to study the categories of emotion names - the similarities between target emotion names are obtained by comparing the contexts in which they appear in texts retrieved from the World Wide Web. This comparison does not account for any explicit semantic information; it simply counts the number of common words or lexical items used in the contexts. This procedure allows us to write the entries of the similarity matrix as dot products in a linear vector space of contexts. The properties of this matrix were then explored using Multidimensional Scaling Analysis and Hierarchical Clustering. Our main findings, namely, the underlying dimension of the emotion space and the categories of emotion names, were consistent with those based on people's judgments of emotion names similarities.

cs.CL↗

arXiv2012

A structural model of emotions of cognitive dissonances

Cognitive dissonance is the stress that comes from holding two conflicting thoughts simultaneously in the mind, usually arising when people are asked to choose between two detrimental or two beneficial options. In view of the well-established role of emotions in decision making, here we investigate whether the conventional structural models used to represent the relationships among basic emotions, such as the Circumplex model of affect, can describe the emotions of cognitive dissonance as well. We presented a questionnaire to 34 anonymous participants, where each question described a decision to be made among two conflicting motivations and asked the participants to rate analogically the pleasantness and the intensity of the experienced emotion. We found that the results were compatible with the predictions of the Circumplex model for basic emotions.

q-bio.NC↗

arXiv2010

Social interaction as a heuristic for combinatorial optimization problems

We investigate the performance of a variant of Axelrod's model for dissemination of culture - the Adaptive Culture Heuristic (ACH) - on solving an NP-Complete optimization problem, namely, the classification of binary input patterns of size $F$ by a Boolean Binary Perceptron. In this heuristic, $N$ agents, characterized by binary strings of length $F$ which represent possible solutions to the optimization problem, are fixed at the sites of a square lattice and interact with their nearest neighbors only. The interactions are such that the agents' strings (or cultures) become more similar to the low-cost strings of their neighbors resulting in the dissemination of these strings across the lattice. Eventually the dynamics freezes into a homogeneous absorbing configuration in which all agents exhibit identical solutions to the optimization problem. We find through extensive simulations that the probability of finding the optimal solution is a function of the reduced variable $F/N^{1/4}$ so that the number of agents must increase with the fourth power of the problem size, $N \propto F^ 4$, to guarantee a fixed probability of success. In this case, we find that the relaxation time to reach an absorbing configuration scales with $F^ 6$ which can be interpreted as the overall computational cost of the ACH to find an optimal set of weights for a Boolean Binary Perceptron, given a fixed probability of success.

cs.DS↗

arXiv2010

Statistics of opinion domains of the majority-vote model on a square lattice

The existence of juxtaposed regions of distinct cultures in spite of the fact that people's beliefs have a tendency to become more similar to each other's as the individuals interact repeatedly is a puzzling phenomenon in the social sciences. Here we study an extreme version of the frequency-dependent bias model of social influence in which an individual adopts the opinion shared by the majority of the members of its extended neighborhood, which includes the individual itself. This is a variant of the majority-vote model in which the individual retains its opinion in case there is a tie among the neighbors' opinions. We assume that the individuals are fixed in the sites of a square lattice of linear size $L$ and that they interact with their nearest neighbors only. Within a mean-field framework, we derive the equations of motion for the density of individuals adopting a particular opinion in the single-site and pair approximations. Although the single-site approximation predicts a single opinion domain that takes over the entire lattice, the pair approximation yields a qualitatively correct picture with the coexistence of different opinion domains and a strong dependence on the initial conditions. Extensive Monte Carlo simulations indicate the existence of a rich distribution of opinion domains or clusters, the number of which grows with $L^2$ whereas the size of the largest cluster grows with $\ln L^2$. The analysis of the sizes of the opinion domains shows that they obey a power-law distribution for not too large sizes but that they are exponentially distributed in the limit of very large clusters. In addition, similarly to other well-known social influence model -- Axelrod's model -- we found that these opinion domains are unstable to the effect of a thermal-like noise.

physics.comp-ph↗

arXiv2009

The optimization and shock waves in evolution dynamics

We consider the optimal dynamics in the infinite population evolution models with general symmetric fitness landscape. The search of optimal evolution trajectories are complicated due to sharp transitions (like shock waves) in evolution dynamics with smooth fitness landscapes, which exist even in case of popular quadratic fitness. We found exact analytical solutions for discontinuous dynamics at the large genome length limit. We found the optimal mutation rates for the fixed fitness landscape. The single peak fitness landscape gives the fastest dynamics to send the vast majority of the population from the initial sequence to the neighborhood of the final sequence.

