PyPhi: A toolbox for integrated information theory.
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ABSTRACT:
SUBMITTER: Mayner WGP
PROVIDER: S-EPMC6080800 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Integrated Information Theory was developed to explain and quantify consciousness, arguing that conscious systems consist of elements that are integrated through their causal properties. This study presents an implementation of Integrated Information Theory 3.0, the latest version of this framework, to functional MRI data. Data were acquired from 17 healthy subjects who underwent sedation with propofol, a short-acting anaesthetic. Using the PyPhi software package, we systematically analyze how Φmax, a measure of integrated information, is modulated by the sedative in different resting-state networks. We compare Φmax to other proposed measures of conscious level, including the previous version of integrated information, Granger causality, and correlation-based functional connectivity. Our results indicate that Φmax presents a variety of sedative-induced behaviours for different networks. Notably, changes to Φmax closely reflect changes to subjects' conscious level in the frontoparietal and dorsal attention networks, which are responsible for higher-order cognitive functions. In conclusion, our findings present important insight into different measures of conscious level that will be useful in future implementations to functional MRI and other forms of neuroimaging.
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Project description:Collective behaviours are known to be the result of diverse dynamics and are sometimes likened to living systems. Although many studies have revealed the dynamics of various collective behaviours, their main focus has been on the information processing performed by the collective, not on interactions within the collective. For example, the qualitative difference between three and four elements in a system has rarely been investigated. Tononi et al. proposed integrated information theory (IIT) to measure the degree of consciousness ?. IIT postulates that the amount of information loss caused by the minimum information partition is equivalent to the degree of information integration in the system. This measure is not only useful for estimating the degree of consciousness but can also be applied to more general network systems. Here, we obtained two main results from the application of IIT (in particular, IIT 3.0) to the analysis of real fish schools (Plecoglossus altivelis). First, we observed that the discontinuity on ??(N)? distributions emerges for a school of four or more fish. This transition was not observed by measuring the mutual information or the sum of the transfer entropy. We also analysed the IIT on Boids simulations with respect to different coupling strengths; however, the results of the Boids model were found to be quite different from those of real fish. Second, we found a correlation between this discontinuity and the emergence of leadership. We discriminate leadership in this paper from its traditional meaning (e.g. defined by transfer entropy) because IIT-induced leadership refers not to group behaviour, as in other methods, but the degree of autonomy (i.e. group integrity). These results suggest that integrated information ? can reveal the emergence of a new type of leadership which cannot be observed using other measures.
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Project description:This paper presents Integrated Information Theory (IIT) of consciousness 3.0, which incorporates several advances over previous formulations. IIT starts from phenomenological axioms: information says that each experience is specific--it is what it is by how it differs from alternative experiences; integration says that it is unified--irreducible to non-interdependent components; exclusion says that it has unique borders and a particular spatio-temporal grain. These axioms are formalized into postulates that prescribe how physical mechanisms, such as neurons or logic gates, must be configured to generate experience (phenomenology). The postulates are used to define intrinsic information as "differences that make a difference" within a system, and integrated information as information specified by a whole that cannot be reduced to that specified by its parts. By applying the postulates both at the level of individual mechanisms and at the level of systems of mechanisms, IIT arrives at an identity: an experience is a maximally irreducible conceptual structure (MICS, a constellation of concepts in qualia space), and the set of elements that generates it constitutes a complex. According to IIT, a MICS specifies the quality of an experience and integrated information ?Max its quantity. From the theory follow several results, including: a system of mechanisms may condense into a major complex and non-overlapping minor complexes; the concepts that specify the quality of an experience are always about the complex itself and relate only indirectly to the external environment; anatomical connectivity influences complexes and associated MICS; a complex can generate a MICS even if its elements are inactive; simple systems can be minimally conscious; complicated systems can be unconscious; there can be true "zombies"--unconscious feed-forward systems that are functionally equivalent to conscious complexes.
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Project description:Networks distribute energy, materials and information to the components of a variety of natural and human-engineered systems, including organisms, brains, the Internet and microprocessors. Distribution networks enable the integrated and coordinated functioning of these systems, and they also constrain their design. The similar hierarchical branching networks observed in organisms and microprocessors are striking, given that the structure of organisms has evolved via natural selection, while microprocessors are designed by engineers. Metabolic scaling theory (MST) shows that the rate at which networks deliver energy to an organism is proportional to its mass raised to the 3/4 power. We show that computational systems are also characterized by nonlinear network scaling and use MST principles to characterize how information networks scale, focusing on how MST predicts properties of clock distribution networks in microprocessors. The MST equations are modified to account for variation in the size and density of transistors and terminal wires in microprocessors. Based on the scaling of the clock distribution network, we predict a set of trade-offs and performance properties that scale with chip size and the number of transistors. However, there are systematic deviations between power requirements on microprocessors and predictions derived directly from MST. These deviations are addressed by augmenting the model to account for decentralized flow in some microprocessor networks (e.g. in logic networks). More generally, we hypothesize a set of constraints between the size, power and performance of networked information systems including transistors on chips, hosts on the Internet and neurons in the brain.
