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1. 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))

   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 datamore »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.« less
2. On Studying CPU Performance of CloudLab Hardware

   https://doi.org/10.1109/ICNP.2019.8888128  

   Duplyakin, Dmitry ; Uta, Alexandru ; Maricq, Aleksander ; Ricci, Robert ( October 2019 , Proceedings of the Worksop on Midscale Education and Research Infrastructure and Tools (MERIT))

   Empirical performance measurements of computer systems almost always exhibit variability and anomalies. Run-to-run and server-to-server variations are common for CPU, memory, disk, and network performance characteristics. In our previous work, we focused on taming performance variability for memory, disk, and network and established an interactive analysis service at: https://confirm.fyi/ to help users of the CloudLab testbed better plan and conduct their experiments. In this paper, we describe our analysis of CPU variability based on over 1.3M performance measurements from nearly 1,800 servers and present our initial findings. The focus of this work is on capturing hardware variability, which can make repeatable experiments more difficult and can impact conclusions; it it this important for systems researchers to understand. (We note that, though we do not study it in this work, in the cloud, multi-tenancy and resource sharing an exacerbate the problem.) Variability also inevitably impacts performance and operation of middleware and high-level applications, contributing to the straggler problems in many domains, including HPC, Big Data, and Machine Learning, and on many types of cyberinfrastructures. We analyze the data from the CloudLab servers allocated in an exclusive fashion, with no virtualization. While our analysis focuses on the testbed that aims to promotemore »reproducible research, we believe our approach and the findings can be of value to people who manage, analyze, and utilize shared computing resources in supercomputers, clouds, and datacenters.« less
3. Elementary Teachers’ Verbal Support of Engineering Integration in an Interdisciplinary Project

   Lilly, S. C. ; McAlister, A. M. ; Chiu, J. L. ( July 2021 , 2021 ASEE Annual Conference proceedings)

   This study investigates how teachers verbally support students to engage in integrated engineering, science, and computer science activities across the implementation of an engineering project. This is important as recent research has focused on understanding how precollege students’ engagement in engineering practices is supported by teachers (Watkins et al., 2018) and the benefits of integrating engineering in precollege classes, including improved achievement in science, ability to engage in science and engineering practices inherent to engineering (i.e., engineering design), and increased awareness of engineering (National Academy of Engineering and the National Research Council; Katehi et al., 2009). Further, there is a national emphasis on integrating engineering, science, and computer science practices and concepts in science classrooms (NGSS Lead States, 2013). Yet little research has considered how teachers implement these disciplines together within one classroom, particularly elementary teachers who often have little prior experience in teaching engineering and may need support to integrate engineering design into elementary science classroom settings. In particular, this study explores how elementary teachers verbally support science and computer science concepts and practices to be implicitly and explicitly integrated into an engineering project by implementing support intended by curricular materials and/or adding their own verbal support. Implicit usemore »of integration included students engaging in integrated practices without support to know that they were doing so; explicit use of integration included teachers providing support for students to know how and why they were integrating disciplines. Our research questions include: (1) To what extent did teachers provide implicit and explicit verbal support of integration in implementation versus how it was intended in curricular materials? (2) Does this look different between two differently-tracked class sections? Participants include two fifth-grade teachers who co-led two fifth-grade classes through a four-week engineering project. The project focused on redesigning school surfaces to mitigate water runoff. Teachers integrated disciplines by supporting students to create computational models of underlying scientific concepts to develop engineering solutions. One class had a larger proportion of students who were tracked into accelerated mathematics; the other class had a larger proportion of students with individualized educational plans (IEPs). Transcripts of whole class discussion were analyzed for instances that addressed the integration of disciplines or supported students to engage in integrated activities. Results show that all instances of integration were implicit for the class with students in advanced mathematics while most were explicit for the class with students with IEPs. Additionally, support was mainly added by the teachers rather than suggested by curricular materials. Most commonly, teachers added integration between computer science and engineering. Implications of this study are an important consideration for the support that teachers need to engage in the important, but challenging, work of integrating science and computer science practices through engineering lessons within elementary science classrooms. Particularly, we consider how to assist teachers with their verbal supports of integrated curricula through engineering lessons in elementary classrooms. This study then has the potential to significantly impact the state of knowledge in interdisciplinary learning through engineering for elementary students.« less
4. 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,more »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.« less
5. Towards an Experimental News User Community as Infrastructure for Recommendation Research

   Konstan, Joseph A. ; Burke, Robin ; Malthouse, Edward C. ( September 2021 , Proceedings of INRA'21: 9th International Workshop on News Recommendation and Analytics)

   While substantial advances have been made in recommender systems -- both in general and for news -- using datasets, offline analyses, and one-shot experiments, longitudinal studies of real users remain the gold standard, and the only way to effectively measure the impact of recommender system designs (algorithmic and otherwise) on long-term user experience and behavior. While such infrastructure exists for studies within some individual organizations, the extensive cost and effort to build the systems, content streams, and user base make it prohibitive for most researchers to conduct such studies. We propose to develop shared research infrastructure for the research community, and have received funding to gather community input on requirements, resources, and research goals for such an infrastructure. If the full infrastructure proposal is funded, it would result in recruiting a community of thousands of users who agree to use a news delivery application within which various researchers would be install and conduct experiments. In this short paper we outline what we have heard and learned so far and present a set of questions to be directed to INRA attendees to gather their feedback at the workshop.