Pádraig Cunningham

Advances in Case-Based Reasoning

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Tracking the Evolution of Communities in Dynamic Social Networks

Real-world social networks from a variety of domains can naturally be modelled as dynamic graphs. However, approaches to detecting communities have largely focused on identifying communities in static graphs. Recently, researchers have begun to consider the problem of tracking the evolution of groups of users in dynamic scenarios. Here we describe a model for tracking the progress of communities over time in a dynamic network, where each community is characterised by a series of significant evolutionary events. This model is used to motivate a community-matching strategy for efficiently identifying and tracking dynamic communities. Evaluations on synthetic graphs containing embedded events demonstrate that this strategy can successfully track communities over time in volatile networks. In addition, we describe experiments exploring the dynamic communities detected in a real mobile operator network containing millions of users.

Diversity in search strategies for ensemble feature selection

Ensembles of learnt models constitute one of the main current directions in machine learning and data mining. Ensembles allow us to achieve higher accuracy, which is often not achievable with single models. It was shown theoretically and experimentally that in order for an ensemble to be effective, it should consist of base classifiers that have diversity in their predictions. One technique, which proved to be effective for constructing an ensemble of diverse base classifiers, is the use of different feature subsets, or so-called ensemble feature selection. Many ensemble feature selection strategies incorporate diversity as an objective in the search for the best collection of feature subsets. A number of ways are known to quantify diversity in ensembles of classifiers, and little research has been done about their appropriateness to ensemble feature selection. In this paper, we compare five measures of diversity with regard to their possible use in ensemble feature selection. We conduct experiments on 21 data sets from the UCI machine learning repository, comparing the ensemble accuracy and other characteristics for the ensembles built with ensemble feature selection based on the considered measures of diversity. We consider four search strategies for ensemble feature selection together with the simple random subspacing: genetic search, hill-climbing, and ensemble forward and backward sequential selection. In the experiments, we show that, in some cases, the ensemble feature selection process can be sensitive to the choice of the diversity measure, and that the question of the superiority of a particular measure depends on the context of the use of diversity and on the data being processed. In many cases and on average, the plain disagreement measure is the best. Genetic search, kappa, and dynamic voting with selection form the best combination of a search strategy, diversity measure and integration method.

A case-based technique for tracking concept drift in spam filtering

Spam filtering is a particularly challenging machine learning task as the data distribution and concept being learned changes over time. It exhibits a particularly awkward form of concept drift as the change is driven by spammers wishing to circumvent spam filters. In this paper we show that lazy learning techniques are appropriate for such dynamically changing contexts. We present a case-based system for spam filtering that can learn dynamically. We evaluate its performance as the case-base is updated with new cases. We also explore the benefit of periodically redoing the feature selection process to bring new features into play. Our evaluation shows that these two levels of model update are effective in tracking concept drift.

Diversity versus Quality in Classification Ensembles Based on Feature Selection

Feature subset-selection has emerged as a useful technique for creating diversity in ensembles - particularly in classification ensembles. In this paper we argue that this diversity needs to be monitored in the creation of the ensemble. We propose an entropy measure of the outputs of the ensemble members as a useful measure of the ensemble diversity. Further, we show that using the associated conditional entropy as a loss function (error measure) works well and the entropy in the ensemble predicts well the reduction in error due to the ensemble. These measures are evaluated on a medical prediction problem and are shown to predict the performance of the ensemble well. We also show that the entropy measure of diversity has the added advantage that it seems to model the change in diversity with the size of the ensemble.

Using diversity in preparing ensembles of classifiers based on different feature subsets to minimize generalization error

It is well known that ensembles of predictors produce better accuracy than a single predictor provided there is diversity in the ensemble. This diversity manifests itself as disagreement or ambiguity among the ensemble members. In this paper we focus on ensembles of classifiers based on different feature subsets and we present a process for producing such ensembles that emphasizes diversity (ambiguity) in the ensemble members. This emphasis on diversity produces ensembles with low generalization errors from ensemble members with comparatively high generalization error. We compare this with ensembles produced focusing only on the error of the ensemble members (without regard to overall diversity) and find that the ensembles based on ambiguity have lower generalization error. Further, we find that the ensemble members produced focusing on ambiguity have less features on average that those based on error only. We suggest that this indicates that these ensemble members are local learners.

