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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. MAPPER: Managing Application Performance via Parallel Efficiency Regulation

   https://doi.org/10.1145/3501767  

   Srikanthan, Sharanyan ; Chakraborti, Sayak ; Ferro, Princeton ; Dwarkadas, Sandhya ( June 2022 , ACM Transactions on Architecture and Code Optimization)

   State-of-the-art systems, whether in servers or desktops, provide ample computational and storage resources to allow multiple simultaneously executing potentially parallel applications. However, performance tends to be unpredictable, being a function of algorithmic design, resource allocation choices, and hardware resource limitations. In this article, we introduce MAPPER, a manager of application performance via parallel efficiency regulation. MAPPER uses a privileged daemon to monitor (using hardware performance counters) and coordinate all participating applications by making two coupled decisions: the degree of parallelism to allow each application to improve system efficiency while guaranteeing quality of service (QoS), and which specific CPU cores to schedule applications on. The QoS metric may be chosen by the application and could be in terms of execution time, throughput, or tail latency, relative to the maximum performance achievable on the machine. We demonstrate that using a normalized parallel efficiency metric allows comparison across and cooperation among applications to guarantee their required QoS. While MAPPER may be used without application or runtime modification, use of a simple interface to communicate application-level knowledge improves MAPPER’s efficacy. Using a QoS guarantee of 85% of the IPC achieved with a fair share of resources on the machine, MAPPER achieves up to 3.3 \( \times \) speedup relative to unmodified Linux and runtime systems, with an average improvement of 17% in our test cases. At the same time, MAPPER violates QoS for only 2% of the applications (compared to 23% for Linux), while placing much tighter bounds on the worst case. MAPPER relieves hardware bottlenecks via task-to-CPU placement and allocates more CPU contexts to applications that exhibit higher parallel efficiency while guaranteeing QoS, resulting in both individual application performance predictability and overall system efficiency. 

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3. FlexCNN: An End-to-End Framework for Composing CNN Accelerators on FPGA

   https://doi.org/10.1145/3570928  

   Basalama, Suhail ; Sohrabizadeh, Atefeh ; Wang, Jie ; Guo, Licheng ; Cong, Jason ( December 2022 , ACM Transactions on Reconfigurable Technology and Systems)

   With reduced data reuse and parallelism, recent convolutional neural networks (CNNs) create new challenges for FPGA acceleration. Systolic arrays (SAs) are efficient, scalable architectures for convolutional layers, but without proper optimizations, their efficiency drops dramatically for reasons: 1) the different dimensions within same-type layers, 2) the different convolution layers especially transposed and dilated convolutions, and 3) CNN’s complex dataflow graph. Furthermore, significant overheads arise when integrating FPGAs into machine learning frameworks. Therefore, we present a flexible, composable architecture called FlexCNN, which delivers high computation efficiency by employing dynamic tiling, layer fusion, and data layout optimizations. Additionally, we implement a novel versatile SA to process normal, transposed, and dilated convolutions efficiently. FlexCNN also uses a fully-pipelined software-hardware integration that alleviates the software overheads. Moreover, with an automated compilation flow, FlexCNN takes a CNN in the ONNX representation, performs a design space exploration, and generates an FPGA accelerator. The framework is tested using three complex CNNs: OpenPose, U-Net, and E-Net. The architecture optimizations achieve 2.3 × performance improvement. Compared to a standard SA, the versatile SA achieves close-to-ideal speedups, with up to 15.98 × and 13.42 × for transposed and dilated convolutions, with a 6% average area overhead. The pipelined integration leads to a 5 × speedup for OpenPose. 

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4. Asynchronous Automata Processing on GPUs

   https://doi.org/10.1145/3579453  

   Liu, Hongyuan ; Pai, Sreepathi ; Jog, Adwait ( February 2023 , Proceedings of the ACM on Measurement and Analysis of Computing Systems)

   Finite-state automata serve as compute kernels for many application domains such as pattern matching and data analytics. Existing approaches on GPUs exploit three levels of parallelism in automata processing tasks: 1)~input stream level, 2)~automaton-level and 3)~state-level. Among these, only state-level parallelism is intrinsic to automata while the other two levels of parallelism depend on the number of automata and input streams to be processed. As GPU resources increase, a parallelism-limited automata processing task can underutilize GPU compute resources. To this end, we propose AsyncAP, a low-overhead approach that optimizes for both scalability and throughput. Our insight is that most automata processing tasks have an additional source of parallelism originating from the input symbols which has not been leveraged before. Making the matching process associated with the automata tasks asynchronous, i.e., parallel GPU threads start processing an input stream from different input locations instead of processing it serially, improves throughput significantly, and scales with input length. When the task does not have enough parallelism to utilize all the GPU cores, detailed evaluation across 12 evaluated applications shows that AsyncAP achieves up to 58× speedup on average over the state-of-the-art GPU automata processing engine. When the tasks have enough parallelism to utilize GPU cores, AsyncAP still achieves 2.4× speedup. 

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5. SHMEM-ML: Leveraging OpenSHMEM and Apache Arrow for Scalable, Composable Machine Learning

   Grossman, Max ; Poole, Steve ; Pritchard, Howard ; Sarkar, Vivek ( May 2022 , Lecture notes in computer science)

   Poole, Steve ; Hernandez, Oscar ; Baker, Matthew ; Curtis, Tony (Ed.)

   SHMEM-ML is a domain specific library for distributed array computations and machine learning model training & inference. Like other projects at the intersection of machine learning and HPC (e.g. dask, Arkouda, Legate Numpy), SHMEM-ML aims to leverage the performance of the HPC software stack to accelerate machine learning workflows. However, it differs in a number of ways. First, SHMEM-ML targets the full machine learning workflow, not just model training. It supports a general purpose nd-array abstraction commonly used in Python machine learning applications, and efficiently distributes transformation and manipulation of this ndarray across the full system. Second, SHMEM-ML uses OpenSHMEM as its underlying communication layer, enabling high performance networking across hundreds or thousands of distributed processes. While most past work in high performance machine learning has leveraged HPC message passing communication models as a way to efficiently exchange model gradient updates, SHMEM-ML’s focus on the full machine learning lifecycle means that a more flexible and adaptable communication model is needed to support both fine and coarse grain communication. Third, SHMEM-ML works to interoperate with the broader Python machine learning software ecosystem. While some frameworks aim to rebuild that ecosystem from scratch on top of the HPC software stack, SHMEM-ML is built on top of Apache Arrow, an in-memory standard for data formatting and data exchange between libraries. This enables SHMEM-ML to share data with other libraries without creating copies of data. This paper describes the design, implementation, and evaluation of SHMEM-ML – demonstrating a general purpose system for data transformation and manipulation while achieving up to a 38× speedup in distributed training performance relative to the industry standard Horovod framework without a regression in model metrics. 

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