Quantitative Biology

Feedforward Convolutional Neural Networks (ffCNNs) have become state-of-the-art models both in computer vision and neuroscience. However, human-like performance of ffCNNs does not necessarily imply human-like computations. Previous studies have suggested that current ffCNNs do not make use of global shape information. However, it is currently unclear whether this reflects fundamental differences between ffCNN and human processing or is merely an artefact of how ffCNNs are trained. Here, we use visual crowding as a well-controlled, specific probe to test global shape computations. Our results provide evidence that ffCNNs cannot produce human-like global shape computations for principled architectural reasons. We lay out approaches that may address shortcomings of ffCNNs to provide better models of the human visual system.

Brain-Computer Interfaces (BCI) arose as systems that merge computing systems with the human brain to facilitate recording, stimulation, and inhibition of neural activity. Over the years, the development of BCI technologies has shifted towards miniaturization of devices that can be seamlessly embedded into the brain and can target single neuron or small population sensing and control. We present a motivating example highlighting vulnerabilities of two promising micron-scale BCI technologies, demonstrating the lack of security and privacy principles in existing solutions. This situation opens the door to a novel family of cyberattacks, called neuronal cyberattacks, affecting neuronal signaling. This paper defines the first two neural cyberattacks, Neuronal Flooding (FLO) and Neuronal Scanning (SCA), where each threat can affect the natural activity of neurons. This work implements these attacks in a neuronal simulator to determine their impact over the spontaneous neuronal behavior, defining three metrics: number of spikes, percentage of shifts, and dispersion of spikes. Several experiments demonstrate that both cyberattacks produce a reduction of spikes compared to spontaneous behavior, generating a rise in temporal shifts and a dispersion increase. Mainly, SCA presents a higher impact than FLO in the metrics focused on the number of spikes and dispersion, where FLO is slightly more damaging, considering the percentage of shifts. Nevertheless, the intrinsic behavior of each attack generates a differentiation on how they alter neuronal signaling. FLO is adequate to generate an immediate impact on the neuronal activity, whereas SCA presents higher effectiveness for damages to the neural signaling in the long-term.

This paper proposes a novel approach that uses deep neural networks for classifying imagined speech, significantly increasing the classification accuracy. The proposed approach employs only the EEG channels over specific areas of the brain for classification, and derives distinct feature vectors from each of those channels. This gives us more data to train a classifier, enabling us to use deep learning approaches. Wavelet and temporal domain features are extracted from each channel. The final class label of each test trial is obtained by applying a majority voting on the classification results of the individual channels considered in the trial. This approach is used for classifying all the 11 prompts in the KaraOne dataset of imagined speech. The proposed architecture and the approach of treating the data have resulted in an average classification accuracy of 57.15%, which is an improvement of around 35% over the state-of-the-art results.

-Background. Network neuroscience examines the brain as a complex system represented by a network (or connectome), providing deeper insights into the brain morphology and function, allowing the identification of atypical brain connectivity alterations, which can be used as diagnostic markers of neurological disorders. -Existing Methods. Graph embedding methods which map data samples (e.g., brain networks) into a low dimensional space have been widely used to explore the relationship between samples for classification or prediction tasks. However, the majority of these works are based on modeling the pair-wise relationships between samples, failing to capture their higher-order relationships. -New Method. In this paper, inspired by the nascent field of geometric deep learning, we propose Hypergraph U-Net (HUNet), a novel data embedding framework leveraging the hypergraph structure to learn low-dimensional embeddings of data samples while capturing their high-order relationships. Specifically, we generalize the U-Net architecture, naturally operating on graphs, to hypergraphs by improving local feature aggregation and preserving the high-order relationships present in the data. -Results. We tested our method on small-scale and large-scale heterogeneous brain connectomic datasets including morphological and functional brain networks of autistic and demented patients, respectively. -Conclusion. Our HUNet outperformed state-of-the-art geometric graph and hypergraph data embedding techniques with a gain of 4-14% in classification accuracy, demonstrating both scalability and generalizability. HUNet code is available at this https URL.

How an individual's unique brain connectivity determines that individual's cognition, behavior, and risk for pathology is a fundamental question in basic and clinical neuroscience. In seeking answers, many have turned to machine learning, with some noting the particular promise of deep neural networks in modelling complex non-linear functions. However, it is not clear that complex functions actually exist between brain connectivity and behavior, and thus if deep neural networks necessarily outperform simpler linear models, or if their results would be interpretable. Here we show that, across 52 subject measures of cognition and behavior, deep neural networks fit to each brain region's connectivity outperform linear regression, particularly for the brain's connector hubs--regions with diverse brain connectivity--whereas the two approaches perform similarly when fit to brain systems. Critically, averaging deep neural network predictions across brain regions results in the most accurate predictions, demonstrating the ability of deep neural networks to easily model the various functions that exists between regional brain connectivity and behavior, carving the brain at its joints. Finally, we shine light into the black box of deep neural networks using multislice network models. We determined that the relationship between connector hubs and behavior is best captured by modular deep neural networks. Our results demonstrate that both simple and complex relationships exist between brain connectivity and behavior, and that deep neural networks can fit both. Moreover, deep neural networks are particularly powerful when they are first fit to the various functions of a system independently and then combined. Finally, deep neural networks are interpretable when their architectures are structurally characterized using multislice network models.

