Finding common RNA pseudoknot structures in polynomial time

AbstractThis paper presents the first polynomial time algorithm for finding common RNA substructures that include pseudoknots and similar structures. While a more general problem is known to be NP-hard, this algorithm exploits special features of RNA structures to match RNA bonds correctly in polynomial time. Although the theoretical upper bound on the algorithmʼs time and space usage is high, the data-driven nature of its computation enables it to avoid computing unnecessary cases, dramatically reducing the actual running time. The algorithm works well in practice, and has been tested on sample RNA structures that include pseudoknots and pseudoknot-like tertiary structures

Part-to-whole Registration of Histology and MRI using Shape Elements

Image registration between histology and magnetic resonance imaging (MRI) is a challenging task due to differences in structural content and contrast. Too thick and wide specimens cannot be processed all at once and must be cut into smaller pieces. This dramatically increases the complexity of the problem, since each piece should be individually and manually pre-aligned. To the best of our knowledge, no automatic method can reliably locate such piece of tissue within its respective whole in the MRI slice, and align it without any prior information. We propose here a novel automatic approach to the joint problem of multimodal registration between histology and MRI, when only a fraction of tissue is available from histology. The approach relies on the representation of images using their level lines so as to reach contrast invariance. Shape elements obtained via the extraction of bitangents are encoded in a projective-invariant manner, which permits the identification of common pieces of curves between two images. We evaluated the approach on human brain histology and compared resulting alignments against manually annotated ground truths. Considering the complexity of the brain folding patterns, preliminary results are promising and suggest the use of characteristic and meaningful shape elements for improved robustness and efficiency.Comment: Paper accepted at ICCV Workshop (Bio-Image Computing

Categorified sl(N) invariants of colored rational tangles

We use categorical skew Howe duality to find recursion rules that compute categorified sl(N) invariants of rational tangles colored by exterior powers of the standard representation. Further, we offer a geometric interpretation of these rules which suggests a connection to Floer theory. Along the way we make progress towards two conjectures about the colored HOMFLY homology of rational links.Comment: 45 pages, many figures, uses dcpic.sty, v2: minor changes and new example 5

What Makes the Arc-Preserving Subsequence Problem Hard?

International audienceGiven two arc-annotated sequences (S, P ) and (T, Q) representing RNA structures, the Arc-Preserving Subsequence (APS) problem asks whether (T, Q) can be obtained from (S, P ) by deleting some of its bases (together with their incident arcs, if any). In previous studies [3, 6], this problem has been naturally divided into subproblems reflecting intrinsic complexity of arc structures. We show that APS(Crossing, Plain) is NP-complete, thereby answering an open problem [6]. Furthermore, to get more insight into where actual border of APS hardness is, we refine APS classical subproblems in much the same way as in [11] and give a complete categorization among various restrictions of APS problem complexity

State Cycles, Quasipositive Modification, and Constructing H-thick Knots in Khovanov Homology

We study Khovanov homology classes which have state cycle representatives, and examine how they interact with Jacobsson homomorphisms and Lee's map $\Phi$. As an application, we describe a general procedure, quasipositive modification, for constructing H-thick knots in rational Khovanov homology. Moreover, we show that specific families of such knots cannot be detected by Khovanov's thickness criteria. We also exhibit a sequence of prime links related by quasipositive modification whose width is increasing.Comment: 42 pages, color figures. Version 2 revisions: an error was corrected in Proposition 4.3, which requires a stronger hypothesis. This slightly widens the classification theorem of section 4, and has led to small revisions throughout. Theorem 4.7, which involved even all-1 state cycles, has been removed, as it has grown into a forthcoming pape

3D minutiae extraction in 3D fingerprint scans.

Traditionally, fingerprint image acquisition was based on contact. However the conventional touch-based fingerprint acquisition introduces some problems such as distortions and deformations to the fingerprint image. The most recent technology for fingerprint acquisition is touchless or 3D live scans introducing higher quality fingerprint scans. However, there is a need to develop new algorithms to match 3D fingerprints. In this dissertation, a novel methodology is proposed to extract minutiae in the 3D fingerprint scans. The output can be used for 3D fingerprint matching. The proposed method is based on curvature analysis of the surface. The method used to extract minutiae includes the following steps: smoothing; computing the principal curvature; ridges and ravines detection and tracing; cleaning and connecting ridges and ravines; and minutiae detection. First, the ridges and ravines are detected using curvature tensors. Then, ridges and ravines are traced. Post-processing is performed to obtain clean and connected ridges and ravines based on fingerprint pattern. Finally, minutiae are detected using a graph theory concept. A quality map is also introduced for 3D fingerprint scans. Since a degraded area may occur during the scanning process, especially at the edge of the fingerprint, it is critical to be able to determine these areas. Spurious minutiae can be filtered out after applying the quality map. The algorithm is applied to the 3D fingerprint database and the result is very encouraging. To the best of our knowledge, this is the first minutiae extraction methodology proposed for 3D fingerprint scans

Notes on bordered Floer homology

This is a survey of bordered Heegaard Floer homology, an extension of the Heegaard Floer invariant HF-hat to 3-manifolds with boundary. Emphasis is placed on how bordered Heegaard Floer homology can be used for computations.Comment: 73 pages, 29 figures. Based on lectures at the Contact and Symplectic Topology Summer School in Budapest, July 2012. v2: Fixed many small typo