Dynamic integration of classifiers for handling concept drift

In the real world concepts are often not stable but change with time. A typical example of this in the biomedical context is antibiotic resistance, where pathogen sensitivity may change over time as new pathogen strains develop resistance to antibiotics that were previously effective. This problem, known as concept drift, complicates the task of learning a model from data and requires special approaches, different from commonly used techniques that treat arriving instances as equally important contributors to the final concept. The underlying data distribution may change as well, making previously built models useless. This is known as virtual concept drift. Both types of concept drifts make regular updates of the model necessary. Among the most popular and effective approaches to handle concept drift is ensemble learning, where a set of models built over different time periods is maintained and the best model is selected or the predictions of models are combined, usually according to their expertise level regarding the current concept. In this paper we propose the use of an ensemble integration technique that would help to better handle concept drift at an instance level. In dynamic integration of classifiers, each base classifier is given a weight proportional to its local accuracy with regard to the instance tested, and the best base classifier is selected, or the classifiers are integrated using weighted voting. Our experiments with synthetic data sets simulating abrupt and gradual concept drifts and with a real-world antibiotic resistance data set demonstrate that dynamic integration of classifiers built over small time intervals or fixed-sized data blocks can be significantly better than majority voting and weighted voting, which are currently the most commonly used integration techniques for handling concept drift with ensembles.

Hierarchical Modularity and the Evolution of Genetic Interactomes across Species

To date, cross-species comparisons of genetic interactomes have been restricted to small or functionally related gene sets, limiting our ability to infer evolutionary trends. To facilitate a more comprehensive analysis, we constructed a genome-scale epistasis map (E-MAP) for the fission yeast Schizosaccharomyces pombe, providing phenotypic signatures for ~60% of the nonessential genome. Using these signatures, we generated a catalog of 297 functional modules, and we assigned function to 144 previously uncharacterized genes, including mRNA splicing and DNA damage checkpoint factors. Comparison with an integrated genetic interactome from the budding yeast Saccharomyces cerevisiae revealed a hierarchical model for the evolution of genetic interactions, with conservation highest within protein complexes, lower within biological processes, and lowest between distinct biological processes. Despite the large evolutionary distance and extensive rewiring of individual interactions, both networks retain conserved features and display similar levels of functional crosstalk between biological processes, suggesting general design principles of genetic interactomes.

Stability problems with artificial neural networks and the ensemble solution

Artificial neural networks (ANNs) are very popular as classification or regression mechanisms in medical decision support systems despite the fact that they are unstable predictors. This instability means that small changes in the training data used to build the model (i.e. train the ANN) may result in very different models. A central implication of this is that different sets of training data may produce models with very different generalisation accuracies. In this paper, we show in detail how this can happen in a prediction system for use in in-vitro fertilisation. We argue that claims for the generalisation performance of ANNs used in such a scenario should only be based on k-fold cross-validation tests. We also show how the accuracy of such a predictor can be improved by aggregating the output of several predictors.

A Taxonomy of Similarity Mechanisms for Case-Based Reasoning

Assessing the similarity between cases is a key aspect of the retrieval phase in case-based reasoning (CBR). In most CBR work, similarity is assessed based on feature value descriptions of cases using similarity metrics, which use these feature values. In fact, it might be said that this notion of a feature value representation is a defining part of the CBR worldview-it underpins the idea of a problem space with cases located relative to each other in this space. Recently, a variety of similarity mechanisms have emerged that are not founded on this feature space idea. Some of these new similarity mechanisms have emerged in CBR research and some have arisen in other areas of data analysis. In fact, research on kernel-based learning is a rich source of novel similarity representations because of the emphasis on encoding domain knowledge in the kernel function. In this paper, we present a taxonomy that organizes these new similarity mechanisms and more established similarity mechanisms in a coherent framework.