arXiv subjects

Krešimir Josić

Publications and source records attributed to Krešimir Josić.

At least 19 recordsLinked to original sources

arXiv2025

Complexity and dynamics of partially symmetric random neural networks

Neural circuits exhibit structured connectivity, including an overrepresentation of reciprocal connections between neuron pairs. Despite important advances, a full understanding of how such partial symmetry in connectivity shapes neural dynamics remains elusive. Here we ask how correlations between reciprocal connections in a random, recurrent neural network affect phase-space complexity, defined as the exponential proliferation rate (with network size) of the number of fixed points that accompanies the transition to chaotic dynamics. We find a striking pattern: partial anti-symmetry strongly amplifies complexity, while partial symmetry suppresses it. These opposing trends closely track changes in other measures of dynamical behavior, such as dimensionality, Lyapunov exponents, and transient path length, supporting the view that fixed-point structure is a key determinant of network dynamics. Thus, positive reciprocal correlations favor low-dimensional, slowly varying activity, whereas negative correlations promote high-dimensional, rapidly fluctuating chaotic activity. These results yield testable predictions about the link between connection reciprocity, neural dynamics and function.

physics.bio-ph↗

arXiv2025

From Chaos to Coherence: Effects of High-Order Synaptic Correlations on Neural Dynamics

Recurrent Neural Network models have elucidated the interplay between structure and dynamics in biological neural networks, particularly the emergence of irregular and rhythmic activities in cortex. However, most studies have focused on networks with random or simple connectivity structures. Experimental observations find that high-order cortical connectivity patterns affect the temporal patterns of network activity, but a theory that relates such complex structure to network dynamics has yet to be developed. Here, we show that third- and higher-order cyclic correlations in synaptic connectivities greatly impact neuronal dynamics. Specifically, strong cyclic correlations in a network suppress chaotic dynamics and promote oscillatory or fixed activity. This change in dynamics is related to the form of the unstable eigenvalues of the random connectivity matrix. A phase transition from chaotic to fixed or oscillatory activity coincides with the development of a cusp at the leading edge of the eigenvalue support. We also relate the dimensions of activity to the network structure.

q-bio.NC↗

arXiv2025

Modeling Social Systems: Transparency, Reproducibility, and Responsibility

Mathematical models of complex social systems can enrich social scientific theory, inform interventions, and shape policy. From voting behavior to economic inequality and urban development, such models influence decisions that affect millions of lives. Thus, it is especially important to formulate and present them with transparency, reproducibility, and humility. Modeling in social domains, however, is often uniquely challenging. Unlike in physics or engineering, researchers often lack controlled experiments or abundant, clean data. Observational data is sparse, noisy, partial, and missing in systematic ways. In such an environment, how can we build models that can inform science and decision-making in transparent and responsible ways?

math.HO↗

arXiv2025

Neural Network-Based Parameter Estimation for Non-Autonomous Differential Equations with Discontinuous Signals

Non-autonomous differential equations are crucial for modeling systems influenced by external signals, yet fitting these models to data becomes particularly challenging when the signals change abruptly. To address this problem, we propose a novel parameter estimation method utilizing functional approximations with artificial neural networks. Our approach, termed Harmonic Approximation of Discontinuous External Signals using Neural Networks (HADES-NN), operates in two iterated stages. In the first stage, the algorithm employs a neural network to approximate the discontinuous signal with a smooth function. In the second stage, it uses this smooth approximate signal to estimate model parameters. HADES-NN gives highly accurate and precise parameter estimates across various applications, including circadian clock systems regulated by external light inputs measured via wearable devices and the mating response of yeast to external pheromone signals. HADES-NN greatly extends the range of model systems that can be fit to real-world measurements.

cs.LG↗

arXiv2025

Information-Seeking Decision Strategies Mitigate Risk in Dynamic, Uncertain Environments

To survive in dynamic and uncertain environments, individuals must develop effective decision strategies that balance information gathering and decision commitment. Models of such strategies often prioritize either optimizing tangible payoffs, like reward rate, or gathering information to support a diversity of (possibly unknown) objectives. However, our understanding of the relative merits of these two approaches remains incomplete, in part because direct comparisons have been limited to idealized, static environments that lack the dynamic complexity of the real world. Here we compared the performance of normative reward- and information-seeking strategies in a dynamic foraging task. Both strategies show similar transitions between exploratory and exploitative behaviors as environmental uncertainty changes. However, we find subtle disparities in the actions they take, resulting in meaningful performance differences: whereas reward-seeking strategies generate slightly more reward on average, information-seeking strategies provide more consistent and predictable outcomes. Our findings support the adaptive value of information-seeking behaviors that can mitigate risk with minimal reward loss.

