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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))

   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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2. Challenges and Benchmark Datasets for Machine Learning in the Atmospheric Sciences: Definition, Status, and Outlook

   https://doi.org/10.1175/AIES-D-21-0002.1  

   Dueben, Peter D. ; Schultz, Martin G. ; Chantry, Matthew ; Gagne, David John ; Hall, David Matthew ; McGovern, Amy ( July 2022 , Artificial Intelligence for the Earth Systems)

   Abstract Benchmark datasets and benchmark problems have been a key aspect for the success of modern machine learning applications in many scientific domains. Consequently, an active discussion about benchmarks for applications of machine learning has also started in the atmospheric sciences. Such benchmarks allow for the comparison of machine learning tools and approaches in a quantitative way and enable a separation of concerns for domain and machine learning scientists. However, a clear definition of benchmark datasets for weather and climate applications is missing with the result that many domain scientists are confused. In this paper, we equip the domain of atmospheric sciences with a recipe for how to build proper benchmark datasets, a (nonexclusive) list of domain-specific challenges for machine learning is presented, and it is elaborated where and what benchmark datasets will be needed to tackle these challenges. We hope that the creation of benchmark datasets will help the machine learning efforts in atmospheric sciences to be more coherent, and, at the same time, target the efforts of machine learning scientists and experts of high-performance computing to the most imminent challenges in atmospheric sciences. We focus on benchmarks for atmospheric sciences (weather, climate, and air-quality applications). However, many aspects of this paper will also hold for other aspects of the Earth system sciences or are at least transferable. Significance Statement Machine learning is the study of computer algorithms that learn automatically from data. Atmospheric sciences have started to explore sophisticated machine learning techniques and the community is making rapid progress on the uptake of new methods for a large number of application areas. This paper provides a clear definition of so-called benchmark datasets for weather and climate applications that help to share data and machine learning solutions between research groups to reduce time spent in data processing, to generate synergies between groups, and to make tool developments more targeted and comparable. Furthermore, a list of benchmark datasets that will be needed to tackle important challenges for the use of machine learning in atmospheric sciences is provided. 

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3. Novel Network Services for Supporting Big Data Science Research

   Chung, J. ; Donovan, S. ; Bezerra, J. ; Morgan, H. ; Ibarra, J. ; Clark, R. ; Owen, H ( October 2017 , Gateways 2017)

   Poster Abstract: To interconnect research facilities across wide geographic areas, network operators deploy science networks, also referred to as Research and Education (R&E) networks. These networks allow experimenters to establish dedicated network connections between research facilities for transferring large amounts of data. Recently, R&E networks have started using Software-Defined Networking (SDN) and Software Defined Exchanges (SDX) for deploying these connections. AtlanticWave/SDX is a response to the growing demand to support end-to-end network services spanning multiple SDN domains. However, requesting these services is a challenging task for domain-expert scientists, because the interfaces of the R&E networks have been developed by network operators for network operators. In this paper, we propose interfaces that allow domain expert scientists to reserve resources of the scientific network using abstractions that focus on their data transfer needs for scientific workflow management. Recent trends in the networking field pursue better interfaces for requesting network services (e.g., intent-based networking). Although intents are sufficient for the needs of network operations, they are not abstract enough in most cases to be used by domain-expert scientists. This is an issue we are addressing in the AtlanticWave/SDX design: network operators and domain expert scientists will have their own interfaces focusing on their specific needs. 

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4. Novel Network Services for Supporting Big Data Science Research

   Chung, J. ; Donovan, S. ; Bezerra, J. ; Morgan, H. ; Ibarra, J. ; Clark, R. ; Owen, H ( October 2017 , Gateways 2017)

   To interconnect research facilities across wide geographic areas, network operators deploy science networks, also referred to as Research and Education (R&E) networks. These networks allow experimenters to establish dedicated network connections between research facilities for transferring large amounts of data. Recently, R&E networks have started using Software-Defined Networking (SDN) and Software Defined Exchanges (SDX) for deploying these connections. AtlanticWave/SDX is a response to the growing demand to support end-to-end network services spanning multiple SDN domains. However, requesting these services is a challenging task for domain-expert scientists, because the interfaces of the R&E networks have been developed by network operators for network operators. In this paper, we propose interfaces that allow domain expert scientists to reserve resources of the scientific network using abstractions that focus on their data transfer needs for scientific workflow management. Recent trends in the networking field pursue better interfaces for requesting network services (e.g., intent-based networking). Although intents are sufficient for the needs of network operations, they are not abstract enough in most cases to be used by domain-expert scientists. This is an issue we are addressing in the AtlanticWave/SDX design: network operators and domain-expert scientists will have their own interfaces focusing on their specific needs. 

