On FPGA implementations for bioinformatics, neural prosthetics and reinforcement learning problems.

Mak Sui Tung Terrence.Thesis (M.Phil.)--Chinese University of Hong Kong, 2005.Includes bibliographical references (leaves 132-142).Abstracts in English and Chinese.Abstract --- p.iList of Tables --- p.ivList of Figures --- p.vAcknowledgements --- p.ixChapter 1. --- Introduction --- p.1Chapter 1.1 --- Bioinformatics --- p.1Chapter 1.2 --- Neural Prosthetics --- p.4Chapter 1.3 --- Learning in Uncertainty --- p.5Chapter 1.4 --- The Field Programmable Gate Array (FPGAs) --- p.7Chapter 1.5 --- Scope of the Thesis --- p.10Chapter 2. --- A Hybrid GA-DP Approach for Searching Equivalence Sets --- p.14Chapter 2.1 --- Introduction --- p.16Chapter 2.2 --- Equivalence Set Criterion --- p.18Chapter 2.3 --- Genetic Algorithm and Dynamic Programming --- p.19Chapter 2.3.1 --- Genetic Algorithm Formulation --- p.20Chapter 2.3.2 --- Bounded Mutation --- p.21Chapter 2.3.3 --- Conditioned Crossover --- p.22Chapter 2.3.4 --- Implementation --- p.22Chapter 2.4 --- FPGAs Implementation of GA-DP --- p.24Chapter 2.4.1 --- System Overview --- p.25Chapter 2.4.2 --- Parallel Computation for Transitive Closure --- p.26Chapter 2.4.3 --- Genetic Operation Realization --- p.28Chapter 2.5 --- Discussion --- p.30Chapter 2.6 --- Limitation and Future Work --- p.33Chapter 2.7 --- Conclusion --- p.34Chapter 3. --- An FPGA-based Architecture for Maximum-Likelihood Phylogeny Evaluation --- p.35Chapter 3.1 --- Introduction --- p.36Chapter 3.2 --- Maximum-Likelihood Model --- p.39Chapter 3.3 --- Hardware Mapping for Pruning Algorithm --- p.41Chapter 3.3.1 --- Related Works --- p.41Chapter 3.3.2 --- Number Representation --- p.42Chapter 3.3.3 --- Binary Tree Representation --- p.43Chapter 3.3.4 --- Binary Tree Traversal --- p.45Chapter 3.3.5 --- Maximum-Likelihood Evaluation Algorithm --- p.46Chapter 3.4 --- System Architecture --- p.49Chapter 3.4.1 --- Transition Probability Unit --- p.50Chapter 3.4.2 --- State-Parallel Computation Unit --- p.51Chapter 3.4.3 --- Error Computation --- p.54Chapter 3.5 --- Discussion --- p.56Chapter 3.5.1 --- Hardware Resource Consumption --- p.56Chapter 3.5.2 --- Delay Evaluation --- p.57Chapter 3.6 --- Conclusion --- p.59Chapter 4. --- Field Programmable Gate Array Implementation of Neuronal Ion Channel Dynamics --- p.61Chapter 4.1 --- Introduction --- p.62Chapter 4.2 --- Background --- p.63Chapter 4.2.1 --- Analog VLSI Model for Hebbian Synapse --- p.63Chapter 4.2.2 --- A Unifying Model of Bi-directional Synaptic Plasticity --- p.64Chapter 4.2.3 --- Non-NMDA Receptor Channel Regulation --- p.65Chapter 4.3 --- FPGAs Implementation --- p.65Chapter 4.3.1 --- FPGA Design Flow --- p.65Chapter 4.3.2 --- Digital Model of NMD A and AMPA receptors --- p.65Chapter 4.3.3 --- Synapse Modification --- p.67Chapter 4.4 --- Results --- p.68Chapter 4.4.1 --- Simulation Results --- p.68Chapter 4.5 --- Discussion --- p.70Chapter 4.6 --- Conclusion --- p.71Chapter 5. --- Continuous-Time and Discrete-Time Inference Networks for Distributed Dynamic Programming --- p.72Chapter 5.1 --- Introduction --- p.74Chapter 5.2 --- Background --- p.77Chapter 5.2.1 --- Markov decision process (MDPs) --- p.78Chapter 5.2.2 --- Learning in the MDPs --- p.80Chapter 5.2.3 --- Bellman Optimal Criterion --- p.80Chapter 5.2.4 --- Value Iteration --- p.81Chapter 5.3 --- A Computational Framework for Continuous-Time Inference Network --- p.82Chapter 5.3.1 --- Binary Relation Inference Network --- p.83Chapter 5.3.2 --- Binary Relation Inference Network for MDPs --- p.85Chapter 5.3.3 --- Continuous-Time Inference Network for MDPs --- p.87Chapter 5.4 --- Convergence Consideration --- p.88Chapter 5.5 --- Numerical Simulation --- p.90Chapter 5.5.1 --- Example 1: Random Walk --- p.90Chapter 5.5.2 --- Example 2: Random Walk on a Grid --- p.94Chapter 5.5.3 --- Example 3: Stochastic Shortest Path Problem --- p.97Chapter 5.5.4 --- Relationships Between λ and γ --- p.99Chapter 5.6 --- Discrete-Time Inference Network --- p.100Chapter 5.6.1 --- Results --- p.101Chapter 5.7 --- Conclusion --- p.102Chapter 6. --- On Distributed g-Learning Network --- p.104Chapter 6.1 --- Introduction --- p.105Chapter 6.2 --- Distributed Q-Learniing Network --- p.108Chapter 6.2.1 --- Distributed Q-Learning Network --- p.109Chapter 6.2.2 --- Q-Learning Network Architecture --- p.111Chapter 6.3 --- Experimental Results --- p.114Chapter 6.3.1 --- Random Walk --- p.114Chapter 6.3.2 --- The Shortest Path Problem --- p.116Chapter 6.4 --- Discussion --- p.120Chapter 6.4.1 --- Related Work --- p.121Chapter 6.5 --- FPGAs Implementation --- p.122Chapter 6.5.1 --- Distributed Registering Approach --- p.123Chapter 6.5.2 --- Serial BRAM Storing Approach --- p.124Chapter 6.5.3 --- Comparison --- p.125Chapter 6.5.4 --- Discussion --- p.127Chapter 6.6 --- Conclusion --- p.128Chapter 7. --- Summary --- p.129Bibliography --- p.132AppendixChapter A. --- Simplified Floating-Point Arithmetic --- p.143Chapter B. --- "Logarithm, Exponential and Division Implementation" --- p.144Chapter B.1 --- Introduction --- p.144Chapter B.2 --- Approximation Scheme --- p.145Chapter B.2.1 --- Logarithm --- p.145Chapter B.2.2 --- Exponentiation --- p.147Chapter B.2.3 --- Division --- p.148Chapter C. --- Analog VLSI Implementation --- p.150Chapter C.1 --- Site Function --- p.150Chapter C.1.1 --- Multiplication Cell --- p.150Chapter C.2 --- The Unit Function --- p.153Chapter C.3 --- The Inference Network Computation --- p.154Chapter C.4 --- Layout --- p.157Chapter C.5 --- Fabrication --- p.159Chapter C.5.1 --- Testing and Characterization --- p.16

