An Accurate and Robust Method for Spike Sorting Based on Convolutional Neural Networks

In the fields of neuroscience and biomedical signal processing, spike sorting is a crucial step to extract the information of single neurons from extracellular recordings. In this paper, we propose a novel deep learning approach based on one-dimensional convolutional neural networks (1D-CNNs) to implement accurate and robust spike sorting. The results of the simulated data demonstrated that the clustering accuracy in most datasets was greater than 99%, despite the multiple levels of noise and various degrees of overlapped spikes. Moreover, the proposed method performed significantly better than the state-of-the-art method named “WMsorting” and a deep-learning-based multilayer perceptron (MLP) model. In addition, the experimental data recorded from the primary visual cortex of a macaque monkey were used to evaluate the proposed method in a practical application. It was shown that the method could successfully isolate most spikes of different neurons (ranging from two to five) by training the 1D-CNN model with a small number of manually labeled spikes. Considering the above, the deep learning method proposed in this paper is of great advantage for spike sorting with high accuracy and strong robustness. It lays the foundation for application in more challenging works, such as distinguishing overlapped spikes and the simultaneous sorting of multichannel recordings.

Design and Assessment of a Robust and Generalizable ANN-Based Classifier for the Prediction of Premature Birth by means of Multichannel Electrohysterographic Records

Preterm labor is one of the major causes of neonatal deaths and also the cause of significant health and development impairments in those who survive. However, there are still no reliable and accurate tools for preterm labor prediction in clinical settings. Electrohysterography (EHG) has been proven to provide relevant information on the labor time horizon. Many studies focused on predicting preterm labor by using temporal, spectral, and nonlinear parameters extracted from single EHG recordings. However, multichannel analysis, which includes information from the whole uterus and about coupling between the recording areas, may provide better results. The cross validation method is often used to design classifiers and evaluate their performance. However, when the validation dataset is used to tune the classifier hyperparameters, the performance metrics of this dataset may not properly assess its generalization capacity. In this work, we developed and compared different classifiers, based on artificial neural networks, for predicting preterm labor using EHG features from single and multichannel recordings. A set of temporal, spectral, nonlinear, and synchronization parameters computed from EHG recordings was used as the input features. All the classifiers were evaluated on independent test datasets, which were never “seen” by the models, to determine their generalization capacity. Classifiers’ performance was also evaluated when obstetrical data were included. The experimental results show that the classifier performance metrics were significantly lower in the test dataset (AUC range 76-91%) than in the train and validation sets (AUC range 90-99%). The multichannel classifiers outperformed the single-channel classifiers, especially when information was combined into mean efficiency indexes and included coupling information between channels. Including obstetrical data slightly improved the classifier metrics and reached an AUC of 91.1±2.5% for the test dataset. These results show promise for the transfer of the EHG technique to preterm labor prediction in clinical practice.

Large-scale unsupervised clustering of Orca vocalizations: a model for describing orca communication systems

Killer whales (Orcinus orca) can produce 3 types of signals: clicks, whistles and vocalizations. This study focuses on Orca vocalizations from northern Vancouver Island (Hanson Island) where the NGO Orcalab developed a multi-hydrophone recording station to study Orcas. The acoustic station is composed of 5 hydrophones and extends over 50 km 2 of ocean. Since 2015 we are continuously streaming the hydrophone signals to our laboratory in Toulon, France, yielding nearly 50 TB of synchronous multichannel recordings. In previous work, we trained a Convolutional Neural Network (CNN) to detect Orca vocalizations, using transfer learning from a bird activity dataset. Here, for each detected vocalization, we estimate the pitch contour (fundamental frequency). Finally, we cluster vocalizations by features describing the pitch contour. While preliminary, our results demonstrate a possible route towards automatic Orca call type classification. Furthermore, they can be linked to the presence of particular Orca pods in the area according to the classification of their call types. A large-scale call type classification would allow new insights on phonotactics and ethoacoustics of endangered Orca populations in the face of increasing anthropic pressure.

Large-scale unsupervised clustering of Orca vocalizations: a model for describing orca communication systems

Killer whales (Orcinus orca) can produce 3 types of signals: clicks, whistles and vocalizations. This study focuses on Orca vocalizations from northern Vancouver Island (Hanson Island) where the NGO Orcalab developed a multi-hydrophone recording station to study Orcas. The acoustic station is composed of 5 hydrophones and extends over 50 km 2 of ocean. Since 2015 we are continuously streaming the hydrophone signals to our laboratory in Toulon, France, yielding nearly 50 TB of synchronous multichannel recordings. In previous work, we trained a Convolutional Neural Network (CNN) to detect Orca vocalizations, using transfer learning from a bird activity dataset. Here, for each detected vocalization, we estimate the pitch contour (fundamental frequency). Finally, we cluster vocalizations by features describing the pitch contour. While preliminary, our results demonstrate a possible route towards automatic Orca call type classification. Furthermore, they can be linked to the presence of particular Orca pods in the area according to the classification of their call types. A large-scale call type classification would allow new insights on phonotactics and ethoacoustics of endangered Orca populations in the face of increasing anthropic pressure.

Unsupervised Clusterless Decoding using a Switching Poisson Hidden Markov Model

Spike sorting is a standard preprocessing step to obtain ensembles of single unit data from multiunit, multichannel recordings in neuroscience. However, more recently, some researchers have started doing analyses directly on the unsorted data. Here we present a new computational model that is an extension of the standard (unsupervised) switching Poisson hidden Markov model (where observations are time-binned spike counts from each of N neurons), to a clusterless approximation in which we observe only a d-dimensional mark for each spike. Such an unsupervised yet clusterless approach has the potential to incorporate more information than is typically available from spike-sorted approaches, and to uncover temporal structure in neural data without access to behavioral correlates. We show that our approach can recover model parameters from simulated data, and that it can uncover task-relevant structure from real neural data.

Spike sorting: the overlapping spikes challenge

When recording action potentials (spikes) from many neurons simultaneously via multichannel micro-electrodes the overlapping of spikes from different neurons is a demanding problem for detection and classifi-cation of spikes (spike sorting). Since multichannel electrodes provide better possibilities to separate the superimposed waveforms, we refined an algorithm for separation of overlapping spikes for the use on multichannel recordings and tested it on simulated data with different numbers of signal channels and with several signal parameters. We show that the larger the number of signal channels the better the separation that may be achieved, especially under demanding recording conditions.