A search engine for 3D models of museum artefacts

The National Museum of Ireland has about 5 million artifacts distributed across different physical locations. Essentially this means that only small fraction of these are accessible to the public at any time. Digital Libraries support the 3D browsing and retrieval of cultural museum artefacts and offer a potential solution to this problem. This paper describes a final year project where the objective was to build a search engine that: (1) could operate over a digital library storing digitized 3D model representations of objects, and (2) could be integrated with the existing DigiFact system architecture based in CDVP at DCU

Sketch-based 3D Shape Retrieval using Convolutional Neural Networks

Retrieving 3D models from 2D human sketches has received considerable attention in the areas of graphics, image retrieval, and computer vision. Almost always in state of the art approaches a large amount of "best views" are computed for 3D models, with the hope that the query sketch matches one of these 2D projections of 3D models using predefined features. We argue that this two stage approach (view selection -- matching) is pragmatic but also problematic because the "best views" are subjective and ambiguous, which makes the matching inputs obscure. This imprecise nature of matching further makes it challenging to choose features manually. Instead of relying on the elusive concept of "best views" and the hand-crafted features, we propose to define our views using a minimalism approach and learn features for both sketches and views. Specifically, we drastically reduce the number of views to only two predefined directions for the whole dataset. Then, we learn two Siamese Convolutional Neural Networks (CNNs), one for the views and one for the sketches. The loss function is defined on the within-domain as well as the cross-domain similarities. Our experiments on three benchmark datasets demonstrate that our method is significantly better than state of the art approaches, and outperforms them in all conventional metrics.Comment: CVPR 201

Spherical harmonics coeffcients for ligand-based virtual screening of cyclooxygenase inhibitors

Background: Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. Methodology/Principal Findings: We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. Conclusions/Significance: 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort