9323907
Orientation refinement of virus structures with unknown symmetry
Structural biology, in particular the structure determination of viruses and other large macromolecular complexes lead to data- and compute-intensive problems that require resources well beyond those available on a single system. Thus, there is an imperative need to develop parallel algorithms and programs for clusters and computational grids. We present one of the most challenging computational problems posed by the three-dimensional structure determination of viruses, the orientation refinement.
17633305
The Impact of Cache Organization in Optimizing Microprocessor Power Consumption
In the recent years, power consumption has become increasingly an important design concern as silicon area and performance in modern computer systems design. Several factors have contributed to this trend. Perhaps the most visible have been the remarkable success and growth of Personal Digital Assistants (PDA’s), Cellular phones and pagers, etc .This work is an attempt to explore the impact of feature size shrinkage and cache configuration on optimizing power consumption in modern processors. The work studies two commercially known RISC microprocessors. The StrongARM and the Alpha-21064 microprocessors. The latter is the ancestor of the former and is therefore used here as the baseline in our analysis. Our analysis has illustrated quantitatively great power saving when technology is downsized and cache is well organized
14422830
Compiler-guided register reliability improvement against soft errors
With the scaling of technology, transient errors caused by external particle strikes have become a critical challenge for microprocessor design. As embedded processors are widely used in reliability-sensitive environments, it becomes increasingly important to develop cost-effective techniques to improve the processor reliability against soft errors. This paper focuses on studying the register file immunity against soft errors since modern processors typically employ a large number of registers, which are accessed very frequently. As a result, soft errors occurred in registers can easily propagate to functional units or the memory system, leading to silent data error (SDC) or system crash.To develop cost-effective techniques to fight soft errors for embedded processors, the first step is to understand the register file susceptibility to soft errors and its impact on the system reliability accurately. Toward this goal, this paper proposes the concept of register vulnerability factor (RVF) to characterize the probability that register transient errors can escape the register file and thus potentially impact the system reliability. Built upon the RVF concept, we then propose two cost-effective compiler-guided techniques to improve the register file reliability by lowering the RVF value. Our experiments indicate that on average, the RVF can be reduced to 9.1% and 9.5% by the hyperblock-based instruction re-scheduling and the reliability-oriented register assignment respectively, which can potentially lower the reliability cost significantly while protecting register files against transient errors.
43025995
Processing Probabilistic Range Query over Imprecise Data Based on Quality of Result
Sensors are employed in many applications to monitor entities such as environment temperature or illumination. Because of limited resources (e.g., battery power and wireless bandwidth), it is impractical for the database to track continuous changing readings from sensors at all times. Consequently, database may produce incorrect query results based on recorded data. However, if the error between the recorded value and the actual value is bounded, probabilistic approach can be applied to process queries over the imprecise data in database. The paper proposes a quality of result based probabilistic range query processing method. Two measures are defined to evaluate the quality of result. A probability model is proposed to estimate the quality of returned results. Based on the model, an algorithm is developed to choose the probability threshold according to user’s requirement on the quality of result.
9354212
High-Performance Job-Shop Scheduling With A Time-Delay TD-lambda Network
Job-shop scheduling is an important task for manufacturing industries. We are interested in the particular task of scheduling payload processing for NASA's space shuttle program. This paper summarizes our previous work on formulating this task for solution by the reinforcement learning algorithm T D(). A shortcoming of this previous work was its reliance on hand-engineered input features. This paper shows how to extend the time-delay neural network (TDNN) architecture to apply it to irregular-length schedules. Experimental tests show that this TDNN-TD() network can match the performance of our previous hand-engineered system. The tests also show that both neural network approaches signiicantly out-perform the best previous (non-learning) solution to this problem in terms of the quality of the resulting schedules and the number of search steps required to construct them.
12895493
Improvement of HITS-based algorithms on web documents
In this paper, we present two ways to improve the precision of HITS-based algorithms on Web documents. First, by analyzing the limitations of current HITS-based algorithms, we propose a new weighted HITS-based method that assigns appropriate weights to in-links of root documents. Then, we combine content analysis with HITS-based algorithms and study the effects of four representative relevance scoring methods, VSM, Okapi, TLS, and CDR, using a set of broad topic queries. Our experimental results show that our weighted HITS-based method performs significantly better than Bharat's improved HITS algorithm. When we combine our weighted HITS-based method or Bharat's HITS algorithm with any of the four relevance scoring methods, the combined methods are only marginally better than our weighted HITS-based method. Between the four relevance-scoring methods, there is no significant quality difference when they are combined with a HITS-based algorithm.
