Related papers: Interfacing biology, category theory and mathemati…

Widespread population aging has made it critical to understand death rates at old ages. However, studying mortality at old ages is challenging because the data are sparse: numbers of survivors and deaths get smaller and smaller with age. We…

Causal inference and model interpretability research are gaining increasing attention, especially in the domains of healthcare and bioinformatics. Despite recent successes in this field, decorrelating features under nonlinear environments…

We consider biological individuality in terms of information theoretic and graphical principles. Our purpose is to extract through an algorithmic decomposition system-environment boundaries supporting individuality. We infer or detect…

We study the rate of decay of the probability of error for distinguishing between a sparse signal with noise, modeled as a sparse mixture, from pure noise. This problem has many applications in signal processing, evolutionary biology,…

The closure and the partitioning principles have been used to build various multiple testing procedures in the past three decades. The essence of these two principles is based on parameter space partitioning. In this article, we propose a…

We formulate an info-clustering paradigm based on a multivariate information measure, called multivariate mutual information, that naturally extends Shannon's mutual information between two random variables to the multivariate case…

This paper is Part I of a two-part series devoting to the study of systematic measures in a complex biological network modeled by a system of ordinary differential equations. As the mathematical complement to our previous work [31] with…

In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…

Cellular mechanism-of-action is of fundamental concern in many biological studies. It is of particular interest for identifying the cause of disease and learning the way in which treatments act against disease. However, pinpointing such…

We examine the convergence properties of sequences of nonnegative real numbers that satisfy a particular class of recursive inequalities, from the perspective of proof theory and computability theory. We first establish a number of results…

For a long time, detection and parameter estimation methods for signal processing have relied on asymptotic statistics as the number $n$ of observations of a population grows large comparatively to the population size $N$, i.e. $n/N\to…

In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…

By linking conceptual theories with observed data, generative models can support reasoning in complex situations. They have come to play a central role both within and beyond statistics, providing the basis for power analysis in molecular…

Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…

Heterogeneous data from multiple populations, sub-groups, or sources is often represented as a ``mixture model'' with a single latent class influencing all of the observed covariates. Heterogeneity can be resolved at multiple levels by…

Several different versions of the theory of numerosities have been introduced in the literature. Here, we unify these approaches in a consistent frame through the notion of set of labels, relating numerosities with the Kiesler field of…

Based on Jaynes' maximum entropy principle, exponential random graphs provide a family of principled models that allow the prediction of network properties as constrained by empirical data (observables). However, their use is often hindered…

Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…

Everyone can see that over the last 150 years, theoretical ecology has become considerably more mathematical. But what is the nature of this phenomenon? Are mathematics applied, as in the use of statistical tests, for example, or are they…

Developing effective therapies against epilepsy remains a challenge. The complex and multifaceted nature of this disease still fuels controversies about its origin. In this perspective article, we argue that conflicting hypotheses can be…