Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes

We propose a novel stochastic global optimization algorithm with applications to the refinement stage of protein docking prediction methods. Our approach can process conformations sampled from multiple clusters, each roughly corresponding to a different binding energy funnel. These clusters are obtained using a density-based clustering method. In each cluster, we identify a smooth “permissive” subspace which avoids high-energy barriers and then underestimate the binding energy function using general convex polynomials in this subspace. We use the underestimator to bias sampling towards its global minimum. Sampling and subspace underestimation are repeated several times and the conformations sampled at the last iteration form a refined ensemble. We report computational results on a comprehensive benchmark of 224 protein complexes, establishing that our refined ensemble significantly improves the quality of the conformations of the original set given to the algorithm. We also devise a method to enhance the ensemble from which near-native models are selected.Published versio

Learning to Navigate the Energy Landscape

In this paper, we present a novel and efficient architecture for addressing computer vision problems that use `Analysis by Synthesis'. Analysis by synthesis involves the minimization of the reconstruction error which is typically a non-convex function of the latent target variables. State-of-the-art methods adopt a hybrid scheme where discriminatively trained predictors like Random Forests or Convolutional Neural Networks are used to initialize local search algorithms. While these methods have been shown to produce promising results, they often get stuck in local optima. Our method goes beyond the conventional hybrid architecture by not only proposing multiple accurate initial solutions but by also defining a navigational structure over the solution space that can be used for extremely efficient gradient-free local search. We demonstrate the efficacy of our approach on the challenging problem of RGB Camera Relocalization. To make the RGB camera relocalization problem particularly challenging, we introduce a new dataset of 3D environments which are significantly larger than those found in other publicly-available datasets. Our experiments reveal that the proposed method is able to achieve state-of-the-art camera relocalization results. We also demonstrate the generalizability of our approach on Hand Pose Estimation and Image Retrieval tasks

Recovering 6D Object Pose and Predicting Next-Best-View in the Crowd

Object detection and 6D pose estimation in the crowd (scenes with multiple object instances, severe foreground occlusions and background distractors), has become an important problem in many rapidly evolving technological areas such as robotics and augmented reality. Single shot-based 6D pose estimators with manually designed features are still unable to tackle the above challenges, motivating the research towards unsupervised feature learning and next-best-view estimation. In this work, we present a complete framework for both single shot-based 6D object pose estimation and next-best-view prediction based on Hough Forests, the state of the art object pose estimator that performs classification and regression jointly. Rather than using manually designed features we a) propose an unsupervised feature learnt from depth-invariant patches using a Sparse Autoencoder and b) offer an extensive evaluation of various state of the art features. Furthermore, taking advantage of the clustering performed in the leaf nodes of Hough Forests, we learn to estimate the reduction of uncertainty in other views, formulating the problem of selecting the next-best-view. To further improve pose estimation, we propose an improved joint registration and hypotheses verification module as a final refinement step to reject false detections. We provide two additional challenging datasets inspired from realistic scenarios to extensively evaluate the state of the art and our framework. One is related to domestic environments and the other depicts a bin-picking scenario mostly found in industrial settings. We show that our framework significantly outperforms state of the art both on public and on our datasets.Comment: CVPR 2016 accepted paper, project page: http://www.iis.ee.ic.ac.uk/rkouskou/6D_NBV.htm

Estimating snow cover from publicly available images

In this paper we study the problem of estimating snow cover in mountainous regions, that is, the spatial extent of the earth surface covered by snow. We argue that publicly available visual content, in the form of user generated photographs and image feeds from outdoor webcams, can both be leveraged as additional measurement sources, complementing existing ground, satellite and airborne sensor data. To this end, we describe two content acquisition and processing pipelines that are tailored to such sources, addressing the specific challenges posed by each of them, e.g., identifying the mountain peaks, filtering out images taken in bad weather conditions, handling varying illumination conditions. The final outcome is summarized in a snow cover index, which indicates for a specific mountain and day of the year, the fraction of visible area covered by snow, possibly at different elevations. We created a manually labelled dataset to assess the accuracy of the image snow covered area estimation, achieving 90.0% precision at 91.1% recall. In addition, we show that seasonal trends related to air temperature are captured by the snow cover index.Comment: submitted to IEEE Transactions on Multimedi

Enrichment Procedures for Soft Clusters: A Statistical Test and its Applications

Clusters, typically mined by modeling locality of attribute spaces, are often evaluated for their ability to demonstrate ‘enrichment’ of categorical features. A cluster enrichment procedure evaluates the membership of a cluster for significant representation in pre-defined categories of interest. While classical enrichment procedures assume a hard clustering definition, in this paper we introduce a new statistical test that computes enrichments for soft clusters. We demonstrate an application of this test in refining and evaluating soft clusters for classification of remotely sensed images