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Scalable Analysis of Large Datasets in Life Sciences

Time: Tue 2019-12-03 10.00

Location: Kollegiesalen, Brinellvägen 8, 114 28, Stockholm (English)

Subject area: Computer Science

Doctoral student: Laeeq Ahmed , Beräkningsvetenskap och beräkningsteknik (CST)

Opponent: Research Director Vincent Breton, French National Center for Scientific Research

Supervisor: Professor Erwin Laure, SeRC - Swedish e-Science Research Centre, Parallelldatorcentrum, PDC; Associate Professor Ola Spjuth, Pharmaceutical Bioinformatics, Uppsala University; Ake Edlund, Telia Company

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We are experiencing a deluge of data in all fields of scientific and business research, particularly in the life sciences, due to the development of better instrumentation and the rapid advancements that have occurred in information technology in recent times. There are major challenges when it comes to handling such large amounts of data. These range from the practicalities of managing these large volumes of data, to understanding the meaning and practical implications of the data.

In this thesis, I present parallel methods to efficiently manage, process, analyse and visualize large sets of data from several life sciences fields at a rapid rate, while building and utilizing various machine learning techniques in a novel way. Most of the work is centred on applying the latest Big Data Analytics frameworks for creating efficient virtual screening strategies while working with large datasets. Virtual screening is a method in cheminformatics used for Drug discovery by searching large libraries of molecule structures. I also present a method for the analysis of large Electroencephalography data in real time. Electroencephalography is one of the main techniques used to measure the brain electrical activity.

First, I evaluate the suitability of Spark, a parallel framework for large datasets, for performing parallel ligand-based virtual screening. As a case study, I classify molecular library using prebuilt classification models to filter out the active molecules. I also demonstrate a strategy to create cloud-ready pipelines for structure-based virtual screening. The major advantages of this strategy are increased productivity and high throughput. In this work, I show that Spark can be applied to virtual screening, and that it is, in general, an appropriate solution for large-scale parallel pipelining. Moreover, I illustrate how Big Data analytics are valuable in working with life sciences datasets.

Secondly, I present a method to further reduce the overall time of the structured-based virtual screening strategy using machine learning and a conformal-prediction-based iterative modelling strategy. The idea is to only dock those molecules that have a better than average chance of being an inhibitor when searching for molecules that could potentially be used as drugs. Using machine learning models from this work, I built a web service to predict the target profile of multiple compounds against ready-made models for a list of targets where 3D structures are available. These target predictions can be used to understand off-target effects, for example in the early stages of drug discovery projects.

Thirdly, I present a method to detect seizures in long term Electroencephalography readings - this method works in real time taking the ongoing readings in as live data streams. The method involves tackling the challenges of real-time decision-making, storing large datasets in memory and updating the prediction model with newly produced data at a rapid rate. The resulting algorithm not only classifies seizures in real time, it also learns the threshold in real time. I also present a new feature "top-k amplitude measure" for classifying which parts of the data correspond to seizures. Furthermore, this feature helps to reduce the amount of data that needs to be processed in the subsequent steps.