1151096
MaxSolver: An efficient exact algorithm for (weighted) maximum satisfiability
Maximum Boolean satisfiability (max-SAT) is the optimization counterpart of Boolean satisfiability (SAT), in which a variable assignment is sought to satisfy the maximum number of clauses in a Boolean formula. A branch and bound algorithm based on the Davis-Putnam-Logemann-Loveland procedure (DPLL) is one of the most competitive exact algorithms for solving max-SAT. In this paper, we propose and investigate a number of strategies for max-SAT. The first strategy is a set of unit propagation or unit resolution rules for max-SAT. We summarize three existing unit propagation rules and propose a new one based on a nonlinear programming formulation of max-SAT. The second strategy is an effective lower bound based on linear programming (LP). We show that the LP lower bound can be made effective as the number of clauses increases. The third strategy consists of a binary-clause first rule and a dynamic-weighting variable ordering rule, which are motivated by a thorough analysis of two existing well-known variable orderings. Based on the analysis of these strategies, we develop an exact solver for both max-SAT and weighted max-SAT. Our experimental results on random problem instances and many instances from the max-SAT libraries show that our new solver outperforms most of the existing exact max-SAT solvers, with orders of magnitude of improvement in many cases.
5775171
Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies
We propose an assay to detect and quantify alternative splicing simultaneously for numerous genes in a pool of cellular mRNA. The assay exploits polymerase colonies, a recently developed method for sampling and amplifying large numbers of individual transcript molecules into discrete spots on a gel. The proposed assay combines the advantages of microarrays for transcript quantitation with the sensitivity and precision of methods based on counting single transcript molecules. Given a collection of spots s(i), each containing an unknown splice variant of some known gene G(i), we design a series of hybridizations to short oligonucleotide probes to determine in parallel which exons of G(i) are present in every spot s(i). We give algorithms to minimize the cost of such designs.
18395713
Value Iteration over Belief Subspace
Partially Observable Markov Decision Processes (POMDPs) provide an elegant framework for AI planning tasks with uncertainties. Value iteration is a well-known algorithm for solving POMDPs. It is notoriously difficult because at each step it needs to account for every belief state in a continuous space. In this paper, we show that value iteration can be conducted over a subset of belief space. Then, we study a class of POMDPs, namely informative POMDPs, where each observation provides good albeit incomplete information about world states. For informative POMDPs, value iteration can be conducted over a small subset of belief space. This yields two advantages: First, fewer vectors are in need to represent value functions. Second, value iteration can be accelerated. Empirical studies are presented to demonstrate these two advantages.
60947848
Backbone Guided Local Search for Maximum Satisfiability
Maximum satisfiability (Max-SAT) is more general and more difficult to solve than satisfiability (SAT). In this paper, we first investigate the effectiveness of Walksat, one of the best local search algorithms designed for SAT, on Max-SAT. We show that Walksat is also effective on Max-SAT, while its effectiveness degrades as the problem is more constrained. We then develop a novel method that exploits the backbone information in the local minima from Walksat and applies the backbone information in different ways to improve the performance of the Walksat algorithm. We call our new algorithm backbone guided Walksat (BGWalksat). On large random SAT and Max-SAT problems as well as instances from the SATLIB, BGWalksat significantly improves Walksat's performance.
7867358
Phase Transitions and Backbones of the Asymmetric Traveling Salesman Problem
In recent years, there has been much interest in phase transitions of combinatorial problems. Phase transitions have been successfully used to analyze combinatorial optimization problems, characterize their typical-case features and locate the hardest problem instances. In this paper, we study phase transitions of the asymmetric Traveling Salesman Problem (ATSP), an NP-hard combinatorial optimization problem that has many real-world applications. Using random instances of up to 1,500 cities in which intercity distances are uniformly distributed, we empirically show that many properties of the problem, including the optimal tour cost and backbone size, experience sharp transitions as the precision of intercity distances increases across a critical value. Our experimental results on the costs of the ATSP tours and assignment problem agree with the theoretical result that the asymptotic cost of assignment problem is π26 as the number of cities goes to infinity. In addition, we show that the average computational cost of the well-known branch-and-bound subtour elimination algorithm for the problem also exhibits a thrashing behavior, transitioning from easy to difficult as the distance precision increases. These results answer positively an open question regarding the existence of phase transitions in the ATSP, and provide guidance on how difficult ATSP problem instances should be generated.