Algorithmic specification

Typically, an algorithm will be specified in the form of a nested loop program (NLP) [3]. It is useful to include the specification of a nested loop program as an integral part of the design trajectory, mainly because it can be specified in an easily comprehensible syntax and because such a program often can be found in a library. 

Unfortunately, an NLP does not explicitly show the parallelism of the computations. Therefore, the first step in the design trajectory is to convert the NLP into a dependence graph (see chapter 2) [4]. The resulting DG will have a node for each instance of the calculation of a function, e.g., Floyd in the example below. Its edges will represent the passing of arguments between those functional nodes and hence implement function calls. We will discuss the conversion step in more detail in section 5. Similar functionality is provided in the approach of chapter 5 but for a partly different target domain. 

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In this section, we present a pseudocode for an FEP alchemical transformation based on the dual-topology paradigm. The steps followed in this algorithm, specifically (c)-(f), may be implemented independently of the core of the program that generates an ensemble of configurations at a given A state - either Monte Carlo or molecular dynamics. This is probably the simplest scheme, which may be improved in several ways, as will be discussed in Sect. 2.9. 

MATLAB s polynomial-roots finder roots does not handle repeated or clustered roots very well, but otherwise it is the best 0(n3) root finder available. Note that an operations count of 0(nP) for an algorithm signifies that the algorithm performs K n additions and multiplications (for some algorithm specific constants K and j, but depending on n) to obtain its output from n input data. Most of the polynomial-root finders of the last century unfortunately were even slower 0(n4) algorithms and all in all much too slow and inaccurate. 

The fundamental idea behind training, for all neural network architectures, is this pick a set of weights (often randomly), apply the inputs to the network and see how the network performs with this set of weights. If it doesn t perform well, then modify the weights by some algorithm (specific to each architecture) and repeat the procedure. This iterative process is continued until some pre-specified stopping criterion has been reached. 

R.F. Nelson, J.B. Olson, E.D. Sexton, A.A. Pesaran, M.A. Keyset, ALABC Project No. B-007.2, Development of improved cycle life by design of charge algorithms specifically aimed at VRLA batteries. Progress Report 21 July to 20 September 1999, Advanced Lead-Acid Battery Consortium, Research Triangle Park, NC, USA, 1999. 

In a hybrid method, molecules are displaced in time according to conventional molecular dynamics (MD) algorithms, specifically, by integrating Newton s equations of motion for the system of interest. Once the initial coordinates and momenta of the particles are specified, motion is deterministic (i.e., one can determine with machine precision where the system will be in the near future). In the context of Eq. (2.1), the probability of proposing a transition from a state 0 to a state 1 is determined by the probability with which the initial velocities of the particles are assigned from that point on, motion is deterministic (it occurs with probability one). If initial velocities are sampled at random from a Maxwellian distribution at the temperature of interest, then the transition probability function required by Eq. 

The presence or absence of isomorphism for a pair of graphs is determined by an isomorphism algorithm. Specifically, graph isomorphism, subgraph... 

The traditional method to calculate the K optimal path is defringe algorithm. Specifically, firstly the optimal path is calculated by the Dijkstra algorithm. Then the new optimal path is determined after deleting a random edge of the opti-... 

The book describes numerical methods, high-performance algorithms, specific devices, and innovative techniques and strategies, all of which are implemented in a well-established numerical library the BzzMath library, developed by Prof. Guido Buzzi-Ferraris at the Politecnico di Milano and downloadable from http // www.chem.polimi.it/homes/gbuzzi. 

The final output file contains an evaluation in tabular form of all simulation and optimized force-field parameters, the simulated properties along with their acmal deviations from the experimental reference data at each temperature, the loss function values, and algorithm-specific information. 

All we require for actual synthesis are the coefficients C =< ci,C2,---Ct >, so the problem is to generate the highest probability sequence of these that also obeys the constraints of the delta coefficients AC =< Aci,Ac2,. .Acf >. As we have to find both the observations and the state sequence, we can t use the Viterbi algorithm as above but rather use an algorithm specific to this... 

In the remainder of the chapter we will make a semi-formal tour of HlFi. We will first introduce the general design philosophy in section 2. Next, the algorithm specification model is introduced, and a realistic demonstrator from document processing is presented at this level (section 3). The most important architecture-level elements of the design model are discussed in section 4. This... 

Software applications used in medical centers must be modular and scalable in order to meet the needs of the beneficiaries. To ensure the proper integration of various software modules it is necessary to use HL7 and DICOM standards which provides a set of rules and algorithms specific tothe medical field. 

Additional specificity is derived through the use of a matrix of SAW devices where each of the elements, a separate SAW oscillator, is coated with a different polymer. For example, one of the SAW systems currently under evaluation contain six SAW oscillators and use six different polymers two have affinities for nerve agents, two for blister agents, one for water vapor and one for non-polar compounds such as hydrocarbons. By determination of the magnitudes of frequency shifts for each of the crystals when the device is exposed to a certain compound, a library of patterns of responses can be generated and, by use of appropriate pattern recognition algorithms, specificity of response can be realized [5]. 

A second approach incorporates free energy information into the branch and bound algorithm. Specifically, harmonic entropic contributions are calculated and included at each minima of the upper and lower bounding functions. In this way, the progression of lower and upper bounds includes a temperature-dependent entropic term. A similar modification to the Monte Carlo minimization method has also been proposed [87] and has been shown to be effective in locating low-energy conformers of peptides [88,89]. 

Completeness. The complete design trajectory should be covered, from a verifyable, bit-true algorithmic specification up to a register-transfer (RT) level description of the architecture. This includes well known synthesis tasks like allocation and scheduling, but also novel tasks like the optimisation of background memory (RAM, FIFOs), or the accommodation of the bit-level specifications in the final architecture. 

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