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Title: Text Recycling in Chemistry Research: The Need for Clear and Consistent Guidelines
Like most scientists, chemists frequently have reason to reuse some materials from their own published articles in new ones, especially when producing a series of closely related papers. Text recycling, the reuse of material from one’s own works, has become a source of considerable confusion and frustration for researchers and editors alike. While text recycling does not pose the same level of ethical concern as matters such as data fabrication or plagiarism, it is much more common and complicated. Much of the confusion stems from a lack of clarity and consistency in publisher guidelines and publishing contracts. Matters are even more complicated when manuscripts are coauthored by researchers residing in different countries. This chapter demonstrates the nature of these problems through an analysis of a set of documents from a single publisher, the American Chemical Society (ACS). The ACS was chosen because it is a leading publisher of chemistry research and because its guidelines and publishing contracts address text recycling in unusual detail. The present analysis takes advantage of this detail to show both the importance of clear, thoughtfully designed text recycling policies and the problems that can arise when publishers fail to bring their various documents into close alignment.  more » « less
Award ID(s):
1737093
NSF-PAR ID:
10338117
Author(s) / Creator(s):
Editor(s):
Schelble, Susan M; Elkins, Kelly M
Date Published:
Journal Name:
International Ethics in Chemistry: Developing Common Values across Cultures
Volume:
1401
Page Range / eLocation ID:
125-134
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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  1. Abstract

    Because research in science, engineering and medical fields advances incrementally, researchers routinely write papers that build directly on their prior work. While each new research article is expected to make a novel contribution, researchers often need to repeat some material—method details, background and so on—from their previous articles, a practice called ‘text recycling’. While increasing awareness of text recycling has led to the proliferation of policies, journal editorials and scholarly articles addressing the practice, these documents tend to employ inconsistent terminology—using different terms to name the same key ideas and, even more problematic, using the same terms with different meanings. These inconsistencies make it difficult for readers to know precisely how the ideas or expectations articulated in one document relate to those of others. This paper first clarifies the problems with current terminology, showing how key terms are used inconsistently across publisher policies for authors, guidelines for editors and textbooks on research ethics. It then offers a new taxonomy of text‐recycling practices with terms designed to align with the acceptability of these practices in common research writing and publishing contexts.

     
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  2. Background: Text recycling (hereafter TR)—the reuse of one’s own textual materials from one document in a new document—is a common but hotly debated and unsettled practice in many academic disciplines, especially in the context of peer-reviewed journal articles. Although several analytic systems have been used to determine replication of text—for example, for purposes of identifying plagiarism—they do not offer an optimal way to compare documents to determine the nature and extent of TR in order to study and theorize this as a practice in different disciplines. In this article, we first describe TR as a common phenomenon in academic publishing, then explore the challenges associated with trying to study the nature and extent of TR within STEM disciplines. We then describe in detail the complex processes we used to create a system for identifying TR across large corpora of texts, and the sentence-level string-distance lexical methods used to refine and test the system (White & Joy, 2004). The purpose of creating such a system is to identify legitimate cases of TR across large corpora of academic texts in different fields of study, allowing meaningful cross-disciplinary comparisons in future analyses of published work. The findings from such investigations will extend and refine our understanding of discourse practices in academic and scientific settings. Literature Review: Text-analytic methods have been widely developed and implemented to identify reused textual materials for detecting plagiarism, and there is considerable literature on such methods. (Instead of taking up space detailing this literature, we point readers to several recent reviews: Gupta, 2016; Hiremath & Otari, 2014; and Meuschke & Gipp, 2013). Such methods include fingerprinting, term occurrence analysis, citation analysis (identifying similarity in references and citations), and stylometry (statistically comparing authors’ writing styles; see Meuschke & Gipp, 2013). Although TR occurs in a wide range of situations, recent debate has focused on recycling from one published research paper to another—particularly in STEM fields (see, for example, Andreescu, 2013; Bouville, 2008; Bretag & Mahmud, 2009; Roig, 2008; Scanlon, 2007). An important step in better understanding the practice is seeing how authors actually recycle material in their published work. Standard methods for detecting plagiarism are not directly suitable for this task, as the objective is not to determine the presence or absence of reuse itself, but to study the types and patterns of reuse, including materials that are syntactically but not substantively distinct—such as “patchwriting” (Howard, 1999). In the present account of our efforts to create a text-analytic system for determining TR, we take a conventional alphabetic approach to text, in part because we did not aim at this stage of our project to analyze non-discursive text such as images or other media. However, although the project adheres to conventional definitions of text, with a focus on lexical replication, we also subscribe to context-sensitive approaches to text production. The results of applying the system to large corpora of published texts can potentially reveal varieties in the practice of TR as a function of different discourse communities and disciplines. Writers’ decisions within what appear to be canonical genres are contingent, based on adherence to or deviation from existing rules and procedures if and when these actually exist. Our goal is to create a system for analyzing TR in groups of texts produced by the same authors in order to determine the nature and extent of TR, especially across disciplinary areas, without judgment of scholars’ use of the practice. 
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  3. Key points

    Text recycling is the reuse of material from an author's own prior work in a new document.

    While the ethical aspects of text recycling have received considerable attention, the legal aspects have been largely ignored or inaccurately portrayed.

    Copyright laws and publisher contracts are difficult to interpret and highly variable, making it difficult for authors or editors to know when text recycling in research writing is legal or illegal.

    We argue that publishers should revise their author contracts to make text recycling explicitly legal as long as authors follow ethics‐based guidelines.

     
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Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. 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For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 
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