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1. CyVerse: a Ten-year Perspective on Cyberinfrastructure Development, Collaboration, and Community Building

   Swetnam, T. L. ; Walls, R. ; Devisetty, U. K. ; Merchant, N. ( December 2018 , AGU Fall Meeting Abstracts)

   Adoption of data and compute-intensive research in geosciences is hindered by the same social and technological reasons as other science disciplines - we're humans after all. As a result, many of the new opportunities to advance science in today's rapidly evolving technology landscape are not approachable by domain geoscientists. Organizations must acknowledge and actively mitigate these intrinsic biases and knowledge gaps in their users and staff. Over the past ten years, CyVerse (www.cyverse.org) has carried out the mission "to design, deploy, and expand a national cyberinfrastructure for life sciences research, and to train scientists in its use." During this time, CyVerse has supported and enabled transdisciplinary collaborations across institutions and communities, overseen many successes, and encountered failures. Our lessons learned in user engagement, both social and technical, are germane to the problems facing the geoscience community today. A key element of overcoming social barriers is to set up an effective education, outreach, and training (EOT) team to drive initial adoption as well as continued use. A strong EOT group can reach new users, particularly those in under-represented communities, reduce power distance relationships, and mitigate users' uncertainty avoidance toward adopting new technology. Timely user support across the life of a project, based on mutual respect between the developers' and researchers' different skill sets, is critical to successful collaboration. Without support, users become frustrated and abandon research questions whose technical issues require solutions that are 'simple' from a developer's perspective, but are unknown by the scientist. At CyVerse, we have found there is no one solution that fits all research challenges. Our strategy has been to maintain a system of systems (SoS) where users can choose 'lego-blocks' to build a solution that matches their problem. This SoS ideology has allowed CyVerse users to extend and scale workflows without becoming entangled in problems which reduce productivity and slow scientific discovery. Likewise, CyVerse addresses the handling of data through its entire lifecycle, from creation to publication to future reuse, supporting community driven big data projects and individual researchers. 

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2. Highlights and Outcomes of the 2021 Global Community Consultation

   https://doi.org/10.3897/biss.5.72716  

   Ellwood, Elizabeth R. ; Bentley, Andrew ; Buschbom, Jutta ; Hardisty, Alex ; Mast, Austin ; Miller, Joe ; Monfils, Anna ; Nelson, Gil ; Paul, Deborah L ( August 2021 , Biodiversity Information Science and Standards)

