arXiv subjects

Hernán A. Makse

Publications and source records attributed to Hernán A. Makse.

At least 19 recordsLinked to original sources

arXiv2025

Complexity reduction by symmetry: uncovering the minimal regulatory network for logical computation in bacteria

Symmetry principles play an important role in geometry, and physics, allowing for the reduction of complicated systems to simpler, more comprehensible models that preserve the system's features of interest. Biological systems are often highly complex and may consist of a large number of interacting parts. Using symmetry fibrations, the relevant symmetries for biological "message-passing" networks, we introduce a scheme, called Complexity Reduction by Symmetry or ComSym, to reduce the gene regulatory networks of Escherichia coli and Bacillus subtilis bacteria to core networks in a way that preserves the dynamics and uncovers the computational capabilities of the network. Gene nodes in the original network that share isomorphic input trees are collapsed by the fibration into equivalence classes called fibers, whereby nodes that receive signals with the same "history" belong to one fiber and synchronize. Then we reduce the networks to its minimal computational core via k-core decomposition. This computational core consists of a few strongly connected components or "signal vortices", in which signals can cycle through. While between them, these "signal vortices" transmit signals in a feedforward manner. These connected components perform signal processing and decision making in the bacterial cell by employing a series of genetic toggle-switch circuits that store memory, plus oscillator circuits. These circuits act as the central computation device of the network, whose output signals then spread to the rest of the network. Our reduction method opens the door to narrow the vast complexity of biological systems to their minimal parts in a systematic way by using fundamental theoretical principles of symmetry.

q-bio.CB↗

arXiv2024

Fibration symmetry-breaking supports functional transitions in a brain network engaged in language

In his book 'A Beautiful Question', physicist Frank Wilczek argues that symmetry is 'nature's deep design,' governing the behavior of the universe, from the smallest particles to the largest structures. While symmetry is a cornerstone of physics, it has not yet been found widespread applicability to describe biological systems, particularly the human brain. In this context, we study the human brain network engaged in language and explore the relationship between the structural connectivity (connectome or structural network) and the emergent synchronization of the mesoscopic regions of interest (functional network). We explain this relationship through a different kind of symmetry than physical symmetry, derived from the categorical notion of Grothendieck fibrations. This introduces a new understanding of the human brain by proposing a local symmetry theory of the connectome, which accounts for how the structure of the brain's network determines its coherent activity. Among the allowed patterns of structural connectivity, synchronization elicits different symmetry subsets according to the functional engagement of the brain. We show that the resting state is a particular realization of the cerebral synchronization pattern characterized by a fibration symmetry that is broken in the transition from rest to language. Our findings suggest that the brain's network symmetry at the local level determines its coherent function, and we can understand this relationship from theoretical principles.

q-bio.NC↗

arXiv2024

Symmetries and synchronization from whole-neural activity in {\it C. elegans} connectome: Integration of functional and structural networks

Understanding the dynamical behavior of complex systems from their underlying network architectures is a long-standing question in complexity theory. Therefore, many metrics have been devised to extract network features like motifs, centrality, and modularity measures. It has previously been proposed that network symmetries are of particular importance since they are expected to underly the synchronization of a system's units, which is ubiquitously observed in nervous system activity patterns. However, perfectly symmetrical structures are difficult to assess in noisy measurements of biological systems, like neuronal connectomes. Here, we devise a principled method to infer network symmetries from combined connectome and neuronal activity data. Using nervous system-wide population activity recordings of the \textit{C.elegans} backward locomotor system, we infer structures in the connectome called fibration symmetries, which can explain which group of neurons synchronize their activity. Our analysis suggests functional building blocks in the animal's motor periphery, providing new testable hypotheses on how descending interneuron circuits communicate with the motor periphery to control behavior. Our approach opens a new door to exploring the structure-function relations in other complex systems, like the nervous systems of larger animals.

q-bio.NC↗

arXiv2024

Fibration symmetries and cluster synchronization in the Caenorhabditis elegans connectome