q-bio.PE↗

arXiv2008

The information capacity of hypercycles

Hypercycles are information integration systems which are thought to overcome the information crisis of prebiotic evolution by ensuring the coexistence of several short templates. For imperfect template replication, we derive a simple expression for the maximum number of distinct templates $n_m$ that can coexist in a hypercycle and show that it is a decreasing function of the length $L$ of the templates. In the case of high replication accuracy we find that the product $n_m L$ tends to a constant value, limiting thus the information content of the hypercycle. Template coexistence is achieved either as a stationary equilibrium (stable fixed point) or a stable periodic orbit in which the total concentration of functional templates is nonzero. For the hypercycle system studied here we find numerical evidence that the existence of an unstable fixed point is a necessary condition for the presence of periodic orbits.

q-bio.PE↗

arXiv2007

Preservation of information in a prebiotic package model

The coexistence between different informational molecules has been the preferred mode to circumvent the limitation posed by imperfect replication on the amount of information stored by each of these molecules. Here we reexamine a classic package model in which distinct information carriers or templates are forced to coexist within vesicles, which in turn can proliferate freely through binary division. The combined dynamics of vesicles and templates is described by a multitype branching process which allows us to write equations for the average number of the different types of vesicles as well as for their extinction probabilities. The threshold phenomenon associated to the extinction of the vesicle population is studied quantitatively using finite-size scaling techniques. We conclude that the resultant coexistence is too frail in the presence of parasites and so confinement of templates in vesicles without an explicit mechanism of cooperation does not resolve the information crisis of prebiotic evolution.

q-bio.PE↗

arXiv2006

Template coexistence in prebiotic vesicle models

The coexistence of distinct templates is a common feature of the diverse proposals advanced to resolve the information crisis of prebiotic evolution. However, achieving robust template coexistence turned out to be such a difficult demand that only a class of models, the so-called package models, seems to have met it so far. Here we apply Wright's Island formulation of group selection to study the conditions for the coexistence of two distinct template types confined in packages (vesicles) of finite capacity. In particular, we show how selection acting at the level of the vesicles can neutralize the pressures towards the fixation of any one of the template types (random drift) and of the type with higher replication rate (deterministic competition). We give emphasis to the role of the distinct generation times of templates and vesicles as yet another obstacle to coexistence.

q-bio.PE↗

arXiv2006

Revisiting the nonequilibrium phase transition of the triplet-creation model

The nonequilibrium phase transition in the triplet-creation model is investigated using critical spreading and the conservative diffusive contact process. The results support the claim that at high enough diffusion the phase transition becomes discontinuous. As the diffusion probability increases the critical exponents change continuously from the ordinary directed percolation (DP) class to the compact directed percolation (CDP). The fractal dimension of the critical cluster, however, switches abruptly between those two universality classes. Strong crossover effects in both methods make it difficult, if not impossible, to establish the exact location of the tricritical point.

cond-mat.stat-mech↗

arXiv2003

Shapes of tree representations of spin-glass landscapes

Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure -- a barrier tree -- the leaves and internal nodes of which represent, respectively, the local minima and the lowest energy saddles connecting those minima. Here we apply several statistics used in the study of phylogenetic trees to barrier trees that result from the energy landscapes of p-spin models. These statistics give information about the shape of these barrier trees, in particular about balance and symmetry. We then ask if they can be used to classify different types of landscapes, compare them with results obtained from random trees, and investigate the structure of subtrees of the barrier trees. We conclude that at least one of the used statistics is capable of distinguishing different types of landscapes, that the barrier trees from p-spin energy landscapes are quite different from random trees, and that subtrees of barrier trees do not reflect the overall tree structure, but their structure is correlated with their ``depth'' in the tree.

cond-mat.dis-nn↗

arXiv2002

Catalytic Reaction Sets, Decay, and the Preservation of Information

We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes impossible to maintain a significant concentration of large polymers, while it is still possible to maintain sets of smaller polymers that can maintain the same amount of information. We use a genetic algorithm to evolve reaction sets to generate specific polymer distributions under the influence of decay. In these evolved reaction sets, the beginnings of hypercycle-type structures can be observed, which are believed to have been an important step toward the evolution of the first living cells.

nlin.AO↗