DeepSNP: An End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data.

Clinical decision-making in cancer and other diseases relies on timely and cost-effective genome-wide testing. Classical bioinformatic algorithms, such as Rawcopy, can support genomic analysis by calling genomic breakpoints and copy-number variations (CNVs), but often require manual data curation, which is error prone, time-consuming, and thus substantially increasing costs of genomic testing and hampering timely delivery of test results to the treating physician. We aimed to investigate whether deep learning algorithms can be used to learn from genome-wide single-nucleotide polymorphism array (SNPa) data and improve state-of-the-art algorithms. We developed, applied, and validated a novel deep neural network (DNN), DeepSNP. A manually curated data set of 50 SNPa analyses was used as truth-set. We show that DeepSNP can learn from SNPa data and classify the presence or absence of genomic breakpoints within large genomic windows with high precision and recall. DeepSNP was compared with well-known neural network models as well as with Rawcopy. Moreover, the use of a localization unit indicates the ability to pinpoint genomic breakpoints despite their exact location not being provided while training. DeepSNP results demonstrate the potential of DNN architectures to learn from genomic SNPa data and encourage further adaptation for CNV detection in SNPa and other genomic data types.

An evaluation of linear and non-linear models of expressive dynamics in classical piano and symphonic music.

Expressive interpretation forms an important but complex aspect of music, particularly in Western classical music. Modeling the relation between musical expression and structural aspects of the score being performed is an ongoing line of research. Prior work has shown that some simple numerical descriptors of the score (capturing dynamics annotations and pitch) are effective for predicting expressive dynamics in classical piano performances. Nevertheless, the features have only been tested in a very simple linear regression model. In this work, we explore the potential of non-linear and temporal modeling of expressive dynamics. Using a set of descriptors that capture different types of structure in the musical score, we compare linear and different non-linear models in a large-scale evaluation on three different corpora, involving both piano and orchestral music. To the best of our knowledge, this is the first study where models of musical expression are evaluated on both types of music. We show that, in addition to being more accurate, non-linear models describe interactions between numerical descriptors that linear models do not.