Data mining for heart failure : an investigation into the challenges in real life clinical datasets

Clinical data presents a number of challenges including missing data, class imbalance, high dimensionality and non-normal distribution. A motivation for this research is to investigate and analyse the manner in which the challenges affect the performance of algorithms. The challenges were explored with the help of a real life heart failure clinical dataset known as Hull LifeLab, obtained from a live cardiology clinic at the Hull Royal Infirmary Hospital. A Clinical Data Mining Workflow (CDMW) was designed with three intuitive stages, namely, descriptive, predictive and prescriptive. The naming of these stages reflects the nature of the analysis that is possible within each stage; therefore a number of different algorithms are employed. Most algorithms require the data to be distributed in a normal manner. However, the distribution is not explicitly used within the algorithms. Approaches based on Bayes use the properties of the distributions very explicitly, and thus provides valuable insight into the nature of the data.The first stage of the analysis is to investigate if the assumptions made for Bayes hold, e.g. the strong independence assumption and the assumption of a Gaussian distribution. The next stage is to investigate the role of missing values. Results found that imputation does not affect the performance as much as those records which are initially complete. These records are often not outliers, but contain problem variables. A method was developed to identify these. The effect of skews in the data was also investigated within the CDMW. However, it was found that methods based on Bayes were able to handle these, albeit with a small variability in performance. The thesis provides an insight into the reasons why clinical data often causes problems. Even the issue of imbalanced classes is not an issue, for Bayes is independent of this

Scalable Text Mining with Sparse Generative Models

The information age has brought a deluge of data. Much of this is in text form, insurmountable in scope for humans and incomprehensible in structure for computers. Text mining is an expanding field of research that seeks to utilize the information contained in vast document collections. General data mining methods based on machine learning face challenges with the scale of text data, posing a need for scalable text mining methods. This thesis proposes a solution to scalable text mining: generative models combined with sparse computation. A unifying formalization for generative text models is defined, bringing together research traditions that have used formally equivalent models, but ignored parallel developments. This framework allows the use of methods developed in different processing tasks such as retrieval and classification, yielding effective solutions across different text mining tasks. Sparse computation using inverted indices is proposed for inference on probabilistic models. This reduces the computational complexity of the common text mining operations according to sparsity, yielding probabilistic models with the scalability of modern search engines. The proposed combination provides sparse generative models: a solution for text mining that is general, effective, and scalable. Extensive experimentation on text classification and ranked retrieval datasets are conducted, showing that the proposed solution matches or outperforms the leading task-specific methods in effectiveness, with a order of magnitude decrease in classification times for Wikipedia article categorization with a million classes. The developed methods were further applied in two 2014 Kaggle data mining prize competitions with over a hundred competing teams, earning first and second places