   International collaboration between collections, aggregators, and researchers within the biodiversity community and beyond is becoming increasingly important in our efforts to support biodiversity, conservation and the life of the planet. The social, technical, logistical and financial aspects of an equitable biodiversity data landscape – from workforce training and mobilization of linked specimen data, to data integration, use and publication – must be considered globally and within the context of a growing biodiversity crisis. In recent years, several initiatives have outlined paths forward that describe how digital versions of natural history specimens can be extended and linked with associated data. In the United States, Webster (2017) presented the “extended specimen”, which was expanded upon by Lendemer et al. (2019) through the work of the Biodiversity Collections Network (BCoN). At the same time, a “digital specimen” concept was developed by DiSSCo in Europe (Hardisty 2020). Both the extended and digital specimen concepts depict a digital proxy of an analog natural history specimen, whose digital nature provides greater capabilities such as being machine-processable, linkages with associated data, globally accessible information-rich biodiversity data, improved tracking, attribution and annotation, additional opportunities for data use and cross-disciplinary collaborations forming the basis for FAIR (Findable, Accessible, Interoperable, Reproducible) and equitable sharing of benefits worldwide, and innumerable other advantages, with slight variation in how an extended or digital specimen model would be executed. Recognizing the need to align the two closely-related concepts, and to provide a place for open discussion around various topics of the Digital Extended Specimen (DES; the current working name for the joined concepts), we initiated a virtual consultation on the discourse platform hosted by the Alliance for Biodiversity Knowledge through GBIF. This platform provided a forum for threaded discussions around topics related and relevant to the DES. The goals of the consultation align with the goals of the Alliance for Biodiversity Knowledge: expand participation in the process, build support for further collaboration, identify use cases, identify significant challenges and obstacles, and develop a comprehensive roadmap towards achieving the vision for a global specification for data integration. In early 2021, Phase 1 launched with five topics: Making FAIR data for specimens accessible; Extending, enriching and integrating data; Annotating specimens and other data; Data attribution; and Analyzing/mining specimen data for novel applications. This round of full discussion was productive and engaged dozens of contributors, with hundreds of posts and thousands of views. During Phase 1, several deeper, more technical, or additional topics of relevance were identified and formed the foundation for Phase 2 which began in May 2021 with the following topics: Robust access points and data infrastructure alignment; Persistent identifier (PID) scheme(s); Meeting legal/regulatory, ethical and sensitive data obligations; Workforce capacity development and inclusivity; Transactional mechanisms and provenance; and Partnerships to collaborate more effectively. In Phase 2 fruitful progress was made towards solutions to some of these complex functional and technical long-term goals. Simultaneously, our commitment to open participation was reinforced, through increased efforts to involve new voices from allied and complementary fields. Among a wealth of ideas expressed, the community highlighted the need for unambiguous persistent identifiers and a dedicated agent to assign them, support for a fully linked system that includes robust publishing mechanisms, strong support for social structures that build trustworthiness of the system, appropriate attribution of legacy and new work, a system that is inclusive, removed from colonial practices, and supportive of creative use of biodiversity data, building a truly global data infrastructure, balancing open access with legal obligations and ethical responsibilities, and the partnerships necessary for success. These two consultation periods, and the myriad activities surrounding the online discussion, produced a wide variety of perspectives, strategies, and approaches to converging the digital and extended specimen concepts, and progressing plans for the DES -- steps necessary to improve access to research-ready data to advance our understanding of the diversity and distribution of life. Discussions continue and we hope to include your contributions to the DES in future implementation plans. 

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3. Cyberinfrastructure for sustainability sciences

   https://doi.org/10.1088/1748-9326/acd9dd  

   Song, Carol X. ; Merwade, Venkatesh ; Wang, Shaowen ; Witt, Michael ; Kumar, Vipin ; Irwin, Elena ; Zhao, Lan ; Walton, Amy ( July 2023 , Environmental Research Letters)

   Meeting the United Nation’ Sustainable Development Goals (SDGs) calls for an integrative scientific approach, combining expertise, data, models and tools across many disciplines towards addressing sustainability challenges at various spatial and temporal scales. This holistic approach, while necessary, exacerbates the big data and computational challenges already faced by researchers. Many challenges in sustainability research can be tackled by harnessing the power of advanced cyberinfrastructure (CI). The objective of this paper is to highlight the key components and technologies of CI necessary for meeting the data and computational needs of the SDG research community. An overview of the CI ecosystem in the United States is provided with a specific focus on the investments made by academic institutions, government agencies and industry at national, regional, and local levels. Despite these investments, this paper identifies barriers to the adoption of CI in sustainability research that include, but are not limited to access to support structures; recruitment, retention and nurturing of an agile workforce; and lack of local infrastructure. Relevant CI components such as data, software, computational resources, and human-centered advances are discussed to explore how to resolve the barriers. The paper highlights multiple challenges in pursuing SDGs based on the outcomes of several expert meetings. These include multi-scale integration of data and domain-specific models, availability and usability of data, uncertainty quantification, mismatch between spatiotemporal scales at which decisions are made and the information generated from scientific analysis, and scientific reproducibility. We discuss ongoing and future research for bridging CI and SDGs to address these challenges.

