Proceedings of the Workshop Semantic Content Acquisition and Representation (SCAR) 2007

This is the proceedings of the Workshop on Semantic Content Acquisition and Representation, held in conjunction with NODALIDA 2007, on May 24 2007 in Tartu, Estonia.</p

Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, and Evaluations

Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences\u27 structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes. In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method encapsulates stereo-chemical properties of sequence residues and their substitution probabilities into a tree-structure scoring scheme. This new technique provides a reliable scoring scheme with low computational complexity. In addition to the new scoring scheme, we have designed an overlapping sequence clustering algorithm to use in our new three multiple sequence alignment algorithms. One of our alignment algorithms uses a dynamic weighted guidance tree to perform multiple sequence alignment in progressive fashion. The use of dynamic weighted tree allows errors in the early alignment stages to be corrected in the subsequence stages. Other two algorithms utilize sequence knowledge-bases and sequence consistency to produce biological meaningful sequence alignments. To improve the speed of the multiple sequence alignment, we have developed a parallel algorithm that can be deployed on reconfigurable computer models. Analytically, our parallel algorithm is the fastest progressive multiple sequence alignment algorithm

Robust interactive cutting based on an adaptive octree simulation mesh

We present an adaptive octree based approach for interactive cutting of deformable objects. Our technique relies on efficient refine- and node split-operations. These are sufficient to robustly represent cuts in the mechanical simulation mesh. A high-resolution surface embedded into the octree is employed to represent a cut visually. Model modification is performed in the rest state of the object, which is accomplished by back-transformation of the blade geometry. This results in an improved robustness of our approach. Further, an efficient update of the correspondences between simulation elements and surface vertices is proposed. The robustness and efficiency of our approach is underlined in test examples as well as by integrating it into a prototype surgical simulato

Efficient Learning of Mesh-Based Physical Simulation with BSMS-GNN

Learning the physical simulation on large-scale meshes with flat Graph Neural Networks (GNNs) and stacking Message Passings (MPs) is challenging due to the scaling complexity w.r.t. the number of nodes and over-smoothing. There has been growing interest in the community to introduce \textit{multi-scale} structures to GNNs for physical simulation. However, current state-of-the-art methods are limited by their reliance on the labor-intensive drawing of coarser meshes or building coarser levels based on spatial proximity, which can introduce wrong edges across geometry boundaries. Inspired by the bipartite graph determination, we propose a novel pooling strategy, \textit{bi-stride} to tackle the aforementioned limitations. Bi-stride pools nodes on every other frontier of the breadth-first search (BFS), without the need for the manual drawing of coarser meshes and avoiding the wrong edges by spatial proximity. Additionally, it enables a one-MP scheme per level and non-parametrized pooling and unpooling by interpolations, resembling U-Nets, which significantly reduces computational costs. Experiments show that the proposed framework, \textit{BSMS-GNN}, significantly outperforms existing methods in terms of both accuracy and computational efficiency in representative physical simulations.Comment: Updates summary: * update to the accepted version ICM

Embedded dynamic programming networks for networks-on-chip

PhD ThesisRelentless technology downscaling and recent technological advancements in three dimensional integrated circuit (3D-IC) provide a promising prospect to realize heterogeneous system-on-chip (SoC) and homogeneous chip multiprocessor (CMP) based on the networks-onchip (NoCs) paradigm with augmented scalability, modularity and performance. In many cases in such systems, scheduling and managing communication resources are the major design and implementation challenges instead of the computing resources. Past research efforts were mainly focused on complex design-time or simple heuristic run-time approaches to deal with the on-chip network resource management with only local or partial information about the network. This could yield poor communication resource utilizations and amortize the benefits of the emerging technologies and design methods. Thus, the provision for efficient run-time resource management in large-scale on-chip systems becomes critical. This thesis proposes a design methodology for a novel run-time resource management infrastructure that can be realized efficiently using a distributed architecture, which closely couples with the distributed NoC infrastructure. The proposed infrastructure exploits the global information and status of the network to optimize and manage the on-chip communication resources at run-time. There are four major contributions in this thesis. First, it presents a novel deadlock detection method that utilizes run-time transitive closure (TC) computation to discover the existence of deadlock-equivalence sets, which imply loops of requests in NoCs. This detection scheme, TC-network, guarantees the discovery of all true-deadlocks without false alarms in contrast to state-of-the-art approximation and heuristic approaches. Second, it investigates the advantages of implementing future on-chip systems using three dimensional (3D) integration and presents the design, fabrication and testing results of a TC-network implemented in a fully stacked three-layer 3D architecture using a through-silicon via (TSV) complementary metal-oxide semiconductor (CMOS) technology. Testing results demonstrate the effectiveness of such a TC-network for deadlock detection with minimal computational delay in a large-scale network. Third, it introduces an adaptive strategy to effectively diffuse heat throughout the three dimensional network-on-chip (3D-NoC) geometry. This strategy employs a dynamic programming technique to select and optimize the direction of data manoeuvre in NoC. It leads to a tool, which is based on the accurate HotSpot thermal model and SystemC cycle accurate model, to simulate the thermal system and evaluate the proposed approach. Fourth, it presents a new dynamic programming-based run-time thermal management (DPRTM) system, including reactive and proactive schemes, to effectively diffuse heat throughout NoC-based CMPs by routing packets through the coolest paths, when the temperature does not exceed chip’s thermal limit. When the thermal limit is exceeded, throttling is employed to mitigate heat in the chip and DPRTM changes its course to avoid throttled paths and to minimize the impact of throttling on chip performance. This thesis enables a new avenue to explore a novel run-time resource management infrastructure for NoCs, in which new methodologies and concepts are proposed to enhance the on-chip networks for future large-scale 3D integration.Iraqi Ministry of Higher Education and Scientific Research (MOHESR)