How do humans learn from raw sensory experience? Throughout life, but most obviously in infancy, we learn without explicit instruction. We propose a detailed biological mechanism for the widely-embraced idea that learning is based on the differences between predictions and actual outcomes (i.e., predictive error-driven learning). Specifically, numerous weak projections into the pulvinar nucleus of the thalamus generate top-down predictions, and sparse, focal driver inputs from lower areas supply the actual outcome, originating in layer 5 intrinsic bursting (5IB) neurons. Thus, the outcome is only briefly activated, roughly every 100 msec (i.e., 10 Hz, alpha), resulting in a temporal difference error signal, which drives local synaptic changes throughout the neocortex, resulting in a biologically-plausible form of error backpropagation learning. We implemented these mechanisms in a large-scale model of the visual system, and found that the simulated inferotemporal (IT) pathway learns to systematically categorize 3D objects according to invariant shape properties, based solely on predictive learning from raw visual inputs. These categories match human judgments on the same stimuli, and are consistent with neural representations in IT cortex in primates.

We present a novel methodology for control of neural circuits based on deep reinforcement learning. Our approach achieves aimed behavior by generating external continuous stimulation of existing neural circuits (neuromodulation control) or modulations of neural circuits architecture (connectome control). Both forms of control are challenging due to nonlinear and recurrent complexity of neural activity. To infer candidate control policies, our approach maps neural circuits and their connectome into a grid-world like setting and infers the actions needed to achieve aimed behavior. The actions are inferred by adaptation of deep Q-learning methods known for their robust performance in navigating grid-worlds. We apply our approach to the model of \textit{C. elegans} which simulates the full somatic nervous system with muscles and body. Our framework successfully infers neuropeptidic currents and synaptic architectures for control of chemotaxis. Our findings are consistent with in vivo measurements and provide additional insights into neural control of chemotaxis. We further demonstrate the generality and scalability of our methods by inferring chemotactic neural circuits from scratch.

Active inference is a Bayesian framework for understanding biological intelligence. The underlying theory brings together perception and action under one single imperative: minimizing free energy. However, despite its theoretical utility in explaining intelligence, computational implementations have been restricted to low-dimensional and idealized situations. In this paper, we present a neural architecture for building deep active inference agents operating in complex, continuous state-spaces using multiple forms of Monte-Carlo (MC) sampling. For this, we introduce a number of techniques, novel to active inference. These include: i) selecting free-energy-optimal policies via MC tree search, ii) approximating this optimal policy distribution via a feed-forward `habitual' network, iii) predicting future parameter belief updates using MC dropouts and, finally, iv) optimizing state transition precision (a high-end form of attention). Our approach enables agents to learn environmental dynamics efficiently, while maintaining task performance, in relation to reward-based counterparts. We illustrate this in a new toy environment, based on the dSprites data-set, and demonstrate that active inference agents automatically create disentangled representations that are apt for modeling state transitions. In a more complex Animal-AI environment, our agents (using the same neural architecture) are able to simulate future state transitions and actions (i.e., plan), to evince reward-directed navigation - despite temporary suspension of visual input. These results show that deep active inference - equipped with MC methods - provides a flexible framework to develop biologically-inspired intelligent agents, with applications in both machine learning and cognitive science.

Decoding behavior, perception, or cognitive state directly from neural signals has applications in brain-computer interface research as well as implications for systems neuroscience. In the last decade, deep learning has become the state-of-the-art method in many machine learning tasks ranging from speech recognition to image segmentation. The success of deep networks in other domains has led to a new wave of applications in neuroscience. In this article, we review deep learning approaches to neural decoding. We describe the architectures used for extracting useful features from neural recording modalities ranging from spikes to EEG. Furthermore, we explore how deep learning has been leveraged to predict common outputs including movement, speech, and vision, with a focus on how pretrained deep networks can be incorporated as priors for complex decoding targets like acoustic speech or images. Deep learning has been shown to be a useful tool for improving the accuracy and flexibility of neural decoding across a wide range of tasks, and we point out areas for future scientific development.

Whether it be in a man-made machine or a biological system, form and function are often directly related. In the latter, however, this particular relationship is often unclear due to the intricate nature of biology. Here we developed a geometric deep learning model capable of exploiting the actual structure of the cortex to learn the complex relationship between brain function and anatomy from structural and functional MRI data. Our model was not only able to predict the functional organization of human visual cortex from anatomical properties alone, but it was also able to predict nuanced variations across individuals.