Related papers: Predicting concentration changes via discrete samp…
Real-world vision models in dynamic environments face rapid shifts in domain distributions, leading to decreased recognition performance. Using unlabeled test data, continuous test-time adaptation (CTTA) directly adjusts a pre-trained…
Molecular communication is set to play an important role in the design of complex biological and chemical systems. An important class of molecular communication systems is based on the timing channel, where information is encoded in the…
Escherichia coli is a motile bacterium that moves up a chemoattractant gradient by performing a biased random walk composed of alternating runs and tumbles. Previous models of run and tumble chemotaxis neglect one or more features of the…
The Escherichia coli chemotaxis signaling pathway has served as a model system for studying the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the…
Finding reduced models of spatially-distributed chemical reaction networks requires an estimation of which effective dynamics are relevant. We propose a machine learning approach to this coarse graining problem, where a maximum entropy…
Quantitatively predictive models of biomolecular circuits are important tools for the design of synthetic biology and molecular communication circuits. The information content of typical time-lapse single-cell data for the inference of…
We introduce a novel approach based on stochastic optimization to find the optimal sampling distribution for the data-driven stability analysis of switched linear systems. Our goal is to address limitations of existing approaches, in…
We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from…
The bacterium E. coli maneuvers itself to regions with high chemoattractant concentrations by performing two stereotypical moves: `runs', in which it moves in near straight lines, and `tumbles', in which it does not advance but changes…
In this work we explore encoding strategies learned by statistical models of sensory coding in noisy spiking networks. Early stages of sensory communication in neural systems can be viewed as encoding channels in the information-theoretic…
Obtaining high certainty in predictive models is crucial for making informed and trustworthy decisions in many scientific and engineering domains. However, extensive experimentation required for model accuracy can be both costly and…
Chemotactic cells establish cell polarity in the absence of external guidance cues. Such self-organized polarity is induced by spontaneous symmetry breaking in the intracellular activities, which produces an emergent memory effect…
In an indirect Gaussian sequence space model lower and upper bounds are derived for the concentration rate of the posterior distribution of the parameter of interest shrinking to the parameter value $\theta^\circ$ that generates the data.…
Wet-lab experiments, in which the dynamics within living cells are observed, are usually costly and time consuming. This is particularly true if single-cell measurements are obtained using experimental techniques such as flow-cytometry or…
Transport networks are crucial for the functioning of natural and technological systems. We study a mathematical model of vascular network adaptation, where the network structure dynamically adjusts to changes in blood flow and pressure.…
When cells measure concentrations of chemical signals, they may average multiple measurements over time in order to reduce noise in their measurements. However, when cells are in a environment that changes over time, past measurements may…
The linear response of a dynamical system refers to changes to properties of the system when small external perturbations are applied. We consider the little-studied question of selecting an optimal perturbation so as to (i) maximise the…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Gene-knockout experiments on single-cell organisms have established that expression of a substantial fraction of genes is not needed for optimal growth. This problem acquired a new dimension with the recent discovery that environmental and…
Unraveling bacterial strategies for spatial exploration is crucial for understanding the complexity in the organization of life. Bacterial motility determines the spatio-temporal structure of microbial communities, controls infection…