Diamond-based models for scientific visualization

Hierarchical spatial decompositions are a basic modeling tool in a variety of application domains including scientific visualization, finite element analysis and shape modeling and analysis. A popular class of such approaches is based on the regular simplex bisection operator, which bisects simplices (e.g. line segments, triangles, tetrahedra) along the midpoint of a predetermined edge. Regular simplex bisection produces adaptive simplicial meshes of high geometric quality, while simplifying the extraction of crack-free, or conforming, approximations to the original dataset. Efficient multiresolution representations for such models have been achieved in 2D and 3D by clustering sets of simplices sharing the same bisection edge into structures called diamonds. In this thesis, we introduce several diamond-based approaches for scientific visualization. We first formalize the notion of diamonds in arbitrary dimensions in terms of two related simplicial decompositions of hypercubes. This enables us to enumerate the vertices, simplices, parents and children of a diamond. In particular, we identify the number of simplices involved in conforming updates to be factorial in the dimension and group these into a linear number of subclusters of simplices that are generated simultaneously. The latter form the basis for a compact pointerless representation for conforming meshes generated by regular simplex bisection and for efficiently navigating the topological connectivity of these meshes. Secondly, we introduce the supercube as a high-level primitive on such nested meshes based on the atomic units within the underlying triangulation grid. We propose the use of supercubes to associate information with coherent subsets of the full hierarchy and demonstrate the effectiveness of such a representation for modeling multiresolution terrain and volumetric datasets. Next, we introduce Isodiamond Hierarchies, a general framework for spatial access structures on a hierarchy of diamonds that exploits the implicit hierarchical and geometric relationships of the diamond model. We use an isodiamond hierarchy to encode irregular updates to a multiresolution isosurface or interval volume in terms of regular updates to diamonds. Finally, we consider nested hypercubic meshes, such as quadtrees, octrees and their higher dimensional analogues, through the lens of diamond hierarchies. This allows us to determine the relationships involved in generating balanced hypercubic meshes and to propose a compact pointerless representation of such meshes. We also provide a local diamond-based triangulation algorithm to generate high-quality conforming simplicial meshes

Implementation of MPEG-4s Subdivision Surfaces Tools

This work is about the implementation of a MPEG-4 decoder for subdivision surfaces, which are powerful 3D paradigms allowing to compactly represent piecewise smooth surfaces. This study will take place in the framework of MPEG-4 AFX, the extension of the MPEG-4 standard including the subdivision surfaces. This document will introduce, with some details, the theory of subdivision surfaces in the two forms present in MPEG-4: plain and detailed/ wavelet subdivision surfaces. It will particularly concentrate on wavelet subdivision surfaces, which permit progressive 3D mesh compression

Self-directedness, integration and higher cognition

In this paper I discuss connections between self-directedness, integration and higher cognition. I present a model of self-directedness as a basis for approaching higher cognition from a situated cognition perspective. According to this model increases in sensorimotor complexity create pressure for integrative higher order control and learning processes for acquiring information about the context in which action occurs. This generates complex articulated abstractive information processing, which forms the major basis for higher cognition. I present evidence that indicates that the same integrative characteristics found in lower cognitive process such as motor adaptation are present in a range of higher cognitive process, including conceptual learning. This account helps explain situated cognition phenomena in humans because the integrative processes by which the brain adapts to control interaction are relatively agnostic concerning the source of the structure participating in the process. Thus, from the perspective of the motor control system using a tool is not fundamentally different to simply controlling an arm