A Faster Subquadratic Algorithm for the Longest Common Increasing Subsequence Problem

The Longest Common Increasing Subsequence (LCIS) is a variant of the classical Longest Common Subsequence (LCS), in which we additionally require the common subsequence to be strictly increasing. While the well-known "Four Russians" technique can be used to find LCS in subquadratic time, it does not seem applicable to LCIS. Recently, Duraj [STACS 2020] used a completely different method based on the combinatorial properties of LCIS to design an $\mathcal{O}(n^2(\log\log n)^2/\log^{1/6}n)$ time algorithm. We show that an approach based on exploiting tabulation can be used to construct an asymptotically faster $\mathcal{O}(n^2 \log\log n/\sqrt{\log n})$ time algorithm. As our solution avoids using the specific combinatorial properties of LCIS, it can be also adapted for the Longest Common Weakly Increasing Subsequence (LCWIS)

On the Separation of Topology-Free Rank Inequalities for the Max Stable Set Problem

In the context of finding the largest stable set of a graph, rank inequalities prescribe that a stable set can contain, from any induced subgraph of the original graph, at most as many vertices as the stability number of the former. Although these inequalities subsume many of the valid inequalities known for the problem, their exact separation has only been investigated in few special cases obtained by restricting the induced subgraph to a specific topology. In this work, we propose a different approach in which, rather than imposing topological restrictions on the induced subgraph, we assume the right-hand side of the inequality to be fixed to a given (but arbitrary) constant. We then study the arising separation problem, which corresponds to the problem of finding a maximum weight subgraph with a bounded stability number. After proving its hardness and giving some insights on its polyhedral structure, we propose an exact branch-and-cut method for its solution. Computational results show that the separation of topology-free rank inequalities with a fixed right-hand side yields a substantial improvement over the bound provided by the fractional clique polytope (which is obtained with rank inequalities where the induced subgraph is restricted to a clique), often better than that obtained with Lovasz's Theta function via semidefmite programming

Tight Conditional Lower Bounds for Longest Common Increasing Subsequence

We consider the canonical generalization of the well-studied Longest Increasing Subsequence problem to multiple sequences, called k-LCIS: Given k integer sequences X_1,...,X_k of length at most n, the task is to determine the length of the longest common subsequence of X_1,...,X_k that is also strictly increasing. Especially for the case of k=2 (called LCIS for short), several algorithms have been proposed that require quadratic time in the worst case. Assuming the Strong Exponential Time Hypothesis (SETH), we prove a tight lower bound, specifically, that no algorithm solves LCIS in (strongly) subquadratic time. Interestingly, the proof makes no use of normalization tricks common to hardness proofs for similar problems such as LCS. We further strengthen this lower bound to rule out O((nL)^{1-epsilon}) time algorithms for LCIS, where L denotes the solution size, and to rule out O(n^{k-epsilon}) time algorithms for k-LCIS. We obtain the same conditional lower bounds for the related Longest Common Weakly Increasing Subsequence problem

Image processing techniques for high-speed atomic force microscopy

Atomic force microscopy (AFM) is a powerful tool for imaging topography or other characteristics of sample surfaces at nanometer-scale spatial resolution by recording the interaction of a sharp probe with the surface. Dispute its excellent spatial resolution, one of the enduring challenges in AFM imaging is its poor temporal resolution relative to the rate of dynamics in many systems of interest. This has led to a large research effort on the development of high-speed AFM (HS-AFM). Most of these efforts focus on mechanical improvement and control algorithm design. This dissertation investigates a complementary HS-AFM approach based on the idea of undersampling which aims at increasing the imaging rate of the instrument by reducing the number of pixels in the sample surface that need to be acquired to create a high-quality image. The first part of this work focuses on the reconstruction of images sub-sampled according to a scheme known as μ path patterns. These patterns consist of randomly placed short and disjoint scans and are designed specifically for fast, efficient, and consistent data acquisition in AFM. We compare compressive sensing (CS) reconstruction methods with inpainting methods on recovering μ-path undersampled images. The results illustrate that the reconstruction quality depends on the choice of reconstruction methods and the sample under study, with CS generally producing a superior result for samples with sparse frequency content and inpainting performing better for samples with information limited to low frequencies. Motivated by the comparison, a basis pursuit vertical variation (BPVV) method, combing CS and inpainting, is proposed. Based on single image reconstruction results, we also extend our analysis to the problem of multiple AFM frames, in which higher overall video reconstruction quality is achieved by pixel sharing among different frames. The second part of the thesis considers patterns for sub-sampling in AFM. The allocation of measurements plays an important role in producing accurate reconstructions of the sample surface. We analyze the expected image reconstruction error using a greedy CS algorithm of our design, termed simplified matching pursuit (SMP), and propose a Monte Carlo-based strategy to create μ-path patterns that minimize the expected error. Because these μ path patterns involve a collection of disjoint scan paths, they require the tip of the instrument to be repeatedly lifted from and re-engaged to the surface. In many cases, the re-engagements make up a significant portion of the total data acquisition time. We therefore extend our Monte Carlo design strategy to find continuous scan patterns that minimize the reconstruction error without requiring the tip to be lifted from the surface. For the final part of the work, we provide a hardware demonstration on a commercial AFM. We describe hardware implementation details and image a calibration grating using the proposed μ-path and continuous scan patterns. The sample surface is reconstructed from acquired data using CS and inpainting methods. The recovered image quality and achievable imaging rate are compared to full raster-scans of the sample. The experimental results show that the proposed scanning combining with reconstruction methods can produce higher image quality with less imaging time

