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Luis A. N. Amaral

Publications and source records attributed to Luis A. N. Amaral.

18 recordsLinked to original sources
arXiv2022

A new approach for extracting information from protein dynamics

Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.

q-bio.MN↗
arXiv2019

A new evaluation framework for topic modeling algorithms based on synthetic corpora

Topic models are in widespread use in natural language processing and beyond. Here, we propose a new framework for the evaluation of probabilistic topic modeling algorithms based on synthetic corpora containing an unambiguously defined ground truth topic structure. The major innovation of our approach is the ability to quantify the agreement between the planted and inferred topic structures by comparing the assigned topic labels at the level of the tokens. In experiments, our approach yields novel insights about the relative strengths of topic models as corpus characteristics vary, and the first evidence of an "undetectable phase" for topic models when the planted structure is weak. We also establish the practical relevance of the insights gained for synthetic corpora by predicting the performance of topic modeling algorithms in classification tasks in real-world corpora.

cs.CL↗
arXiv2012

Rationality, irrationality and escalating behavior in lowest unique bid auctions

Information technology has revolutionized the traditional structure of markets. The removal of geographical and time constraints has fostered the growth of online auction markets, which now include millions of economic agents worldwide and annual transaction volumes in the billions of dollars. Here, we analyze bid histories of a little studied type of online auctions --- lowest unique bid auctions. Similarly to what has been reported for foraging animals searching for scarce food, we find that agents adopt Levy flight search strategies in their exploration of "bid space". The Levy regime, which is characterized by a power-law decaying probability distribution of step lengths, holds over nearly three orders of magnitude. We develop a quantitative model for lowest unique bid online auctions that reveals that agents use nearly optimal bidding strategies. However, agents participating in these auctions do not optimize their financial gain. Indeed, as long as there are many auction participants, a rational profit optimizing agent would choose not to participate in these auction markets.

physics.soc-ph↗
arXiv2010

The role of mentorship in protege performance

The role of mentorship on protege performance is a matter of importance to academic, business, and governmental organizations. While the benefits of mentorship for proteges, mentors and their organizations are apparent, the extent to which proteges mimic their mentors' career choices and acquire their mentorship skills is unclear. Here, we investigate one aspect of mentor emulation by studying mentorship fecundity---the number of proteges a mentor trains---with data from the Mathematics Genealogy Project, which tracks the mentorship record of thousands of mathematicians over several centuries. We demonstrate that fecundity among academic mathematicians is correlated with other measures of academic success. We also find that the average fecundity of mentors remains stable over 60 years of recorded mentorship. We further uncover three significant correlations in mentorship fecundity. First, mentors with small mentorship fecundity train proteges that go on to have a 37% larger than expected mentorship fecundity. Second, in the first third of their career, mentors with large fecundity train proteges that go on to have a 29% larger than expected fecundity. Finally, in the last third of their career, mentors with large fecundity train proteges that go on to have a 31% smaller than expected fecundity.

physics.soc-ph↗
arXiv2009

Characterizing Individual Communication Patterns

The increasing availability of electronic communication data, such as that arising from e-mail exchange, presents social and information scientists with new possibilities for characterizing individual behavior and, by extension, identifying latent structure in human populations. Here, we propose a model of individual e-mail communication that is sufficiently rich to capture meaningful variability across individuals, while remaining simple enough to be interpretable. We show that the model, a cascading non-homogeneous Poisson process, can be formulated as a double-chain hidden Markov model, allowing us to use an efficient inference algorithm to estimate the model parameters from observed data. We then apply this model to two e-mail data sets consisting of 404 and 6,164 users, respectively, that were collected from two universities in different countries and years. We find that the resulting best-estimate parameter distributions for both data sets are surprisingly similar, indicating that at least some features of communication dynamics generalize beyond specific contexts. We also find that variability of individual behavior over time is significantly less than variability across the population, suggesting that individuals can be classified into persistent "types". We conclude that communication patterns may prove useful as an additional class of attribute data, complementing demographic and network data, for user classification and outlier detection--a point that we illustrate with an interpretable clustering of users based on their inferred model parameters.

