Developing electrophysiological recordings of brain neuronal activity and their analysis provide a basis for exploring the structure of brain function and nervous system investigation. The recorded signals are typically a combination of spikes and noise. High amounts of background noise and possibility of electric signaling recording from several neurons adjacent to the recording site have led scientists to develop neuronal signal processing tools such as spike sorting to facilitate brain data analysis. Spike sorting plays a pivotal role in understanding the electrophysiological activity of neuronal networks. This process prepares recorded data for interpretations of neurons interactions and understanding the overall structure of brain functions. Spike sorting consists of three steps: spike detection, feature extraction, and spike clustering. There are several methods to implement each of spike sorting steps. This paper provides a systematic comparison of various spike sorting sub-techniques applied to real extracellularly recorded data from a rat brain basolateral amygdala. An efficient sorted data resulted from careful choice of spike sorting sub-methods leads to better interpretation of the brain structures connectivity under different conditions, which is a very sensitive concept in diagnosis and treatment of neurological disorders. Here, spike detection is performed by appropriate choice of threshold level via three different approaches. Feature extraction is done through PCA and Kernel PCA methods, which Kernel PCA outperforms. We have applied four different algorithms for spike clustering including K-means, Fuzzy C-means, Bayesian and Fuzzy maximum likelihood estimation. As one requirement of most clustering algorithms, optimal number of clusters is achieved through validity indices for each method. Finally, the sorting results are evaluated using inter-spike interval histograms.

Finding a code to unravel the population of neural responses that leads to a distinct animal behavior has been a long-standing question in the field of neuroscience. With the recent advances in machine learning, it is shown that the hierarchically Deep Neural Networks (DNNs) perform optimally in decoding unique features out of complex datasets. In this study, we utilize the power of a DNN to explore the computational principles in the mammalian brain by exploiting the Neuropixel data from Allen Brain Institute. We decode the neural responses from mouse visual cortex to predict the presented stimuli to the animal for natural (bear, trees, cheetah, etc.) and artificial (drifted gratings, orientated bars, etc.) classes. Our results indicate that neurons in mouse visual cortex encode the features of natural and artificial objects in a distinct manner, and such neural code is consistent across animals. We investigate this by applying transfer learning to train a DNN on the neural responses of a single animal and test its generalized performance across multiple animals. Within a single animal, DNN is able to decode the neural responses with as much as 100% classification accuracy. Across animals, this accuracy is reduced to 91%. This study demonstrates the potential of utilizing the DNN models as a computational framework to understand the neural coding principles in the mammalian brain.

Two types of zeroth-order stochastic algorithms have recently been designed for nonconvex optimization respectively based on the first-order techniques SVRG and SARAH/SPIDER. This paper addresses several important issues that are still open in these methods. First, all existing SVRG-type zeroth-order algorithms suffer from worse function query complexities than either zeroth-order gradient descent (ZO-GD) or stochastic gradient descent (ZO-SGD). In this paper, we propose a new algorithm ZO-SVRG-Coord-Rand and develop a new analysis for an existing ZO-SVRG-Coord algorithm proposed in Liu et al. 2018b, and show that both ZO-SVRG-Coord-Rand and ZO-SVRG-Coord (under our new analysis) outperform other exiting SVRG-type zeroth-order methods as well as ZO-GD and ZO-SGD. Second, the existing SPIDER-type algorithm SPIDER-SZO (Fang et al. 2018) has superior theoretical performance, but suffers from the generation of a large number of Gaussian random variables as well as a $\sqrt{\epsilon}$-level stepsize in practice. In this paper, we develop a new algorithm ZO-SPIDER-Coord, which is free from Gaussian variable generation and allows a large constant stepsize while maintaining the same convergence rate and query complexity, and we further show that ZO-SPIDER-Coord automatically achieves a linear convergence rate as the iterate enters into a local PL region without restart and algorithmic modification.

State-of-art deep neural networks (DNN) are vulnerable to attacks by adversarial examples: a carefully designed small perturbation to the input, that is imperceptible to human, can mislead DNN. To understand the root cause of adversarial examples, we quantify the probability of adversarial example existence for linear classifiers. Previous mathematical definition of adversarial examples only involves the overall perturbation amount, and we propose a more practical relevant definition of strong adversarial examples that separately limits the perturbation along the signal direction also. We show that linear classifiers can be made robust to strong adversarial examples attack in cases where no adversarial robust linear classifiers exist under the previous definition. The quantitative formulas are confirmed by numerical experiments using a linear support vector machine (SVM) classifier. The results suggest that designing general strong-adversarial-robust learning systems is feasible but only through incorporating human knowledge of the underlying classification problem.

