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1. COMPaaS DLV: Composable Infrastructure for Deep Learning in an Academic Research Environment

   https://doi.org/10.1109/ICNP.2019.8888070  

   Brown, Maxine ; Renambot, Luc ; Long, Lance ; Bargo, Timothy ; Johnson, Andrew E. ( October 2019 , 2019 IEEE 27th International Conference on Network Protocols (ICNP))

   In today's Big Data era, data scientists require new computational instruments in order to quickly analyze large-scale datasets using complex codes and quicken the rate of scientific progress. While Federally-funded computer resources, from supercomputers to clouds, are beneficial, they are often limiting - particularly for deep learning and visualization - as they have few Graphics Processing Units (GPUs). GPUs are at the center of modern high-performance computing and artificial intelligence, efficiently performing mathematical operations that can be massively parallelized, speeding up codes used for deep learning, visualization and image processing, more so than general-purpose microprocessors, or Central Processing Units (CPUs). The University of Illinois at Chicago is acquiring a much-in-demand GPU-based instrument, COMPaaS DLV - COMposable Platform as a Service Instrument for Deep Learning & Visualization, based on composable infrastructure, an advanced architecture that disaggregates the underlying compute, storage, and network resources for scaling needs, but operates as a single cohesive infrastructure for management and workload purposes. We are experimenting with a small system and learning a great deal about composability, and we believe COMPaaS DLV users will benefit from the varied workflow that composable infrastructure allows. 

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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))

   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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3. Issues in the Reproducibility of Deep Learning Results

   https://doi.org/10.1109/SPMB47826.2019.9037840  

   Jean-Paul, S. ; Elseify, T. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. ; Selesnik, I. ; Picone, J. (Ed.)

   The Neuronix high-performance computing cluster allows us to conduct extensive machine learning experiments on big data [1]. This heterogeneous cluster uses innovative scheduling technology, Slurm [2], that manages a network of CPUs and graphics processing units (GPUs). The GPU farm consists of a variety of processors ranging from low-end consumer grade devices such as the Nvidia GTX 970 to higher-end devices such as the GeForce RTX 2080. These GPUs are essential to our research since they allow extremely compute-intensive deep learning tasks to be executed on massive data resources such as the TUH EEG Corpus [2]. We use TensorFlow [3] as the core machine learning library for our deep learning systems, and routinely employ multiple GPUs to accelerate the training process. Reproducible results are essential to machine learning research. Reproducibility in this context means the ability to replicate an existing experiment – performance metrics such as error rates should be identical and floating-point calculations should match closely. Three examples of ways we typically expect an experiment to be replicable are: (1) The same job run on the same processor should produce the same results each time it is run. (2) A job run on a CPU and GPU should produce identical results. (3) A job should produce comparable results if the data is presented in a different order. System optimization requires an ability to directly compare error rates for algorithms evaluated under comparable operating conditions. However, it is a difficult task to exactly reproduce the results for large, complex deep learning systems that often require more than a trillion calculations per experiment [5]. This is a fairly well-known issue and one we will explore in this poster. Researchers must be able to replicate results on a specific data set to establish the integrity of an implementation. They can then use that implementation as a baseline for comparison purposes. A lack of reproducibility makes it very difficult to debug algorithms and validate changes to the system. Equally important, since many results in deep learning research are dependent on the order in which the system is exposed to the data, the specific processors used, and even the order in which those processors are accessed, it becomes a challenging problem to compare two algorithms since each system must be individually optimized for a specific data set or processor. This is extremely time-consuming for algorithm research in which a single run often taxes a computing environment to its limits. Well-known techniques such as cross-validation [5,6] can be used to mitigate these effects, but this is also computationally expensive. These issues are further compounded by the fact that most deep learning algorithms are susceptible to the way computational noise propagates through the system. GPUs are particularly notorious for this because, in a clustered environment, it becomes more difficult to control which processors are used at various points in time. Another equally frustrating issue is that upgrades to the deep learning package, such as the transition from TensorFlow v1.9 to v1.13, can also result in large fluctuations in error rates when re-running the same experiment. Since TensorFlow is constantly updating functions to support GPU use, maintaining an historical archive of experimental results that can be used to calibrate algorithm research is quite a challenge. This makes it very difficult to optimize the system or select the best configurations. The overall impact of all of these issues described above is significant as error rates can fluctuate by as much as 25% due to these types of computational issues. Cross-validation is one technique used to mitigate this, but that is expensive since you need to do multiple runs over the data, which further taxes a computing infrastructure already running at max capacity. GPUs are preferred when training a large network since these systems train at least two orders of magnitude faster than CPUs [7]. Large-scale experiments are simply not feasible without using GPUs. However, there is a tradeoff to gain this performance. Since all our GPUs use the NVIDIA CUDA® Deep Neural Network library (cuDNN) [8], a GPU-accelerated library of primitives for deep neural networks, it adds an element of randomness into the experiment. When a GPU is used to train a network in TensorFlow, it automatically searches for a cuDNN implementation. NVIDIA’s cuDNN implementation provides algorithms that increase the performance and help the model train quicker, but they are non-deterministic algorithms [9,10]. Since our networks have many complex layers, there is no easy way to avoid this randomness. Instead of comparing each epoch, we compare the average performance of the experiment because it gives us a hint of how our model is performing per experiment, and if the changes we make are efficient. In this poster, we will discuss a variety of issues related to reproducibility and introduce ways we mitigate these effects. For example, TensorFlow uses a random number generator (RNG) which is not seeded by default. TensorFlow determines the initialization point and how certain functions execute using the RNG. The solution for this is seeding all the necessary components before training the model. This forces TensorFlow to use the same initialization point and sets how certain layers work (e.g., dropout layers). However, seeding all the RNGs will not guarantee a controlled experiment. Other variables can affect the outcome of the experiment such as training using GPUs, allowing multi-threading on CPUs, using certain layers, etc. To mitigate our problems with reproducibility, we first make sure that the data is processed in the same order during training. Therefore, we save the data from the last experiment and to make sure the newer experiment follows the same order. If we allow the data to be shuffled, it can affect the performance due to how the model was exposed to the data. We also specify the float data type to be 32-bit since Python defaults to 64-bit. We try to avoid using 64-bit precision because the numbers produced by a GPU can vary significantly depending on the GPU architecture [11-13]. Controlling precision somewhat reduces differences due to computational noise even though technically it increases the amount of computational noise. We are currently developing more advanced techniques for preserving the efficiency of our training process while also maintaining the ability to reproduce models. In our poster presentation we will demonstrate these issues using some novel visualization tools, present several examples of the extent to which these issues influence research results on electroencephalography (EEG) and digital pathology experiments and introduce new ways to manage such computational issues. 

