Industry-scale application and evaluation of deep learning for drug target prediction

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.Web of Science121art. no. 2

Doctor of Philosophy

dissertationEmerging trends such as growing architectural diversity and increased emphasis on energy and power efficiency motivate the need for code that adapts to its execution context (input dataset and target architecture). Unfortunately, writing such code remains difficult, and is typically attempted only by a small group of motivated expert programmers who are highly knowledgeable about the relationship between software and its hardware mapping. In this dissertation, we introduce novel abstractions and techniques based on automatic performance tuning that enable both experts and nonexperts (application developers) to produce adaptive code. We present two new frameworks for adaptive programming: Nitro and Surge. Nitro enables expert programmers to specify code variants, or alternative implementations of the same computation, together with meta-information for selecting among them. It then utilizes supervised classification to select an optimal code variant at runtime based on characteristics of the execution context. Surge, on the other hand, provides a high-level nested data-parallel programming interface for application developers to specify computations. It then employs a two-level mechanism to automatically generate code variants and then tunes them using Nitro. The resulting code performs on par with or better than handcrafted reference implementations on both CPUs and GPUs. In addition to abstractions for expressing code variants, this dissertation also presents novel strategies for adaptively tuning them. First, we introduce a technique for dynamically selecting an optimal code variant at runtime based on characteristics of the input dataset. On five high-performance GPU applications, variants tuned using this strategy achieve over 93% of the performance of variants selected through exhaustive search. Next, we present a novel approach based on multitask learning to develop a code variant selection model on a target architecture from training on different source architectures. We evaluate this approach on a set of six benchmark applications and a collection of six NVIDIA GPUs from three distinct architecture generations. Finally, we implement support for combined code variant and frequency selection based on multiple objectives, including power and energy efficiency. Using this strategy, we construct a GPU sorting implementation that provides improved energy and power efficiency with less than a proportional drop in sorting throughput

Efficient Image Gallery Representations at Scale Through Multi-Task Learning

Image galleries provide a rich source of diverse information about a product which can be leveraged across many recommendation and retrieval applications. We study the problem of building a universal image gallery encoder through multi-task learning (MTL) approach and demonstrate that it is indeed a practical way to achieve generalizability of learned representations to new downstream tasks. Additionally, we analyze the relative predictive performance of MTL-trained solutions against optimal and substantially more expensive solutions, and find signals that MTL can be a useful mechanism to address sparsity in low-resource binary tasks.Comment: Proceedings of the 43rd International ACM SIGIR Conference on Research and Development in Information Retrieva

Evolutionary neural architecture search for deep learning

Deep neural networks (DNNs) have produced state-of-the-art results in many benchmarks and problem domains. However, the success of DNNs depends on the proper configuration of its architecture and hyperparameters. DNNs are often not used to their full potential because it is difficult to determine what architectures and hyperparameters should be used. While several approaches have been proposed, computational complexity of searching large design spaces makes them impractical for large modern DNNs. This dissertation introduces an efficient evolutionary algorithm (EA) for simultaneous optimization of DNN architecture and hyperparameters. It builds upon extensive past research of evolutionary optimization of neural network structure. Various improvements to the core algorithm are introduced, including: (1) discovering DNN architectures of arbitrary complexity; (1) generating modular, repetitive modules commonly seen in state-of-the-art DNNs; (3) extending to the multitask learning and multiobjective optimization domains; (4) maximizing performance and reducing wasted computation through asynchronous evaluations. Experimental results in image classification, image captioning, and multialphabet character recognition show that the approach is able to evolve networks that are competitive with or even exceed hand-designed networks. Thus, the method enables an automated and streamlined process to optimize DNN architectures for a given problem and can be widely applied to solve harder tasks.Computer Science

Multi-Path Region-Based Convolutional Neural Network for Accurate Detection of Unconstrained "Hard Faces"

Large-scale variations still pose a challenge in unconstrained face detection. To the best of our knowledge, no current face detection algorithm can detect a face as large as 800 x 800 pixels while simultaneously detecting another one as small as 8 x 8 pixels within a single image with equally high accuracy. We propose a two-stage cascaded face detection framework, Multi-Path Region-based Convolutional Neural Network (MP-RCNN), that seamlessly combines a deep neural network with a classic learning strategy, to tackle this challenge. The first stage is a Multi-Path Region Proposal Network (MP-RPN) that proposes faces at three different scales. It simultaneously utilizes three parallel outputs of the convolutional feature maps to predict multi-scale candidate face regions. The "atrous" convolution trick (convolution with up-sampled filters) and a newly proposed sampling layer for "hard" examples are embedded in MP-RPN to further boost its performance. The second stage is a Boosted Forests classifier, which utilizes deep facial features pooled from inside the candidate face regions as well as deep contextual features pooled from a larger region surrounding the candidate face regions. This step is included to further remove hard negative samples. Experiments show that this approach achieves state-of-the-art face detection performance on the WIDER FACE dataset "hard" partition, outperforming the former best result by 9.6% for the Average Precision.Comment: 11 pages, 7 figures, to be presented at CRV 201

On Multilingual Training of Neural Dependency Parsers

We show that a recently proposed neural dependency parser can be improved by joint training on multiple languages from the same family. The parser is implemented as a deep neural network whose only input is orthographic representations of words. In order to successfully parse, the network has to discover how linguistically relevant concepts can be inferred from word spellings. We analyze the representations of characters and words that are learned by the network to establish which properties of languages were accounted for. In particular we show that the parser has approximately learned to associate Latin characters with their Cyrillic counterparts and that it can group Polish and Russian words that have a similar grammatical function. Finally, we evaluate the parser on selected languages from the Universal Dependencies dataset and show that it is competitive with other recently proposed state-of-the art methods, while having a simple structure.Comment: preprint accepted into the TSD201