Using machine learning tools for protein database biocuration assistance

Biocuration in the omics sciences has become paramount, as research in these fields rapidly evolves towards increasingly data-dependent models. As a result, the management of web-accessible publicly-available databases becomes a central task in biological knowledge dissemination. One relevant challenge for biocurators is the unambiguous identification of biological entities. In this study, we illustrate the adequacy of machine learning methods as biocuration assistance tools using a publicly available protein database as an example. This database contains information on G Protein-Coupled Receptors (GPCRs), which are part of eukaryotic cell membranes and relevant in cell communication as well as major drug targets in pharmacology. These receptors are characterized according to subtype labels. Previous analysis of this database provided evidence that some of the receptor sequences could be affected by a case of label noise, as they appeared to be too consistently misclassified by machine learning methods. Here, we extend our analysis to recent and quite substantially modified new versions of the database and reveal their now extremely accurate labeling using several machine learning models and different transformations of the unaligned sequences. These findings support the adequacy of our proposed method to identify problematic labeling cases as a tool for database biocuration.Peer ReviewedPostprint (published version

Automatic semantic and geometric enrichment of CityGML 3D building models of varying architectural styles with HOG-based template matching

While the number of 3D geo-spatial digital models of buildings with cultural heritage interest is burgeoning, most lack semantic annotation that could be used to inform users of mobile and desktop applications about the architectural features and origins of the buildings. Additionally, while automated reconstruction of 3D building models is an active research area, the labelling of architectural features (objects) is comparatively less well researched, while distinguishing between different architectural styles is less well researched still. Meanwhile, the successful automatic identification of architectural objects, typified by a comparatively less symmetrical or less regular distribution of objects on façades, particularly on older buildings, has so far eluded researchers. This research has addressed these issues by automating the semantic and geometric enrichment of existing 3D building models by using Histogram of Oriented Gradients (HOG)-based template matching. The methods are applied to the texture maps of 3D building models of 20th century styles, of Georgian-Regency (1715-1830) style and of the Norman (1066 to late 12th century) style, where the amalgam of styles present on buildings of the latter style necessitates detection of styles of the Gothic tradition (late 12th century to present day). The most successful results were obtained when applying a set of heuristics including the use of real world dimensions, while a Support Vector Machine (SVM)-based machine learning approach was found effective in obviating the need for thresholds on matchscores when making detection decisions