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Mapping human brain function is a long-standing goal of neuroscience that promises to inform the development of new treatments for brain disorders. Early maps of human brain function were based on locations of brain damage or brain stimulation that caused a functional change. Over time, this approach was largely replaced by technologies such as functional neuroimaging, which identify brain regions in which activity is correlated with behaviours or symptoms. Despite their advantages, these technologies reveal correlations, not causation. This creates challenges for interpreting the data generated from these tools and using them to develop treatments for brain disorders. A return to causal mapping of human brain function based on brain lesions and brain stimulation is underway. New approaches can combine these causal sources of information with modern neuroimaging and electrophysiology techniques to gain new insights into the functions of specific brain areas. In this Review, we provide a definition of causality for translational research, propose a continuum along which to assess the relative strength of causal information from human brain mapping studies and discuss recent advances in causal brain mapping and their relevance for developing treatments.In this Review, Siddiqi et al. examine causal approaches to mapping human brain function. They provide a definition of causality for translational research, propose a framework for assessing causality strength in brain mapping studies and cover advances in techniques and their use in developing treatments for brain disorders.

Recurrently connected networks of spiking neurons underlie the astounding information processing capabilities of the brain. Yet in spite of extensive research, how they can learn through synaptic plasticity to carry out complex network computations remains unclear. We argue that two pieces of this puzzle were provided by experimental data from neuroscience. A mathematical result tells us how these pieces need to be combined to enable biologically plausible online network learning through gradient descent, in particular deep reinforcement learning. This learning method–called e-prop–approaches the performance of backpropagation through time (BPTT), the best-known method for training recurrent neural networks in machine learning. In addition, it suggests a method for powerful on-chip learning in energy-efficient spike-based hardware for artificial intelligence. Bellec et al. present a mathematically founded approximation for gradient descent training of recurrent neural networks without backwards propagation in time. This enables biologically plausible training of spike-based neural network models with working memory and supports on-chip training of neuromorphic hardware.

Neurobiological abnormalities associated with psychiatric disorders do not map well to existing diagnostic categories. High co-morbidity suggests dimensional circuit-level abnormalities that cross diagnoses. Here we seek to identify brain-based dimensions of psychopathology using sparse canonical correlation analysis in a sample of 663 youths. This analysis reveals correlated patterns of functional connectivity and psychiatric symptoms. We find that four dimensions of psychopathology – mood, psychosis, fear, and externalizing behavior – are associated ( r  = 0.68–0.71) with distinct patterns of connectivity. Loss of network segregation between the default mode network and executive networks emerges as a common feature across all dimensions. Connectivity linked to mood and psychosis becomes more prominent with development, and sex differences are present for connectivity related to mood and fear. Critically, findings largely replicate in an independent dataset ( n  = 336). These results delineate connectivity-guided dimensions of psychopathology that cross clinical diagnostic categories, which could serve as a foundation for developing network-based biomarkers in psychiatry. Co-morbidity and symptom overlap make it difficult to associate psychiatric disorders with unique neural signatures. Here, the authors use a data-driven approach to show that the symptom dimensions of mood, psychosis, fear and externalizing behavior exhibit unique patterns of functional dysconnectivity.

