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Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology

JOURNAL OF EVOLUTIONARY BIOLOGY 2023年第10期36卷 1347-1356页

作者： Ivimey-Cook, Edward R. Pick, Joel L. Bairos-Novak, Kevin R. Culina, Antica Gould, Elliot Grainger, Matthew Marshall, Benjamin M. Moreau, David Paquet, Matthieu Royaute, Raphael Sanchez-Tojar, Alfredo Silva, Ines Windecker, Saras M. Univ Glasgow Sch Biodivers One Hlth & Vet Med Glasgow Scotland Univ Edinburgh Inst Ecol & Evolut Edinburgh Scotland James Cook Univ Australian Res Council Ctr Excellence Coral Reef Studies Townsville Qld Australia James Cook Univ Coll Sci & Engn Townsville Qld Australia Rudjer Boskovic Inst Zagreb Croatia NIOO KNAW Netherlands Inst Ecol Wageningen Netherlands Univ Melbourne Sch Ecosyst & Forest Sci Melbourne Vic Australia Norwegian Inst Nat Res Trondheim Norway Univ Stirling Fac Nat Sci Biol & Environm Sci Stirling Scotland Univ Auckland Ctr Brain Res Sch Psychol Auckland New Zealand Univ Bordeaux Inst Math Bordeaux CNRS Bordeaux INP Talence France Univ ParisSaclay INRAE AgroParisTech UMR EcoSys Palaiseau France Bielefeld Univ Dept Evolutionary Biol Bielefeld Germany Helmholtz Zentrum Dresden Rossendorf eV HZDR Ctr Adv Syst Understanding CASUS Gorlitz Germany

Code review increases reliability and improves reproducibility of research. As such, code review is an inevitable step in software development and is common in fields such as computer science. However, despite its importance, code review is noticeably lacking in ecology and evolutionary biology. This is problematic as it facilitates the propagation of coding errors and a reduction in reproducibility and reliability of published results. To address this, we provide a detailed commentary on how to effectively review code, how to set up your project to enable this form of review and detail its possible implementation at several stages throughout the research process. This guide serves as a primer for code review, and adoption of the principles and advice here will go a long way in promoting more open, reliable, and transparent ecology and evolutionary biology.

关键词： coding errors open science reliability reproducibility research process software development transparency

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Discussion: "Comprehensive approach to verification and validation of CFD simulations - Part 1: Methodology and procedures" ( Stern, F., Wilson, R. V.., Coleman, H. W.., and Paterson, E. G.., 2001, ASME J. FLUIDS ENG., 123, pp. 793-802)

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JOURNAL OF FLUIDS ENGINEERING-TRANSACTIONS OF THE ASME 2002年第3期124卷 809-810页

作者： Oberkampf, WL Validation and Uncertainty Estimation Dept. MS 0828 Sandia National Laboratories Albuquerque New Mexico 87185

The paper by Stern et al. proposes a comprehensive approach to verification and validation of computational fluid dynamics simulations. Although the authors present a new perspective for quantifying verification and validation, I believe there is a conceptual flaw in the proposed approach to validation. Three criticisms follow. 1 The authors define verification as “…a process for assessing simulation numerical uncertainty…” I agree with the authors when they say that their definition of verification is not contradictory with the broader definitions developed by Roache 1 and the AIAA Guide 2. However, as pointed out clearly by Roache and others, there are two other important facets of verification: code verification and software quality assurance. Code verification deals with assessing the correctness of the computer program in implementing the discrete form of the partial differential equations, as well as the numerical algorithms needed to solve the discrete...

关键词： errors computational fluid dynamics computer software modelling Fluids Simulation Modeling Computational fluid dynamics coding errors Computer software numerical analysis numerical stability flow simulation

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Quality Improvement of Medical Diagnostic coding through Computer-assisted Error Prevention

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ZEITSCHRIFT FUR EVIDENZ FORTBILDUNG UND QUALITAET IM GESUNDHEITSWESEN 2008年第2期102卷 101-109页

作者： Koch, Heinz Graubner, Bernd Kerek-Bodden, Hedy Brenner, Gerhard von Stillfried, Dominik Graf Zent Inst Kassenarzliche Versorgung Bundesrepubl D-10623 Berlin Germany

