Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers

<p>Abstract</p> <p>Background</p> <p>Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs.</p> <p>Results</p> <p>We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies.</p> <p>Conclusions</p> <p>Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy.</p

Data-driven Soft Sensors in the Process Industry

In the last two decades Soft Sensors established themselves as a valuable alternative to the traditional means for the acquisition of critical process variables, process monitoring and other tasks which are related to process control. This paper discusses characteristics of the process industry data which are critical for the development of data-driven Soft Sensors. These characteristics are common to a large number of process industry fields, like the chemical industry, bioprocess industry, steel industry, etc. The focus of this work is put on the data-driven Soft Sensors because of their growing popularity, already demonstrated usefulness and huge, though yet not completely realised, potential. A comprehensive selection of case studies covering the three most important Soft Sensor application fields, a general introduction to the most popular Soft Sensor modelling techniques as well as a discussion of some open issues in the Soft Sensor development and maintenance and their possible solutions are the main contributions of this work

Evolving interval-based representation for multiple classifier fusion.

Designing an ensemble of classifiers is one of the popular research topics in machine learning since it can give better results than using each constituent member. Furthermore, the performance of ensemble can be improved using selection or adaptation. In the former, the optimal set of base classifiers, meta-classifier, original features, or meta-data is selected to obtain a better ensemble than using the entire classifiers and features. In the latter, the base classifiers or combining algorithms working on the outputs of the base classifiers are made to adapt to a particular problem. The adaptation here means that the parameters of these algorithms are trained to be optimal for each problem. In this study, we propose a novel evolving combining algorithm using the adaptation approach for the ensemble systems. Instead of using numerical value when computing the representation for each class, we propose to use the interval-based representation for the class. The optimal value of the representation is found through Particle Swarm Optimization. During classification, a test instance is assigned to the class with the interval-based representation that is closest to the base classifiers’ prediction. Experiments conducted on a number of popular dataset confirmed that the proposed method is better than the well-known ensemble systems using Decision Template and Sum Rule as combiner, L2-loss Linear Support Vector Machine, Multiple Layer Neural Network, and the ensemble selection methods based on GA-Meta-data, META-DES, and ACO

Automated Adaptation Strategies for Stream Learning

Automation of machine learning model development is increasingly becoming an established research area. While automated model selection and automated data pre-processing have been studied in depth, there is, however, a gap concerning automated model adaptation strategies when multiple strategies are available. Manually developing an adaptation strategy can be time consuming and costly. In this paper we address this issue by proposing the use of flexible adaptive mechanism deployment for automated development of adaptation strategies. Experimental results after using the proposed strategies with five adaptive algorithms on 36 datasets confirm their viability. These strategies achieve better or comparable performance to the custom adaptation strategies and the repeated deployment of any single adaptive mechanism

A Review of Meta-level Learning in the Context of Multi-component, Multi-level Evolving Prediction Systems.

The exponential growth of volume, variety and velocity of data is raising the need for investigations of automated or semi-automated ways to extract useful patterns from the data. It requires deep expert knowledge and extensive computational resources to find the most appropriate mapping of learning methods for a given problem. It becomes a challenge in the presence of numerous configurations of learning algorithms on massive amounts of data. So there is a need for an intelligent recommendation engine that can advise what is the best learning algorithm for a dataset. The techniques that are commonly used by experts are based on a trial and error approach evaluating and comparing a number of possible solutions against each other, using their prior experience on a specific domain, etc. The trial and error approach combined with the expert’s prior knowledge, though computationally and time expensive, have been often shown to work for stationary problems where the processing is usually performed off-line. However, this approach would not normally be feasible to apply on non-stationary problems where streams of data are continuously arriving. Furthermore, in a non-stationary environment the manual analysis of data and testing of various methods every time when there is a change in the underlying data distribution would be very difficult or simply infeasible. In that scenario and within an on-line predictive system, there are several tasks where Meta-learning can be used to effectively facilitate best recommendations including: 1) pre processing steps, 2) learning algorithms or their combination, 3) adaptivity mechanisms and their parameters, 4) recurring concept extraction, and 5) concept drift detection. However, while conceptually very attractive and promising, the Meta-learning leads to several challenges with the appropriate representation of the problem at a meta-level being one of the key ones. The goal of this review and our research is, therefore, to investigate Meta learning in general and the associated challenges in the context of automating the building, deployment and adaptation of multi-level and multi-component predictive system that evolve over time

