相关论文: Positional information, positional error, and read…
During development, morphogen gradients precisely determine the position of gene expression boundaries despite the inevitable presence of fluctuations. Recent experiments suggest that some morphogen gradients may be interpreted prior to…
Convergent extension of epithelial tissue is a key motif of animal morphogenesis. On a coarse scale, cell motion resembles laminar fluid flow; yet in contrast to a fluid, epithelial cells adhere to each other and maintain the tissue layer…
This paper lays the foundations for a unified framework for numerically and computationally applying methods drawn from a range of currently distinct geometrical approaches to statistical modelling. In so doing, it extends information…
Advances in imaging technology now provide us with detailed 3D data on gene expression patterns in developing embryos. This information can be used to build predictive mathematical models of embryogenesis. Current modelling approaches are,…
Using a dynamical model to make predictions about a system has many sources of error. These can include errors in how the model was initialised but also errors in the dynamics of the model itself. For many applications in data assimilation,…
Gene expression is a stochastic process in which cells produce biomolecules essential to the function of life. Modern experimental methods allow for the measurement of biomolecules at single-cell and single-molecule resolution over time.…
Artificial intelligence research to a great degree focuses on the brain and behaviors that the brain generates. But the brain, an extremely complex structure resulting from millions of years of evolution, can be viewed as a solution to…
In genetic networks, information of relevance to the organism is represented by the concentrations of transcription factor molecules. In order to extract this information the cell must effectively "measure"' these concentrations, but there…
This report investigates the modular organisation of the Central region in the Drosophila connectome. We identify groups of neurones amongst which information circulates rapidly before spreading to the rest of the network using Infomap. We…
Single-cell gene expression measurements encode variability spanning molecular noise, cell-to-cell heterogeneity, and technical artifacts. Mechanistic stochastic models provide powerful approaches to disentangle these sources, yet inferring…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Autoregressive language models achieve remarkable performance, yet a unified theory explaining their internal mechanisms, how training shapes representations, and why these representations support complex behavior remains incomplete. We…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…
A large body of work in psycholinguistics has focused on the idea that online language comprehension can be shallow or `good enough': given constraints on time or available computation, comprehenders may form interpretations of their input…
The problem of planning sensing trajectories for a mobile robot to collect observations of a target and predict its future trajectory is known as active target tracking. Enabled by probabilistic motion models, one may solve this problem by…
The ability to represent intracellular biochemical dynamics via deterministic and stochastic modelling is one of the crucial components to move biological sciences in the observe-predict-control-design knowledge ladder. Compared to the…
Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of…
This chapter describes a novel approach for the treatment of model error in geophysical data assimilation. In this method, model error is treated as a deterministic process fully correlated in time. This allows for the derivation of the…
The relationship between intelligence and evolution is bidirectional: while evolution can help evolve intelligences, the degree of intelligence itself can impact evolution (Baldwin, 1896). In the field of Evolutionary Computation, the…
This work introduces a framework for quantifying the information content of logical propositions through the use of implication hypergraphs. We posit that a proposition's informativeness is primarily determined by its relationships with…