Capturing how the Caenorhabditis elegans connectome structure gives rise to its neuron functionality remains unclear. It is through fiber symmetries found in its neuronal connectivity that synchronization of a group of neurons can be determined. To understand these we investigate graph symmetries and search for such in the symmetrized versions of the forward and backward locomotive sub-networks of the Caenorhabditi elegans worm neuron network. The use of ordinarily differential equations simulations admissible to these graphs are used to validate the predictions of these fiber symmetries and are compared to the more restrictive orbit symmetries. Additionally fibration symmetries are used to decompose these graphs into their fundamental building blocks which reveal units formed by nested loops or multilayered fibers. It is found that fiber symmetries of the connectome can accurately predict neuronal synchronization even under not idealized connectivity as long as the dynamics are within stable regimes of simulations.

q-bio.NC↗

arXiv2022

Symmetry-driven network reconstruction through pseudobalanced coloring optimization

Symmetries found through automorphisms or graph fibrations provide important insights in network analysis. Symmetries identify clusters of robust synchronization in the network which improves the understanding of the functionality of complex biological systems. Network symmetries can be determined by finding a {\it balanced coloring} of the graph, which is a node partition in which each cluster of nodes receives the same information (color) from the rest of the graph. In recent work we saw that biological networks such as gene regulatory networks, metabolic networks and neural networks in organisms ranging from bacteria to yeast and humans are rich in fibration symmetries related to the graph balanced coloring. Networks based on real systems, however, are built on experimental data which are inherently incomplete, due to missing links, collection errors, and natural variations within specimens of the same biological species. Therefore, it is fair to assume that some of the existing symmetries were not detected in our analysis. For that reason, a method to find pseudosymmetries and repair networks based on those symmetries is important when analyzing real world networks. In this paper we introduce the {\it pseudobalanced coloring} \eqref{eq:mainip} problem, and provide an integer programming formulation which (a) calculates a pseudobalanced coloring of the graph taking into account the missing data, and (b) optimally repairs the graph with the minimal number of added/removed edges to maximize the symmetry of the graph. We apply our formulation to the {\it C. elegans} connectome to find pseudocoloring and the optimal graph repair. Our solution compares well with a manually curated ground-truth {\it C. elegans} graph as well as solutions generated by other methods of missing link prediction.

q-bio.QM↗

arXiv2021

Quasifibrations of Graphs to Find Symmetries in Biological Networks

A fibration of graphs is an homomorphism that is a local isomorphism of in-neighbourhoods, much in the same way a covering projection is a local isomorphism of neighbourhoods. Recently, it has been shown that graph fibrations are useful tools to uncover symmetries and synchronization patterns in biological networks ranging from gene, protein,and metabolic networks to the brain. However, the inherent incompleteness and disordered nature of biological data precludes the application of the definition of fibration as it is; as a consequence, also the currently known algorithms to identify fibrations fail in these domains. In this paper, we introduce and develop systematically the theory of quasifibrations which attempts to capture more realistic patterns of almost-synchronization of units in biological networks. We provide an algorithmic solution to the problem of finding quasifibrations in networks where the existence of missing links and variability across samples preclude the identification of perfect symmetries in the connectivity structure. We test the algorithm against other strategies to repair missing links in incomplete networks using real connectome data and synthetic networks. Quasifibrations can be applied to reconstruct any incomplete network structure characterized by underlying symmetries and almost synchronized clusters.

q-bio.QM↗

arXiv2021

Centralities in complex networks

In network science complex systems are represented as a mathematical graphs consisting of a set of nodes representing the components and a set of edges representing their interactions. The framework of networks has led to significant advances in the understanding of the structure, formation and function of complex systems. Social and biological processes such as the dynamics of epidemics, the diffusion of information in social media, the interactions between species in ecosystems or the communication between neurons in our brains are all actively studied using dynamical models on complex networks. In all of these systems, the patterns of connections at the individual level play a fundamental role on the global dynamics and finding the most important nodes allows one to better understand and predict their behaviors. An important research effort in network science has therefore been dedicated to the development of methods allowing to find the most important nodes in networks. In this short entry, we describe network centrality measures based on the notions of network traversal they rely on. This entry aims at being an introduction to this extremely vast topic, with many contributions from several fields, and is by no means an exhaustive review of all the literature about network centralities.