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)

Using materialized views for answering graph pattern queries

Discovering patterns in graphs by evaluating graph pattern queries involving direct (edge-to-edge mapping) and reachability (edge-to-path mapping) relationships under homomorphisms on data graphs has been extensively studied. Previous studies have aimed to reduce the evaluation time of graph pattern queries due to the potentially numerous matches on large data graphs. In this work, the concept of the summary graph is developed to improve the evaluation of tree pattern queries and graph pattern queries. The summary graph first filters out candidate matches which violate certain reachability constraints, and then finds local matches of query edges. This reduces redundancy in the representation of the query results and allows for computation sharing during the generation of these results. Methods using materialized graph pattern views are developed to improve the efficiency of graph pattern query evaluation. A view is materialized as a summary graph, which compactly records all the homomorphisms of the view to the data graph. View usability is characterized in terms of query edge coverage to provide necessary and sufficient conditions for answering queries using views, and algorithms are developed for determining view usability and for summary graph construction. Experimental evaluation shows that the methods using summary graphs and its related concepts outperform previous state-of-the-art approaches. It also demonstrates that the view materialization method outperforms, by several orders of magnitude, a state-of-the-art approach which does not use materialized views, and substantially improves upon its scalability

The Fine-Grained Complexity of Problems Expressible by First-Order Logic and Its Extensions

This dissertation studies the fine-grained complexity of model checking problems for fixed logical formulas on sparse input structures. The Orthogonal Vectors problem is an important and well-studied problem in fine-grained complexity: its hardness is implied by the Strong Exponential Time Hypothesis, and its hardness implies the hardness of many other interesting problems. We show that the Orthogonal Vectors problem is complete in the class of first-order model checking on sparse structures, under fine-grained reductions. In other words, the hardness of Orthogonal Vectors and the hardness of first-order model checking imply each other. This also gives us an improved algorithm for first-order model checking problems. Among all first-order logic formulas in prenex normal form, we have reasons to believe that quantifier structures $\exists \dots \exists \forall$ and $\forall \dots \forall \exists$ may be the hardest in computational complexity: If the Nondeterministic version of the Strong Exponential Time Hypothesis is true, formulas of these forms are the only hard ones under the Strong Exponential Time Hypothesis. We can add extensions to first-order logic to strengthen its expressive power. This work also studies the fine-grained complexity of first-order formulas with comparison on structures with total order, first-order formulas with transitive closure operations, first-order formulas of fixed quantifier rank, and first-order formulas of fixed variable complexity. We also introduce a technique that can be used to reduce from sequential problems on graphs to parallel problems on sets, which can be applied to extending the Least Weight Subsequence problems from linear structures to some special classes of graphs

Topological and algebraic characterization of coverings sets obtained in rough sets discretization and attribute reduction algorithms

Abstract. A systematic study on approximation operators in covering based rough sets and some relations with relation based rough sets are presented. Two different frameworks of approximation operators in covering based rough sets were unified in a general framework of dual pairs. This work establishes some relationships between the most important generalization of rough set theory: Covering based and relation based rough sets. A structured genetic algorithm to discretize, to find reducts and to select approximation operators for classification problems is presented.Se presenta un estudio sistemático de los diferentes operadores de aproximación en conjuntos aproximados basados en cubrimientos y operadores de aproximación basados en relaciones binarias. Se unifican dos marcos de referencia sobre operadores de aproximación basados en cubrimientos en un único marco de referencia con pares duales. Se establecen algunas relaciones entre operadores de aproximación de dos de las más importantes generalizaciones de la teoría de conjuntos aproximados. Finalmente, se presenta un algoritmo genético estructurado, para discretizar, reducir atributos y seleccionar operadores de aproximación, en problemas de clasificación.Doctorad