DeepMatching: Hierarchical Deformable Dense Matching

We introduce a novel matching algorithm, called DeepMatching, to compute dense correspondences between images. DeepMatching relies on a hierarchical, multi-layer, correlational architecture designed for matching images and was inspired by deep convolutional approaches. The proposed matching algorithm can handle non-rigid deformations and repetitive textures and efficiently determines dense correspondences in the presence of significant changes between images. We evaluate the performance of DeepMatching, in comparison with state-of-the-art matching algorithms, on the Mikolajczyk (Mikolajczyk et al 2005), the MPI-Sintel (Butler et al 2012) and the Kitti (Geiger et al 2013) datasets. DeepMatching outperforms the state-of-the-art algorithms and shows excellent results in particular for repetitive textures.We also propose a method for estimating optical flow, called DeepFlow, by integrating DeepMatching in the large displacement optical flow (LDOF) approach of Brox and Malik (2011). Compared to existing matching algorithms, additional robustness to large displacements and complex motion is obtained thanks to our matching approach. DeepFlow obtains competitive performance on public benchmarks for optical flow estimation

Stereo and ToF Data Fusion by Learning from Synthetic Data

Time-of-Flight (ToF) sensors and stereo vision systems are both capable of acquiring depth information but they have complementary characteristics and issues. A more accurate representation of the scene geometry can be obtained by fusing the two depth sources. In this paper we present a novel framework for data fusion where the contribution of the two depth sources is controlled by confidence measures that are jointly estimated using a Convolutional Neural Network. The two depth sources are fused enforcing the local consistency of depth data, taking into account the estimated confidence information. The deep network is trained using a synthetic dataset and we show how the classifier is able to generalize to different data, obtaining reliable estimations not only on synthetic data but also on real world scenes. Experimental results show that the proposed approach increases the accuracy of the depth estimation on both synthetic and real data and that it is able to outperform state-of-the-art methods

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.

Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply the method to human data and discover a number of potentially new repeats sequences that have been missed by previous repeat annotations. Many of these sequences are incorporated into various parasite genomes, possibly because the filtering process for host DNA involved in the sequencing of the parasite genomes failed to exclude the host derived repeat sequences. REPdenovo is a new powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families. The software tool, REPdenovo, is available for download at https://github.com/Reedwarbler/REPdenovo