physics.soc-ph↗
arXiv2009

A Poissonian explanation for heavy-tails in e-mail communication

Patterns of deliberate human activity and behavior are of utmost importance in areas as diverse as disease spread, resource allocation, and emergency response. Because of its widespread availability and use, e-mail correspondence provides an attractive proxy for studying human activity. Recently, it was reported that the probability density for the inter-event time $τ$ between consecutively sent e-mails decays asymptotically as $τ^{-α}$, with $α\approx 1$. The slower than exponential decay of the inter-event time distribution suggests that deliberate human activity is inherently non-Poissonian. Here, we demonstrate that the approximate power-law scaling of the inter-event time distribution is a consequence of circadian and weekly cycles of human activity. We propose a cascading non-homogeneous Poisson process which explicitly integrates these periodic patterns in activity with an individual's tendency to continue participating in an activity. Using standard statistical techniques, we show that our model is consistent with the empirical data. Our findings may also provide insight into the origins of heavy-tailed distributions in other complex systems.

physics.soc-ph↗
arXiv2006

Log-normal statistics in e-mail communication patterns

Following up on Barabasi's recent letter to Nature [435, 207--211 (2005)], we systematically investigate the time series of e-mail usage for 3,188 users at a university. We focus on two quantities for each user: the time interval between consecutively sent e-mails (interevent time), and the time interval between when a user sends an e-mail and when a recipient sends an e-mail back to the original sender (waiting time). We perform a standard Bayesian model selection analysis that demonstrates that the interevent times are well-described by a single log-normal while the waiting times are better described by the superposition of two log-normals. Our analysis rejects the possibility that either measure could be described by truncated power-law distributions with exponent $α\simeq 1$. We also critically evaluate the priority queuing model proposed by Barabási to describe the distribution of the waiting times. We show that neither the assumptions nor the predictions of the model are plausible, and conclude that a theoretical description of human e-mail communication patterns remains an open problem.

physics.data-an↗
arXiv2005

Comment on Barabasi, Nature 435, 207 (2005)

In a recent letter, Barabasi claims that the dynamics of a number of human activities are scale-free [1]. He specifically reports that the probability distribution of time intervals tau between consecutive e-mails sent by a single user and time delays for e-mail replies follow a power-law with an exponent -1, and proposes a priority-queuing process as an explanation of the bursty nature of human activity. Here, we quantitatively demonstrate that the reported power-law distributions are solely an artifact of the analysis of the empirical data and that the proposed model is not representative of e-mail communication patterns.

physics.data-an↗
arXiv2005

Canalizing Kauffman networks: non-ergodicity and its effect on their critical behavior

Boolean Networks have been used to study numerous phenomena, including gene regulation, neural networks, social interactions, and biological evolution. Here, we propose a general method for determining the critical behavior of Boolean systems built from arbitrary ensembles of Boolean functions. In particular, we solve the critical condition for systems of units operating according to canalizing functions and present strong numerical evidence that our approach correctly predicts the phase transition from order to chaos in such systems.

cond-mat.dis-nn↗
arXiv2004

Emergence of Complex Dynamics in a Simple Model of Signaling Networks

A variety of physical, social and biological systems generate complex fluctuations with correlations across multiple time scales. In physiologic systems, these long-range correlations are altered with disease and aging. Such correlated fluctuations in living systems have been attributed to the interaction of multiple control systems; however, the mechanisms underlying this behavior remain unknown. Here, we show that a number of distinct classes of dynamical behaviors, including correlated fluctuations characterized by $1/f$-scaling of their power spectra, can emerge in networks of simple signaling units. We find that under general conditions, complex dynamics can be generated by systems fulfilling two requirements: i) a ``small-world'' topology and ii) the presence of noise. Our findings support two notable conclusions: first, complex physiologic-like signals can be modeled with a minimal set of components; and second, systems fulfilling conditions (i) and (ii) are robust to some degree of degradation, i.e., they will still be able to generate $1/f$-dynamics.