A survey of multiple classifier systems as hybrid systems

A current focus of intense research in pattern classification is the combination of several classifier systems, which can be built following either the same or different models and/or datasets building approaches. These systems perform information fusion of classification decisions at different levels overcoming limitations of traditional approaches based on single classifiers. This paper presents an up-to-date survey on multiple classifier system (MCS) from the point of view of Hybrid Intelligent Systems. The article discusses major issues, such as diversity and decision fusion methods, providing a vision of the spectrum of applications that are currently being developed

Building well-performing classifier ensembles: model and decision level combination.

There is a continuing drive for better, more robust generalisation performance from classification systems, and prediction systems in general. Ensemble methods, or the combining of multiple classifiers, have become an accepted and successful tool for doing this, though the reasons for success are not always entirely understood. In this thesis, we review the multiple classifier literature and consider the properties an ensemble of classifiers - or collection of subsets - should have in order to be combined successfully. We find that the framework of Stochastic Discrimination provides a well-defined account of these properties, which are shown to be strongly encouraged in a number of the most popular/successful methods in the literature via differing algorithmic devices. This uncovers some interesting and basic links between these methods, and aids understanding of their success and operation in terms of a kernel induced on the training data, with form particularly well suited to classification. One property that is desirable in both the SD framework and in a regression context, the ambiguity decomposition of the error, is de-correlation of individuals. This motivates the introduction of the Negative Correlation Learning method, in which neural networks are trained in parallel in a way designed to encourage de-correlation of the individual networks. The training is controlled by a parameter λ governing the extent to which correlations are penalised. Theoretical analysis of the dynamics of training results in an exact expression for the interval in which we can choose λ while ensuring stability of the training, and a value λ∗ for which the training has some interesting optimality properties. These values depend only on the size N of the ensemble. Decision level combination methods often result in a difficult to interpret model, and NCL is no exception. However in some applications, there is a need for understandable decisions and interpretable models. In response to this, we depart from the standard decision level combination paradigm to introduce a number of model level combination methods. As decision trees are one of the most interpretable model structures used in classification, we chose to combine structure from multiple individual trees to build a single combined model. We show that extremely compact, well performing models can be built in this way. In particular, a generalisation of bottom-up pruning to a multiple-tree context produces good results in this regard. Finally, we develop a classification system for a real-world churn prediction problem, illustrating some of the concepts introduced in the thesis, and a number of more practical considerations which are of importance when developing a prediction system for a specific problem

On robust and adaptive soft sensors.