From 2009, morbidity measured by medical diagnoses and its change over time will be one of the factors to determine the remuneration of physicians in Germany. Other factors include changes in the scope of medical service profiles and in the development of practice costs. In preparation of the physician payment reform, the National Association of Statutory Health Insurance Physicians (KBV) started to introduce measures in 2004 to check the plausibility of diagnosis codes recorded in the ambulatory care setting to prevent coding errors. Their development has been supported professionally by the Central Research Institute of Ambulatory Health Care (ZI), which continues to analyse the outcome of these measures. Theresults in coding improvements are illustrated using a time series. We compare the frequencies of errors from the first quarter of the year 2000, in which coding based on a German version of the ICD-10 became mandatory in ambulatory care, up to the first quarter of 2006. A notable decline in the frequencies of all monitored coding errors after the introduction of an obligatory automated plausibility check for recorded diagnoses in 2005 can be demonstrated. This automated plausibility check which is embedded in all practice data processing systems applies to obvious coding errors (implausible reference to age and sex, and "exotic'', very rare and notifiable diseases). The introduction of the morbidity-related payment system is likely to raise the necessary quality standards for coding. Automated plausibility checks contribute to improved coding quality while minimizing the efforts physicians need to make.

关键词： ambulatory medical care ICD-10 diagnosis codes coding errors evaluation of diagnoses quality of coding

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Design of Codes for One Insertion and at Most Two Consecutive Deletion errors

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IEEE Transactions on Communications 2024年

作者： Khuat, Thi-Huong Kim, Sunghwan Telecommunications Faculty 1 Posts and Telecommunications Institute of Technology Hanoi Viet Nam Kyonggi University School of Electronic Engineering Korea Republic of

This paper proposes a novel binary code to correct one insertion and at most two consecutive deletion errors simultaneously occurring in a codeword. Our proposed code is intended first to isolate the possible error cases among all the error scenarios, and then correct the errors. Furthermore, we provide detailed descriptions of the code construction and also suggest a decoding strategy for the proposed code. According to the proposed code, 5 log2 n + O(1) redundancy bits are required to correct one insertion and at most two consecutive deletion errors occurring in a codeword. In addition, a decoding procedure of the proposed code is comprehensively presented for all error scenarios including a single insertion error, an insertion and a deletion error, and an insertion and two consecutive deletion errors. © 1972-2012 IEEE.

关键词： coding errors

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ADAPTIVE RATE ERROR CONTROL FOR THE LAND-MOBILE SATELLITE CHANNEL

ADAPTIVE RATE ERROR CONTROL FOR THE LAND-MOBILE SATELLITE CH...

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1994 IEEE International Conference on Communications (SUPERCOMM/ICC 94): Serving Humanity Through Communications

作者： RICE, M BRIGHAM YOUNG UNIV DEPT ELECT & COMP ENGNPROVOUT 84602

ISBN: (纸本)0780318250

An adaptive rate error control system is presented for communication over a land mobile satellite channel described by a finite state Markov chain. In channel states where the fading is moderate, the code rate is high thus providing increased throughput. In channel states where the fading is more severe, a low rate code is used to provide the necessary error protection. Retransmission requests used by hybrid-ARQ error control are incorporated into the Viterbi decoder following a modification proposed by Yamamoto and Itoh. The decision to change code rates is made by a sequential statistical test which monitors the frequency of retransmissions. The essentials are presented in an example which illustrates the significant performance improvements realized by the adaptive system.

关键词： coding errors

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A random coding error exponent for joint quantization and watermarking of Gaussian sources under memoryless Gaussian attacks

A random coding error exponent for joint quantization and wa...

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10th Canadian Workshop on Information Theory

作者： Wang, Yadong Alajaji, Fady Linder, Tamas Queens Univ Dept Math & Stat Kingston ON K7L 3N6 Canada

ISBN: (纸本)9781424407682

We study joint quantization and watermarking of a memoryless Gaussian source under memoryless additive Gaussian attacks in a private scenario. The achievable region involving the quantization and the watermarking rate pairs has been established by Karakos and Papamarcou (2003). In this paper, we refine the analysis of the watermarking decoding error probability for given achievable rate pairs by deriving a computable random coding lower bound to the error exponent. The random coding exponent is positive within almost the entire achievable region of Karakos and Papamarcou.