    

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4. The Deep Learning Epilepsy Detection Challenge: Design, Implementation, and Test of a New Crowd-Sourced AI Challenge Ecosystem

   Kiral, Isabell ; Roy, Subhrajit ; Mummert, Todd ; Braz, Alan ; Tsay, Jason ; Tang, Jianbin ; Asif, Umar ; Schaffter, Thomas ; Mehmet, Eren ; Picone, Joseph ; et al ( April 2019 , Challenges in Machine Learning Competitions for All (CiML))

   null (Ed.)

   The DeepLearningEpilepsyDetectionChallenge: design, implementation, andtestofanewcrowd-sourced AIchallengeecosystem Isabell Kiral*, Subhrajit Roy*, Todd Mummert*, Alan Braz*, Jason Tsay, Jianbin Tang, Umar Asif, Thomas Schaffter, Eren Mehmet, The IBM Epilepsy Consortium◊ , Joseph Picone, Iyad Obeid, Bruno De Assis Marques, Stefan Maetschke, Rania Khalaf†, Michal Rosen-Zvi† , Gustavo Stolovitzky† , Mahtab Mirmomeni† , Stefan Harrer† * These authors contributed equally to this work † Corresponding authors: rkhalaf@us.ibm.com, rosen@il.ibm.com, gustavo@us.ibm.com, mahtabm@au1.ibm.com, sharrer@au.ibm.com ◊ Members of the IBM Epilepsy Consortium are listed in the Acknowledgements section J. Picone and I. Obeid are with Temple University, USA. T. Schaffter is with Sage Bionetworks, USA. E. Mehmet is with the University of Illinois at Urbana-Champaign, USA. All other authors are with IBM Research in USA, Israel and Australia. Introduction This decade has seen an ever-growing number of scientific fields benefitting from the advances in machine learning technology and tooling. More recently, this trend reached the medical domain, with applications reaching from cancer diagnosis [1] to the development of brain-machine-interfaces [2]. While Kaggle has pioneered the crowd-sourcing of machine learning challenges to incentivise data scientists from around the world to advance algorithm and model design, the increasing complexity of problem statements demands of participants to be expert data scientists, deeply knowledgeable in at least one other scientific domain, and competent software engineers with access to large compute resources. People who match this description are few and far between, unfortunately leading to a shrinking pool of possible participants and a loss of experts dedicating their time to solving important problems. Participation is even further restricted in the context of any challenge run on confidential use cases or with sensitive data. Recently, we designed and ran a deep learning challenge to crowd-source the development of an automated labelling system for brain recordings, aiming to advance epilepsy research. A focus of this challenge, run internally in IBM, was the development of a platform that lowers the barrier of entry and therefore mitigates the risk of excluding interested parties from participating. The challenge: enabling wide participation With the goal to run a challenge that mobilises the largest possible pool of participants from IBM (global), we designed a use case around previous work in epileptic seizure prediction [3]. In this “Deep Learning Epilepsy Detection Challenge”, participants were asked to develop an automatic labelling system to reduce the time a clinician would need to diagnose patients with epilepsy. Labelled training and blind validation data for the challenge were generously provided by Temple University Hospital (TUH) [4]. TUH also devised a novel scoring metric for the detection of seizures that was used as basis for algorithm evaluation [5]. In order to provide an experience with a low barrier of entry, we designed a generalisable challenge platform under the following principles: 1. No participant should need to have in-depth knowledge of the specific domain. (i.e. no participant should need to be a neuroscientist or epileptologist.) 2. No participant should need to be an expert data scientist. 3. No participant should need more than basic programming knowledge. (i.e. no participant should need to learn how to process fringe data formats and stream data efficiently.) 4. No participant should need to provide their own computing resources. In addition to the above, our platform should further • guide participants through the entire process from sign-up to model submission, • facilitate collaboration, and • provide instant feedback to the participants through data visualisation and intermediate online leaderboards. The platform The architecture of the platform that was designed and developed is shown in Figure 1. The entire system consists of a number of interacting components. (1) A web portal serves as the entry point to challenge participation, providing challenge information, such as timelines and challenge rules, and scientific background. The portal also facilitated the formation of teams and provided participants with an intermediate leaderboard of submitted results and a final leaderboard at the end of the challenge. (2) IBM Watson Studio [6] is the umbrella term for a number of services offered by IBM. Upon creation