2,941 research outputs found
Wavelet feature extraction and genetic algorithm for biomarker detection in colorectal cancer data
Biomarkers which predict patient’s survival can play an important role in medical diagnosis and
treatment. How to select the significant biomarkers from hundreds of protein markers is a key step in
survival analysis. In this paper a novel method is proposed to detect the prognostic biomarkers ofsurvival in colorectal cancer patients using wavelet analysis, genetic algorithm, and Bayes classifier. One dimensional discrete wavelet transform (DWT) is normally used to reduce the dimensionality of biomedical data. In this study one dimensional continuous wavelet transform (CWT) was proposed to extract the features of colorectal cancer data. One dimensional CWT has no ability to reduce
dimensionality of data, but captures the missing features of DWT, and is complementary part of DWT. Genetic algorithm was performed on extracted wavelet coefficients to select the optimized features, using Bayes classifier to build its fitness function. The corresponding protein markers were
located based on the position of optimized features. Kaplan-Meier curve and Cox regression model 2 were used to evaluate the performance of selected biomarkers. Experiments were conducted on colorectal cancer dataset and several significant biomarkers were detected. A new protein biomarker CD46 was found to significantly associate with survival time
Learning Bayesian network equivalence classes using ant colony optimisation
Bayesian networks have become an indispensable tool in the modelling of uncertain
knowledge. Conceptually, they consist of two parts: a directed acyclic graph called the
structure, and conditional probability distributions attached to each node known as the
parameters. As a result of their expressiveness, understandability and rigorous mathematical basis, Bayesian networks have become one of the first methods investigated,
when faced with an uncertain problem domain. However, a recurring problem persists
in specifying a Bayesian network. Both the structure and parameters can be difficult for
experts to conceive, especially if their knowledge is tacit.To counteract these problems, research has been ongoing, on learning both the structure
and parameters of Bayesian networks from data. Whilst there are simple methods for
learning the parameters, learning the structure has proved harder. Part ofthis stems from
the NP-hardness of the problem and the super-exponential space of possible structures.
To help solve this task, this thesis seeks to employ a relatively new technique, that has
had much success in tackling NP-hard problems. This technique is called ant colony
optimisation. Ant colony optimisation is a metaheuristic based on the behaviour of ants
acting together in a colony. It uses the stochastic activity of artificial ants to find good
solutions to combinatorial optimisation problems. In the current work, this method is
applied to the problem of searching through the space of equivalence classes of Bayesian
networks, in order to find a good match against a set of data. The system uses operators
that evaluate potential modifications to a current state. Each of the modifications is
scored and the results used to inform the search. In order to facilitate these steps, other
techniques are also devised, to speed up the learning process. The techniques includeThe techniques are tested by sampling data from gold standard networks and learning
structures from this sampled data. These structures are analysed using various goodnessof-fit measures to see how well the algorithms perform. The measures include structural
similarity metrics and Bayesian scoring metrics. The results are compared in depth
against systems that also use ant colony optimisation and other methods, including
evolutionary programming and greedy heuristics. Also, comparisons are made to well
known state-of-the-art algorithms and a study performed on a real-life data set. The
results show favourable performance compared to the other methods and on modelling
the real-life data
Recognizing Teamwork Activity In Observations Of Embodied Agents
This thesis presents contributions to the theory and practice of team activity recognition. A particular focus of our work was to improve our ability to collect and label representative samples, thus making the team activity recognition more efficient. A second focus of our work is improving the robustness of the recognition process in the presence of noisy and distorted data. The main contributions of this thesis are as follows: We developed a software tool, the Teamwork Scenario Editor (TSE), for the acquisition, segmentation and labeling of teamwork data. Using the TSE we acquired a corpus of labeled team actions both from synthetic and real world sources. We developed an approach through which representations of idealized team actions can be acquired in form of Hidden Markov Models which are trained using a small set of representative examples segmented and labeled with the TSE. We developed set of team-oriented feature functions, which extract discrete features from the high-dimensional continuous data. The features were chosen such that they mimic the features used by humans when recognizing teamwork actions. We developed a technique to recognize the likely roles played by agents in teams even before the team action was recognized. Through experimental studies we show that the feature functions and role recognition module significantly increase the recognition accuracy, while allowing arbitrary shuffled inputs and noisy data
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