Related papers: Cell assemblies at multiple time scales with arbit…
The synaptic connectivity of cortex is plastic, with experience shaping the ongoing interactions between neurons. Theoretical studies of spike timing-dependent plasticity (STDP) have focused on either just pairs of neurons or large-scale…
Neural computation is associated with the emergence, reconfiguration and dissolution of cell assemblies in the context of varying oscillatory states. Here, we describe the complex spatio-temporal dynamics of cell assemblies through temporal…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
We revisit the planning problem in the blocks world, and we implement a known heuristic for this task. Importantly, our implementation is biologically plausible, in the sense that it is carried out exclusively through the spiking of…
In this paper we propose a novel algorithm to combine two or more cellular complexes, providing a minimal fragmentation of the cells of the resulting complex. We introduce here the idea of arrangement generated by a collection of cellular…
The spontaneous generation of electrical activity underpins a number of essential physiological processes, and is observed even in tissues where specialized pacemaker cells have not been identified. The emergence of periodic oscillations in…
Biological systems represent time from microseconds to years. An important gap in our knowledge concerns the mechanisms for encoding time intervals of hundreds of milliseconds to minutes that matter for tasks like navigation, communication,…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
Deep learning dominates speech processing but relies on massive datasets, global backpropagation-guided weight updates, and produces entangled representations. Assembly Calculus (AC), which models sparse neuronal assemblies via Hebbian…
Many fields, such as neuroscience, are experiencing the vast proliferation of cellular data, underscoring the need for organizing and interpreting large datasets. A popular approach partitions data into manageable subsets via hierarchical…
The discovery of general principles underlying the complexity and diversity of cellular and developmental systems is a central and long-standing aim of biology. Whilst new technologies collect data at an ever-accelerating rate, there is…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
We study hierarchical clusterings of metric spaces that change over time. This is a natural geometric primitive for the analysis of dynamic data sets. Specifically, we introduce and study the problem of finding a temporally coherent…
Many mathematical models of synaptic plasticity have been proposed to explain the diversity of plasticity phenomena observed in biological organisms. These models range from simple interpretations of Hebb's postulate, which suggests that…
The principles of neural encoding and computations are inherently collective and usually involve large populations of interacting neurons with highly correlated activities. While theories of neural function have long recognized the…
The process of collecting and organizing sets of observations represents a common theme throughout the history of science. However, despite the ubiquity of scientists measuring, recording, and analyzing the dynamics of different processes,…
Neurodegenerative diseases are driven by the accumulation of protein aggregates in the brain of affected individuals. The aggregation behaviour in vitro is well understood and driven by the equilibration of a super-saturated protein…
We show that the unavoidable increase in neuronal response latency to ongoing stimulation serves as a nonuniform gradual stretching of neuronal circuit delay loops and emerges as an essential mechanism in the formation of various types of…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…