iSeqQC: a tool for expression-based quality control in RNA sequencing.

BACKGROUND: Quality Control in any high-throughput sequencing technology is a critical step, which if overlooked can compromise an experiment and the resulting conclusions. A number of methods exist to identify biases during sequencing or alignment, yet not many tools exist to interpret biases due to outliers. RESULTS: Hence, we developed iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers. It can be utilized through command-line (Github: https://github.com/gkumar09/iSeqQC) or web-interface (http://cancerwebpa.jefferson.edu/iSeqQC). A local shiny installation can also be obtained from github (https://github.com/gkumar09/iSeqQC). CONCLUSION: iSeqQC is a fast, light-weight, expression-based QC tool that detects outliers by implementing various statistical approaches

Handwriting styles: benchmarks and evaluation metrics

Evaluating the style of handwriting generation is a challenging problem, since it is not well defined. It is a key component in order to develop in developing systems with more personalized experiences with humans. In this paper, we propose baseline benchmarks, in order to set anchors to estimate the relative quality of different handwriting style methods. This will be done using deep learning techniques, which have shown remarkable results in different machine learning tasks, learning classification, regression, and most relevant to our work, generating temporal sequences. We discuss the challenges associated with evaluating our methods, which is related to evaluation of generative models in general. We then propose evaluation metrics, which we find relevant to this problem, and we discuss how we evaluate the evaluation metrics. In this study, we use IRON-OFF dataset. To the best of our knowledge, there is no work done before in generating handwriting (either in terms of methodology or the performance metrics), our in exploring styles using this dataset.Comment: Submitted to IEEE International Workshop on Deep and Transfer Learning (DTL 2018

Machine Learning Theory and Practice as a Source of Insight into Universal Grammar

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BinaryConnect: Training Deep Neural Networks with binary weights during propagations

Deep Neural Networks (DNN) have achieved state-of-the-art results in a wide range of tasks, with the best results obtained with large training sets and large models. In the past, GPUs enabled these breakthroughs because of their greater computational speed. In the future, faster computation at both training and test time is likely to be crucial for further progress and for consumer applications on low-power devices. As a result, there is much interest in research and development of dedicated hardware for Deep Learning (DL). Binary weights, i.e., weights which are constrained to only two possible values (e.g. -1 or 1), would bring great benefits to specialized DL hardware by replacing many multiply-accumulate operations by simple accumulations, as multipliers are the most space and power-hungry components of the digital implementation of neural networks. We introduce BinaryConnect, a method which consists in training a DNN with binary weights during the forward and backward propagations, while retaining precision of the stored weights in which gradients are accumulated. Like other dropout schemes, we show that BinaryConnect acts as regularizer and we obtain near state-of-the-art results with BinaryConnect on the permutation-invariant MNIST, CIFAR-10 and SVHN.Comment: Accepted at NIPS 2015, 9 pages, 3 figure