Spatial resolution is critical for observing and monitoring environmental phenomena. Acquiring high-resolution bathymetry data directly from satellites is not always feasible due to limitations on equipment, so spatial data scientists and researchers turn to single image super-resolution (SISR) methods that utilize deep learning techniques as an alternative method to increase pixel density. While super resolution residual networks (e.g., SR-ResNet) are promising for this purpose, several challenges still need to be addressed: (1) Earth data such as bathymetry is expensive to obtain and relatively limited in its data record amount; (2) certain domain knowledge needs to be complied with during model training; (3) certain areas of interest require more accurate measurements than other areas. To address these challenges, following the transfer learning principle, we study how to leverage an existing pre-trained super-resolution deep learning model, namely SR-ResNet, for high-resolution bathymetry data generation. We further enhance the SR-ResNet model to add corresponding loss functions based on domain knowledge. To let the model perform better for certain spatial areas, we add additional loss functions to increase the penalty of the areas of interest. Our experiments show our approaches achieve higher accuracy than most baseline models when evaluating using metrics including MSE, PSNR, and SSIM.

Abstract Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner. Results: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences. Availability and supplementary information: http://www.ebi.ac.uk/research/cgg/annotation/cteval/ Contact: [email protected] * To whom correspondence should be addressed. † INA-EKETA, GR-57001 Thessaloniki, Greece ‡ Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA § Aetion Technologies LLC, Worthington, OH 43085, USA ¶ Institut Curie, F-75248 Paris, France ∥ CNRS, UMR6543, F-06108 Nice, France ** Alma Bioinformatics, E-28760 Madrid, Spain †† Cap Gemini Ernst & Young, London SW1X 7LX, UK ‡‡ Univ. of Rome ‘La Sapienza’, I-00185 Rome, Italy §§ MWG-Biotech AG, Ebersberg, D-85560 Berlin, Germany ¶¶ Wellcome Trust Biocentre, Univ. of Dundee, Dundee DD1 5HN, UK