Related papers: A Spatial Filtering Approach to Biological Pattern…
A complex system comprises multiple interacting entities whose interdependencies form a unified whole, exhibiting emergent behaviours not present in individual components. Examples include the human brain, living cells, soft matter, Earth's…
We derive gain-tuning rules for the positive and negative spatial-feedback loops of a spatially-distributed filter to change the resolution of its spatial band-pass characteristic accordingly to a wavelet zoom, while preserving temporal…
Noise and spatial degrees of freedom characterize most ecosystems. Some aspects of their influence on the coevolution of populations with cyclic interspecies competition have been demonstrated in recent experiments [e.g. B. Kerr et al.,…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
Many image processing operations involve the modification of the spatial frequency content of images. Here we demonstrate object-plane spatial frequency filtering utilizing the angular sensitivity of a commercial spectral bandstop filter.…
Model diffing methods aim to identify how fine-tuning changes a model's internal representations. Crosscoders approach this by learning shared dictionaries of interpretable latent directions between base and fine-tuned models. However,…
We introduce a dynamical spatio-temporal model formalized as a recurrent neural network for forecasting time series of spatial processes, i.e. series of observations sharing temporal and spatial dependencies. The model learns these…
In this paper, we investigate the complex dynamics of a spatial plankton-fish system with Holling type III functional responses. We have carried out the analytical study for both one and two dimensional system in details and found out a…
A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…
Emergence of regular spatial patterns is a hallmark in living matter ranging from subcellular organelles to developing embryos and to ecosystems. Mechanisms for the formation of ordered spatial patterns in biology often require chemical…
Recent works on deep non-linear spatially selective filters demonstrate exceptional enhancement performance with computationally lightweight architectures for stationary speakers of known directions. However, to maintain this performance in…
In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in…
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in…
We consider systems that are well modelled as a networks that evolve in time, which we call {\it Moving Neighborhood Networks}. These models are relevant in studying cooperative behavior of swarms and other phenomena where emergent…
The understanding of neural activity patterns is fundamentally linked to an understanding of how the brain's network architecture shapes dynamical processes. Established approaches rely mostly on deviations of a given network from certain…
We introduce bio-inspired artificial neural networks consisting of neurons that are additionally characterized by spatial positions. To simulate properties of biological systems we add the costs penalizing long connections and the proximity…
Many systems in biology, physics and engineering can be described by systems of ordinary differential equation containing many parameters. When studying the dynamic behavior of these large, nonlinear systems, it is useful to identify and…
In this paper mathematical models for the evolutionary conserved Notch-Delta pathway are developed and analyzed in order to better understand how two neighboring biological cells can become different. We pursue a structure-based…