Improving Academic Plagiarism Detection for STEM Documents by Analyzing Mathematical Content and Citations

Identifying academic plagiarism is a pressing task for educational and research institutions, publishers, and funding agencies. Current plagiarism detection systems reliably find instances of copied and moderately reworded text. However, reliably detecting concealed plagiarism, such as strong paraphrases, translations, and the reuse of nontextual content and ideas is an open research problem. In this paper, we extend our prior research on analyzing mathematical content and academic citations. Both are promising approaches for improving the detection of concealed academic plagiarism primarily in Science, Technology, Engineering and Mathematics (STEM). We make the following contributions: i) We present a two-stage detection process that combines similarity assessments of mathematical content, academic citations, and text. ii) We introduce new similarity measures that consider the order of mathematical features and outperform the measures in our prior research. iii) We compare the effectiveness of the math-based, citation-based, and text-based detection approaches using confirmed cases of academic plagiarism. iv) We demonstrate that the combined analysis of math-based and citation-based content features allows identifying potentially suspicious cases in a collection of 102K STEM documents. Overall, we show that analyzing the similarity of mathematical content and academic citations is a striking supplement for conventional text-based detection approaches for academic literature in the STEM disciplines.Comment: Proceedings of the ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL) 2019. The data and code of our study are openly available at https://purl.org/hybridP

Acoustic analysis of the knee joint in the study of osteoarthritis detection during walking

This thesis investigates the potential of non-invasive detection of knee Osteoarthritis (OA) using the sounds emitted by the knee joint during walking and captured by a single microphone. This is a novel application since, until now, there are no other methods that considered this type of signals. Clinical detection of knee OA relies on imaging techniques such as X-radiology and Magnetic Resonance Imaging. Some of these methods are expensive and impractical while others pose health risks due to radiation. Knee sounds on the other hand may offer a quick, practical and cost-effective alternative for the detection of the disease. In this thesis, the knee sound signal structure is investigated using signal processing methods for information extraction from the time, frequency, cepstral and modulation domains. Feature representations are obtained and their discriminant properties are studied using statistical methods such as the Bhattacharyya distance and supervised learning techniques such as Support Vector Machine. From this work, a statistical feature parameterisation is proposed and its efficacy for the task of healthy vs OA knee condition classification is investigated using a comprehensive experimental framework proposed in this thesis. Feature-based representations that incorporate spatiotemporal information using gait pattern variables, were also investigated for classification. Using the waveform characteristics of the acoustic pulse events detected in the signal, such representations are proposed and evaluated. This approach utilised a novel stride detection and segmentation algorithm that is based on dynamic programming and is also proposed in the thesis. This algorithm opens up potential applications in other research fields such as gait analysis.Open Acces

Discretization schemes and numerical approximations of PDE impainting models and a comparative evaluation on novel real world MRI reconstruction applications

While various PDE models are in discussion since the last ten years and are widely applied nowadays in image processing and computer vision tasks, including restoration, filtering, segmentation and object tracking, the perspective adopted in the majority of the relevant reports is the view of applied mathematician, attempting to prove the existence theorems and devise exact numerical methods for solving them. Unfortunately, such solutions are exact for the continuous PDEs but due to the discrete approximations involved in image processing, the results yielded might be quite unsatisfactory. The major contribution of This work is, therefore, to present, from an engineering perspective, the application of PDE models in image processing analysis, from the algorithmic point of view, the discretization and numerical approximation schemes used for solving them. It is of course impossible to tackle all PDE models applied in image processing in this report from the computational point of view. It is, therefore, focused on image impainting PDE models, that is on PDEs, including anisotropic diffusion PDEs, higher order non-linear PDEs, variational PDEs and other constrained/regularized and unconstrained models, applied to image interpolation/ reconstruction. Apart from this novel computational critical overview and presentation of the PDE image impainting models numerical analysis, the second major contribution of This work is to evaluate, especially the anisotropic diffusion PDEs, in novel real world image impainting applications related to MRI