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

Sparse Signal Processing Concepts for Efficient 5G System Design

As it becomes increasingly apparent that 4G will not be able to meet the emerging demands of future mobile communication systems, the question what could make up a 5G system, what are the crucial challenges and what are the key drivers is part of intensive, ongoing discussions. Partly due to the advent of compressive sensing, methods that can optimally exploit sparsity in signals have received tremendous attention in recent years. In this paper we will describe a variety of scenarios in which signal sparsity arises naturally in 5G wireless systems. Signal sparsity and the associated rich collection of tools and algorithms will thus be a viable source for innovation in 5G wireless system design. We will discribe applications of this sparse signal processing paradigm in MIMO random access, cloud radio access networks, compressive channel-source network coding, and embedded security. We will also emphasize important open problem that may arise in 5G system design, for which sparsity will potentially play a key role in their solution.Comment: 18 pages, 5 figures, accepted for publication in IEEE Acces

A Double Error Dynamic Asymptote Model of Associative Learning

In this paper a formal model of associative learning is presented which incorporates representational and computational mechanisms that, as a coherent corpus, empower it to make accurate predictions of a wide variety of phenomena that so far have eluded a unified account in learning theory. In particular, the Double Error Dynamic Asymptote (DDA) model introduces: 1) a fully-connected network architecture in which stimuli are represented as temporally clustered elements that associate to each other, so that elements of one cluster engender activity on other clusters, which naturally implements neutral stimuli associations and mediated learning; 2) a predictor error term within the traditional error correction rule (the double error), which reduces the rate of learning for expected predictors; 3) a revaluation associability rate that operates on the assumption that the outcome predictiveness is tracked over time so that prolonged uncertainty is learned, reducing the levels of attention to initially surprising outcomes; and critically 4) a biologically plausible variable asymptote, which encapsulates the principle of Hebbian learning, leading to stronger associations for similar levels of cluster activity. The outputs of a set of simulations of the DDA model are presented along with empirical results from the literature. Finally, the predictive scope of the model is discussed

Centralized prevention of denial of service attacks

The world has come to depend on the Internet at an increasing rate for communication, e-commerce, and many other essential services. As such, the Internet has become an integral part of the workings of society at large. This has lead to an increased vulnerability to remotely controlled disruption of vital commercial and government operations---with obvious implications. This disruption can be caused by an attack on one or more specific networks which will deny service to legitimate users or an attack on the Internet itself by creating large amounts of spurious traffic (which will deny services to many or all networks). Individual organizations can take steps to protect themselves but this does not solve the problem of an Internet wide attack. This thesis focuses on an analysis of the different types of Denial of Service attacks and suggests an approach to prevent both categories by centralized detection and limitation of excessive packet flows

EchoFusion: Tracking and Reconstruction of Objects in 4D Freehand Ultrasound Imaging without External Trackers

Ultrasound (US) is the most widely used fetal imaging technique. However, US images have limited capture range, and suffer from view dependent artefacts such as acoustic shadows. Compounding of overlapping 3D US acquisitions into a high-resolution volume can extend the field of view and remove image artefacts, which is useful for retrospective analysis including population based studies. However, such volume reconstructions require information about relative transformations between probe positions from which the individual volumes were acquired. In prenatal US scans, the fetus can move independently from the mother, making external trackers such as electromagnetic or optical tracking unable to track the motion between probe position and the moving fetus. We provide a novel methodology for image-based tracking and volume reconstruction by combining recent advances in deep learning and simultaneous localisation and mapping (SLAM). Tracking semantics are established through the use of a Residual 3D U-Net and the output is fed to the SLAM algorithm. As a proof of concept, experiments are conducted on US volumes taken from a whole body fetal phantom, and from the heads of real fetuses. For the fetal head segmentation, we also introduce a novel weak annotation approach to minimise the required manual effort for ground truth annotation. We evaluate our method qualitatively, and quantitatively with respect to tissue discrimination accuracy and tracking robustness.Comment: MICCAI Workshop on Perinatal, Preterm and Paediatric Image analysis (PIPPI), 201

New acceleration technique for the backpropagation algorithm

Artificial neural networks have been studied for many years in the hope of achieving human like performance in the area of pattern recognition, speech synthesis and higher level of cognitive process. In the connectionist model there are several interconnected processing elements called the neurons that have limited processing capability. Even though the rate of information transmitted between these elements is limited, the complex interconnection and the cooperative interaction between these elements results in a vastly increased computing power; The neural network models are specified by an organized network topology of interconnected neurons. These networks have to be trained in order them to be used for a specific purpose. Backpropagation is one of the popular methods of training the neural networks. There has been a lot of improvement over the speed of convergence of standard backpropagation algorithm in the recent past. Herein we have presented a new technique for accelerating the existing backpropagation without modifying it. We have used the fourth order interpolation method for the dominant eigen values, by using these we change the slope of the activation function. And by doing so we increase the speed of convergence of the backpropagation algorithm; Our experiments have shown significant improvement in the convergence time for problems widely used in benchmarKing Three to ten fold decrease in convergence time is achieved. Convergence time decreases as the complexity of the problem increases. The technique adjusts the energy state of the system so as to escape from local minima

Self-stabilizing cluster routing in Manet using link-cluster architecture

We design a self-stabilizing cluster routing algorithm based on the link-cluster architecture of wireless ad hoc networks. The network is divided into clusters. Each cluster has a single special node, called a clusterhead that contains the routing information about inter and intra-cluster communication. A cluster is comprised of all nodes that choose the corresponding clusterhead as their leader. The algorithm consists of two main tasks. First, the set of special nodes (clusterheads) is elected such that it models the link-cluster architecture: any node belongs to a single cluster, it is within two hops of the clusterhead, it knows the direct neighbor on the shortest path towards the clusterhead, and there exist no two adjacent clusterheads. Second, the routing tables are maintained by the clusterheads to store information about nodes both within and outside the cluster. There are two advantages of maintaining routing tables only in the clusterheads. First, as no two neighboring nodes are clusterheads (as per the link-cluster architecture), there is no need to check the consistency of the routing tables. Second, since all other nodes have significantly less work (they only forward messages), they use much less power than the clusterheads. Therefore, if a clusterhead runs out of power, a neighboring node (that is not a clusterhead) can accept the role of a clusterhead. (Abstract shortened by UMI.)