Bioinformatics and Medicine in the Era of Deep Learning

Many of the current scientific advances in the life sciences have their origin in the intensive use of data for knowledge discovery. In no area this is so clear as in bioinformatics, led by technological breakthroughs in data acquisition technologies. It has been argued that bioinformatics could quickly become the field of research generating the largest data repositories, beating other data-intensive areas such as high-energy physics or astroinformatics. Over the last decade, deep learning has become a disruptive advance in machine learning, giving new live to the long-standing connectionist paradigm in artificial intelligence. Deep learning methods are ideally suited to large-scale data and, therefore, they should be ideally suited to knowledge discovery in bioinformatics and biomedicine at large. In this brief paper, we review key aspects of the application of deep learning in bioinformatics and medicine, drawing from the themes covered by the contributions to an ESANN 2018 special session devoted to this topic.

Metrics for Probabilistic Geometries

We investigate the geometrical structure of probabilistic generative dimensionality reduction models using the tools of Riemannian geometry. We explicitly define a distribution over the natural metric given by the models. We provide the necessary algorithms to compute expected metric tensors where the distribution over mappings is given by a Gaussian process. We treat the corresponding latent variable model as a Riemannian manifold and we use the expectation of the metric under the Gaussian process prior to define interpolating paths and measure distance between latent points. We show how distances that respect the expected metric lead to more appropriate generation of new data.