HAMFAST: Fast Hamming Distance Computation

Pappalardo, Francesco; Calonaci, Cristiano; Pennisi, Marzio; Mastriani, Emilio; Motta, Santo

doi:10.1109/csie.2009.223

Cited by 9 publications

(9 citation statements)

References 13 publications

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“…Our design avoids known problems of such circuits (namely, large capacitive loading at the comparator inputs and multiphase clock operation necessitating the use of DLL circuits) by using a We next report on the results of HSPICE evaluation of our design and a representative prior design [9] suitable for 0.15 lm CMOS technology. Similar comparisons based on different CMOS technologies have been reported in [9,10,13,16,17]. Our HSPICE comparison results are shown in Table 4.…”

Section: Speed and Cost Comparisonmentioning

confidence: 62%

“…Most recent digital Hamming-based designs [9,10,13,16,17] also have cost-performance figures in the same general range. However, the uniqueness of our design and its broader functionality have the potential of leading to further application domains, as reported in [10].…”

Section: Speed and Cost Comparisonmentioning

confidence: 86%

“…(21), our design covers comparisons, Hamming distance measurements, and filtering of pre-selected Hamming weights. Most previously proposed Hamming-related module designs [9,10,13,16,17], by contrast, are aimed at measuring distances between, or comparing, bit-vectors, entailing only one comparison instead of two parallel ones. Additionally, the aforementioned functionalities of our design are applicable to N-bit input XH, with YHL and YHU potentially being of same width or narrower.…”

Section: Speed and Cost Comparisonmentioning

confidence: 95%

“…Many circuits in the latter class have been designed to cater to specific applications or application domains involving Hamming vectors and weights. Among the many available options, one finds all-digital designs [9][10][11][12], digital designs based on the technology-ratioed approach [13][14][15], designs using lookup tables and approximations [16][17][18], and, in the case of our prior contributions, mixed digital-analog designs that are more compact and use highspeed parallel evaluation [19,20]. A general view, covering both radix-based weights and unit weights, is the assignment of arbitrary ''importance'' to various features [21].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A mixed analog–digital fast hamming-weight filtering circuit using switched-capacitor arrays

Abdel-Hafeez

Parhami

Alhammouri

2015

Analog Integr Circ Sig Process

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Many circuit design applications rely on an intermediate sequence to carry a decision to the next circuit stage. The decision may be carried by a weighted pattern of N bits, with the weights being selected in a way that optimizes the circuit implementation or some aspect of performance. For example, when the weights are consecutive powers of 2 beginning with 1 = 2 0 , we have the standard binary representation. As another example, when all the weights are 1, we have the unary representation that encodes a value k by k asserted bits and N-k unasserted bits (a weightk bit vector of length N). In this paper, we present the design of a circuit that screens a unary representation to verify that the represented value falls between preset lower and upper limits l and u, passing through any string that represents a value in the interval [l, u] and outputting the all-0 s bit pattern otherwise. Our mixed analog-digital circuit implementation, based on switched-capacitor arrays, provides a decision output within a clock cycle of 4 ns for 16-bit unary representation, when realized with 0.15 lm TSMC technology. The latter results were obtained with normal, per-bit capacitance of 200 fF and single-clock-cycle operation. As an added benefit, our filtering circuit can form the basis for designing a cost-effective Hamming decoder circuit.

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Section: Speed and Cost Comparisonmentioning

confidence: 62%

Section: Speed and Cost Comparisonmentioning

confidence: 86%

Section: Speed and Cost Comparisonmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A mixed analog–digital fast hamming-weight filtering circuit using switched-capacitor arrays

Abdel-Hafeez

Parhami

Alhammouri

2015

Analog Integr Circ Sig Process

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“…The calculation of pairwise Hamming distances is one of the most common tasks in string metrics to measure the edit distance between two sequences [Pinheiro et al, 2012]. There are numerous algorithms to determine Hamming distances [Pappalardo et al, 2009;Zhang et al, 2013;Kopelowitz et al, 2018] and some of them are implemented as functions in programming languages (e.g. hamming_distance(x, y) in Python 2.3+ or hamming.distance(x, y) in R).…”

Section: Introductionmentioning

confidence: 99%

HamHeat: A fast and simple package for calculating Hamming distance from multiple sequence data for heatmap visualization

Rakov

Schifferli

Liu

et al. 2020

Preprint

Self Cite

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The problem of fast calculation of Hamming distance inferred from many sequence datasets is still not a trivial task. Here, we present HamHeat, as a new software package to efficiently calculate Hamming distance for hundreds of aligned protein or DNA sequences of a large number of residues or nucleotides, respectively. HamHeat uses a unique algorithm with many advantages, including its ease of use and the execution of fast runs for large amounts of data. The package consists of three consecutive modules. In the first module, the software ranks the sequences from the most to the least frequent variant. The second module uses the most common variant as the reference sequence to calculate the Hamming distance of each additional sequence based on the number of residue or nucleotide changes. A final module formats all the results in a comprehensive table that displays the sequence ranks and Hamming distances. Availability and implementation:HamHeat is based on Python 3 and AWK, runs on Linux system and is available under the MIT License at: https://github.com/alexeyrakov/HamHeat.

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Verification of an agent‐based disease model of human Mycobacterium tuberculosis infection

Curreli

Pappalardo

Russo

et al. 2021

Numer Methods Biomed Eng

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HAMFAST: Fast Hamming Distance Computation

Cited by 9 publications

References 13 publications

A mixed analog–digital fast hamming-weight filtering circuit using switched-capacitor arrays

A mixed analog–digital fast hamming-weight filtering circuit using switched-capacitor arrays

HamHeat: A fast and simple package for calculating Hamming distance from multiple sequence data for heatmap visualization

Verification of an agent‐based disease model of human Mycobacterium tuberculosis infection

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