Related papers: Positional information, positional error, and read…
The expected position error in many cases is far from feasible to be estimated experimentally using real satellite measurements which makes the model-based position dilution of precision (PDOP) crucial in positioning and navigation…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
The fundamental biological processes of development of tissues and organs in multicellular organisms is governed by various signaling molecules, which are called morphogens. It is known that spatial and temporal variations in concentration…
Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's…
In a sequential decision-making problem, the information structure is the description of how events in the system occurring at different points in time affect each other. Classical models of reinforcement learning (e.g., MDPs, POMDPs)…
Expression of the Drosophila segment polarity genes is initiated by a prepattern of pair-rule gene products and maintained by a network of regulatory interactions throughout several stages of embryonic development. Analysis of a model of…
During development of biological organisms, multiple complex structures are formed. In many instances, these structures need to exhibit a high degree of order to be functional, although many of their constituents are intrinsically…
Cell fate decisions in multicellular organisms are precisely coordinated, leading to highly reproducible macroscopic outcomes of developmental processes. The origins of this reproducibility can be found at the molecular level during the…
Gene transcription is a critical step in gene expression. The currently accepted physical model of transcription predicts the existence of a physical limit on the maximal rate of transcription, which does not depend on the transcribed gene.…
Most animals possess the ability to actuate a vast diversity of movements, ostensibly constrained only by morphology and physics. In practice, however, a frequent assumption in behavioral science is that most of an animal's activities can…
3D human pose estimation from 2D images is a challenging problem due to depth ambiguity and occlusion. Because of these challenges the task is underdetermined, where there exists multiple -- possibly infinite -- poses that are plausible…
Information Theory provides a fundamental basis for analysis, and for a variety of subsequent methodological approaches, in relation to uncertainty quantification. The transversal character of concepts and derived results justifies its…
The positioning of new cellular walls during cell division plays a key role in shaping plant tissue organization. The influence of cell geometry on the positioning of division planes has been previously captured into various geometrical…
Multiple types of inference are available for probabilistic graphical models, e.g., marginal, maximum-a-posteriori, and even marginal maximum-a-posteriori. Which one do researchers mean when they talk about "planning as inference"? There is…
Multicellular tissues are the building blocks of many biological systems and organs. These tissues are not static, but dynamically change over time. Even if the overall structure remains the same there is a turnover of cells within the…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
The deterministic notions of capacity and entropy are studied in the context of communication and storage of information using square-integrable, bandlimited signals subject to perturbation. The $(\epsilon,\delta)$-capacity, that extends…
The task of modelling and forecasting a dynamical system is one of the oldest problems, and it remains challenging. Broadly, this task has two subtasks - extracting the full dynamical information from a partial observation; and then…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…