t-SNE Visualization of Large-Scale Neural Recordings

Electrophysiology is entering the era of big data. Multiple probes, each with hundreds to thousands of individual electrodes, are now capable of simultaneously recording from many brain regions. The major challenge confronting these new technologies is transforming the raw data into physiologically meaningful signals, that is, single unit spikes. Sorting the spike events of individual neurons from a spatiotemporally dense sampling of the extracellular electric field is a problem that has attracted much attention (Rey, Pedreira, & Quian Quiroga, 2015; Rossant et al., 2016) but is still far from solved. Current methods still rely on human input and thus become unfeasible as the size of the data sets grows exponentially. Here we introduce the -student stochastic neighbor embedding (t-SNE) dimensionality reduction method (Van der Maaten & Hinton, 2008) as a visualization tool in the spike sorting process. t-SNE embeds the -dimensional extracellular spikes ( = number of features by which each spike is decomposed) into a low- (usually two-) dimensional space. We show that such embeddings, even starting from different feature spaces, form obvious clusters of spikes that can be easily visualized and manually delineated with a high degree of precision. We propose that these clusters represent single units and test this assertion by applying our algorithm on labeled data sets from both hybrid (Rossant et al., 2016) and paired juxtacellular/extracellular recordings (Neto et al., 2016). We have released a graphical user interface (GUI) written in Python as a tool for the manual clustering of the t-SNE embedded spikes and as a tool for an informed overview and fast manual curation of results from different clustering algorithms. Furthermore, the generated visualizations offer evidence in favor of the use of probes with higher density and smaller electrodes. They also graphically demonstrate the diverse nature of the sorting problem when spikes are recorded with different methods and arise from regions with different background spiking statistics

Knowledge Transfer from Weakly Labeled Audio using Convolutional Neural Network for Sound Events and Scenes

In this work we propose approaches to effectively transfer knowledge from weakly labeled web audio data. We first describe a convolutional neural network (CNN) based framework for sound event detection and classification using weakly labeled audio data. Our model trains efficiently from audios of variable lengths; hence, it is well suited for transfer learning. We then propose methods to learn representations using this model which can be effectively used for solving the target task. We study both transductive and inductive transfer learning tasks, showing the effectiveness of our methods for both domain and task adaptation. We show that the learned representations using the proposed CNN model generalizes well enough to reach human level accuracy on ESC-50 sound events dataset and set state of art results on this dataset. We further use them for acoustic scene classification task and once again show that our proposed approaches suit well for this task as well. We also show that our methods are helpful in capturing semantic meanings and relations as well. Moreover, in this process we also set state-of-art results on Audioset dataset, relying on balanced training set.Comment: ICASSP 201

Fast and accurate classification of echocardiograms using deep learning

Echocardiography is essential to modern cardiology. However, human interpretation limits high throughput analysis, limiting echocardiography from reaching its full clinical and research potential for precision medicine. Deep learning is a cutting-edge machine-learning technique that has been useful in analyzing medical images but has not yet been widely applied to echocardiography, partly due to the complexity of echocardiograms' multi view, multi modality format. The essential first step toward comprehensive computer assisted echocardiographic interpretation is determining whether computers can learn to recognize standard views. To this end, we anonymized 834,267 transthoracic echocardiogram (TTE) images from 267 patients (20 to 96 years, 51 percent female, 26 percent obese) seen between 2000 and 2017 and labeled them according to standard views. Images covered a range of real world clinical variation. We built a multilayer convolutional neural network and used supervised learning to simultaneously classify 15 standard views. Eighty percent of data used was randomly chosen for training and 20 percent reserved for validation and testing on never seen echocardiograms. Using multiple images from each clip, the model classified among 12 video views with 97.8 percent overall test accuracy without overfitting. Even on single low resolution images, test accuracy among 15 views was 91.7 percent versus 70.2 to 83.5 percent for board-certified echocardiographers. Confusional matrices, occlusion experiments, and saliency mapping showed that the model finds recognizable similarities among related views and classifies using clinically relevant image features. In conclusion, deep neural networks can classify essential echocardiographic views simultaneously and with high accuracy. Our results provide a foundation for more complex deep learning assisted echocardiographic interpretation.Comment: 31 pages, 8 figure

Look, Listen and Learn

We consider the question: what can be learnt by looking at and listening to a large number of unlabelled videos? There is a valuable, but so far untapped, source of information contained in the video itself -- the correspondence between the visual and the audio streams, and we introduce a novel "Audio-Visual Correspondence" learning task that makes use of this. Training visual and audio networks from scratch, without any additional supervision other than the raw unconstrained videos themselves, is shown to successfully solve this task, and, more interestingly, result in good visual and audio representations. These features set the new state-of-the-art on two sound classification benchmarks, and perform on par with the state-of-the-art self-supervised approaches on ImageNet classification. We also demonstrate that the network is able to localize objects in both modalities, as well as perform fine-grained recognition tasks.Comment: Appears in: IEEE International Conference on Computer Vision (ICCV) 201