of a user account through the web portal, an IBM Watson Studio account was automatically created for each participant that allowed users access to IBM's Data Science Experience (DSX), the analytics engine Watson Machine Learning (WML), and IBM's Cloud Object Storage (COS) [7], all of which will be described in more detail in further sections. (3) The user interface and starter kit were hosted on IBM's Data Science Experience platform (DSX) and formed the main component for designing and testing models during the challenge. DSX allows for real-time collaboration on shared notebooks between team members. A starter kit in the form of a Python notebook, supporting the popular deep learning libraries TensorFLow [8] and PyTorch [9], was provided to all teams to guide them through the challenge process. Upon instantiation, the starter kit loaded necessary python libraries and custom functions for the invisible integration with COS and WML. In dedicated spots in the notebook, participants could write custom pre-processing code, machine learning models, and post-processing algorithms. The starter kit provided instant feedback about participants' custom routines through data visualisations. Using the notebook only, teams were able to run the code on WML, making use of a compute cluster of IBM's resources. The starter kit also enabled submission of the final code to a data storage to which only the challenge team had access. (4) Watson Machine Learning provided access to shared compute resources (GPUs). Code was bundled up automatically in the starter kit and deployed to and run on WML. WML in turn had access to shared storage from which it requested recorded data and to which it stored the participant's code and trained models. (5) IBM's Cloud Object Storage held the data for this challenge. Using the starter kit, participants could investigate their results as well as data samples in order to better design custom algorithms. (6) Utility Functions were loaded into the starter kit at instantiation. This set of functions included code to pre-process data into a more common format, to optimise streaming through the use of the NutsFlow and NutsML libraries [10], and to provide seamless access to the all IBM services used. Not captured in the diagram is the final code evaluation, which was conducted in an automated way as soon as code was submitted though the starter kit, minimising the burden on the challenge organising team. Figure 1: High-level architecture of the challenge platform Measuring success The competitive phase of the "Deep Learning Epilepsy Detection Challenge" ran for 6 months. Twenty-five teams, with a total number of 87 scientists and software engineers from 14 global locations participated. All participants made use of the starter kit we provided and ran algorithms on IBM's infrastructure WML. Seven teams persisted until the end of the challenge and submitted final solutions. The best performing solutions reached seizure detection performances which allow to reduce hundred-fold the time eliptologists need to annotate continuous EEG recordings. Thus, we expect the developed algorithms to aid in the diagnosis of epilepsy by significantly shortening manual labelling time. Detailed results are currently in preparation for publication. Equally important to solving the scientific challenge, however, was to understand whether we managed to encourage participation from non-expert data scientists. Figure 2: Primary occupation as reported by challenge participants Out of the 40 participants for whom we have occupational information, 23 reported Data Science or AI as their main job description, 11 reported being a Software Engineer, and 2 people had expertise in Neuroscience. Figure 2 shows that participants had a variety of specialisations, including some that are in no way related to data science, software engineering, or neuroscience. No participant had deep knowledge and experience in data science, software engineering and neuroscience. Conclusion Given the growing complexity of data science problems and increasing dataset sizes, in order to solve these problems, it is imperative to enable collaboration between people with differences in expertise with a focus on inclusiveness and having a low barrier of entry. We designed, implemented, and tested a challenge platform to address exactly this. Using our platform, we ran a deep-learning challenge for epileptic seizure detection. 87 IBM employees from several business units including but not limited to IBM Research with a variety of skills, including sales and design, participated in this highly technical challenge. 

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5. A Text-Analytic Method for Identifying Text Recycling in STEM Research Reports

   Anson, Ian G ; Moskovitz, Cary ; Anson, Chris M ( November 2019 , The journal of writing analytics)

   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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