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Causal discovery, the task of inferring causal structure from data, has the potential to uncover mechanistic insights from biological experiments, especially those involving perturbations. However, causal discovery algorithms over larger…

Machine Learning · Computer Science 2025-04-01 Menghua Wu , Yujia Bao , Regina Barzilay , Tommi Jaakkola

Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…

Cell Behavior · Quantitative Biology 2025-08-20 Ramya Deshpande , Francesco Mottes , Ariana-Dalia Vlad , Michael P. Brenner , Alma dal Co

Discovering the underlying dynamics of complex systems from data is an important practical topic. Constrained optimization algorithms are widely utilized and lead to many successes. Yet, such purely data-driven methods may bring about…

Dynamical Systems · Mathematics 2023-05-17 Nan Chen , Yinling Zhang

We present experiments on the behavior of reaction fronts in ordered and disordered cellular flows with imposed winds. Fronts in a chain of alternating vortices are found to freeze (pin to the separatrix) for a wide range of imposed winds…

Pattern Formation and Solitons · Physics 2007-07-31 M. E. Schwartz , T. H. Solomon

We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of "fast" and "slow" self-propelled Brownian particles is considered in the presence of a…

Soft Condensed Matter · Physics 2023-02-08 Mauricio Rojas-Vega , Pablo de Castro , Rodrigo Soto

The remarkable range of biological forms in and around us, such as the undulating shape of a leaf or flower in the garden, the coils in our gut, or the folds in our brain, raise a number of questions at the interface of biology, physics and…

General Mathematics · Mathematics 2021-05-13 Marta Lewicka , L. Mahadevan

Although transformer-based models have shown exceptional empirical performance, the fundamental principles governing their training dynamics are inadequately characterized beyond configuration-specific studies. Inspired by empirical…

Machine Learning · Computer Science 2025-10-09 Zheng-An Chen , Tao Luo

Non-stationary sequences arise naturally in control, forecasting, and decision-making. The data-generating process shifts at unknown times, and models must detect the change, discard or downweight obsolete evidence, and adapt to new…

Machine Learning · Computer Science 2026-04-21 Carson Dudley , Yutong Bi , Xiaofeng Liu , Samet Oymak

In this paper, we develop new methods for the analysis of decentralized control systems and we apply them to formation control problems. The basic set-up consists of a system with multiple agents corresponding to the nodes of a graph whose…

Optimization and Control · Mathematics 2011-01-20 M. -A. Belabbas

Understanding pattern formation in crossing pedestrian flows is essential for analyzing and managing high-density crowd dynamics in urban environments. This study presents two complementary methodological approaches to detect and…

Physics and Society · Physics 2025-04-24 Piotr Nyczka , Pratik Mullick

We study the patterns formed by adding $N$ sand-grains at a single site on an initial periodic background in the Abelian sandpile models, and relaxing the configuration. When the heights at all sites in the initial background are low…

Statistical Mechanics · Physics 2014-11-18 Tridib Sadhu , Deepak Dhar

We consider the motion of planar phase-transition fronts in first-order phase transitions of the Universe. We find the steady state wall velocity as a function of a friction coefficient and thermodynamical parameters, taking into account…

Cosmology and Nongalactic Astrophysics · Physics 2012-08-17 Ariel Megevand , Alejandro D. Sanchez

Many patterning events in multi-cellular organisms rely on cell-to-cell contact signaling, such as the Notch pathway in metazoans. A particularly interesting phenomenon in this form of communication is lateral inhibition where a cell that…

Dynamical Systems · Mathematics 2012-01-09 Murat Arcak

The existence, stability properties, and bifurcation diagrams of localized patterns and hole solutions in one-dimensional extended systems is studied from the point of view of front interactions. An adequate envelope equation is derived…

Pattern Formation and Solitons · Physics 2009-11-11 M. G. Clerc , C. Falcon

Using dynamical density functional theory we calculate the speed of solidification fronts advancing into a quenched two-dimensional model fluid of soft-core particles. We find that solidification fronts can advance via two different…

Soft Condensed Matter · Physics 2014-10-22 A. J. Archer , M. C. Walters , U. Thiele , E. Knobloch

We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse grained models can be…

Understanding how growth induces form is a longstanding biological question. Many studies concentrated on the shapes of plant cells, fungi or bacteria. Some others have shown the importance of the mechanical properties of bacterial walls…

Biological Physics · Physics 2007-05-23 Arezki Boudaoud

Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…

Biological Physics · Physics 2024-05-15 Tom Burkart , Benedikt J. Müller , Erwin Frey

This work deals with the presence of topological structures in models of two real scalar fields in the two-dimensional spacetime. The subject concerns the presence of a geometric constriction, which appears with a modification of the…

High Energy Physics - Theory · Physics 2024-03-11 D. Bazeia , M. A. Feitosa , R. Menezes , G. S. Santiago

This article was motivated by the discovery of a potential new foundation for mainstream mathematics. The goals are to clarify the relationships between primitives, foundations, and deductive practice; to understand how to determine what…

History and Overview · Mathematics 2025-02-18 Frank Quinn