A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Optical techniques for 3D surface reconstruction in computer-assisted laparoscopic surgery

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-opera- tive morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilites by observ- ing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted in- struments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This paper reviews the state-of-the-art methods for optical intra-operative 3D reconstruction in laparoscopic surgery and discusses the technical challenges and future perspectives towards clinical translation. With the recent paradigm shift of surgical practice towards MIS and new developments in 3D opti- cal imaging, this is a timely discussion about technologies that could facilitate complex CAS procedures in dynamic and deformable anatomical regions

Large-scale interactive exploratory visual search

Large scale visual search has been one of the challenging issues in the era of big data. It demands techniques that are not only highly effective and efficient but also allow users conveniently express their information needs and refine their intents. In this thesis, we focus on developing an exploratory framework for large scale visual search. We also develop a number of enabling techniques in this thesis, including compact visual content representation for scalable search, near duplicate video shot detection, and action based event detection. We propose a novel scheme for extremely low bit rate visual search, which sends compressed visual words consisting of vocabulary tree histogram and descriptor orientations rather than descriptors. Compact representation of video data is achieved through identifying keyframes of a video which can also help users comprehend visual content efficiently. We propose a novel Bag-of-Importance model for static video summarization. Near duplicate detection is one of the key issues for large scale visual search, since there exist a large number nearly identical images and videos. We propose an improved near-duplicate video shot detection approach for more effective shot representation. Event detection has been one of the solutions for bridging the semantic gap in visual search. We particular focus on human action centred event detection. We propose an enhanced sparse coding scheme to model human actions. Our proposed approach is able to significantly reduce computational cost while achieving recognition accuracy highly comparable to the state-of-the-art methods. At last, we propose an integrated solution for addressing the prime challenges raised from large-scale interactive visual search. The proposed system is also one of the first attempts for exploratory visual search. It provides users more robust results to satisfy their exploring experiences

Design of a High-Speed Architecture for Stabilization of Video Captured Under Non-Uniform Lighting Conditions

Video captured in shaky conditions may lead to vibrations. A robust algorithm to immobilize the video by compensating for the vibrations from physical settings of the camera is presented in this dissertation. A very high performance hardware architecture on Field Programmable Gate Array (FPGA) technology is also developed for the implementation of the stabilization system. Stabilization of video sequences captured under non-uniform lighting conditions begins with a nonlinear enhancement process. This improves the visibility of the scene captured from physical sensing devices which have limited dynamic range. This physical limitation causes the saturated region of the image to shadow out the rest of the scene. It is therefore desirable to bring back a more uniform scene which eliminates the shadows to a certain extent. Stabilization of video requires the estimation of global motion parameters. By obtaining reliable background motion, the video can be spatially transformed to the reference sequence thereby eliminating the unintended motion of the camera. A reflectance-illuminance model for video enhancement is used in this research work to improve the visibility and quality of the scene. With fast color space conversion, the computational complexity is reduced to a minimum. The basic video stabilization model is formulated and configured for hardware implementation. Such a model involves evaluation of reliable features for tracking, motion estimation, and affine transformation to map the display coordinates of a stabilized sequence. The multiplications, divisions and exponentiations are replaced by simple arithmetic and logic operations using improved log-domain computations in the hardware modules. On Xilinx\u27s Virtex II 2V8000-5 FPGA platform, the prototype system consumes 59% logic slices, 30% flip-flops, 34% lookup tables, 35% embedded RAMs and two ZBT frame buffers. The system is capable of rendering 180.9 million pixels per second (mpps) and consumes approximately 30.6 watts of power at 1.5 volts. With a 1024×1024 frame, the throughput is equivalent to 172 frames per second (fps). Future work will optimize the performance-resource trade-off to meet the specific needs of the applications. It further extends the model for extraction and tracking of moving objects as our model inherently encapsulates the attributes of spatial distortion and motion prediction to reduce complexity. With these parameters to narrow down the processing range, it is possible to achieve a minimum of 20 fps on desktop computers with Intel Core 2 Duo or Quad Core CPUs and 2GB DDR2 memory without a dedicated hardware

Reasoning & Querying – State of the Art

Various query languages for Web and Semantic Web data, both for practical use and as an area of research in the scientific community, have emerged in recent years. At the same time, the broad adoption of the internet where keyword search is used in many applications, e.g. search engines, has familiarized casual users with using keyword queries to retrieve information on the internet. Unlike this easy-to-use querying, traditional query languages require knowledge of the language itself as well as of the data to be queried. Keyword-based query languages for XML and RDF bridge the gap between the two, aiming at enabling simple querying of semi-structured data, which is relevant e.g. in the context of the emerging Semantic Web. This article presents an overview of the field of keyword querying for XML and RDF