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4. Moving from Composable to Programmable

   https://doi.org/10.1109/IPDPSW55747.2022.00209  

   Chen, Zhongyi ; Renambot, Luc ; Long, Lance ; Brown, Maxine ; Johnson, Andrew E. ( May 2022 , 36th IEEE International Parallel & Distributed Processing Symposium Workshops (IPDPSW))

   In today’s Big Data era, data scientists require modern workflows to quickly analyze large-scale datasets using complex codes to maintain the rate of scientific progress. These scientists often rely on available campus resources or off-the-shelf computational systems for their applications. Unified infrastructure or over-provisioned servers can quickly become bottlenecks for specific tasks, wasting time and resources. Composable infrastructure helps solve these problems by providing users with new ways to increase resource utilization. Composable infrastructure disaggregates a computer’s components – CPU, GPU (accelerators), storage and networking – into fluid pools of resources, but typically relies upon infrastructure engineers to architect individual machines. Infrastructure is either managed with specialized command-line utilities, user interfaces or specification files. These management models are cumbersome and difficult to incorporate into data-science workflows. We developed a high-level software API, Composastructure, which, when integrated into modern workflows, can be used by infrastructure engineers as well as data scientists to reorganize composable resources on demand. Composastructure enables infrastructures to be programmable, secure, persistent and reproducible. Our API composes machines, frees resources, supports multi-rack operations, and includes a Python module for Jupyter Notebooks. 

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5. Cloud and on-premises data center usage, expenditures, and approaches to return on investment: A survey of academic research computing organizations

   https://doi.org/https://doi.org/10.1145/3311790.3396642  

   Chalker, Alan ; Hillegas, Curtis W. ; Sill, Alan ; Broude Geva, Sharon ; Stewart, Craig A. ( July 2020 , PEARC '20: Practice and Experience in Advanced Research Computing)

   The landscape of research in science and engineering is heavily reliant on computation and data processing. There is continued and expanded usage by disciplines that have historically used advanced computing resources, new usage by disciplines that have not traditionally used HPC, and new modalities of the usage in Data Science, Machine Learning, and other areas of AI. Along with these new patterns have come new advanced computing resource methods and approaches, including the availability of commercial cloud resources. The Coalition for Academic Scientific Computation (CASC) has long been an advocate representing the needs of academic researchers using computational resources, sharing best practices and offering advice to create a national cyberinfrastructure to meet US science, engineering, and other academic computing needs. CASC has completed the first of what we intend to be an annual survey of academic cloud and data center usage and practices in analyzing return on investment in cyberinfrastructure. Critically important findings from this first survey include the following: many of the respondents are engaged in some form of analysis of return in research computing investments, but only a minority currently report the results of such analyses to their upper-level administration. Most respondents are experimenting with use of commercial cloud resources but no respondent indicated that they have found use of commercial cloud services to create financial benefits compared to their current methods. There is clear correlation between levels of investment in research cyberinfrastructure and the scale of both cpu core-hours delivered and the financial level of supported research grants. Also interesting is that almost every respondent indicated that they participate in some sort of national cooperative or nationally provided research computing infrastructure project and most were involved in academic computing-related organizations, indicating a high degree of engagement by institutions of higher education in building and maintaining national research computing ecosystems. Institutions continue to evaluate cloud-based HPC service models, despite having generally concluded that so far cloud HPC is too expensive to use compared to their current methods. 

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