Related papers: Stable developmental patterns of gene expression w…
A new class of pattern forming systems is identified and investigated: anisotropic systems that are spatially inhomogeneous along the direction perpendicular to the preferred one. By studying the generic amplitude equation of this new class…
In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy molecular process, is regulated to…
When dynamics in a system proceeds under suppressive external bias, the system can undergo an abrupt phase transition, as it occurs for example in the epidemic spreading. Recently, an explosive percolation (EP) model was introduced in line…
Motivated by certain problems of statistical physics we consider a stationary stochastic process in which deterministic evolution is interrupted at random times by upward jumps of a fixed size. If the evolution consists of linear decay, the…
Graph neural networks (GNNs) are learning architectures that rely on knowledge of the graph structure to generate meaningful representations of large-scale network data. GNN stability is thus important as in real-world scenarios there are…
Despite their claimed biological plausibility, most self organizing networks have strict topological constraints and consequently they cannot take into account a wide range of external stimuli. Furthermore their evolution is conditioned by…
Stable diffusion models represent the state-of-the-art in data synthesis across diverse domains and hold transformative potential for applications in science and engineering, e.g., by facilitating the discovery of novel solutions and…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
Mini-proteins and peptides manifest dynamic conformational fluctuation and involve mutual interconversion among metastable states. A robust mapping of the conformational landscape underlying mini-proteins and peptides often requires…
Stabilized regression aims to identify a set of predictors whose conditional relationship with a response variable remains invariant across different environments. Existing graphical characterizations of the stable blanket are mainly…
Deriving emergent patterns from models of biological processes is a core concern of mathematical biology. In the context of partial differential equations (PDEs), these emergent patterns sometimes appear as local minimisers of a…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Steering vectors offer a training-free mechanism for controlling reasoning behaviors in large language models, but constructing effective vectors requires identifying genuine behavioral signals in the model's hidden states. For behaviors…
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
Biological systems are typically highly open, non-equilibrium systems that are very challenging to understand from a statistical mechanics perspective. While statistical treatments of evolutionary biological systems have a long and rich…
Advances in sensing technology have made it possible to collect large volumes of high-dimensional time-series data. In fields like genetics and neuroscience, key questions concern whether directed relationships between variables can be…
We introduce a model for amorphous grain boundaries in graphene, and find that stable structures can exist along the boundary that are responsible for local density of states enhancements both at zero and finite (~0.5 eV) energies. Such…
The Free Energy Principle (FEP) states that self-organizing systems must minimize variational free energy to persist, but the path from principle to implementable algorithm has remained unclear. We present a constructive proof that the FEP…
We propose a generative model for single-channel EEG that incorporates the constraints experts actively enforce during visual scoring. The framework takes the form of a dynamic Bayesian network with depth in both the latent variables and…