Quantitative Biology

When presented with information of any type, from music to language to mathematics, the human mind subconsciously arranges it into a network. A network puts pieces of information like musical notes, syllables or mathematical concepts into context by linking them together. These networks help our minds organize information and anticipate what is coming. Here we present two questions about network building. 1) Can humans more easily learn some types of networks than others? 2) Do humans find some links between ideas more surprising than others? The answer to both questions is "Yes," and we explain why. The findings provide much-needed insight into the ways that humans learn about the networked world around them. Moreover, the study paves the way for future efforts seeking to optimize how information is presented to accelerate human learning.

We tracked the eye movements of seven young and seven older adults performing a conjunctive visual search task similar to that performed by two highly trained monkeys in an original influential study of Motter and Belky (1998a, 1998b). We obtained results consistent with theirs regarding elements of perception, selection, attention and object recognition, but we found a much greater role played by long-range memory. A design inadequacy in the original Motter-Belky study is not sufficient to explain such discrepancy, nor is the high level of training of their monkeys. Perhaps monkeys and humans do not use mnemonic resources compatibly already in basic visual search tasks, contrary to a common expectation, further supported by cortical representation studies. We also found age-related differences in various measures of eye movements, consistently indicating slightly reduced conspicuity areas for the older adults, hence, correspondingly reduced processing and memory capacities. However, because of sample size and age differential limitations, statistically significant differences were found only for a few variables, most notably overall reaction times. Results reported here provide the basis for demonstrating the formation of spiraling or circulating patterns in the eye movement trajectories and for developing corresponding computational models and simulations.

The origins of spontaneous movements have been investigated in human as well as in other vertebrates. Studies have reported an increase in neuronal activity one second before the onset of a given movement: this is known as readiness potential. The mechanisms underlying this increase are still unclear. Zebrafish larva is an ideal animal model to study the neuronal basis of spontaneous movements. Because of its small size and transparency, this vertebrate is an ideal candidate to apply optical recording methods. In order to understand what neuronal activity causes the execution of a specific tail movement at a given time, we will mainly use a prediction approach.

In this paper, we show that organisms can be modeled as hierarchical Bayesian control systems with small world and information bottleneck (bow-tie) network structure. Such systems combine hierarchical perception with hierarchical goal setting and hierarchical action control. We argue that hierarchical Bayesian control systems produce deep hierarchies of goal states, from which it follows that organisms must have some form of 'highest goals'. For all organisms, these involve internal (self) models, external (social) models and overarching (normative) models. We show that goal hierarchies tend to decompose in a top-down manner under severe and prolonged levels of stress. This produces behavior that favors short-term and self-referential goals over long term, social and/or normative goals. The collapse of goal hierarchies is universally accompanied by an increase in entropy (disorder) in control systems that can serve as an early warning sign for tipping points (disease or death of the organism). In humans, learning goal hierarchies corresponds to personality development (maturation). The failure of goal hierarchies to mature properly corresponds to personality deficits. A top-down collapse of such hierarchies under stress is identified as a common factor in all forms of episodic mental disorders (psychopathology). The paper concludes by discussing ways of testing these hypotheses empirically.

It is proposed that both human creativity and human consciousness are (unintended) consequences of the human brain's extraordinary energy efficiency. The topics of creativity and consciousness are treated separately, though have a common sub-structure. It is argued that creativity arises from a synergy between two cognitive modes of the human brain (which broadly coincide with Kahneman's Systems 1 and 2). In the first, available energy is spread across a relatively large network of neurons. As such, the amount of energy per active neuron is so small that the operation of such neurons is susceptible to thermal (ultimately quantum decoherent) noise. In the second, available energy is focussed on a small enough subset of neurons to guarantee a deterministic operation. An illustration of how this synergy can lead to creativity with implications for computing in silicon are discussed. Starting with a discussion of the concept of free will, the notion of consciousness is defined in terms of an awareness of what are perceived to be nearby counterfactual worlds in state space. It is argued that such awareness arises from an interplay between our memories on the one hand, and quantum physical mechanisms (where, unlike in classical physics, nearby counterfactual worlds play an indispensable dynamical role) in the ion channels of neural networks. As with the brain's susceptibility to noise, it is argued that in situations where quantum physics plays a role in the brain, it does so for reasons of energy efficiency. As an illustration of this definition of consciousness, a novel proposal is outlined as to why quantum entanglement appears so counter-intuitive.