关键词： coding errors

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High-speed error correcting code LSI with throughput of 5 to 48 Gbps

High-speed error correcting code LSI with throughput of 5 to...

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IEEE International Symposium on Information Theory

作者： Hamasuna, Y Hata, M Taktumi, I DDS Inc Nakagawa Ku Nagoya Aichi 4540012 Japan

ISBN: (纸本)0780377281

We proved that the hardware implementation of the proposed code and the new packet synchronization system was effectively realized by using a unique circuit configuration. A three-dimensional size-five coder and decoding-synchronization system was implemented on FPGA. The developed FPGA was applied to a high-speed MPEG communication device, which can transmit a movie signal of 20 Mbps.

关键词： coding errors

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Error-Correcting Codes for Combinatorial Composite DNA

Error-Correcting Codes for Combinatorial Composite DNA

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IEEE International Symposium on Information Theory (ISIT)

作者： Sabary, Omer Preuss, Inbal Gabrys, Ryan Yakhini, Zohar Anavy, Leon Yaakobi, Eitan Technion Israel Inst Technol Fac Comp Sci Haifa Israel Reichman Univ Fac Comp Sci Hezliya Israel Univ Calif San Diego Dept Elect & Comp Engn La Jolla CA 92093 USA

ISBN: (纸本)9798350382853;9798350382846

Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This approach extends the DNA alphabet by harnessing short DNA fragment reagents, known as shortmers. The shortmers are building blocks of the alphabet symbols, each consisting of a fixed number of shortmers. Thus, when information is read, it is possible that one of the shortmers that forms part of the composition of a symbol is missing and therefore the symbol cannot be determined. In this paper, we model this type of error as a type of asymmetric error and propose code constructions that can correct such errors in this setup. We also provide a lower bound on the redundancy of such error-correcting codes and give an explicit encoder and decoder for our construction. Our suggested error model is also supported by an analysis of data from actual experiments that produced DNA according to the combinatorial scheme. Lastly, we also provide a statistical evaluation of the probability of observing such error events, as a function of read depth.

关键词： coding errors

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On a Problem of Massey

On a Problem of Massey

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Information Theory and Applications Workshop (ITA)

作者： Hamkins, Jon CALTECH Jet Prop Lab Pasadena CA 91109 USA

ISBN: (纸本)9781479935901

In 1976, Massey introduced a method to compute the confidence interval for the frame error rate of a coded communications system based on the simulation of just a few frame errors [1]. He commented that his approach did not apply to bit error rate confidence intervals, because bit errors are not independent in a coded system. In this paper, we show how to overcome the limitation Massey recognized, and present a method to compute a confidence interval of the bit error rate of a coded communications system from a simulation of bit and frame error events. The proposed interval may be easily computed from the first and second sample moments of the number of bits errors per frame.

关键词： coding errors error statistics modulation coding Massey simulations bit error rate coded communication system confidence interval computation frame error rate Accuracy Approximation methods Bismuth Bit error rate Computational modeling Decoding Signal to noise ratio

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Practical Short-Length coding Schemes for Binary Distributed Hypothesis Testing

Practical Short-Length Coding Schemes for Binary Distributed...

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IEEE International Symposium on Information Theory (ISIT)

作者： Dupraz, Elsa Adamou, Ismaila Salihou Asvadi, Reza Matsumoto, Tad IMT Atlantique CNRS UMR 6285 Lab STICC Brest France Shahid Beheshti Univ Fac Elect Engn Tehran Iran JAIST Oulu Finland Univ Oulu Oulu Finland

ISBN: (纸本)9798350382853;9798350382846

This paper investigates practical coding schemes for Distributed Hypothesis Testing (DHT). While the literature has extensively analyzed the information-theoretic performance of DHT and established bounds on Type-II error exponents through quantize and quantize-binning achievability schemes, the practical implementation of DHT coding schemes has not yet been investigated. Therefore, this paper introduces practical implementations of quantizers and quantize-binning schemes for DHT, leveraging short-length binary linear block codes. Furthermore, it provides exact analytical expressions for Type-I and Type-II error probabilities associated with each proposed coding scheme. Numerical results show the accuracy of the proposed analytical error probability expressions, and enable to compare the performance of the proposed schemes.

关键词： coding errors

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