- Award ID(s):
- NSF-PAR ID:
- Date Published:
- Journal Name:
- Proceedings of the 1st International Workshop on Software Engineering for High Performance Computing in Computational and Data-enabled Science & Engineering
- Page Range / eLocation ID:
- 9 to 12
- Medium: X
- Sponsoring Org:
- National Science Foundation
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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: firstname.lastname@example.org, email@example.com, firstname.lastname@example.org, email@example.com, firstname.lastname@example.org ◊ 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  to the development of brain-machine-interfaces . 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 . 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) . TUH also devised a novel scoring metric for the detection of seizures that was used as basis for algorithm evaluation . 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  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) , 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  and PyTorch , 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 , 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.more » « less
Binder is a publicly accessible online service for executing interactive notebooks based on Git repositories. Binder dynamically builds and deploys containers following a recipe stored in the repository, then gives the user a browser-based notebook interface. The Binder group periodically releases a log of container launches from the public Binder service. Archives of launch records are available here. These records do not include identifiable information like IP addresses, but do give the source repo being launched along with some other metadata. The main content of this dataset is in the
binder.sqlitefile. This SQLite database includes launch records from 2018-11-03 to 2021-06-06 in the
eventstable, which has the following schema.
CREATE TABLE events( version INTEGER, timestamp TEXT, provider TEXT, spec TEXT, origin TEXT, ref TEXT, guessed_ref TEXT ); CREATE INDEX idx_timestamp ON events(timestamp);
versionindicates the version of the record as assigned by Binder. The
originfield became available with version 3, and the
reffield with version 4. Older records where this information was not recorded will have the corresponding fields set to null.
timestampis the ISO timestamp of the launch
providergives the type of source repo being launched ("GitHub" is by far the most common). The rest of the explanations assume GitHub, other providers may differ.
specgives the particular branch/release/commit being built. It consists of
originindicates which backend was used. Each has its own storage, compute, etc. so this info might be important for evaluating caching and performance. Note that only recent records include this field. May be null.
refspecifies the git commit that was actually used, rather than the named branch referenced by
spec. Note that this was not recorded from the beginning, so only the more recent entries include it. May be null.
- For records where
refis not available, we attempted to clone the named reference given by
specrather than the specific commit (see below). The
guessed_reffield records the commit found at the time of cloning. If the branch was updated since the container was launched, this will not be the exact version that was used, and instead will refer to whatever was available at the time (early 2021). Depending on the application, this might still be useful information. Selecting only records with version 4 (or non-null
ref) will exclude these guessed commits. May be null.
The Binder launch dataset identifies the source repos that were used, but doesn't give any indication of their contents. We crawled GitHub to get the actual specification files in the repos which were fed into repo2docker when preparing the notebook environments, as well as filesystem metadata of the repos. Some repos were deleted/made private at some point, and were thus skipped. This is indicated by the absence of any row for the given commit (or absence of both
eventstable). The schema is as follows.
CREATE TABLE spec_files ( ref TEXT NOT NULL PRIMARY KEY, ls TEXT, runtime BLOB, apt BLOB, conda BLOB, pip BLOB, pipfile BLOB, julia BLOB, r BLOB, nix BLOB, docker BLOB, setup BLOB, postbuild BLOB, start BLOB );
eventstable. For each repo, we collected spec files into the following fields (see the repo2docker docs for details on what these are). The records in the database are simply the verbatim file contents, with no parsing or further processing performed.
lsfield gives a metadata listing of the repo contents (excluding the
.gitdirectory). This field is JSON encoded with the following structure based on JSON types:
- Object: filesystem directory. Keys are file names within it. Values are the contents, which can be regular files, symlinks, or subdirectories.
- String: symlink. The string value gives the link target.
- Number: regular file. The number value gives the file size in bytes.
CREATE TABLE clean_specs ( ref TEXT NOT NULL PRIMARY KEY, conda_channels TEXT, conda_packages TEXT, pip_packages TEXT, apt_packages TEXT );
clean_specstable provides parsed and validated specifications for some of the specification files (currently Pip, Conda, and APT packages). Each column gives either a JSON encoded list of package requirements, or null. APT packages have been validated using a regex adapted from the repo2docker source. Pip packages have been parsed and normalized using the Requirement class from the pkg_resources package of setuptools. Conda packages have been parsed and normalized using the
conda.models.match_spec.MatchSpecclass included with the library form of Conda (distinct from the command line tool). Users might want to use these parsers when working with the package data, as the specifications can become fairly complex.
missingtable gives the repos that were not accessible, and
event_logsrecords which log files have already been added. These tables are used for updating the dataset and should not be of interest to users.
