ExpaRNA-P : simultaneous exact pattern matching and folding of RNAs

Background: Identifying sequence-structure motifs common to two RNAs can speed up the comparison of structural RNAs substantially. The core algorithm of the existent approach ExpaRNA solves this problem for a priori known input structures. However, such structures are rarely known; moreover, predicting them computationally is no rescue, since single sequence structure prediction is highly unreliable. Results: The novel algorithm ExpaRNA-P computes exactly matching sequence-structure motifs in entire Boltzmann-distributed structure ensembles of two RNAs; thereby we match and fold RNAs simultaneously, analogous to the well-known “simultaneous alignment and folding” of RNAs. While this implies much higher flexibility compared to ExpaRNA, ExpaRNA-P has the same very low complexity (quadratic in time and space), which is enabled by its novel structure ensemble-based sparsification. Furthermore, we devise a generalized chaining algorithm to compute compatible subsets of ExpaRNA-P’s sequence-structure motifs. Resulting in the very fast RNA alignment approach ExpLoc-P, we utilize the best chain as anchor constraints for the sequence-structure alignment tool LocARNA. ExpLoc-P is benchmarked in several variants and versus state-of-the-art approaches. In particular, we formally introduce and evaluate strict and relaxed variants of the problem; the latter makes the approach sensitive to compensatory mutations. Across a benchmark set of typical non-coding RNAs, ExpLoc-P has similar accuracy to LocARNA but is four times faster (in both variants), while it achieves a speed-up over 30-fold for the longest benchmark sequences (≈400nt). Finally, different ExpLoc-P variants enable tailoring of the method to specific application scenarios. ExpaRNA-P and ExpLoc-P are distributed as part of the LocARNA package. The source code is freely available at http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P webcite. Conclusions: ExpaRNA-P’s novel ensemble-based sparsification reduces its complexity to quadratic time and space. Thereby, ExpaRNA-P significantly speeds up sequence-structure alignment while maintaining the alignment quality. Different ExpaRNA-P variants support a wide range of applications

Proof of the middle levels conjecture

Define the middle layer graph as the graph whose vertex set consists of all bitstrings of length $2n+1$ that have exactly $n$ or $n+1$ entries equal to 1, with an edge between any two vertices for which the corresponding bitstrings differ in exactly one bit. The middle levels conjecture asserts that this graph has a Hamilton cycle for every $n\geq 1$. This conjecture originated probably with Havel, Buck and Wiedemann, but has also been attributed to Dejter, Erd{\H{o}}s, Trotter and various others, and despite considerable efforts it resisted all attacks during the last 30 years. In this paper we prove the middle levels conjecture. In fact, we construct $2^{2^{\Omega(n)}}$ different Hamilton cycles in the middle layer graph, which is best possible

Single View Modeling and View Synthesis

This thesis develops new algorithms to produce 3D content from a single camera. Today, amateurs can use hand-held camcorders to capture and display the 3D world in 2D, using mature technologies. However, there is always a strong desire to record and re-explore the 3D world in 3D. To achieve this goal, current approaches usually make use of a camera array, which suffers from tedious setup and calibration processes, as well as lack of portability, limiting its application to lab experiments. In this thesis, I try to produce the 3D contents using a single camera, making it as simple as shooting pictures. It requires a new front end capturing device rather than a regular camcorder, as well as more sophisticated algorithms. First, in order to capture the highly detailed object surfaces, I designed and developed a depth camera based on a novel technique called light fall-off stereo (LFS). The LFS depth camera outputs color+depth image sequences and achieves 30 fps, which is necessary for capturing dynamic scenes. Based on the output color+depth images, I developed a new approach that builds 3D models of dynamic and deformable objects. While the camera can only capture part of a whole object at any instance, partial surfaces are assembled together to form a complete 3D model by a novel warping algorithm. Inspired by the success of single view 3D modeling, I extended my exploration into 2D-3D video conversion that does not utilize a depth camera. I developed a semi-automatic system that converts monocular videos into stereoscopic videos, via view synthesis. It combines motion analysis with user interaction, aiming to transfer as much depth inferring work from the user to the computer. I developed two new methods that analyze the optical flow in order to provide additional qualitative depth constraints. The automatically extracted depth information is presented in the user interface to assist with user labeling work. In this thesis, I developed new algorithms to produce 3D contents from a single camera. Depending on the input data, my algorithm can build high fidelity 3D models for dynamic and deformable objects if depth maps are provided. Otherwise, it can turn the video clips into stereoscopic video

Stable Marriage Problem Based Adaptation for Clone Detection and Service Selection

Current software engineering topics such as clone detection and service selection need to improve the capability of detection process and selection process. The clone detection is the process of finding duplicated code through the system for several purposes such as removal of repeated portions as maintenance part of legacy system. Service selection is the process of finding the appropriate web service which meets the consumer’s request. Both problems can be converted into a matching problem. Matching process forms an essential part of software engineering activities. In this research, a well-known mathematical algorithm Stable Marriage Problem (SMP) and its variations are investigated to fulfil the purposes of matching processes in software engineering area. We aim to provide a competitive matching algorithm that can help to detect cloned software accurately and ensure high scalability, precision and recall. We also aim to apply matching algorithm on incoming request and service profile to deal with the web service as a clever independent object so that we can allow the services to accept or decline requests (equal opportunity) rather than the current state of service selection (search-based), in which service lacks of interacting as an independent candidate. In order to meet the above aims, the traditional SMP algorithm has been extended to achieve the cardinality of many-to-many. This adaptation is achieved by defining the selective strategy which is the main engine of the new adaptations. Two adaptations, Dual-Proposed and Dual-Multi-Allocation, have been proposed to both service selection and clone detection process. The proposed approach (SMP-based) shows very competitive results compare to existing software clone approaches, especially in identifying type 3 (copy with further modifications such update, add and delete statements) of cloned software. It performs the detection process with a relatively high precision and recall compare to the CloneDR tool and shows good scalability on a middle sized program. For service selection, the proposed approach has several advantages such as service protection and service quality. The services gain equal opportunity against the incoming requests. Therefore, the intelligent service interaction is achieved, and both stability and satisfaction of the candidates are ensured. This dissertation contributes to several contributions firstly, the new extended SMP algorithm by introducing selective strategy to accommodate many-to-many matching problems, to improve overall features. Secondly, a new SMP-based clone detection approach to detect cloned software accurately and ensures high precision and recall. Ultimately, a new SMPbased service selection approach allows equal opportunity between services and requests. This led to improve service protection and service quality. Case studies are carried out for experiments with the proposed approach, which show that the new adaptations can be applied effectively to clone detection and service selection processes with several features (e.g. accuracy). It can be concluded that the match based approach is feasible and promising in software engineering domain.Royal Embassy of Saudi Arabi