35045189
New Born Radii Deriving Method for Generalized Born Model
Here we report a method to calculate Born radii, an important parameter used in a Generalized Born model. Traditional methods to derive Born radii are mostly based on a complicated formula, while our method is easier and more direct. Atoms are classified according to their atom type, and the Born radii of each type are obtained by fitting to experimental solvation free energy. The SMARTS language is used for the exact definition of atoms types, and Ullmann's subgraph isomorphism algorithm is used to deduce the environment. A generic algorithm is used for the parameter fitting because of its efficiency in searching a huge phase space, and its results are then optimized by using the conjugate gradient method. The final parameter set is fitting from a training set containing 357 molecules and is tested using a test set of 44 small organic molecules, and the average error is 0.58 kcal/mol for 36 neutral molecules and is 1.67 kcal/mol for 8 ions. The model is further tested under organic molecules, biopolymers, and a protein-inhibitor complex and yields reliable results in all these cases. This method can be used to accelerate molecular docking calculations.
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.
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.
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.
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.
52800785
Association-Based Multiple Imputation in Multivariate Datasets: A Summary
There are two general approaches to handling missing data. The rst one ignores missing data, by discarding the records with missing values from a dataset or taking unknown attribute values as special, null values and processing them during the process of answering queries. The second approach is called imputations, which attempts to ll in missing data with plausible values. There are two major existing methods of this approach. The rst uses statistical relationships among the variables under consideration, and builds statistical models for the variables, namely linear regression models for numerical values and statistical classi cation rules for categorical values. A possible value of an unspeci ed item is then estimated using the statistical models. The second method is multiple imputations that replaces each missing value by multiple simulated values. After the multiple imputations are obtained, each plausible value is analyzed, using EM algorithm and Gibbs sampling, to produce an inferential conclusion that include uncertainty caused by missing data. Note that the multiple imputationmethod can only apply to numerical attributes.
207099457
Improved sparse least-squares support vector machine classifiers
The least-squares support vector machines (LS-SVM) can be obtained by solving a simpler optimization problem than that in standard support vector machines (SVM). Its shortcoming is the loss of sparseness and this usually results in slow testing speed. Several pruning methods have been proposed. It is found that these methods can be further improved for classification problems. In this paper a different reduced training set is selected to re-train LS-SVM. Then a new procedure is proposed to obtain the sparseness. The performance of the proposed method is compared with other typical ones and the results indicate that it is more effective.
34728545
Data dissemination with ring-based index for wireless sensor networks
In current sensor networks, sensor nodes are capable of not only measuring real world phenomena, but also storing, processing and transferring these measurements. Many data dissemination techniques have been proposed for sensor networks. However, these techniques may not work well in a large scale sensor network where a huge amount of sensing data are generated, but only a small portion of them are queried. In this paper, we propose an index-based data dissemination scheme to address the problem. This scheme is based on the idea that sensing data are collected, processed and stored at the nodes close to the detecting nodes, and the location information of these storing nodes is pushed to some index nodes, which act as the rendezvous points for sinks and sources. We further extend the scheme with an adaptive ring-based index (ARI) technique, in which the index nodes for one event type form a ring surrounding the location which is determined by the event type, and the ring can be dynamically reconfigured for fault tolerance and load balance. Analysis and simulations are conducted to evaluate the performance of the proposed index-based scheme. The results show that the index-based scheme outperforms the external storage-based scheme, the DCS scheme, and the local storage-based schemes with flood-response style. The results also show that using ARI can tolerate clustering failures and achieve load balance.
27275411
Distributed breakout algorithm for distributed constraint optimization problems -- DBArelax
2214133
A Novel Local Search Algorithm for the Traveling Salesman Problem that Exploits Backbones
We present and investigate a new method for the Traveling Salesman Problem (TSP) that incorporates backbone information into the well known and widely applied Lin-Kernighan (LK) local search family of algorithms for the problem. We consider how heuristic backbone information can be obtained and develop methods to make biased local perturbations in the LK algorithm and its variants by exploiting heuristic backbone information to improve their efficacy. We present extensive experimental results, using large instances from the TSP Challenge suite and real-world instances in TSPLIB, showing the significant improvement that the new method can provide over the original algorithms.