In this survey, we provide a detailed review of recent advances in the recovery of continuous domain multidimensional signals from their few nonuniform (multichannel) measurements using structured low-rank matrix completion formulation. This framework is centered on the fundamental duality between the compactness (e.g., sparsity) of the continuous signal and the rank of a structured matrix, whose entries are functions of the signal. This property enables the reformulation of the signal recovery as a low-rank structured matrix completion, which comes with performance guarantees. We will also review fast algorithms that are comparable in complexity to current compressed sensing methods, which enables the application of the framework to large-scale magnetic resonance (MR) recovery problems. The remarkable flexibility of the formulation can be used to exploit signal properties that are difficult to capture by current sparse and low-rank optimization strategies. We demonstrate the utility of the framework in a wide range of MR imaging (MRI) applications, including highly accelerated imaging, calibration-free acquisition, MR artifact correction, and ungated dynamic MRI. The slow nature of signal acquisition in magnetic resonance imaging (MRI), where the image is formed from a sequence of Fourier samples, often restricts the achievable spatial and temporal resolution in multidimensional static and dynamic imaging applications. Discrete compressed sensing (CS) methods provided a major breakthrough to accelerate the magnetic resonance (MR) signal acquisition by reducing the sampling burden. As described in an introductory article in this special issue [1] these algorithms exploited the sparsity of the discrete signal in a transform domain to recover the images from a few measurements. In this paper, we review a continuous domain extension of CS using a structured low-rank (SLR) framework for the recovery of an image or a series of images from a few measurements using various compactness assumptions [2]-[22]. The general strategy of the SLR framework starts with defining a lifting operation to construct a structured matrix, whose entries are functions of the signal samples. The SLR algorithms exploit the dual relationships between the signal compactness properties (e.g. This dual relationship allows recovery of the signal from a few samples in the measurement domain as an SLR optimization problem. MJ and MM are with the University of Iowa, Iowa City, IA 52242 (emails: mathews-jacob@uiowa.edu,merry-mani@uiowa.edu). JCY is with the Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea (email: jong.ye@kaist.ac.kr).

Human brain development is rapid during infancy and early childhood. Many disease processes impair this development. Therefore, brain developmental age estimation (BDAE) is essential for all diseases affecting cognitive development. Brain magnetic resonance imaging (MRI) of infants shows brain growth and morphologic patterns during childhood. Therefore, we can estimate the developmental age from brain images. However, MRI analysis is time-consuming because each scan contains millions of data points (voxels). We investigated the three-dimensional convolutional neural network (3D CNN), a deep learning algorithm, to rapidly classify neurodevelopmental age with high accuracy based on MRIs. MRIs from normal newborns were obtained from the National Institute of Mental Health (NIMH) Data Archive. Age categories of pediatric MRIs were 3 wks + 1 wk, 1 yr + 2 wks, and 3 yrs + 4 wks. We trained a BDAE method using T1, T2, and proton density (PD) images from MRI scans of 112 individuals using 3D CNN. Compared with the known age, our method has a sensitivity of 99% and specificity of 98.3%. Moreover, our 3D CNN model has better performance in neurodevelopmental age estimation than does 2D CNN.

We study the safe reinforcement learning problem with nonlinear function approximation, where policy optimization is formulated as a constrained optimization problem with both the objective and the constraint being nonconvex functions. For such a problem, we construct a sequence of surrogate convex constrained optimization problems by replacing the nonconvex functions locally with convex quadratic functions obtained from policy gradient estimators. We prove that the solutions to these surrogate problems converge to a stationary point of the original nonconvex problem. Furthermore, to extend our theoretical results, we apply our algorithm to examples of optimal control and multi-agent reinforcement learning with safety constraints.

Graph convolutional neural networks (GCNN) have been successfully applied to many different graph based learning tasks including node and graph classification, matrix completion, and learning of node embeddings. Despite their impressive performance, the techniques have a limited capability to incorporate the uncertainty in the underlined graph structure. In order to address this issue, a Bayesian GCNN (BGCN) framework was recently proposed. In this framework, the observed graph is considered to be a random realization from a parametric random graph model and the joint Bayesian inference of the graph and GCNN weights is performed. In this paper, we propose a non-parametric generative model for graphs and incorporate it within the BGCN framework. In addition to the observed graph, our approach effectively uses the node features and training labels in the posterior inference of graphs and attains superior or comparable performance in benchmark node classification tasks.

In recent years there has been a rapid increase in classification methods on graph structured data. Both in graph kernels and graph neural networks, one of the implicit assumptions of successful state-of-the-art models was that incorporating graph isomorphism features into the architecture leads to better empirical performance. However, as we discover in this work, commonly used data sets for graph classification have repeating instances which cause the problem of isomorphism bias, i.e. artificially increasing the accuracy of the models by memorizing target information from the training set. This prevents fair competition of the algorithms and raises a question of the validity of the obtained results. We analyze 54 data sets, previously extensively used for graph-related tasks, on the existence of isomorphism bias, give a set of recommendations to machine learning practitioners to properly set up their models, and open source new data sets for the future experiments.

We present a framework based on neural networks to extract music scores directly from polyphonic audio in an end-to-end fashion. Most previous Automatic Music Transcription (AMT) methods seek a piano-roll representation of the pitches, that can be further transformed into a score by incorporating tempo estimation, beat tracking, key estimation or rhythm quantization. Unlike these methods, our approach generates music notation directly from the input audio in a single stage. For this, we use a Convolutional Recurrent Neural Network (CRNN) with Connectionist Temporal Classification (CTC) loss function which does not require annotated alignments of audio frames with the score rhythmic information. We trained our model using as input Haydn, Mozart, and Beethoven string quartets and Bach chorales synthesized with different tempos and expressive performances. The output is a textual representation of four-voice music scores based on **kern format. Although the proposed approach is evaluated in a simplified scenario, results show that this model can learn to transcribe scores directly from audio signals, opening a promising avenue towards complete AMT.