Co-regularised support vector regression

We consider a semi-supervised learning scenario for regression, where only few labelled examples, many unlabelled instances and different data representations (multiple views) are available. For this setting, we extend support vector regression with a co-regularisation term and obtain co-regularised support vector regression (CoSVR). In addition to labelled data, co-regularisation includes information from unlabelled examples by ensuring that models trained on different views make similar predictions. Ligand affinity prediction is an important real-world problem that fits into this scenario. The characterisation of the strength of protein-ligand bonds is a crucial step in the process of drug discovery and design. We introduce variants of the base CoSVR algorithm and discuss their theoretical and computational properties. For the CoSVR function class we provide a theoretical bound on the Rademacher complexity. Finally, we demonstrate the usefulness of CoSVR for the affinity prediction task and evaluate its performance empirically on different protein-ligand datasets. We show that CoSVR outperforms co-regularised least squares regression as well as existing state-of-the-art approaches for affinity prediction

Black-Box Parallelization for Machine Learning

The landscape of machine learning applications is changing rapidly: large centralized datasets are replaced by high volume, high velocity data streams generated by a vast number of geographically distributed, loosely connected devices, such as mobile phones, smart sensors, autonomous vehicles or industrial machines. Current learning approaches centralize the data and process it in parallel in a cluster or computing center. This has three major disadvantages: (i) it does not scale well with the number of data-generating devices since their growth exceeds that of computing centers, (ii) the communication costs for centralizing the data are prohibitive in many applications, and (iii) it requires sharing potentially privacy-sensitive data. Pushing computation towards the data-generating devices alleviates these problems and allows to employ their otherwise unused computing power. However, current parallel learning approaches are designed for tightly integrated systems with low latency and high bandwidth, not for loosely connected distributed devices. Therefore, I propose a new paradigm for parallelization that treats the learning algorithm as a black box, training local models on distributed devices and aggregating them into a single strong one. Since this requires only exchanging models instead of actual data, the approach is highly scalable, communication-efficient, and privacy-preserving. Following this paradigm, this thesis develops black-box parallelizations for two broad classes of learning algorithms. One approach can be applied to incremental learning algorithms, i.e., those that improve a model in iterations. Based on the utility of aggregations it schedules communication dynamically, adapting it to the hardness of the learning problem. In practice, this leads to a reduction in communication by orders of magnitude. It is analyzed for (i) online learning, in particular in the context of in-stream learning, which allows to guarantee optimal regret and for (ii) batch learning based on empirical risk minimization where optimal convergence can be guaranteed. The other approach is applicable to non-incremental algorithms as well. It uses a novel aggregation method based on the Radon point that allows to achieve provably high model quality with only a single aggregation. This is achieved in polylogarithmic runtime on quasi-polynomially many processors. This relates parallel machine learning to Nick's class of parallel decision problems and is a step towards answering a fundamental open problem about the abilities and limitations of efficient parallel learning algorithms. An empirical study on real distributed systems confirms the potential of the approaches in realistic application scenarios

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested

Co-regularised support vector regression

We consider a semi-supervised learning scenario for regression, where only few labelled examples, many unlabelled instances and different data representations (multiple views) are available. For this setting, we extend support vector regression with a co-regularisation term and obtain co-regularised support vector regression (CoSVR). In addition to labelled data, co-regularisation includes information from unlabelled examples by ensuring that models trained on different views make similar predictions. Ligand affinity prediction is an important real-world problem that fits into this scenario. The characterisation of the strength of protein-ligand bonds is a crucial step in the process of drug discovery and design. We introduce variants of the base CoSVR algorithm and discuss their theoretical and computational properties. For the CoSVR function class we provide a theoretical bound on the Rademacher complexity. Finally, we demonstrate the usefulness of CoSVR for the affinity prediction task and evaluate its performance empirically on different protein-ligand datasets. We show that CoSVR outperforms co-regularised least squares regression as well as existing state-of-the-art approaches for affinity prediction

Ligand-based virtual screening with co-regularised support vector regression

We consider the problem of ligand affinity prediction as a regression task, typically with few labelled examples, many unlabelled instances, and multiple views on the data. In chemoinformatics, the prediction of binding affinities for protein ligands is an important but also challenging task. As protein-ligand bonds trigger biochemical reactions, their characterisation is a crucial step in the process of drug discovery and design. However, the practical determination of ligand affinities is very expensive, whereas unlabelled compounds are available in abundance. Additionally, many different vectorial representations for compounds (molecular fingerprints) exist that cover different sets of features. To this task we propose to apply a co-regularisation approach, which extracts information from unlabelled examples by ensuring that individual models trained on different fingerprints make similar predictions. We extend support vector regression similarly to the existing co-regularised least squares regression (CoRLSR) and obtain a co-regularised support vector regression (CoSVR). We empirically evaluate the performance of CoSVR on various protein-ligand datasets. We show that CoSVR outperforms CoRLSR as well as existing state-of-the- art approaches that do not take unlabelled molecules into account. Additionally, we provide a theoretical bound on the Rademacher complexity for CoSVR