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Register a new userIntroducing ReQuEST: an Open Platform for Reproducible and Quality-Efficient Systems-ML Tournaments
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Co-designing efficient machine learning based systems across the whole hardware/software stack to trade off speed, accuracy, energy and costs is becoming extremely complex and time consuming. Researchers often struggle to evaluate and compare different published works across rapidly evolving software frameworks, heterogeneous hardware platforms, compilers, libraries, algorithms, data sets, models, and environments. We present our community effort to develop an open co-design tournament platform with an online public scoreboard. It will gradually incorporate best research practices while providing a common way for multidisciplinary researchers to optimize and compare the quality vs. efficiency Pareto optimality of various workloads on diverse and complete hardware/software systems. We want to leverage the open-source Collective Knowledge framework and the ACM artifact evaluation methodology to validate and share the complete machine learning system implementations in a standardized, portable, and reproducible fashion. We plan to hold regular multi-objective optimization and co-design tournaments for emerging workloads such as deep learning, starting with ASPLOS18 (ACM conference on Architectural Support for Programming Languages and Operating Systems - the premier forum for multidisciplinary systems research spanning computer architecture and hardware, programming languages and compilers, operating systems and networking) to build a public repository of the most efficient machine learning algorithms and systems which can be easily customized, reused and built upon.
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We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii) perform reproducible evaluations of their methods, and iii) easily share data and results within their institution and with external collaborators. The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI and PET data), as well as tools for statistics, machine learning and deep learning. It relies on the brain imaging data structure (BIDS) for the organization of raw neuroimaging datasets and on established tools written by the community to build its pipelines. It also provides converters of public neuroimaging datasets to BIDS (currently ADNI, AIBL, OASIS and NIFD). Processed data include image-valued scalar fields (e.g. tissue probability maps), meshes, surface-based scalar fields (e.g. cortical thickness maps) or scalar outputs (e.g. regional averages). These data follow the ClinicA Processed Structure (CAPS) format which shares the same philosophy as BIDS. Consistent organization of raw and processed neuroimaging files facilitates the execution of single pipelines and of sequences of pipelines, as well as the integration of processed data into statistics or machine learning frameworks. The target audience of Clinica is neuroscientists or clinicians conducting clinical neuroscience studies involving multimodal imaging, and researchers developing advanced machine learning algorithms applied to neuroimaging data.
We introduce a recent symplectic integration scheme derived for solving physically motivated systems with non-separable Hamiltonians. We show its relevance to Riemannian manifold Hamiltonian Monte Carlo (RMHMC) and provide an alternative to the currently used generalised leapfrog symplectic integrator, which relies on solving multiple fixed point iterations to convergence. Via this approach, we are able to reduce the number of higher-order derivative calculations per leapfrog step. We explore the implications of this integrator and demonstrate its efficacy in reducing the computational burden of RMHMC. Our code is provided in a new open-source Python package, hamiltorch.
Data analysis in fundamental sciences nowadays is an essential process that pushes frontiers of our knowledge and leads to new discoveries. At the same time we can see that complexity of those analyses increases fast due to a)~enormous volumes of datasets being analyzed, b)~variety of techniques and algorithms one have to check inside a single analysis, c)~distributed nature of research teams that requires special communication media for knowledge and information exchange between individual researchers. There is a lot of resemblance between techniques and problems arising in the areas of industrial information retrieval and particle physics. To address those problems we propose Reproducible Experiment Platform (REP), a software infrastructure to support collaborative ecosystem for computational science. It is a Python based solution for research teams that allows running computational experiments on shared datasets, obtaining repeatable results, and consistent comparisons of the obtained results. We present some key features of REP based on case studies which include trigger optimization and physics analysis studies at the LHCb experiment.
In many academic settings, medical students start their scientific work already during their studies. Like at our institution, they often work in interdisciplinary teams with more or less experienced (postgraduate) researchers of pharmaceutical sciences, natural sciences in general, or biostatistics. All of them should be taught good research practices as an integral part of their education, especially in terms of statistical analysis. This includes reproducibility as a central aspect of modern research. Acknowledging that even educators might be unfamiliar with necessary aspects of a perfectly reproducible workflow, I agreed to give a lecture series on reproducible research (RR) for medical students and postgraduate pharmacists involved in several areas of clinical research. Thus, I designed a piloting lecture series to highlight definitions of RR, reasons for RR, potential merits of RR, and ways to work accordingly. In trying to actually reproduce a published analysis, I encountered several practical obstacles. In this article, I focus on this working example to emphasize the manifold facets of RR, to provide possible explanations and solutions, and argue that harmonized curricula for (quantitative) clinical researchers should include RR principles. I therefore hope these experiences are helpful to raise awareness among educators and students. RR working habits are not only beneficial for ourselves or our students, but also for other researchers within an institution, for scientific partners, for the scientific community, and eventually for the public profiting from research findings.
MLModelCI provides multimedia researchers and developers with a one-stop platform for efficient machine learning (ML) services. The system leverages DevOps techniques to optimize, test, and manage models. It also containerizes and deploys these optimized and validated models as cloud services (MLaaS). In its essence, MLModelCI serves as a housekeeper to help users publish models. The models are first automatically converted to optimized formats for production purpose and then profiled under different settings (e.g., batch size and hardware). The profiling information can be used as guidelines for balancing the trade-off between performance and cost of MLaaS. Finally, the system dockerizes the models for ease of deployment to cloud environments. A key feature of MLModelCI is the implementation of a controller, which allows elastic evaluation which only utilizes idle workers while maintaining online service quality. Our system bridges the gap between current ML training and serving systems and thus free developers from manual and tedious work often associated with service deployment. We release the platform as an open-source project on GitHub under Apache 2.0 license, with the aim that it will facilitate and streamline more large-scale ML applications and research projects.
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