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1. Generating Connected Synthetic Electronic Health Records and Social Media Data for Modeling and Simulation

   Tall, Anne M. ; Zou, Cliff C. ; Wang, Jun ( December 2020 , Interservice/Industry Training, Simulation and Education Conference (I/ITSEC))

   Research and experimentation using big data sets, specifically large sets of electronic health records (EHR) and social media data, is demonstrating the potential to understand the spread of diseases and a variety of other issues. Applications of advanced algorithms, machine learning, and artificial intelligence indicate a potential for rapidly advancing improvements in public health. For example, several reports indicate that social media data can be used to predict disease outbreak and spread (Brown, 2015). Since real-world EHR data has complicated security and privacy issues preventing it from being widely used by researchers, there is a real need to synthetically generate EHR data that is realistic and representative. Current EHR generators, such as Syntheaä (Walonoski et al., 2018) only simulate and generate pure medical-related data. However, adding patients’ social media data with their simulated EHR data would make combined data more comprehensive and realistic for healthcare research. This paper presents a patients’ social media data generator that extends an EHR data generator. By adding coherent social media data to EHR data, a variety of issues can be examined for emerging interests, such as where a contagious patient may have been and others with whom they may have been in contact. Socialmore »media data, specifically Twitter data, is generated with phrases indicating the onset of symptoms corresponding to the synthetically generated EHR reports of simulated patients. This enables creation of an open data set that is scalable up to a big-data size, and is not subject to the security, privacy concerns, and restrictions of real healthcare data sets. This capability is important to the modeling and simulation community, such as scientists and epidemiologists who are developing algorithms to analyze the spread of diseases. It enables testing a variety of analytics without revealing real-world private patient information.« less
2. 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
3. Role-Based Ecosystem for the Design, Development, and Deployment of Secure Multi-Party Data Analytics Applications

   https://doi.org/10.1109/SecDev.2019.00015  

   Lapets, Andrei ; Albab, Kinan ; Issa, Rawane ; Qin, Lucy ; Varia, Mayank ; Bestavros, Azer ; Jansen, Frederick ( September 2019 , IEEE SecDev)

   Software applications that employ secure multi-party computation (MPC) can empower individuals and organizations to benefit from privacy-preserving data analyses when data sharing is encumbered by confidentiality concerns, legal constraints, or corporate policies. MPC is already being incorporated into software solutions in some domains; however, individual use cases do not fully convey the variety, extent, and complexity of the opportunities of MPC. This position paper articulates a role-based perspective that can provide some insight into how future research directions, infrastructure development and evaluation approaches, and deployment practices for MPC may evolve. Drawing on our own lessons from existing real-world deployments and the fundamental characteristics of MPC that make it a compelling technology, we propose a role-based conceptual framework for describing MPC deployment scenarios. Our framework acknowledges and leverages a novel assortment of roles that emerge from the fundamental ways in which MPC protocols support federation of functionalities and responsibilities. Defining these roles using the new opportunities for federation that MPC enables in turn can help identify and organize the capabilities, concerns, incentives, and trade-offs that affect the entities (software engineers, government regulators, corporate executives, end-users, and others) that participate in an MPC deployment scenario. This framework can not only guide themore »development of an ecosystem of modular and composable MPC tools, but can make explicit some of the opportunities that researchers and software engineers (and any organizations they form) have to differentiate and specialize the artifacts and services they choose to design, develop, and deploy. We demonstrate how this framework can be used to describe existing MPC deployment scenarios, how new opportunities in a scenario can be observed by disentangling roles inhabited by the involved parties, and how this can motivate the development of MPC libraries and software tools that specialize not by application domain but by role.« less
4. Polymath: Low-Latency MPC via Secure Polynomial Evaluations and Its Applications

   https://doi.org/10.2478/popets-2022-0020  

   Lu, Donghang ; Yu, Albert ; Kate, Aniket ; Maji, Hemanta ( November 2021 , Proceedings on Privacy Enhancing Technologies)

   Abstract While the practicality of secure multi-party computation (MPC) has been extensively analyzed and improved over the past decade, we are hitting the limits of efficiency with the traditional approaches of representing the computed functionalities as generic arithmetic or Boolean circuits. This work follows the design principle of identifying and constructing fast and provably-secure MPC protocols to evaluate useful high-level algebraic abstractions; thus, improving the efficiency of all applications relying on them. We present Polymath, a constant-round secure computation protocol suite for the secure evaluation of (multi-variate) polynomials of scalars and matrices, functionalities essential to numerous data-processing applications. Using precise natural precomputation and high-degree of parallelism prevalent in the modern computing environments, Polymath can make latency of secure polynomial evaluations of scalars and matrices independent of polynomial degree and matrix dimensions. We implement our protocols over the HoneyBadgerMPC library and apply it to two prominent secure computation tasks: privacy-preserving evaluation of decision trees and privacy-preserving evaluation of Markov processes. For the decision tree evaluation problem, we demonstrate the feasibility of evaluating high-depth decision tree models in a general n -party setting. For the Markov process application, we demonstrate that Poly-math can compute large powers of transition matrices with better onlinemore »time and less communication.« less
5. Sharing personal ECG time-series data privately

   https://doi.org/10.1093/jamia/ocac047  

   Bonomi, Luca ; Wu, Zeyun ; Fan, Liyue ( April 2022 , Journal of the American Medical Informatics Association)

   Emerging technologies (eg, wearable devices) have made it possible to collect data directly from individuals (eg, time-series), providing new insights on the health and well-being of individual patients. Broadening the access to these data would facilitate the integration with existing data sources (eg, clinical and genomic data) and advance medical research. Compared to traditional health data, these data are collected directly from individuals, are highly unique and provide fine-grained information, posing new privacy challenges. In this work, we study the applicability of a novel privacy model to enable individual-level time-series data sharing while maintaining the usability for data analytics.

   We propose a privacy-protecting method for sharing individual-level electrocardiography (ECG) time-series data, which leverages dimensional reduction technique and random sampling to achieve provable privacy protection. We show that our solution provides strong privacy protection against an informed adversarial model while enabling useful aggregate-level analysis.

   We conduct our evaluations on 2 real-world ECG datasets. Our empirical results show that the privacy risk is significantly reduced after sanitization while the data usability is retained for a variety of clinical tasks (eg, predictive modeling and clustering).

   Our study investigates the privacy risk in sharing individual-level ECG time-series data. We demonstrate thatmore »individual-level data can be highly unique, requiring new privacy solutions to protect data contributors.

   The results suggest our proposed privacy-protection method provides strong privacy protections while preserving the usefulness of the data.

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