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Shin Fujishiro

Publications and source records attributed to Shin Fujishiro.

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Distinct weak asymmetric interactions shape human brain functions as probability fluxes

The functional computation of the human brain arises from the collective behaviour of the underlying neural network. The emerging technology enables the recording of population activity in neurons, and the theory of neural networks is expected to explain and extract functional computations from the data. Thermodynamically, a large proportion of the whole-body energy is consumed by the brain, and functional computation of the human brain seems to involve high energy consumption. The human brain, however, does not increase its energy consumption with its function, and most of its energy consumption is not involved in specific brain function: how can the human brain perform its wide repertoire of functional computations without drastically changing its energy consumption? Here, we present a mechanism to perform functional computation by subtle modification of the interaction network among the brain regions. We first show that, by analyzing the data of spontaneous and task-induced whole-cerebral-cortex activity, the probability fluxes, which are the microscopic irreversible measure of state transitions, exhibit unique patterns depending on the task being performed, indicating that the human brain function is a distinct sequence of the brain state transitions. We then fit the parameters of Ising spin systems with asymmetric interactions, where we reveal that the symmetric interactions among the brain regions are strong and task-independent, but the antisymmetric interactions are subtle and task-dependent, and the inferred model reproduces most of the observed probability flux patterns. Our results indicate that the human brain performs its functional computation by subtly modifying the antisymmetric interaction among the brain regions, which might be possible with a small amount of energy.

physics.bio-ph

Landscapes and nonequilibrium fluctuations of eukaryotic gene regulation

Understanding the interplay among processes that occur over different timescales is a challenging issue in the physics of systems regulation. In gene regulation, the timescales for changes in chromatin states can differ from those for changes in the concentration of product protein, raising questions about how to understand their coupled dynamics. In this study, we examine the effects of these different timescales on eukaryotic gene regulation using a stochastic model that describes the landscapes and probability currents of nonequilibrium fluctuations.This model shows that slow, nonadiabatic transitions of chromatin states significantly impact gene-regulation dynamics. The simulated circular flow of the probability currents indicates a maximum entropy production when the rates of chromatin-state transitions are low in the intensely nonadiabatic regime. In the mildly nonadiabatic regime, this circular flow fosters hysteresis, suggesting that changes in chromatin states precede changes in transcription activity. Furthermore, calculations using a model of a circuit involving three core genes in mouse embryonic stem cells illustrate how the timescale difference can tune fluctuations in individual genes. These findings highlight the rich effects of nonadiabatic chromatin-state transitions on gene regulation in eukaryotic cells.

physics.bio-ph

Orthogonal projections of hypercubes

Projections of hypercubes have been applied to visualize high-dimensional binary state spaces in various scientific fields. Conventional methods for projecting hypercubes, however, face practical difficulties. Manual methods require nontrivial adjustments of the projection basis, while optimization-based algorithms limit the interpretability and reproducibility of the resulting plots. These limitations motivate us to explore theoretically analyzable projection algorithms such as principal component analysis (PCA). Here, we investigate the mathematical properties of PCA-projected hypercubes. Our numerical and analytical results show that PCA effectively captures polarized distributions within the hypercubic state space. This property enables the assessment of the asymptotic distribution of projected vertices and error bounds, which characterize the performance of PCA in the projected space. We demonstrate the application of PCA to visualize the hypercubic energy landscapes of Ising spin systems, specifically finite artificial spin-ice systems, including those with geometric frustration. By adding projected hypercubic edges, these visualizations reveal pathways of correlated spin flips. We confirm that the time-integrated probability flux exhibits patterns consistent with the pathways identified in the projected hypercubic energy landscapes. Using the mean-field model, we show that dominant state transition pathways tend to emerge around the periphery of the projected hypercubes. Our work provides a better understanding of how PCA discovers hidden patterns in high-dimensional binary data.

physics.data-an