Quantitative Biology

In science, macro level descriptions of the causal interactions within complex, dynamical systems are typically deemed convenient, but ultimately reducible to a complete causal account of the underlying micro constituents. Yet, such a reductionist perspective is hard to square with several issues related to autonomy and agency: (1) agents require (causal) borders that separate them from the environment, (2) at least in a biological context, agents are associated with macroscopic systems, and (3) agents are supposed to act upon their environment. Integrated information theory (IIT) (Oizumi et al., 2014) offers a quantitative account of causation based on a set of causal principles, including notions such as causal specificity, composition, and irreducibility, that challenges the reductionist perspective in multiple ways. First, the IIT formalism provides a complete account of a system's causal structure, including irreducible higher-order mechanisms constituted of multiple system elements. Second, a system's amount of integrated information ( Φ ) measures the causal constraints a system exerts onto itself and can peak at a macro level of description (Hoel et al., 2016; Marshall et al., 2018). Finally, the causal principles of IIT can also be employed to identify and quantify the actual causes of events ("what caused what"), such as an agent's actions (Albantakis et al., 2019). Here, we demonstrate this framework by example of a simulated agent, equipped with a small neural network, that forms a maximum of Φ at a macro scale.

We introduce a mean-field model for analysing the dynamics of human consciousness. In particular, inspired by the Giulio Tononi's Integrated Information Theory and by the Max Tegmark's representation of consciousness, we study order-disorder phase transitions on Curie-Weiss models generated by processing EEG signals. The latter have been recorded on healthy individuals undergoing deep sedation. Then, we implement a machine learning tool for classifying mental states using, as input, the critical temperatures computed in the Curie-Weiss models. Results show that, by the proposed method, it is possible to discriminate between states of awareness and states of deep sedation. Besides, we identify a state space for representing the path between mental states, whose dimensions correspond to critical temperatures computed over different frequency bands of the EEG signal. Beyond possible theoretical implications in the study of human consciousness, resulting from our model, we deem relevant to emphasise that the proposed method could be exploited for clinical applications.

Oscillatory systems arise in the different science fields. Complex mathematical formulations with differential equations have been proposed to model the dynamics of these systems. While they have the advantage of having a direct physiological meaning, they are not useful in practice as a result of the parameter adjustment complexity and the presence of noise. In this paper, a signal plus error model is proposed to analyze oscillations, where the signal is a multicomponent FMM and the noise is assumed Gaussian. The signal formulation is also a novel decomposition approach in AM-FM components, competing with Fourier and other decompositions. Several interesting theoretical properties are derived including the Ordinary Differential Equations describing the signal. Furthermore, the usefulness in real practice is demonstrate to analyze signals associated to neuron synapses and by addressing other questions in Neuroscience.

The increasing popularity of naturalistic paradigms in fMRI (such as movie watching) demands novel strategies for multi-subject data analysis, such as use of neural encoding models. In the present study, we propose a shared convolutional neural encoding method that accounts for individual-level differences. Our method leverages multi-subject data to improve the prediction of subject-specific responses evoked by visual or auditory stimuli. We showcase our approach on high-resolution 7T fMRI data from the Human Connectome Project movie-watching protocol and demonstrate significant improvement over single-subject encoding models. We further demonstrate the ability of the shared encoding model to successfully capture meaningful individual differences in response to traditional task-based facial and scenes stimuli. Taken together, our findings suggest that inter-subject knowledge transfer can be beneficial to subject-specific predictive models.

Spatial Semantic Pointers (SSPs) have recently emerged as a powerful tool for representing and transforming continuous space, with numerous applications to cognitive modelling and deep learning. Fundamental to SSPs is the notion of "similarity" between vectors representing different points in n -dimensional space -- typically the dot product or cosine similarity between vectors with rotated unit-length complex coefficients in the Fourier domain. The similarity measure has previously been conjectured to be a Gaussian function of Euclidean distance. Contrary to this conjecture, we derive a simple trigonometric formula relating spatial displacement to similarity, and prove that, in the case where the Fourier coefficients are uniform i.i.d., the expected similarity is a product of normalized sinc functions: ∏ n k=1 sinc( a k ) , where a∈ R n is the spatial displacement between the two n -dimensional points. This establishes a direct link between space and the similarity of SSPs, which in turn helps bolster a useful mathematical framework for architecting neural networks that manipulate spatial structures.