Cancer tumor classification based on morphological characteristics alone has been shown to have serious limitations. Breast, lung, colorectal, thyroid, and ovarian are the most commonly diagnosed cancers among women. Precise classification of cancers into their types is considered a vital problem for cancer diagnosis and therapy. In this paper, we proposed a stacking ensemble deep learning model based on one-dimensional convolutional neural network (1D-CNN) to perform a multi-class classification on the five common cancers among women based on RNASeq data. The RNASeq gene expression data was downloaded from Pan-Cancer Atlas using GDCquery function of the TCGAbiolinks package in the R software. We used least absolute shrinkage and selection operator (LASSO) as feature selection method. We compared the results of the new proposed model with and without LASSO with the results of the single 1D-CNN and machine learning methods which include support vector machines with radial basis function, linear, and polynomial kernels; artificial neural networks; k-nearest neighbors; bagging trees. The results show that the proposed model with and without LASSO has a better performance compared to other classifiers. Also, the results show that the machine learning methods (SVM-R, SVM-L, SVM-P, ANN, KNN, and bagging trees) with under-sampling have better performance than with over-sampling techniques. This is supported by the statistical significance test of accuracy where the p -values for differences between the SVM-R and SVM-P, SVM-R and ANN, SVM-R and KNN are found to be p  = 0.003, p  =  < 0.001, and p  =  < 0.001, respectively. Also, SVM-L had a significant difference compared to ANN p  = 0.009. Moreover, SVM-P and ANN, SVM-P and KNN are found to be significantly different with p -values p  =  < 0.001 and p  =  < 0.001, respectively. In addition, ANN and bagging trees, ANN and KNN were found to be significantly different with p -values p  =  < 0.001 and p  = 0.004, respectively. Thus, the proposed model can help in the early detection and diagnosis of cancer in women, and hence aid in designing early treatment strategies to improve survival.

Neural network models are potential tools for improving our understanding of complex brain functions. To address this goal, these models need to be neurobiologically realistic. However, although neural networks have advanced dramatically in recent years and even achieve human-like performance on complex perceptual and cognitive tasks, their similarity to aspects of brain anatomy and physiology is imperfect. Here, we discuss different types of neural models, including localist, auto-associative, hetero-associative, deep and whole-brain networks, and identify aspects under which their biological plausibility can be improved. These aspects range from the choice of model neurons and of mechanisms of synaptic plasticity and learning to implementation of inhibition and control, along with neuroanatomical properties including areal structure and local and long-range connectivity. We highlight recent advances in developing biologically grounded cognitive theories and in mechanistically explaining, on the basis of these brain-constrained neural models, hitherto unaddressed issues regarding the nature, localization and ontogenetic and phylogenetic development of higher brain functions. In closing, we point to possible future clinical applications of brain-constrained modelling.Neural network models have potential for improving our understanding of brain functions. In this Perspective, Pulvermüller and colleagues examine various aspects of such models that may need to be constrained to make them more neurobiologically realistic and therefore better tools for understanding brain function.

Epidural electrical stimulation (EES) of the spinal cord restores locomotion in animal models of spinal cord injury but is less effective in humans. Here we hypothesized that this interspecies discrepancy is due to interference between EES and proprioceptive information in humans. Computational simulations and preclinical and clinical experiments reveal that EES blocks a significant amount of proprioceptive input in humans, but not in rats. This transient deafferentation prevents modulation of reciprocal inhibitory networks involved in locomotion and reduces or abolishes the conscious perception of leg position. Consequently, continuous EES can only facilitate locomotion within a narrow range of stimulation parameters and is unable to provide meaningful locomotor improvements in humans without rehabilitation. Simulations showed that burst stimulation and spatiotemporal stimulation profiles mitigate the cancellation of proprioceptive information, enabling robust control over motor neuron activity. This demonstrates the importance of stimulation protocols that preserve proprioceptive information to facilitate walking with EES.

The authors used new network-analysis algorithms to examine how distributed networks of brain areas are reorganized as humans learn a new motor skill. Using fMRI, the authors found that learning induced autonomy of sensorimotor systems and that a release of cognitive control hubs predicted individual differences in learning. Distributed networks of brain areas interact with one another in a time-varying fashion to enable complex cognitive and sensorimotor functions. Here we used new network-analysis algorithms to test the recruitment and integration of large-scale functional neural circuitry during learning. Using functional magnetic resonance imaging data acquired from healthy human participants, we investigated changes in the architecture of functional connectivity patterns that promote learning from initial training through mastery of a simple motor skill. Our results show that learning induces an autonomy of sensorimotor systems and that the release of cognitive control hubs in frontal and cingulate cortices predicts individual differences in the rate of learning on other days of practice. Our general statistical approach is applicable across other cognitive domains and provides a key to understanding time-resolved interactions between distributed neural circuits that enable task performance.

