classification of oncologic data with genetic programming

Discovering the models explaining the hidden relationship between genetic material and tumor pathologies is one of the most important open challenges in biology and medicine. Given the large amount of data made available by the DNA Microarray technique, Machine Learning is becoming a popular tool for this kind of investigations. In the last few years, we have been particularly involved in the study of Genetic Programming for mining large sets of biomedical data. In this paper, we present a comparison between four variants of Genetic Programming for the classification of two different oncologic datasets: the first one contains data from healthy colon tissues and colon tissues affected by cancer; the second one contains data from patients affected by two kinds of leukemia (acute myeloid leukemia and acute lymphoblastic leukemia). We report experimental results obtained using two different fitness criteria: the receiver operating characteristic and the percentage of correctly classified instances. These results, and their comparison with the ones obtained by three nonevolutionary Machine Learning methods (Support Vector Machines, MultiBoosting, and Random Forests) on the same data, seem to hint that Genetic Programming is a promising technique for this kind of classification

A neural network approach to audio-assisted movie dialogue detection

A novel framework for audio-assisted dialogue detection based on indicator functions and neural networks is investigated. An indicator function defines that an actor is present at a particular time instant. The cross-correlation function of a pair of indicator functions and the magnitude of the corresponding cross-power spectral density are fed as input to neural networks for dialogue detection. Several types of artificial neural networks, including multilayer perceptrons, voted perceptrons, radial basis function networks, support vector machines, and particle swarm optimization-based multilayer perceptrons are tested. Experiments are carried out to validate the feasibility of the aforementioned approach by using ground-truth indicator functions determined by human observers on 6 different movies. A total of 41 dialogue instances and another 20 non-dialogue instances is employed. The average detection accuracy achieved is high, ranging between 84.78%±5.499% and 91.43%±4.239%

Improving multiclass pattern recognition by the combination of two strategies

We present a new method of multiclass classification based on the combination of one- vs- all method and a modification of one- vs- one method. This combination of one- vs- all and one- vs- one methods proposed enforces the strength of both methods. A study of the behavior of the two methods identifies some of the sources of their failure. The performance of a classifier can be improved if the two methods are combined in one, in such a way that the main sources of their failure are partially avoided

Meta-Learning and the Full Model Selection Problem

When working as a data analyst, one of my daily tasks is to select appropriate tools from a set of existing data analysis techniques in my toolbox, including data preprocessing, outlier detection, feature selection, learning algorithm and evaluation techniques, for a given data project. This indeed was an enjoyable job at the beginning, because to me finding patterns and valuable information from data is always fun. Things become tricky when several projects needed to be done in a relatively short time. Naturally, as a computer science graduate, I started to ask myself, "What can be automated here?"; because, intuitively, part of my work is more or less a loop that can be programmed. Literally, the loop is "choose, run, test and choose again... until some criterion/goals are met". In other words, I use my experience or knowledge about machine learning and data mining to guide and speed up the process of selecting and applying techniques in order to build a relatively good predictive model for a given dataset for some purpose. So the following questions arise: "Is it possible to design and implement a system that helps a data analyst to choose from a set of data mining tools? Or at least that provides a useful recommendation about tools that potentially save some time for a human analyst." To answer these questions, I decided to undertake a long-term study on this topic, to think, define, research, and simulate this problem before coding my dream system. This thesis presents research results, including new methods, algorithms, and theoretical and empirical analysis from two directions, both of which try to propose systematic and efficient solutions to the questions above, using different resource requirements, namely, the meta-learning-based algorithm/parameter ranking approach and the meta-heuristic search-based full-model selection approach. Some of the results have been published in research papers; thus, this thesis also serves as a coherent collection of results in a single volume

Adabook and Multibook: adaptive boosting with chance correction

There has been considerable interest in boosting and bagging, including the combination of the adaptive techniques of AdaBoost with the random selection with replacement techniques of Bagging. At the same time there has been a revisiting of the way we evaluate, with chance-corrected measures like Kappa, Informedness, Correlation or ROC AUC being advocated. This leads to the question of whether learning algorithms can do better by optimizing an appropriate chance corrected measure. Indeed, it is possible for a weak learner to optimize Accuracy to the detriment of the more reaslistic chance-corrected measures, and when this happens the booster can give up too early. This phenomenon is known to occur with conventional Accuracy-based AdaBoost, and the MultiBoost algorithm has been developed to overcome such problems using restart techniques based on bagging. This paper thus complements the theoretical work showing the necessity of using chance-corrected measures for evaluation, with empirical work showing how use of a chance-corrected measure can improve boosting. We show that the early surrender problem occurs in MultiBoost too, in multiclass situations, so that chance-corrected AdaBook and Multibook can beat standard Multiboost or AdaBoost, and we further identify which chance-corrected measures to use when

BiasBed -- Rigorous Texture Bias Evaluation

The well-documented presence of texture bias in modern convolutional neural networks has led to a plethora of algorithms that promote an emphasis on shape cues, often to support generalization to new domains. Yet, common datasets, benchmarks and general model selection strategies are missing, and there is no agreed, rigorous evaluation protocol. In this paper, we investigate difficulties and limitations when training networks with reduced texture bias. In particular, we also show that proper evaluation and meaningful comparisons between methods are not trivial. We introduce BiasBed, a testbed for texture- and style-biased training, including multiple datasets and a range of existing algorithms. It comes with an extensive evaluation protocol that includes rigorous hypothesis testing to gauge the significance of the results, despite the considerable training instability of some style bias methods. Our extensive experiments, shed new light on the need for careful, statistically founded evaluation protocols for style bias (and beyond). E.g., we find that some algorithms proposed in the literature do not significantly mitigate the impact of style bias at all. With the release of BiasBed, we hope to foster a common understanding of consistent and meaningful comparisons, and consequently faster progress towards learning methods free of texture bias. Code is available at https://github.com/D1noFuzi/BiasBe