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5. Geometric deep optical sensing

   https://doi.org/10.1126/science.ade1220  

   Yuan, Shaofan ; Ma, Chao ; Fetaya, Ethan ; Mueller, Thomas ; Naveh, Doron ; Zhang, Fan ; Xia, Fengnian ( March 2023 , Science)

   BACKGROUND Optical sensing devices measure the rich physical properties of an incident light beam, such as its power, polarization state, spectrum, and intensity distribution. Most conventional sensors, such as power meters, polarimeters, spectrometers, and cameras, are monofunctional and bulky. For example, classical Fourier-transform infrared spectrometers and polarimeters, which characterize the optical spectrum in the infrared and the polarization state of light, respectively, can occupy a considerable portion of an optical table. Over the past decade, the development of integrated sensing solutions by using miniaturized devices together with advanced machine-learning algorithms has accelerated rapidly, and optical sensing research has evolved into a highly interdisciplinary field that encompasses devices and materials engineering, condensed matter physics, and machine learning. To this end, future optical sensing technologies will benefit from innovations in device architecture, discoveries of new quantum materials, demonstrations of previously uncharacterized optical and optoelectronic phenomena, and rapid advances in the development of tailored machine-learning algorithms. ADVANCES Recently, a number of sensing and imaging demonstrations have emerged that differ substantially from conventional sensing schemes in the way that optical information is detected. A typical example is computational spectroscopy. In this new paradigm, a compact spectrometer first collectively captures the comprehensive spectral information of an incident light beam using multiple elements or a single element under different operational states and generates a high-dimensional photoresponse vector. An advanced algorithm then interprets the vector to achieve reconstruction of the spectrum. This scheme shifts the physical complexity of conventional grating- or interference-based spectrometers to computation. Moreover, many of the recent developments go well beyond optical spectroscopy, and we discuss them within a common framework, dubbed “geometric deep optical sensing.” The term “geometric” is intended to emphasize that in this sensing scheme, the physical properties of an unknown light beam and the corresponding photoresponses can be regarded as points in two respective high-dimensional vector spaces and that the sensing process can be considered to be a mapping from one vector space to the other. The mapping can be linear, nonlinear, or highly entangled; for the latter two cases, deep artificial neural networks represent a natural choice for the encoding and/or decoding processes, from which the term “deep” is derived. In addition to this classical geometric view, the quantum geometry of Bloch electrons in Hilbert space, such as Berry curvature and quantum metrics, is essential for the determination of the polarization-dependent photoresponses in some optical sensors. In this Review, we first present a general perspective of this sensing scheme from the viewpoint of information theory, in which the photoresponse measurement and the extraction of light properties are deemed as information-encoding and -decoding processes, respectively. We then discuss demonstrations in which a reconfigurable sensor (or an array thereof), enabled by device reconfigurability and the implementation of neural networks, can detect the power, polarization state, wavelength, and spatial features of an incident light beam. OUTLOOK As increasingly more computing resources become available, optical sensing is becoming more computational, with device reconfigurability playing a key role. On the one hand, advanced algorithms, including deep neural networks, will enable effective decoding of high-dimensional photoresponse vectors, which reduces the physical complexity of sensors. Therefore, it will be important to integrate memory cells near or within sensors to enable efficient processing and interpretation of a large amount of photoresponse data. On the other hand, analog computation based on neural networks can be performed with an array of reconfigurable devices, which enables direct multiplexing of sensing and computing functions. We anticipate that these two directions will become the engineering frontier of future deep sensing research. On the scientific frontier, exploring quantum geometric and topological properties of new quantum materials in both linear and nonlinear light-matter interactions will enrich the information-encoding pathways for deep optical sensing. In addition, deep sensing schemes will continue to benefit from the latest developments in machine learning. Future highly compact, multifunctional, reconfigurable, and intelligent sensors and imagers will find applications in medical imaging, environmental monitoring, infrared astronomy, and many other areas of our daily lives, especially in the mobile domain and the internet of things. Schematic of deep optical sensing. The n -dimensional unknown information ( w ) is encoded into an m -dimensional photoresponse vector ( x ) by a reconfigurable sensor (or an array thereof), from which w′ is reconstructed by a trained neural network ( n ′ = n and w′   ≈   w ). Alternatively, x may be directly deciphered to capture certain properties of w . Here, w , x , and w′ can be regarded as points in their respective high-dimensional vector spaces ℛ n , ℛ m , and ℛ n ′ . 

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