In process industries, there is a great demand for additional process information such as the product quality level or the exact process state estimation. At the same time, there is a large amount of process data like temperatures, pressures, etc. measured and stored every moment. This data is mainly measured for process control and monitoring purposes but its potential reaches far beyond these applications. The task of soft sensors is the maximal exploitation of this potential by extracting and transforming the latent information from the data into more useful process knowledge. Theoretically, achieving this goal should be straightforward since the process data as well as the tools for soft sensor development in the form of computational learning methods, are both readily available. However, contrary to this evidence, there are still several obstacles which prevent soft sensors from broader application in the process industry. The identification of the sources of these obstacles and proposing a concept for dealing with them is the general purpose of this work. The proposed solution addressing the issues of current soft sensors is a conceptual architecture for the development of robust and adaptive soft sensing algorithms. The architecture reflects the results of two review studies that were conducted during this project. The first one focuses on the process industry aspects of soft sensor development and application. The main conclusions of this study are that soft sensor development is currently being done in a non-systematic, ad-hoc way which results in a large amount of manual work needed for their development and maintenance. It is also found that a large part of the issues can be related to the process data upon which the soft sensors are built. The second review study dealt with the same topic but this time it was biased towards the machine learning viewpoint. The review focused on the identification of machine learning tools, which support the goals of this work. The machine learning concepts which are considered are: (i) general regression techniques for building of soft sensors; (ii) ensemble methods; (iii) local learning; (iv) meta-learning; and (v) concept drift detection and handling. The proposed architecture arranges the above techniques into a three-level hierarchy, where the actual prediction-making models operate at the bottom level. Their predictions are flexibly merged by applying ensemble methods at the next higher level. Finally from the top level, the underlying algorithm is managed by means of metalearning methods. The architecture has a modular structure that allows new pre-processing, predictive or adaptation methods to be plugged in. Another important property of the architecture is that each of the levels can be equipped with adaptation mechanisms, which aim at prolonging the lifetime of the resulting soft sensors. The relevance of the architecture is demonstrated by means of a complex soft sensing algorithm, which can be seen as its instance. This algorithm provides mechanisms for autonomous selection of data preprocessing and predictive methods and their parameters. It also includes five different adaptation mechanisms, some of which can be applied on a sample-by-sample basis without any requirement to store the on-line data. Other, more complex ones are started only on-demand if the performance of the soft sensor drops below a defined level. The actual soft sensors are built by applying the soft sensing algorithm to three industrial data sets. The different application scenarios aim at the analysis of the fulfilment of the defined goals. It is shown that the soft sensors are able to follow changes in dynamic environment and keep a stable performance level by exploiting the implemented adaptation mechanisms. It is also demonstrated that, although the algorithm is rather complex, it can be applied to develop simple and transparent soft sensors. In another experiment, the soft sensors are built without any manual model selection or parameter tuning, which demonstrates the ability of the algorithm to reduce the effort required for soft sensor development. However, if desirable, the algorithm is at the same time very flexible and provides a number of parameters that can be manually optimised. Evidence of the ability of the algorithm to deploy soft sensors with minimal training data and as such to provide the possibility to save the time consuming and costly training data collection is also given in this work

Multimedia Decision Fusion

Ph.DDOCTOR OF PHILOSOPH

Multiple adaptive mechanisms for predictive models on streaming data.

Making predictions on non-stationary streaming data remains a challenge in many application areas. Changes in data may cause a decrease in predictive accuracy, which in a streaming setting require a prompt response. In recent years many adaptive predictive models have been proposed for dealing with these issues. Most of these methods use more than one adaptive mechanism, deploying all of them at the same time at regular intervals or in some other fixed manner. However, this manner is often determined in an ad-hoc way, as the effects of adaptive mechanisms are largely unexplored. This thesis therefore investigates different aspects of adaptation with multiple adaptive mechanisms with the aim to increase knowledge in the area, and propose heuristic approaches for more accurate adaptive predictive models. This is done by systematising and formalising the “adaptive mechanism” notion, proposing a categorisation of adaptive mechanisms and a metric to measure their usefulness, comparing the results after deployment of different orders of adaptive mechanisms during the run of the predictive method, and suggesting techniques on how to select the most appropriate adaptive mechanisms. The literature review suggests that during the prediction process, adaptive mechanisms are selected to be deployed in a certain order which is usually fixed beforehand at the design time of the algorithm. For this reason, it was investigated whether changing the selection method for the adaptive mechanisms significantly affects predictive accuracy and whether there are certain deployment orders which provide better results than others. Commonly used adaptive mechanism selection methods are then examined and new methods are proposed. A novel regression ensemble method which uses several common adaptive mechanisms has been developed to be used as a vehicle for the experimentation. The predictive accuracy and behaviour of adaptive mechanisms while predicting on different real world datasets from the process industry were analysed. Empirical results suggest that different selection of adaptive mechanisms result in significantly different performance. It has been found that while some adaptive mechanisms adapt the predictive model better than others, there is none which is the best at all times. Finally, flexible orders of adaptive mechanisms generated using the proposed selection techniques often result in significantly more accurate models than fixed orders commonly used in literature