Deep learning, especially in the form of convolutional neural networks (CNNs), has triggered substantial improvements in computer vision and related fields in recent years. This progress is attributed to the shift from designing features and subsequent individual subsystems towards learning features and recognition systems end to end from nearly unprocessed data. For speaker clustering, however, it is still common to use handcrafted processing chains such as MFCC features and GMM-based models. In this paper, we use simple spectrograms as input to a CNN and study the optimal design of those networks for speaker identification and clustering. Furthermore, we elaborate on the question how to transfer a network, trained for speaker identification, to speaker clustering. We demonstrate our approach on the well known TIMIT dataset, achieving results comparable with the state of the art-without the need for handcrafted features.

Deep learning methods are currently outperforming traditional state-of-the-art computer vision algorithms in diverse applications and recently even surpassed human performance in object recognition. Here we demonstrate the potential of deep learning methods to high-content screening-based phenotype classification. We trained a deep learning classifier in the form of convolutional neural networks with approximately 40,000 publicly available single-cell images from samples treated with compounds from four classes known to lead to different phenotypes. The input data consisted of multichannel images. The construction of appropriate feature definitions was part of the training and carried out by the convolutional network, without the need for expert knowledge or handcrafted features. We compare our results against the recent state-of-the-art pipeline in which predefined features are extracted from each cell using specialized software and then fed into various machine learning algorithms (support vector machine, Fisher linear discriminant, random forest) for classification. The performance of all classification approaches is evaluated on an untouched test image set with known phenotype classes. Compared to the best reference machine learning algorithm, the misclassification rate is reduced from 8.9% to 6.6%.

Recent technological advances in high-content screening instrumentation have increased its ease of use and throughput, expanding the application of high-content screening to the early stages of drug discovery. However, high-content screens produce complex data sets, presenting a challenge for both extraction and interpretation of meaningful information. This shifts the high-content screening process bottleneck from the experimental to the analytical stage. In this article, the authors discuss different approaches of data analysis, using a phenotypic neurite outgrowth screen as an example. Distance measurements and hierarchical clustering methods lead to a profound understanding of different high-content screening readouts. In addition, the authors introduce a hit selection procedure based on machine learning methods and demonstrate that this method increases the hit verification rate significantly (up to a factor of 5), compared to conventional hit selection based on single readouts only. (Journal of Biomolecular

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At present, the majority of the proposed Deep Learning (DL) methods provide point predictions without quantifying the model's uncertainty. However, a quantification of the reliability of automated image analysis is essential, in particular in medicine when physicians rely on the results for making critical treatment decisions. In this work, we provide an entire framework to diagnose ischemic stroke patients incorporating Bayesian uncertainty into the analysis procedure. We present a Bayesian Convolutional Neural Network (CNN) yielding a probability for a stroke lesion on 2D Magnetic Resonance (MR) images with corresponding uncertainty information about the reliability of the prediction. For patientlevel diagnoses, different aggregation methods are proposed and evaluated, which combine the single image-level predictions. Those methods take advantage of the uncertainty in image predictions and report model uncertainty at the patient-level. In a cohort of 511 patients, our Bayesian CNN achieved an accuracy of 95.33% at the image-level representing a significant improvement of 2% over a non-Bayesian counterpart. The best patient aggregation method yielded 95.89% of accuracy. Integrating uncertainty information about image predictions in aggregation models resulted in higher uncertainty measures to false patient classifications, which enabled to filter critical patient diagnoses that are supposed to be closer examined by a medical doctor. We therefore recommend using Bayesian approaches not only for improved image-level prediction and uncertainty estimation but also for the detection of uncertain aggregations at the patient-level.

Recent work has shown that convolutional neural networks (CNNs) trained in a supervised fashion for speaker identification are able to extract features from spectrograms which can be used for speaker clustering. These features are represented by the activations of a certain hidden layer and are called embeddings. However, previous approaches require plenty of additional speaker data to learn the embedding, and although the clustering results are then on par with more traditional approaches using MFCC features etc., room for improvements stems from the fact that these embeddings are trained with a surrogate task that is rather far away from segregating unknown voices-namely, identifying few specific speakers. We address both problems by training a CNN to extract embeddings that are similar for equal speakers (regardless of their specific identity) using weakly labeled data. We demonstrate our approach on the well-known TIMIT dataset that has often been used for speaker clustering experiments in the past. We exceed the clustering performance of all previous approaches, but require just 100 instead of 590 unrelated speakers to learn an embedding suited for clustering.

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