How to Knit Your Own Markov Blanket

Hohwy (Hohwy 2016, Hohwy 2017) argues there is a tension between the free energy principle and leading depictions of mind as embodied, enactive, and extended (so-called ‘EEE1 cognition’). The tension is traced to the importance, in free energy formulations, of a conception of mind and agency that depends upon the presence of a ‘Markov blanket’ demarcating the agent from the surrounding world. In what follows I show that the Markov blanket considerations do not, in fact, lead to the kinds of tension that Hohwy depicts. On the contrary, they actively favour the EEE story. This is because the Markov property, as exemplified in biological agents, picks out neither a unique nor a stationary boundary. It is this multiplicity and mutability– rather than the absence of agent-environment boundaries as such - that EEE cognition celebrates

Improving the Efficiency of Genomic Selection

We investigate two approaches to increase the efficiency of phenotypic prediction from genome-wide markers, which is a key step for genomic selection (GS) in plant and animal breeding. The first approach is feature selection based on Markov blankets, which provide a theoretically-sound framework for identifying non-informative markers. Fitting GS models using only the informative markers results in simpler models, which may allow cost savings from reduced genotyping. We show that this is accompanied by no loss, and possibly a small gain, in predictive power for four GS models: partial least squares (PLS), ridge regression, LASSO and elastic net. The second approach is the choice of kinship coefficients for genomic best linear unbiased prediction (GBLUP). We compare kinships based on different combinations of centring and scaling of marker genotypes, and a newly proposed kinship measure that adjusts for linkage disequilibrium (LD). We illustrate the use of both approaches and examine their performances using three real-world data sets from plant and animal genetics. We find that elastic net with feature selection and GBLUP using LD-adjusted kinships performed similarly well, and were the best-performing methods in our study.Comment: 17 pages, 5 figure

How to entrain your evil demon

The notion that the brain is a prediction error minimizer entails, via the notion of Markov blankets and self-evidencing, a form of global scepticism — an inability to rule out evil demon scenarios. This type of scepticism is viewed by some as a sign of a fatally flawed conception of mind and cognition. Here I discuss whether this scepticism is ameliorated by acknowledging the role of action in the most ambitious approach to prediction error minimization, namely under the free energy principle. I argue that the scepticism remains but that the role of action in the free energy principle constrains the demon’s work. This yields new insights about the free energy principle, epistemology, and the place of mind in nature

A probabilistic model for information and sensor validation

This paper develops a new theory and model for information and sensor validation. The model represents relationships between variables using Bayesian networks and utilizes probabilistic propagation to estimate the expected values of variables. If the estimated value of a variable differs from the actual value, an apparent fault is detected. The fault is only apparent since it may be that the estimated value is itself based on faulty data. The theory extends our understanding of when it is possible to isolate real faults from potential faults and supports the development of an algorithm that is capable of isolating real faults without deferring the problem to the use of expert provided domain-specific rules. To enable practical adoption for real-time processes, an any time version of the algorithm is developed, that, unlike most other algorithms, is capable of returning improving assessments of the validity of the sensors as it accumulates more evidence with time. The developed model is tested by applying it to the validation of temperature sensors during the start-up phase of a gas turbine when conditions are not stable; a problem that is known to be challenging. The paper concludes with a discussion of the practical applicability and scalability of the model

A Multi-scale View of the Emergent Complexity of Life: A Free-energy Proposal

We review some of the main implications of the free-energy principle (FEP) for the study of the self-organization of living systems – and how the FEP can help us to understand (and model) biotic self-organization across the many temporal and spatial scales over which life exists. In order to maintain its integrity as a bounded system, any biological system - from single cells to complex organisms and societies - has to limit the disorder or dispersion (i.e., the long-run entropy) of its constituent states. We review how this can be achieved by living systems that minimize their variational free energy. Variational free energy is an information theoretic construct, originally introduced into theoretical neuroscience and biology to explain perception, action, and learning. It has since been extended to explain the evolution, development, form, and function of entire organisms, providing a principled model of biotic self-organization and autopoiesis. It has provided insights into biological systems across spatiotemporal scales, ranging from microscales (e.g., sub- and multicellular dynamics), to intermediate scales (e.g., groups of interacting animals and culture), through to macroscale phenomena (the evolution of entire species). A crucial corollary of the FEP is that an organism just is (i.e., embodies or entails) an implicit model of its environment. As such, organisms come to embody causal relationships of their ecological niche, which, in turn, is influenced by their resulting behaviors. Crucially, free-energy minimization can be shown to be equivalent to the maximization of Bayesian model evidence. This allows us to cast natural selection in terms of Bayesian model selection, providing a robust theoretical account of how organisms come to match or accommodate the spatiotemporal complexity of their surrounding niche. In line with the theme of this volume; namely, biological complexity and self-organization, this chapter will examine a variational approach to self-organization across multiple dynamical scales