q-bio.OT↗
arXiv2004

Modularity from Fluctuations in Random Graphs and Complex Networks

The mechanisms by which modularity emerges in complex networks are not well understood but recent reports have suggested that modularity may arise from evolutionary selection. We show that finding the modularity of a network is analogous to finding the ground-state energy of a spin system. Moreover, we demonstrate that, due to fluctuations, stochastic network models give rise to modular networks. Specifically, we show both numerically and analytically that random graphs and scale-free networks have modularity. We argue that this fact must be taken into consideration to define statistically-significant modularity in complex networks.

cond-mat.dis-nn↗
arXiv2002

Analytical solution of a model for complex food webs

We investigate numerically and analytically a recently proposed model for food webs [Nature {\bf 404}, 180 (2000)] in the limit of large web sizes and sparse interaction matrices. We obtain analytical expressions for several quantities with ecological interest, in particular the probability distributions for the number of prey and the number of predators. We find that these distributions have fast-decaying exponential and Gaussian tails, respectively. We also find that our analytical expressions are robust to changes in the details of the model.

cond-mat.dis-nn↗
arXiv2001

Scaling in the growth of geographically subdivided populations: invariant patterns from a continent-wide biological survey

We consider statistical patterns of variation in growth rates for over 400 species of breeding birds across North America surveyed from 1966 to 1998. We report two results. First, the standard deviation of population growth rates decays as a power-law function of total population size with an exponent $β= 0.36\pm0.02$. Second, the number of subpopulations, measured as the number of survey locations with non-zero counts, scales to the 3/4-power of total number of birds counted in a given species. We show how these patterns may be related, and discuss a simple stochastic growth model for a geographically subdivided population that formalizes the relationship. We also examine reasons that may explain why some species deviate from these scaling-laws.

cond-mat.stat-mech↗
arXiv1999

Small-world networks: Evidence for a crossover picture

Watts and Strogatz [Nature 393, 440 (1998)] have recently introduced a model for disordered networks and reported that, even for very small values of the disorder $p$ in the links, the network behaves as a small-world. Here, we test the hypothesis that the appearance of small-world behavior is not a phase-transition but a crossover phenomenon which depends both on the network size $n$ and on the degree of disorder $p$. We propose that the average distance $\ell$ between any two vertices of the network is a scaling function of $n / n^*$. The crossover size $n^*$ above which the network behaves as a small-world is shown to scale as $n^*(p \ll 1) \sim p^{-τ}$ with $τ\approx 2/3$.

cond-mat.stat-mech↗
arXiv1998

Environmental changes, co-extinction, and patterns in the fossil record

We introduce a new model for large scale evolution and extinction in which species are organized into food chains. The system evolves by two processes: origination/speciation and extinction. In the model, extinction of a given species can be due to an externally induced change in the environment or due to the extinction of all preys of that species (co-extinction). The model is able to reproduce the empirical observations, such as the statistical fractality of the fossil record or the scale-free distribution of extinction events, without invoking extinctions due to competition between species.

cond-mat.stat-mech↗
arXiv1998

Universal features in the growth dynamics of complex organizations

We analyze the fluctuations in the gross domestic product (GDP) of 152 countries for the period 1950--1992. We find that (i) the distribution of annual growth rates for countries of a given GDP decays with ``fatter'' tails than for a Gaussian, and (ii) the width of the distribution scales as a power law of GDP with a scaling exponent $β\approx 0.15$. Both findings are in surprising agreement with results on firm growth. These results are consistent with the hypothesis that the evolution of organizations with complex structure is governed by similar growth mechanisms.

cond-mat.stat-mech↗
arXiv1997

Stochastic Feedback and the Regulation of Biological Rhythms

We propose a general approach to the question of how biological rhythms spontaneously self-regulate, based on the concept of ``stochastic feedback''. We illustrate this approach by considering the neuroautonomic regulation of the heart rate. The model generates complex dynamics and successfully accounts for key characteristics of cardiac variability, including the $1/f$ power spectrum, the functional form and scaling of the distribution of variations, and correlations in the Fourier phases. Our results suggest that in healthy systems the control mechanisms operate to drive the system away from extreme values while not allowing it to settle down to a constant output.

cond-mat.stat-mech↗