Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting

Copyright @ 2014 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Over the 16 years, the Bio-Ontologies SIG at ISMB has provided a forum for vibrant discussions of the latest and most innovative advances in the research area of bio-ontologies, its applications to biomedicine and more generally in the organisation, sharing and re-use of knowledge in biomedicine and the life sciences. The six papers selected for this supplement span a wide range of topics including: ontology-based data integration, ontology-based annotation of scientific literature, ontology and data model development, representation of scientific results and gene candidate prediction

Finding Temporally Consistent Occlusion Boundaries in Videos using Geometric Context

We present an algorithm for finding temporally consistent occlusion boundaries in videos to support segmentation of dynamic scenes. We learn occlusion boundaries in a pairwise Markov random field (MRF) framework. We first estimate the probability of an spatio-temporal edge being an occlusion boundary by using appearance, flow, and geometric features. Next, we enforce occlusion boundary continuity in a MRF model by learning pairwise occlusion probabilities using a random forest. Then, we temporally smooth boundaries to remove temporal inconsistencies in occlusion boundary estimation. Our proposed framework provides an efficient approach for finding temporally consistent occlusion boundaries in video by utilizing causality, redundancy in videos, and semantic layout of the scene. We have developed a dataset with fully annotated ground-truth occlusion boundaries of over 30 videos ($5000 frames). This dataset is used to evaluate temporal occlusion boundaries and provides a much needed baseline for future studies. We perform experiments to demonstrate the role of scene layout, and temporal information for occlusion reasoning in dynamic scenes.Comment: Applications of Computer Vision (WACV), 2015 IEEE Winter Conference o

Probabilistic methods in the analysis of protein interaction networks

Imperial Users onl

Unsupervised Deep Single-Image Intrinsic Decomposition using Illumination-Varying Image Sequences

Machine learning based Single Image Intrinsic Decomposition (SIID) methods decompose a captured scene into its albedo and shading images by using the knowledge of a large set of known and realistic ground truth decompositions. Collecting and annotating such a dataset is an approach that cannot scale to sufficient variety and realism. We free ourselves from this limitation by training on unannotated images. Our method leverages the observation that two images of the same scene but with different lighting provide useful information on their intrinsic properties: by definition, albedo is invariant to lighting conditions, and cross-combining the estimated albedo of a first image with the estimated shading of a second one should lead back to the second one's input image. We transcribe this relationship into a siamese training scheme for a deep convolutional neural network that decomposes a single image into albedo and shading. The siamese setting allows us to introduce a new loss function including such cross-combinations, and to train solely on (time-lapse) images, discarding the need for any ground truth annotations. As a result, our method has the good properties of i) taking advantage of the time-varying information of image sequences in the (pre-computed) training step, ii) not requiring ground truth data to train on, and iii) being able to decompose single images of unseen scenes at runtime. To demonstrate and evaluate our work, we additionally propose a new rendered dataset containing illumination-varying scenes and a set of quantitative metrics to evaluate SIID algorithms. Despite its unsupervised nature, our results compete with state of the art methods, including supervised and non data-driven methods.Comment: To appear in Pacific Graphics 201