cs.AI↗

arXiv2025

From Opinion Polarization to Climate Action: A Social-Climate Model of the Opinion Spectrum

We developed a coupled social-climate network model to understand the interaction between climate change opinion spread and the climate system and determine the role of this interaction in shaping collective actions and global temperature changes. In contrast to previous social-climate models that discretized opinions, we assumed opinions on climate change form a continuum, and were thereby able to capture more nuanced interactions. The model shows that resistance to behaviour change, elevated mitigation costs, and slow response to climate events can result in a global temperature anomaly in excess of 2°C. However, this outcome could be avoided by lowering mitigation costs and increasing the rate of interactions between individuals with differing opinions (social learning). Our model is the first to demonstrate the emergence of opinion polarization in a human-environment system. We predict that polarization of opinions in a population can be extinguished, and the population will adopt mitigation practices, when the response to temperature change is sensitive, even at higher mitigation costs. It also indicates that even with polarized opinion, an average pro-mitigative opinion in the population can reduce emissions. Finally, our model underscores how frequent and unexpected social or environmental changes, such as policy changes or extreme weather events, can slow climate change mitigation. This analysis helps identify the factors that support achieving international climate goals, such as leveraging peer influence and decreasing stubbornness in individuals, reducing mitigation costs, and encouraging climate-friendly lifestyles. Our model offers a valuable new framework for exploring the integration of social and natural sciences, particularly in the domain of human behavioural change.

math.DS↗

arXiv2024

Fast decisions reflect biases, slow decisions do not

Decisions are often made by heterogeneous groups of individuals, each with distinct initial biases and access to information of different quality. We show that in large groups of independent agents who accumulate evidence the first to decide are those with the strongest initial biases. Their decisions align with their initial bias, regardless of the underlying truth. In contrast, agents who decide last make decisions as if they were initially unbiased, and hence make better choices. We obtain asymptotic expressions in the large population limit that quantify how agents' initial inclinations shape early decisions. Our analysis shows how bias, information quality, and decision order interact in non-trivial ways to determine the reliability of decisions in a group.

physics.soc-ph↗

arXiv2023

Correlated Information Reduces Accuracy of Pioneering Decision-Makers

Normative models are often used to describe how humans and animals make decisions. These models treat deliberation as the accumulation of uncertain evidence that terminates with a commitment to a choice. When extended to social groups, such models often assume that individuals make independent observations. However, individuals typically gather evidence from common sources, and their observations are rarely independent. Here we ask: For a group of ideal observers who do not exchange information, what is the impact of correlated evidence on decision accuracy? We show that even when agents are identical, correlated evidence causes decision accuracy to depend on temporal decision order. Surprisingly, the first decider is less accurate than a lone observer. Early deciders are less accurate than late deciders. These phenomena occur despite the fact that the rational observers use the same decision criterion, so they are equally confident in their decisions. We analyze discrete and continuum evidence-gathering models to explain why the first decider is less accurate than a lone observer when evidence is correlated. Pooling the decisions of early deciders using a majority rule does not rescue accuracy in the sense that such pooling results in only modest accuracy gain. Although we analyze an idealized model, we believe that our analysis offers insights that do not depend on exactly how groups integrate evidence and form decisions.

physics.soc-ph↗

arXiv2022

Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies

Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new, specific cost functional. This minimization is implemented by dedicated Boltzmann machines (stochastic recurrent neural networks). Automated detection of cell divisions is handled similarly by successive minimizations of two cost functions, alternating the identification of children pairs and parent identification. We validate the proposed automatic cell tracking algorithm using (i) recordings of simulated cell colonies that closely mimic the growth dynamics of E. coli in microfluidic traps and (ii) real data. On a batch of 1100 simulated image frames, cell registration accuracies per frame ranged from 94.5% to 100%, with a high average. Our initial tests using experimental image sequences (i.e., real data) of E. coli colonies also yield convincing results, with a registration accuracy ranging from 90% to 100%.

cs.CV↗

arXiv2021

Incorporating Computational Challenges into a Multidisciplinary Course on Stochastic Processes

Quantitative methods and mathematical modeling are playing an increasingly important role across disciplines. As a result, interdisciplinary mathematics courses are increasing in popularity. However, teaching such courses at an advanced level can be challenging. Students often arrive with different mathematical backgrounds, different interests, and divergent reasons for wanting to learn the material. Here we describe a course on stochastic processes in biology, delivered between September and December 2020 to a mixed audience of mathematicians and biologists. In addition to traditional lectures and homeworks, we incorporated a series of weekly computational challenges into the course. These challenges served to familiarize students with the main modeling concepts, and provide them with an introduction on how to implement them in a research-like setting. In order to account for the different academic backgrounds of the students, they worked on the challenges in small groups, and presented their results and code in a dedicated discussion class each week. We discuss our experience designing and implementing an element of problem-based learning in an applied mathematics course through computational challenges. We also discuss feedback from students, and describe the content of the challenges presented in the course. We provide all materials, along with example code for a number of challenges.

q-bio.OT↗

arXiv2020

Synaptic Plasticity in Correlated Balanced Networks

The dynamics of local cortical networks are irregular, but correlated. Dynamic excitatory--inhibitory balance is a plausible mechanism that generates such irregular activity, but it remains unclear how balance is achieved and maintained in plastic neural networks. In particular, it is not fully understood how plasticity induced changes in the network affect balance, and in turn, how correlated, balanced activity impacts learning. How does the dynamics of balanced networks change under different plasticity rules? How does correlated spiking activity in recurrent networks change the evolution of weights, their eventual magnitude, and structure across the network? To address these questions, we develop a general theory of plasticity in balanced networks. We show that balance can be attained and maintained under plasticity induced weight changes. We find that correlations in the input mildly, but significantly affect the evolution of synaptic weights. Under certain plasticity rules, we find an emergence of correlations between firing rates and synaptic weights. Under these rules, synaptic weights converge to a stable manifold in weight space with their final configuration dependent on the initial state of the network. Lastly, we show that our framework can also describe the dynamics of plastic balanced networks when subsets of neurons receive targeted optogenetic input.

q-bio.NC↗

arXiv2020

Bayesian Evidence Accumulation on Social Networks

To make decisions we are guided by the evidence we collect, as well as the opinions of friends and neighbors. How do we integrate our private beliefs with information we obtain from our social network? To understand the strategies humans use to do so it is useful to compare them to observers that optimally integrate all evidence. Here we derive network models of rational (Bayes optimal) agents who accumulate private measurements and observe decisions of their neighbors to make an irreversible choice between two options. The resulting information exchange dynamics has interesting properties: When one option is preferred, the absence of a decision can be increasingly informative over time. In recurrent networks an absence of a decision can lead to a sequence of belief updates akin to those in the literature on common knowledge. Information obtained from observing repeated non-decisions is independent of realization, unless the private information of agents is redundant. On the other hand, in larger networks a single decision can trigger a cascade of agreements and disagreements that depend on the private information agents have gathered. Our approach provides a bridge between social decision making models in the economics literature, which largely ignore the temporal dynamics of decisions, and the single-observer evidence accumulator models used widely in neuroscience and psychology.

physics.soc-ph↗

arXiv2020

Linking structure and activity in nonlinear spiking networks

Recent experimental advances are producing an avalanche of data on both neural connectivity and neural activity. To take full advantage of these two emerging datasets we need a framework that links them, revealing how collective neural activity arises from the structure of neural connectivity and intrinsic neural dynamics. This problem of {\it structure-driven activity} has drawn major interest in computational neuroscience. Existing methods for relating activity and architecture in spiking networks rely on linearizing activity around a central operating point and thus fail to capture the nonlinear responses of individual neurons that are the hallmark of neural information processing. Here, we overcome this limitation and present a new relationship between connectivity and activity in networks of nonlinear spiking neurons by developing a diagrammatic fluctuation expansion based on statistical field theory. We explicitly show how recurrent network structure produces pairwise and higher-order correlated activity, and how nonlinearities impact the networks' spiking activity. Our findings open new avenues to investigating how single-neuron nonlinearities---including those of different cell types---combine with connectivity to shape population activity and function.