Background: In patients with psychotic disorders, sleep spindles are reduced, supporting the hypothesis that the thalamus and glutamate receptors play a crucial etio-pathophysiological role, whose underlying mechanisms remain unknown. We hypothesized that a reduced function of NMDA receptors is involved in the spindle deficit observed in schizophrenia. Methods: An electrophysiological multisite cell-to-network exploration was used to investigate, in pentobarbital-sedated rats, the effects of a single psychotomimetic dose of the NMDA glutamate receptor antagonist ketamine in the sensorimotor and associative/cognitive thalamocortical (TC) systems. Results: Under the control condition, spontaneously-occurring spindles (intra-frequency: 10-16 waves/s) and delta-frequency (1-4Hz) oscillations were recorded in the frontoparietal cortical EEG, in thalamic extracellular recordings, in dual juxtacellularly recorded GABAergic thalamic reticular nucleus (TRN) and glutamatergic TC neurons, and in intracellularly recorded TC neurons. The TRN cells rhythmically exhibited robust high-frequency bursts of action potentials (7 to 15 APs at 200-700Hz). A single administration of low-dose ketamine fleetingly reduced TC spindles and delta oscillations, amplified ongoing gamma-(30-80Hz) and higher-frequency oscillations, and switched the firing pattern of both TC and TRN neurons from a burst mode to a single AP mode. Furthermore, ketamine strengthened the gamma-frequency band TRN-TC connectivity. The antipsychotic clozapine consistently prevented the ketamine effects on spindles, delta- and gamma-/higher-frequency TC oscillations. Conclusion: The present findings support the hypothesis that NMDA receptor hypofunction is involved in the reduction in sleep spindles and delta oscillations. The ketamine-induced swift conversion of ongoing TC-TRN activities may have involved at least both the ascending reticular activating system and the corticothalamic pathway.

Myelinated neurons are characterized by the presence of myelin, a multilaminated wrapping around the axons formed by specialized neuroglial cells. Myelin acts as an electrical insulator and therefore, in myelinated neurons, the action potentials do not propagate within the axons but happen only at the nodes of Ranvier which are gaps in the axonal myelination. Recent advancements in brain science have shown that the shapes, timings, and propagation speeds of these so-called saltatory action potentials are controlled by various biochemical interactions among neurons, glial cells, and the extracellular space. Given the complexity of brain's structure and processes, the work hypothesis made in this paper is that non-local effects are involved in the optimal propagation of action potentials. A space-fractional cable equation for the action potentials propagation in myelinated neurons is proposed that involves spatial derivatives of fractional order. The effects of non-locality on the distribution of the membrane potential are investigated using numerical simulations.

As the limits of traditional von Neumann computing come into view, the brain's ability to communicate vast quantities of information using low-power spikes has become an increasing source of inspiration for alternative architectures. Key to the success of these largescale neural networks is a power-efficient spiking element that is scalable and easily interfaced with traditional control electronics. In this work, we present a spiking element fabricated from superconducting nanowires that has pulse energies on the order of ~10 aJ. We demonstrate that the device reproduces essential characteristics of biological neurons, such as a refractory period and a firing threshold. Through simulations using experimentally measured device parameters, we show how nanowire-based networks may be used for inference in image recognition, and that the probabilistic nature of nanowire switching may be exploited for modeling biological processes and for applications that rely on stochasticity.

How the brain processes information from external stimuli in order to perceive the world and act on it is one of the greatest questions in neuroscience. To address this question different time series analyzes techniques have been employed to characterize the statistical properties of brain signals during cognitive tasks. Typically response-specific processes are addressed by comparing the time course of average event-related potentials in different trials type. Here we analyze monkey Local Field Potentials data during visual pattern discrimination called Go/No-Go task in the light of information theory quantifiers. We show that the Bandt-Pompe symbolization methodology to calculate entropy and complexity of data is a useful tool to distinguish response-related differences between Go and No-Go trials. We propose to use an asymmetry index to statistically validate trial type differences. Moreover, by using the multi-scale approach and embedding time delays to downsample the data we can estimate the important time scales in which the relevant information is been processed.

We design a physical wave-pulse neural network (WPNN) for both wave and pulse propagation, which gives more degrees of freedom for neural coding than spike neural networks (SNN). We define the rules and the information entropy of this kind of neural network, where the signal speed, arrival time, and the length of connections between neurons all become crucial parameters for signal coding. We call it quasi-quantum coding (QQC) since the combination of wave and pulse signals here behaves like a classical mimic of quantum wave-particle duality, and can be studied by borrowing some concepts form quantum mechanics. We present that the quasi-quantum coding can give efficient methods for both sound and image recognitions. We also discuss the possibility of the wave-pulse neural network and the quasi-quantum coding methods running on it in biological brains where both neural oscillations and action potentials are important to cognition.