physics.soc-ph↗

arXiv2021

Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria

Background: Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the questions whether it is possible to predict gene synchronization from network structure alone. We have recently shown that synchronized gene expression may be predicted from symmetries in the gene regulatory networks (GRN) and described by the concept of symmetry fibrations. We showed that symmetry fibrations partition the genes into groups called fibers based on the symmetries of their 'input trees', the set of paths in the network through which signals can reach a gene. In idealized dynamic gene expression models, all genes in a fiber are perfectly synchronized, while less idealized models - with gene input functions differencing between genes - predict symmetry breaking and desynchronization. Results: To study the functional role of gene fibers and to test whether some of the fiber-induced coexpression remains in reality, we analyze gene fibrations for the gene regulatory networks of E. coli and B. subtilis and confront them with expression data. We find approximate gene coexpression patterns consistent with symmetry fibrations with idealized gene expression dynamics. This shows that network structure alone provides useful information about gene synchronization, and suggest that gene input functions within fibers may be further streamlined by evolutionary pressures to realize a coexpression of genes. Conclusions: Thus, gene fibrations provides a sound conceptual tool to describe tunable coexpression induced by network topology and shaped by mechanistic details of gene expression.

q-bio.MN↗

arXiv2021

Superspreading k-cores at the center of COVID-19 pandemic persistence

The spread of COVID-19 caused by the recently discovered SARS-CoV-2 virus has become a worldwide problem with devastating consequences. To slow down the spread of the pandemic, mass quarantines have been implemented globally, provoking further social and economic disruptions. Here, we implement a comprehensive contact tracing network analysis to find an optimized quarantine protocol to dismantle the chain of transmission of coronavirus with minimal disruptions to society. We track billions of anonymized GPS human mobility datapoints from a compilation of hundreds of mobile apps deployed in Latin America to monitor the evolution of the contact network of disease transmission before and after the confinements. As a consequence of the lockdowns, people's mobility across the region decreases by $\sim$53\%, which results in a drastic disintegration of the transmission network by $\sim$90\%. However, this disintegration did not halt the spreading of the disease. Our analysis indicates that superspreading k-core structures persist in the transmission network to prolong the pandemic. Once the k-cores are identified, an optimized strategy to break the chain of transmission is to quarantine a minimal number of 'weak links' with high betweenness centrality connecting the large k-cores. As countries built contact tracing apps to fight the pandemic, our results could turn into a valuable resource to help deploy quarantine protocols with minimized disruptions.

physics.soc-ph↗

arXiv2020

Monolingual and bilingual language networks in healthy subjects using functional MRI and graph theory

Pre-surgical language mapping with functional magnetic resonance imaging (fMRI) is routinely conducted to assist the neurosurgeon in preventing damage to brain regions responsible for language. Functional differences exist between the monolingual versus the bilingual brain, whereas clinical fMRI tasks are typically conducted in a single language. The presence of secondary language processing mechanisms is a potential source of error in the inferred language map. From fMRI data of healthy bilingual and monolingual subjects we obtain language maps as functional networks. Our results show a sub-network "core" architecture consisting of the Broca's, pre-supplementary motor, and premotor areas present across all subjects. Wernicke's Area was found to connect to the "core" to a different extent across groups. The $k$ core centrality measure shows "core" areas belong to the maximum core while WA and other fROIs vary across groups. The results may provide a benchmark to preserve equal treatment outcomes for bilingual patients.

