Towards Automated Single Channel Source Separation using Neural Networks

Many applications of single channel source separation (SCSS) including automatic speech recognition (ASR), hearing aids etc. require an estimation of only one source from a mixture of many sources. Treating this special case as a regular SCSS problem where in all constituent sources are given equal priority in terms of reconstruction may result in a suboptimal separation performance. In this paper, we tackle the one source separation problem by suitably modifying the orthodox SCSS framework and focus only on one source at a time. The proposed approach is a generic framework that can be applied to any existing SCSS algorithm, improves performance, and scales well when there are more than two sources in the mixture unlike most existing SCSS methods. Additionally, existing SCSS algorithms rely on fine hyper-parameter tuning hence making them difficult to use in practice. Our framework takes a step towards automatic tuning of the hyper-parameters thereby making our method better suited for the mixture to be separated and thus practically more useful. We test our framework on a neural network based algorithm and the results show an improved performance in terms of SDR and SAR

ICLabel: An automated electroencephalographic independent component classifier, dataset, and website

The electroencephalogram (EEG) provides a non-invasive, minimally restrictive, and relatively low cost measure of mesoscale brain dynamics with high temporal resolution. Although signals recorded in parallel by multiple, near-adjacent EEG scalp electrode channels are highly-correlated and combine signals from many different sources, biological and non-biological, independent component analysis (ICA) has been shown to isolate the various source generator processes underlying those recordings. Independent components (IC) found by ICA decomposition can be manually inspected, selected, and interpreted, but doing so requires both time and practice as ICs have no particular order or intrinsic interpretations and therefore require further study of their properties. Alternatively, sufficiently-accurate automated IC classifiers can be used to classify ICs into broad source categories, speeding the analysis of EEG studies with many subjects and enabling the use of ICA decomposition in near-real-time applications. While many such classifiers have been proposed recently, this work presents the ICLabel project comprised of (1) an IC dataset containing spatiotemporal measures for over 200,000 ICs from more than 6,000 EEG recordings, (2) a website for collecting crowdsourced IC labels and educating EEG researchers and practitioners about IC interpretation, and (3) the automated ICLabel classifier. The classifier improves upon existing methods in two ways: by improving the accuracy of the computed label estimates and by enhancing its computational efficiency. The ICLabel classifier outperforms or performs comparably to the previous best publicly available method for all measured IC categories while computing those labels ten times faster than that classifier as shown in a rigorous comparison against all other publicly available EEG IC classifiers.Comment: Intended for NeuroImage. Updated from version one with minor editorial and figure change

QFlow lite dataset: A machine-learning approach to the charge states in quantum dot experiments

Over the past decade, machine learning techniques have revolutionized how research is done, from designing new materials and predicting their properties to assisting drug discovery to advancing cybersecurity. Recently, we added to this list by showing how a machine learning algorithm (a so-called learner) combined with an optimization routine can assist experimental efforts in the realm of tuning semiconductor quantum dot (QD) devices. Among other applications, semiconductor QDs are a candidate system for building quantum computers. The present-day tuning techniques for bringing the QD devices into a desirable configuration suitable for quantum computing that rely on heuristics do not scale with the increasing size of the quantum dot arrays required for even near-term quantum computing demonstrations. Establishing a reliable protocol for tuning that does not rely on the gross-scale heuristics developed by experimentalists is thus of great importance. To implement the machine learning-based approach, we constructed a dataset of simulated QD device characteristics, such as the conductance and the charge sensor response versus the applied electrostatic gate voltages. Here, we describe the methodology for generating the dataset, as well as its validation in training convolutional neural networks. We show that the learner's accuracy in recognizing the state of a device is ~96.5 % in both current- and charge-sensor-based training. We also introduce a tool that enables other researchers to use this approach for further research: QFlow lite - a Python-based mini-software suite that uses the dataset to train neural networks to recognize the state of a device and differentiate between states in experimental data. This work gives the definitive reference for the new dataset that will help enable researchers to use it in their experiments or to develop new machine learning approaches and concepts.Comment: 18 pages, 6 figures, 3 table

Highly accurate model for prediction of lung nodule malignancy with CT scans

Computed tomography (CT) examinations are commonly used to predict lung nodule malignancy in patients, which are shown to improve noninvasive early diagnosis of lung cancer. It remains challenging for computational approaches to achieve performance comparable to experienced radiologists. Here we present NoduleX, a systematic approach to predict lung nodule malignancy from CT data, based on deep learning convolutional neural networks (CNN). For training and validation, we analyze >1000 lung nodules in images from the LIDC/IDRI cohort. All nodules were identified and classified by four experienced thoracic radiologists who participated in the LIDC project. NoduleX achieves high accuracy for nodule malignancy classification, with an AUC of ~0.99. This is commensurate with the analysis of the dataset by experienced radiologists. Our approach, NoduleX, provides an effective framework for highly accurate nodule malignancy prediction with the model trained on a large patient population. Our results are replicable with software available at http://bioinformatics.astate.edu/NoduleX

Sustained synchronized neuronal network activity in a human astrocyte co-culture system

Impaired neuronal network function is a hallmark of neurodevelopmental and neurodegenerative disorders such as autism, schizophrenia, and Alzheimer's disease and is typically studied using genetically modified cellular and animal models. Weak predictive capacity and poor translational value of these models urge for better human derived in vitro models. The implementation of human induced pluripotent stem cells (hiPSCs) allows studying pathologies in differentiated disease-relevant and patient-derived neuronal cells. However, the differentiation process and growth conditions of hiPSC-derived neurons are non-trivial. In order to study neuronal network formation and (mal) function in a fully humanized system, we have established an in vitro co-culture model of hiPSC-derived cortical neurons and human primary astrocytes that recapitulates neuronal network synchronization and connectivity within three to four weeks after final plating. Live cell calcium imaging, electrophysiology and high content image analyses revealed an increased maturation of network functionality and synchronicity over time for co-cultures compared to neuronal monocultures. The cells express GABAergic and glutamatergic markers and respond to inhibitors of both neurotransmitter pathways in a functional assay. The combination of this co-culture model with quantitative imaging of network morphofunction is amenable to high throughput screening for lead discovery and drug optimization for neurological diseases