To make informed decisions in natural environments that change over time, humans must update their beliefs as new observations are gathered. Studies exploring human inference as a dynamical process that unfolds in time have focused on situations in which the statistics of observations are history-independent. Yet temporal structure is everywhere in nature, and yields history-dependent observations. Do humans modify their inference processes depending on the latent temporal statistics of their observations? We investigate this question experimentally and theoretically using a change-point inference task. We show that humans adapt their inference process to fine aspects of the temporal structure in the statistics of stimuli. As such, humans behave qualitatively in a Bayesian fashion, but, quantitatively, deviate away from optimality. Perhaps more importantly, humans behave suboptimally in that their responses are not deterministic, but variable. We show that this variability itself is modulated by the temporal statistics of stimuli. To elucidate the cognitive algorithm that yields this behavior, we investigate a broad array of existing and new models that characterize different sources of suboptimal deviations away from Bayesian inference. While models with 'output noise' that corrupts the response-selection process are natural candidates, human behavior is best described by sampling-based inference models, in which the main ingredient is a compressed approximation of the posterior, represented through a modest set of random samples and updated over time. This result comes to complement a growing literature on sample-based representation and learning in humans.

Using language makes human beings surpass animals in wisdom. To let machines understand, learn, and use language flexibly, we propose a human-like general language processing (HGLP) architecture, which contains sensorimotor, association, and cognitive systems. The HGLP network learns from easy to hard like a child, understands word meaning by coactivating multimodal neurons, comprehends and generates sentences by real-time constructing a virtual world model, and can express the whole thinking process verbally. HGLP rapidly learned 10+ different tasks including object recognition, sentence comprehension, imagination, attention control, query, inference, motion judgement, mixed arithmetic operation, digit tracing and writing, and human-like iterative thinking process guided by language. Language in the HGLP framework is not matching nor correlation statistics, but a script that can describe and control the imagination.

The dynamical mechanism underlying the processes of anesthesia-induced loss of consciousness and recovery is key to gaining insights into the working of the nervous system. Previous experiments revealed an asymmetry between neural signals during the anesthesia and recovery processes. Here we obtain experimental evidence for the hysteresis loop and articulate the dynamical mechanism based on percolation on multilayer complex networks with self-similarity. Model analysis reveals that, during anesthesia, the network is able to maintain its neural pathways despite the loss of a substantial fraction of the edges. A predictive and potentially testable result is that, in the forward process of anesthesia, the average shortest path and the clustering coefficient of the neural network are markedly smaller than those associated with the recovery process. This suggests that the network strives to maintain certain neurological functions by adapting to a relatively more compact structure in response to anesthesia.

Identify the directions of signal flows in neural networks is one of the most important stages for understanding the intricate information dynamics of a living brain. Using a dataset of 213 projection neurons distributed in different regions of Drosophila brain, we develop a powerful machine learning algorithm: node-based polarity identifier of neurons (NPIN). The proposed model is trained by nodal information only and includes both Soma Features (which contain spatial information from a given node to a soma) and Local Features (which contain morphological information of a given node). After including the spatial correlations between nodal polarities, our NPIN provided extremely high accuracy (>96.0%) for the classification of neuronal polarity, even for complex neurons with more than two dendrite/axon clusters. Finally, we further apply NPIN to classify the neuronal polarity of the blowfly, which has much less neuronal data available. Our results demonstrate that NPIN is a powerful tool to identify the neuronal polarity of insects and to map out the signal flows in the brain's neural networks.

Brain function relies on a precisely coordinated and dynamic balance between the functional integration and segregation of distinct neural systems. Characterizing the way in which neural systems reconfigure their interactions to give rise to distinct but hidden brain states remains an open challenge. In this paper, we propose a Bayesian model-based characterization of latent brain states and showcase a novel method based on posterior predictive discrepancy using the latent block model to detect transitions between latent brain states in blood oxygen level-dependent (BOLD) time series. The set of estimated parameters in the model includes a latent label vector that assigns network nodes to communities, and also block model parameters that reflect the weighted connectivity within and between communities. Besides extensive in-silico model evaluation, we also provide empirical validation (and replication) using the Human Connectome Project (HCP) dataset of 100 healthy adults. Our results obtained through an analysis of task-fMRI data during working memory performance show appropriate lags between external task demands and change-points between brain states, with distinctive community patterns distinguishing fixation, low-demand and high-demand task conditions.