Evidence shows that developer reputation is extremely important when accepting pull requests or resolving reported issues. It is particularly salient in Free/Libre Open Source Software since the developers are distributed around the world, do not work for the same organization and, in most cases, never meet face to face. The existing solutions to expose developer reputation tend to be forge specific (GitHub), focus on activity instead of impact, do not leverage social or technical networks, and do not correct often misspelled developer identities. We aim to remedy this by amalgamating data from all public Git repositories, measuring the impact of developer work, expose developer's collaborators, and correct notoriously problematic developer identity data. We leverage World of Code (WoC), a collection of an almost complete (and continuously updated) set of Git repositories by first allowing developers to select which of the 34 million(M) Git commit author IDs belong to them and then generating their profiles by treating the selected collection of IDs as that single developer. As a side-effect, these selections serve as a training set for a supervised learning algorithm that merges multiple identity strings belonging to a single individual. As we evaluate the tool and the proposed impact measure, we expect to build on these findings to develop reputation badges that could be associated with pull requests and commits so developers could easier trust and prioritize them.more » « less
One of the activities of the Pacific Rim Applications and Grid Middleware Assembly (PRAGMA) is fostering Virtual Biodiversity Expeditions by bringing domain scientists and cyber infrastructure specialists together as a team. Over the past few years, PRAGMA members have been collaborating on virtualizing the Lifemapper software. Virtualization and cloud computing have introduced great flexibility and efficiency into IT projects. Virtualization refers to the technologies that provide a layer of abstraction between server hardware system and software that runs on it. This abstraction enables a logical view of computing resources and allows multiple servers to run on the same hardware. With this project, we are virtualizing Lifemapper by enabling its installation and configuration on a virtual cluster. Virtualization provides application scalability, maximizes resources utilization, and creates a more efficient, agile, and automated infrastructure. However, there are downsides to the complexity inherent in these environments, including the need for special techniques to deploy cluster hosts, dependence on virtual environments, and challenging application installation, management, and configuration. In this study, we report on progress of the Lifemapper virtualization framework focused on a reproducible and highly configurable infrastructure capable of fast deployment.
Lifemapper is a distributed software application developed by the Biodiversity Institute at The University of Kansas. Lifemapper creates and maintains a publicly accessible archive of species distribution maps calculated from public specimen data. Lifemapper software also provides a suite of tools for biodiversity researchers that calculate single and multispecies distribution predictions and macroecological analyses through application programming interfaces. Our goal is to create a viable solution that can be easily adopted and reused by scientists from multiple institutions or projects. This solution (1) allows fast deployment of ready‐made cluster images, (2) reproduces the complete Lifemapper processing pipeline on demand at multiple sites and in different hosting environments, and (3) enables scientists to perform Lifemapper‐facilitated data processing on restricted‐use data, very large datasets, or other unique data.
A key contribution of this work is describing the practical experience in taking a complex, clustered, domain‐specific, data analysis, and simulation system and enabling its operation on a variety of system configurations. Uses of this portability range from whole cluster replication to teaching and experimentation on a single laptop. System virtualization is used to practically define and make portable the full application stack, including all of its complex set of supporting software and allows Lifemapper deployment in a variety of environments.
Transparent environments and social-coding platforms asGitHub help developers to stay abreast of changes during the development and maintenance phase of a project. Especially, notification feeds can help developers to learn about relevant changes in other projects. Unfortunately, transparent environments can quickly overwhelm developers with too many notifications, such that they lose the important ones in a sea of noise. Complementing existing prioritization and filtering strategies based on binary compatibility and code ownership, we develop an anomaly detection mechanism to identify unusual commits in a repository, which stand out with respect to other changes in the same repository or by the same developer. Among others, we detect exceptionally large commits, commits at unusual times, and commits touching rarely changed file types given the characteristics of a particular repository or developer. We automatically flag unusual commits on GitHub through a browser plug-in. In an interactive survey with 173 active GitHub users, rating commits in a project of their interest, we found that, although our unusual score is only a weak predictor of whether developers want to be notified about a commit, information about unusual characteristics of a commit changes how developers regard commits. Our anomaly detection mechanism is a building block for scaling transparent environments.more » « less