q-bio.NC↗

arXiv2018

The k-core as a predictor of structural collapse in mutualistic ecosystems

Collapses of dynamical systems into irrecoverable states are observed in ecosystems, human societies, financial systems and network infrastructures. Despite their widespread occurrence and impact, these events remain largely unpredictable. In searching for the causes for collapse and instability, theoretical investigations have so far been unable to determine quantitatively the influence of the structural features of the network formed by the interacting species. Here, we derive the condition for the stability of a mutualistic ecosystem as a constraint on the strength of the dynamical interactions between species and a topological invariant of the network: the k-core. Our solution predicts that when species located at the maximum k-core of the network go extinct, as a consequence of sufficiently weak interaction strengths, the system will reach the tipping point of its collapse. As a key variable involved in collapse phenomena, monitoring the k-core of the network may prove a powerful method to anticipate catastrophic events in the vast context that stretches from ecological and biological networks to finance.

nlin.AO↗

arXiv2018

Finding influential nodes for integration in brain networks using optimal percolation theory

Global integration of information in the brain results from complex interactions of segregated brain networks. Identifying the most influential neuronal populations that efficiently bind these networks is a fundamental problem of systems neuroscience. Here we apply optimal percolation theory and pharmacogenetic interventions in-vivo to predict and subsequently target nodes that are essential for global integration of a memory network in rodents. The theory predicts that integration in the memory network is mediated by a set of low-degree nodes located in the nucleus accumbens. This result is confirmed with pharmacogenetic inactivation of the nucleus accumbens, which eliminates the formation of the memory network, while inactivations of other brain areas leave the network intact. Thus, optimal percolation theory predicts essential nodes in brain networks. This could be used to identify targets of interventions to modulate brain function.

q-bio.NC↗

arXiv2018

A worldwide model for boundaries of urban settlements

The shape of urban settlements plays a fundamental role in their sustainable planning. Properly defining the boundaries of cities is challenging and remains an open problem in the Science of Cities. Here, we propose a worldwide model to define urban settlements beyond their administrative boundaries through a bottom-up approach that takes into account geographical biases intrinsically associated with most societies around the world, and reflected in their different regional growing dynamics. The generality of the model allows to study the scaling laws of cities at all geographical levels: countries, continents, and the entire world. Our definition of cities is robust and holds to one of the most famous results in Social Sciences: Zipf's law. According to our results, the largest cities in the world are not in line with what was recently reported by the United Nations. For example, we find that the largest city in the world is an agglomeration of several small settlements close to each other, connecting three large settlements: Alexandria, Cairo, and Luxor. Our definition of cities opens the doors to the study of the economy of cities in a systematic way independently of arbitrary definitions that employ administrative boundaries.

physics.soc-ph↗

arXiv2018

Theories for influencer identification in complex networks

In social and biological systems, the structural heterogeneity of interaction networks gives rise to the emergence of a small set of influential nodes, or influencers, in a series of dynamical processes. Although much smaller than the entire network, these influencers were observed to be able to shape the collective dynamics of large populations in different contexts. As such, the successful identification of influencers should have profound implications in various real-world spreading dynamics such as viral marketing, epidemic outbreaks and cascading failure. In this chapter, we first summarize the centrality-based approach in finding single influencers in complex networks, and then discuss the more complicated problem of locating multiple influencers from a collective point of view. Progress rooted in collective influence theory, belief-propagation and computer science will be presented. Finally, we present some applications of influencer identification in diverse real-world systems, including online social platforms, scientific publication, brain networks and socioeconomic systems.

