Knowing one's place: a free-energy approach to pattern regulation

Abstract

Understanding how organisms establish their form during embryogenesis and regeneration represents a major knowledge gap in biological pattern formation. It has been recently suggested that morphogenesis could be understood in terms of cellular information processing and the ability of cell groups to model shape. Here, we offer a proof of principle that self-assembly is an emergent property of cells that share a common (genetic and epigenetic) model of organismal form. This behaviour is formulated in terms of variational free-energy minimization—of the sort that has been used to explain action and perception in neuroscience. In brief, casting the minimization of thermodynamic free energy in terms of variational free energy allows one to interpret (the dynamics of) a system as inferring the causes of its inputs—and acting to resolve uncertainty about those causes. This novel perspective on the coordination of migration and differentiation of cells suggests an interpretation of genetic codes as parametrizing a generative model—predicting the signals sensed by cells in the target morphology—and epigenetic processes as the subsequent inversion of that model. This theoretical formulation may complement bottom-up strategies—that currently focus on molecular pathways—with (constructivist) top-down approaches that have proved themselves in neuroscience and cybernetics.

Where There is Life There is Mind: In Support of a Strong Life-Mind Continuity Thesis

“…It is this knowledge-based formulation that adds the cognitivist assumption. We will unpack what we mean by this, since the FEP is generally taken to imply that internal states engage in Bayesian inference in which internal-comprising a system's generative model-as well as active states can be modeled as minimizing free energy inferentially [29]. So, it is not the issue of inference or the possession of a generative model as such that exemplifies the cognitivist assumption.…”

“…Non-cognitivist FEP casts free energy minimization in physical systems in terms of Shannon "entropy" in information theory [5]. Hence, it is possible to posit the FEP as the unifying principle of life and mind and, at the same time, deny that the most basic features of life and mind involve probabilistic inferences with semantic content, even if the basis of life and mind involves probabilistic inference (see also [10,14,29]). …”

“…In a cell, say, the surface of a cell can be cast as constituting a Markov blanket, thus separating intracellular (internal) and extracellular (external) states. A Markov blanket can itself be further partitioned into perceptual/sensory states and active states [10,29]. Assuming that one can interpret internal states as parametrizing "some arbitrary (variational) density or Bayesian beliefs .…”

“…. about external states, then the dynamics of internal and active states can be described as a gradient descent on variational free energy" ( [29], p. 3). In other words, one can describe the system in virtue of possessing a Markov blanket as maximizing model evidence via approximate Bayesian inference.…”

Термодинамический Подход К Проблеме Определения Числа Кластеров На Основе Тематического Моделирования

“…Термодинамический формализм, реализованный на основе миними-зации свободной энергии, успешно применяется в различных областях, таких как обработка изображений [1], нейронные сети [2], кластерный анализ [3]. Существенное развитие методов кластеризации произошло в рамках тематического моделирования (ТМ) [4,5].…”