Artificial intelligence (AI) is undergoing a revolution thanks to the breakthroughs of machine learning algorithms in computer vision, speech recognition, natural language processing and generative modelling. Recent works on publicly available pharmaceutical data showed that AI methods are highly promising for Drug Target prediction. However, the quality of public data might be different than that of industry data due to different labs reporting measurements, different measurement techniques, fewer samples and less diverse and specialized assays. As part of a European funded project (ExCAPE), that brought together expertise from pharmaceutical industry, machine learning, and high-performance computing, we investigated how well machine learning models obtained from public data can be transferred to internal pharmaceutical industry data. Our results show that machine learning models trained on public data can indeed maintain their predictive power to a large degree when applied to industry data. Moreover, we observed that deep learning derived machine learning models outperformed comparable models, which were trained by other machine learning algorithms, when applied to internal pharmaceutical company datasets. To our knowledge, this is the first large-scale study evaluating the potential of machine learning and especially deep learning directly at the level of industry-scale settings and moreover investigating the transferability of publicly learned target prediction models towards industrial bioactivity prediction pipelines.
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High-Performance Big Data Analytics (HPDA) applications are characterized by huge volumes of distributed and heterogeneous data that require efficient computation for knowledge extraction and decision making. Designers are moving towards a tight integration of computing systems combining HPC, Cloud, and IoT solutions with artificial intelligence (AI). Matching the application and data requirements with the characteristics of the underlying hardware is a key element to improve the predictions thanks to high performance and better use of resources.We present EVEREST, a novel H2020 project started on October 1st, 2020 that aims at developing a holistic environment for the co-design of HPDA applications on heterogeneous, distributed, and secure platforms. EVEREST focuses on programmability issues through a data-driven design approach, the use of hardwareaccelerated AI, and an efficient runtime monitoring with virtualization support. In the different stages, EVEREST combines state-of-the-art programming models, emerging communication standards, and novel domain-specific extensions. We describe the EVEREST approach and the use cases that drive our research.
Real-world scienti c applications often encompass end-to-end data processing pipelines composed of a large number of interconnected computational tasks of various granularity. We introduce Hyper-Loom, an open source platform for de ning and executing such pipelines in distributed environments and providing a Python interface for de ning tasks. HyperLoom is a self-contained system that does not use an external scheduler for the actual execution of the task. We have successfully employed HyperLoom for executing chemogenomics pipelines used in pharmaceutic industry for novel drug discovery.
We have developed HyperLoom-a platform for defining and executing scientific workflows in large-scale HPC systems. The computational tasks in such workflows often have non-trivial dependency patterns, unknown execution time and unknown sizes of generated outputs. HyperLoom enables to efficiently execute the workflows respecting task requirements and cluster resources agnostically to the shape or size of the workflow. Although HPC infrastructures provide an unbeatable performance, they may be unavailable or too expensive especially for small to medium workloads. Moreover, for some workloads, due to HPCs not very flexible resource allocation policy, the system energy efficiency may not be optimal at some stages of the execution. In contrast, current public cloud providers such as Amazon, Google or Exoscale allow users a comfortable and elastic way of deploying, scaling and disposing a virtualized cluster of almost any size. In this paper, we describe HyperLoom virtualization and evaluate its performance in a virtualized environment using workflows of various shapes and sizes. Finally, we discuss the Hyperloom potential for its expansion to cloud environments.
Task graphs provide a simple way to describe scientific workflows (sets of tasks with dependencies) that can be executed on both HPC clusters and in the cloud. An important aspect of executing such graphs is the used scheduling algorithm. Many scheduling heuristics have been proposed in existing works; nevertheless, they are often tested in oversimplified environments. We provide an extensible simulation environment designed for prototyping and benchmarking task schedulers, which contains implementations of various scheduling algorithms and is open-sourced, in order to be fully reproducible. We use this environment to perform a comprehensive analysis of workflow scheduling algorithms with a focus on quantifying the effect of scheduling challenges that have so far been mostly neglected, such as delays between scheduler invocations or partially unknown task durations. Our results indicate that network models used by many previous works might produce results that are off by an order of magnitude in comparison to a more realistic model. Additionally, we show that certain implementation details of scheduling algorithms which are often neglected can have a large effect on the scheduler’s performance, and they should thus be described in great detail to enable proper evaluation.
The quality of an opt imal solut ion of the Vehicle Rout ing Problem is st rongly depended on the sett ing of the configurat ion parameters of the algorithm. The paper is focused on the int roduct ion of hyperparameter search for solving the Vehicle Rout ing Problem using a HyperLoom plat form for defining and execut ing scient ific pipelines in a dist ributed environment . To give a concrete example, we focused on Periodic Vehicle Rout ing Problem for the waste collect ion. HyperLoom plat form was used to define and execute the hyperparameters sweep pipeline. The heurist ic algorithm was tested on a real benchmark of the waste collect ion in Ostrava, Czech Republic. The aim of our ca se was to effect ively combine the minimizat ion of the total t ravelled distance and the opt imizat ion of the fairness of the routes in terms of the standard deviat ion of a tour length. The waste collect ion problem was very extensive and computat ionally demanding, so it was necessary to use high performance comput ing architecture for test ing a large number of different sett ings of configurat ion parameters. The experiments were run on the supercomputer Salomon operated by IT4Innovations Nat ional Supercomput ing Center in the Czech Republic.
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