physics.soc-ph↗

arXiv2017

The price of a vote: diseconomy in proportional elections

The increasing cost of electoral campaigns raises the need for effective campaign planning and a precise understanding of the return of such investment. Interestingly, despite the strong impact of elections on our daily lives, how this investment is translated into votes is still unknown. By performing data analysis and modeling, we show that top candidates spend more money \emph{per vote} than the less successful and poorer candidates, a sublinearity that discloses a diseconomy of scale. We demonstrate that such electoral diseconomy arises from the competition between candidates due to inefficient campaign expenditure. Our approach succeeds in two important tests. First, it reveals that the statistical pattern in the vote distribution of candidates can be explained in terms of the independently conceived, but similarly skewed distribution of money campaign. Second, using a heuristic argument, we are able to predict a turnout percentage for a given election of approximately 63\%. This result is in good agreement with the average turnout rate obtained from real data. Due to its generality, we expect that our approach can be applied to a wide range of problems concerning the adoption process in marketing campaigns.

physics.soc-ph↗

arXiv2017

Edwards Statistical Mechanics for Jammed Granular Matter

In 1989, Sir Sam Edwards made the visionary proposition to treat jammed granular materials using a volume ensemble of equiprobable jammed states in analogy to thermal equilibrium statistical mechanics, despite their inherent athermal features. Since then, the statistical mechanics approach for jammed matter has garnered an extraordinary amount of attention by both theorists and experimentalists. Here, we review a systematic approach to jammed matter based on the Edwards statistical mechanical ensemble. We discuss the construction of microcanonical and canonical ensembles based on the volume function, which replaces the Hamiltonian in jammed systems. The importance of approximation schemes at various levels is emphasized leading to quantitative predictions for ensemble averaged quantities such as packing fractions and contact force distributions. An overview of the phenomenology of jammed states and experiments, simulations, and theoretical models scrutinizing the strong assumptions underlying Edwards' approach is given including recent results suggesting the validity of Edwards ergodic hypothesis for jammed states. A theoretical framework for packings whose constitutive particles range from spherical to non-spherical shapes like dimers, polymers, ellipsoids, spherocylinders or tetrahedra, hard and soft, frictional, frictionless and adhesive, monodisperse and polydisperse particles in any dimensions is discussed providing insight into an unifying phase diagram for all jammed matter. Furthermore, the connection between the Edwards' ensemble of metastable jammed states and metastability in spin-glasses is established. This highlights that the packing problem can be understood as a constraint satisfaction problem for excluded volume and force and torque balance leading to a unifying framework between the Edwards ensemble of equiprobable jammed states and out-of-equilibrium spin-glasses.

cond-mat.soft↗

arXiv2017

Model of Brain Activation Predicts the Neural Collective Influence Map of the Brain

Efficient complex systems have a modular structure, but modularity does not guarantee robustness, because efficiency also requires an ingenious interplay of the interacting modular components. The human brain is the elemental paradigm of an efficient robust modular system interconnected as a network of networks (NoN). Understanding the emergence of robustness in such modular architectures from the interconnections of its parts is a long-standing challenge that has concerned many scientists. Current models of dependencies in NoN inspired by the power grid express interactions among modules with fragile couplings that amplify even small shocks, thus preventing functionality. Therefore, we introduce a model of NoN to shape the pattern of brain activations to form a modular environment that is robust. The model predicts the map of neural collective influencers (NCIs) in the brain, through the optimization of the influence of the minimal set of essential nodes responsible for broadcasting information to the whole-brain NoN. Our results suggest new intervention protocols to control brain activity by targeting influential neural nodes predicted by network theory.

q-bio.NC↗

arXiv2017

Inferring Personal Economic Status from Social Network Location

It is commonly believed that patterns of social ties affect individuals' economic status. Here, we translate this concept into an operational definition at the network level, which allows us to infer the economic wellbeing of individuals through a measure of their location and influence in the social network. We analyze two large-scale sources: telecommunications and financial data of a whole country's population. Our results show that an individual's location, measured as the optimal collective influence to the structural integrity of the social network, is highly correlated with personal economic status. The observed social network patterns of influence mimics the patterns of economic inequality. For pragmatic use and validation, we carry out a marketing campaign that shows a three-fold increase in response rate by targeting individuals identified by our social network metrics as compared to random targeting. Our strategy can also be useful in maximizing the effects of large-scale economic stimulus policies.

physics.soc-ph↗