q-bio.NC↗

arXiv2019

Performance of normative and approximate evidence accumulation on the dynamic clicks task

The aim of a number of psychophysics tasks is to uncover how mammals make decisions in a world that is in flux. Here we examine the characteristics of ideal and near-ideal observers in a task of this type. We ask when and how performance depends on task parameters and design, and, in turn, what observer performance tells us about their decision-making process. In the dynamic clicks task subjects hear two streams (left and right) of Poisson clicks with different rates. Subjects are rewarded when they correctly identify the side with the higher rate, as this side switches unpredictably. We show that a reduced set of task parameters defines regions in parameter space in which optimal, but not near-optimal observers, maintain constant response accuracy. We also show that for a range of task parameters an approximate normative model must be finely tuned to reach near-optimal performance, illustrating a potential way to distinguish between normative models and their approximations. In addition, we show that using the negative log-likelihood and the 0/1-loss functions to fit these types of models is not equivalent: the 0/1-loss leads to a bias in parameter recovery that increases with sensory noise. These findings suggest ways to tease apart models that are hard to distinguish when tuned exactly, and point to general pitfalls in experimental design, model fitting, and interpretation of the resulting data.

q-bio.NC↗

arXiv2019

Analyzing dynamic decision-making models using Chapman-Kolmogorov equations

Decision-making in dynamic environments typically requires adaptive evidence accumulation that weights new evidence more heavily than old observations. Recent experimental studies of dynamic decision tasks require subjects to make decisions for which the correct choice switches stochastically throughout a single trial. In such cases, an ideal observer's belief is described by an evolution equation that is doubly stochastic, reflecting stochasticity in the both observations and environmental changes. In these contexts, we show that the probability density of the belief can be represented using differential Chapman-Kolmogorov equations, allowing efficient computation of ensemble statistics. This allows us to reliably compare normative models to near-normative approximations using, as model performance metrics, decision response accuracy and Kullback-Leibler divergence of the belief distributions. Such belief distributions could be obtained empirically from subjects by asking them to report their decision confidence. We also study how response accuracy is affected by additional internal noise, showing optimality requires longer integration timescales as more noise is added. Lastly, we demonstrate that our method can be applied to tasks in which evidence arrives in a discrete, pulsatile fashion, rather than continuously.

q-bio.NC↗

arXiv2018

Optimal models of decision-making in dynamic environments

Nature is in constant flux, so animals must account for changes in their environment when making decisions. How animals learn the timescale of such changes and adapt their decision strategies accordingly is not well understood. Recent psychophysical experiments have shown humans and other animals can achieve near-optimal performance at two alternative forced choice (2AFC) tasks in dynamically changing environments. Characterization of performance requires the derivation and analysis of computational models of optimal decision-making policies on such tasks. We review recent theoretical work in this area, and discuss how models compare with subjects' behavior in tasks where the correct choice or evidence quality changes in dynamic, but predictable, ways.

q-bio.NC↗

arXiv2017

From the statistics of connectivity to the statistics of spike times in neuronal networks

An essential step toward understanding neural circuits is linking their structure and their dynamics. In general, this relationship can be almost arbitrarily complex. Recent theoretical work has, however, begun to identify some broad principles underlying collective spiking activity in neural circuits. The first is that local features of network connectivity can be surprisingly effective in predicting global statistics of activity across a network. The second is that, for the important case of large networks with excitatory-inhibitory balance, correlated spiking persists or vanishes depending on the spatial scales of recurrent and feedforward connectivity. We close by showing how these ideas, together with plasticity rules, can help to close the loop between network structure and activity statistics.

q-bio.NC↗

arXiv2017

Modeling mechanical interactions in growing populations of rod-shaped bacteria

Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular fluid flow lead to complex, changing arrangements of cells within the population. To rationally engineer and control the behavior of cell collectives we need theoretical and computational tools to understand their emergent spatiotemporal dynamics. Here, we present an agent-based model that allows growing cells to detect and respond to mechanical interactions. Crucially, our model couples the dynamics of cell growth to the cell's environment: Mechanical constraints can affect cellular growth rate and a cell may alter its behavior in response to these constraints. This coupling links the mechanical forces that influence cell growth and emergent behaviors in cell assemblies. We illustrate our approach by showing how mechanical interactions can impact the dynamics of bacterial collectives growing in microfluidic traps.

q-bio.CB↗