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Project description:Integrated information theory (IIT) has established itself as one of the leading theories for the study of consciousness. IIT essentially proposes that quantitative consciousness is identical to maximally integrated conceptual information, quantified by a measure called ?max, and that phenomenological experience corresponds to the associated set of maximally irreducible cause-effect repertoires of a physical system being in a certain state. With the current work, we provide a general formulation of the framework, which comprehensively and parsimoniously expresses ?max in the language of probabilistic models. Here, the stochastic process describing a system under scrutiny corresponds to a first-order time-invariant Markov process, and all necessary mathematical operations for the definition of ?max are fully specified by a system's joint probability distribution over two adjacent points in discrete time. We present a detailed constructive rule for the decomposition of a system into two disjoint subsystems based on flexible marginalization and factorization of this joint distribution. Furthermore, we show that for a given joint distribution, virtualization is identical to a flexible factorization enforcing independence between variable subsets. We then validate our formulation in a previously established discrete example system, in which we also illustrate the previously unexplored theoretical issue of quale underdetermination due to non-unique maximally irreducible cause-effect repertoires. Moreover, we show that the current definition of ? entails its sensitivity to the shape of the conceptual structure in qualia space, thus tying together IIT's measures of quantitative and qualitative consciousness, which we suggest be better disentangled. We propose several modifications of the framework in order to address some of these issues.
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Project description:Providing objective metrics of conscious state is of great interest across multiple research and clinical fields-from neurology to artificial intelligence. Here we approach this challenge by proposing plausible mechanisms for the phenomenon of structured experience. In earlier work, we argued that the experience we call reality is a mental construct derived from information compression. Here we show that algorithmic information theory provides a natural framework to study and quantify consciousness from neurophysiological or neuroimaging data, given the premise that the primary role of the brain is information processing. We take as an axiom that "there is consciousness" and focus on the requirements for structured experience: we hypothesize that the existence and use of compressive models by cognitive systems, e.g. in biological recurrent neural networks, enables and provides the structure to phenomenal experience. Self-awareness is seen to arise naturally (as part of a better model) in cognitive systems interacting bidirectionally with the external world. Furthermore, we argue that by running such models to track data, brains can give rise to apparently complex (entropic but hierarchically organized) data. We compare this theory, named KT for its basis on the mathematical theory of Kolmogorov complexity, to other information-centric theories of consciousness. We then describe methods to study the complexity of the brain's output streams or of brain state as correlates of conscious state: we review methods such as (i) probing the brain through its input streams (e.g. event-related potentials in oddball paradigms or mutual algorithmic information between world and brain), (ii) analyzing spontaneous brain state, (iii) perturbing the brain by non-invasive transcranial stimulation, and (iv) quantifying behavior (e.g. eye movements or body sway).
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Project description:How difficult is it to 'discover' an evolutionary adaptation or innovation? I here suggest that information theory, in combination with high-throughput DNA sequencing, can help answer this question by quantifying a new phenotype's information content. I apply this framework to compute the phenotypic information associated with novel gene regulation and with the ability to use novel carbon sources. The framework can also help quantify how DNA duplications affect evolvability, estimate the complexity of phenotypes and clarify the meaning of 'progress' in Darwinian evolution.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Project description:Different plant defense theories have provided important theoretical guidance in explaining patterns in plant specialized metabolism, but their critical predictions remain to be tested. Here, we systematically explored the metabolomes of Nicotiana attenuata, from single plants to populations, as well as of closely related species, using unbiased tandem mass spectrometry (MS/MS) analyses and processed the abundances of compound spectrum-based MS features within an information theory framework to test critical predictions of optimal defense (OD) and moving target (MT) theories. Information components of plant metabolomes were consistent with the OD theory but contradicted the main prediction of the MT theory for herbivory-induced dynamics of metabolome compositions. From micro- to macroevolutionary scales, jasmonate signaling was confirmed as the master determinant of OD, while ethylene signaling provided fine-tuning for herbivore-specific responses annotated via MS/MS molecular networks.
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Project description:Organisms have evolved sensory mechanisms to extract pertinent information from their environment, enabling them to assess their situation and act accordingly. For social organisms travelling in groups, like the fish in a school or the birds in a flock, sharing information can further improve their situational awareness and reaction times. Data on the benefits and costs of social coordination, however, have largely allowed our understanding of why collective behaviours have evolved to outpace our mechanistic knowledge of how they arise. Recent studies have begun to correct this imbalance through fine-scale analyses of group movement data. One approach that has received renewed attention is the use of information theoretic (IT) tools like mutual information, transfer entropy and causation entropy, which can help identify causal interactions in the type of complex, dynamical patterns often on display when organisms act collectively. Yet, there is a communications gap between studies focused on the ecological constraints and solutions of collective action with those demonstrating the promise of IT tools in this arena. We attempt to bridge this divide through a series of ecologically motivated examples designed to illustrate the benefits and challenges of using IT tools to extract deeper insights into the interaction patterns governing group-level dynamics. We summarize some of the approaches taken thus far to circumvent existing challenges in this area and we conclude with an optimistic, yet cautionary perspective.
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Project description:The study of biocultural diversity requires the use of appropriate concepts and analytical tools. Particularly, there is a need of indices capable to show the degree of stratification in the set of interactions among cultures and groups of plants and animals in a given region. Here, we present a mathematical approach based on the mutual Shannon information theory to study the relationships among cultural and biological groups. Biocultural complexity was described in terms of effective biocultural units, a new concept defined in this work. From the mathematical formulation of biocultural complexity, formulas were derived to measure the specificity of biological groups and the specialization of cultures, based on the association of human societies with plant or animal groups. To exemplify the concepts and tools, two data sets were analyzed; 1) a set that included artificial data in order to demonstrate the use of the formulas and calculate the indices, and 2) a set that included published data on the use of 18 mushroom species by people in five villages of eastern India. Analysis of the first data set revealed a clear case of biocultural complexity, whereas that of the second set showed that the villages and the use of biological resources composed a single biocultural unit. Overall, hypothesis testing of the association among cultures and biological species was consistent with the information that was provided by the new indices.
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