Intelligent recognition methods for classifying non-stationary and non-invasive epileptic diagnoses are essential tools in neurological research. Electroencephalogram (EEG) signals exhibit better temporal characteristics in the detection of epilepsy compared to radiation medical images like computed tomography (CT) and magnetic resonance imaging (MRI), as they provide real-time insights into the disease’ condition. While classical machine learning methods have been used for epilepsy EEG classification, they still often require manual parameter adjustments. Previous studies primarily focused on binary epilepsy recognition (epilepsy vs. healthy subjects) rather than as ternary status recognition (continuous epilepsy vs. intermittent epilepsy vs. healthy subjects). In this study, we propose a novel deep learning method that combines a convolution neural network (CNN) with a long short-term memory (LSTM) network for multi-class classification including both binary and ternary tasks, using a publicly available benchmark database on epilepsy EEGs. The hybrid CNN-LSTM automatically acquires knowledge without the need for extra pre-processing or manual intervention. Besides, the joint network method benefits from memory function and stronger feature extraction ability. Our proposed hybrid CNN-LSTM achieves state-of-the-art performance in ternary classification, outperforming classical machine learning and the latest deep learning models. For the three-class classification, in the method achieves an accuracy, specificity, sensitivity, and ROC of 98%, 97.4, 98.3% and 96.8%, respectively. In binary classification, the method achieves better results, with ACC of 100%, 100%, and 99.8%, respectively. Our dual stream spatiotemporal hybrid network demonstrates superior performance compared to other methods. Notably, it eliminates the need for manual operations, making it more efficient for doctors to diagnose during the clinical process and alleviating the workload of neurologists.

Elucidating brain cell type specific gene expression patterns is critical towards a better understanding of how cell-cell communications may influence brain functions and dysfunctions. We set out to compare and contrast five human and murine cell type-specific transcriptome-wide RNA expression data sets that were generated within the past several years. We defined three measures of brain cell type-relative expression including specificity, enrichment, and absolute expression and identified corresponding consensus brain cell “signatures,” which were well conserved across data sets. We validated that the relative expression of top cell type markers are associated with proxies for cell type proportions in bulk RNA expression data from postmortem human brain samples. We further validated novel marker genes using an orthogonal ATAC-seq dataset. We performed multiscale coexpression network analysis of the single cell data sets and identified robust cell-specific gene modules. To facilitate the use of the cell type-specific genes for cell type proportion estimation and deconvolution from bulk brain gene expression data, we developed an R package, BRETIGEA. In summary, we identified a set of novel brain cell consensus signatures and robust networks from the integration of multiple datasets and therefore transcend limitations related to technical issues characteristic of each individual study.

The analysis of biomedical signals for clinical studies and therapeutic applications can benefit from embedded devices that can process these signals locally and in real-time. An example is the analysis of intracranial EEG (iEEG) from epilepsy patients for the detection of High Frequency Oscillations (HFO), which are a biomarker for epileptogenic brain tissue. Mixed-signal neuromorphic circuits offer the possibility of building compact and low-power neural network processing systems that can analyze data on-line in real-time. Here we present a neuromorphic system that combines a neural recording headstage with a spiking neural network (SNN) processing core on the same die for processing iEEG, and show how it can reliably detect HFO, thereby achieving state-of-the-art accuracy, sensitivity, and specificity. This is a first feasibility study towards identifying relevant features in iEEG in real-time using mixed-signal neuromorphic computing technologies. A major challenge across a variety of fields is how to process the vast quantities of data produced by sensors without large computation resources. Here, the authors present a neuromorphic chip which can detect a relevant signature of epileptogenic tissue from intracranial recordings in patients.