Are screening methods useful in feature selection? An empirical study

Filter or screening methods are often used as a preprocessing step for reducing the number of variables used by a learning algorithm in obtaining a classification or regression model. While there are many such filter methods, there is a need for an objective evaluation of these methods. Such an evaluation is needed to compare them with each other and also to answer whether they are at all useful, or a learning algorithm could do a better job without them. For this purpose, many popular screening methods are partnered in this paper with three regression learners and five classification learners and evaluated on ten real datasets to obtain accuracy criteria such as R-square and area under the ROC curve (AUC). The obtained results are compared through curve plots and comparison tables in order to find out whether screening methods help improve the performance of learning algorithms and how they fare with each other. Our findings revealed that the screening methods were useful in improving the prediction of the best learner on two regression and two classification datasets out of the ten datasets evaluated.Comment: 29 pages, 4 figures, 21 table

An empirical evaluation of imbalanced data strategies from a practitioner's point of view

This research tested the following well known strategies to deal with binary imbalanced data on 82 different real life data sets (sampled to imbalance rates of 5%, 3%, 1%, and 0.1%): class weight, SMOTE, Underbagging, and a baseline (just the base classifier). As base classifiers we used SVM with RBF kernel, random forests, and gradient boosting machines and we measured the quality of the resulting classifier using 6 different metrics (Area under the curve, Accuracy, F-measure, G-mean, Matthew's correlation coefficient and Balanced accuracy). The best strategy strongly depends on the metric used to measure the quality of the classifier. For AUC and accuracy class weight and the baseline perform better; for F-measure and MCC, SMOTE performs better; and for G-mean and balanced accuracy, underbagging

Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Applications Of Machine Learning In Biology And Medicine

Machine learning as a field is defined to be the set of computational algorithms that improve their performance by assimilating data. As such, the field as a whole has found applications in many diverse disciplines from robotics and communication in engineering to economics and finance, and also biology and medicine. It should not come as a surprise that many popular methods in use today have completely different origins. Despite this heterogeneity, different methods can be divided into standard tasks, such as supervised, unsupervised, semi-supervised and reinforcement learning. Although machine learning as a field can be formalized as methods trying to solve certain standard tasks, applying these tasks on datasets from different fields comes with certain caveats, and sometimes is fraught with challenges. In this thesis, we develop general procedures and novel solutions, dealing with practical problems that arise when modeling biological and medical data. Cost sensitive learning is an important area of research in machine learning which addresses the widespread and practical problem of dealing with different costs during the learning and deployment of classification algorithms. In many applications such as credit fraud detection, network intrusion and specifically medical diagnosis domains, prior class distributions are highly skewed, which makes the training examples very much unbalanced. Combining this with uneven misclassification costs renders standard machine learning approaches useless in learning an acceptable decision function. We experimentally show the benefits and shortcomings of various methods that convert cost blind learning algorithms to cost sensitive ones. Using the results and best practices found for cost sensitive learning, we design and develop a machine learning approach to ontology mapping. Next, we present a novel approach to deal with uncertainty in classification when costs are unknown or otherwise hard to assign. Support Vector Machines (SVM) are considered to be among the most successful approaches for classification. However prediction of instances near the decision boundary depends more on the specific parameter selection or noise in data, rather than a clear difference in features. In many applications such as medical diagnosis, these regions should be labeled as uncertain rather than assigned to any particular class. Furthermore, instances may belong to novel disease subtypes that are not from any previously known class. In such applications, declining to make a prediction could be beneficial when more powerful but expensive tests are available. We develop a novel approach for optimal selection of the threshold and show its successful application on three biological and medical datasets. The last part of this thesis provides novel solutions for handling high dimensional data. Although high-dimensional data is ubiquitously found in many disciplines, current life science research almost always involves high-dimensional genomics/proteomics data. The ``omics\u27\u27 data provide a wealth of information and have changed the research landscape in biology and medicine. However, these data are plagued with noise, redundancy and collinearity, which makes the discovery process very difficult and costly. Any method that can accurately detect irrelevant and noisy variables in omics data would be highly valuable. We present Robust Feature Selection (RFS), a randomized feature selection approach dedicated to low-sample high-dimensional data. RFS combines an embedded feature selection method with a randomization procedure for stability. Recent advances in sparse recovery and estimation methods have provided efficient and asymptotically consistent feature selection algorithms. However, these methods lack finite sample error control due to instability. Furthermore, the chances of correct recovery diminish with more collinearity among features. To overcome these difficulties, RFS uses a randomization procedure to provide an accurate and stable feature selection method. We thoroughly evaluate RFS by comparing it to a number of popular univariate and multivariate feature selection methods and show marked prediction accuracy improvement of a diagnostic signature, while preserving a good stability

Abstraction, aggregation and recursion for generating accurate and simple classifiers

An important goal of inductive learning is to generate accurate and compact classifiers from data. In a typical inductive learning scenario, instances in a data set are simply represented as ordered tuples of attribute values. In our research, we explore three methodologies to improve the accuracy and compactness of the classifiers: abstraction, aggregation, and recursion;Firstly, abstraction is aimed at the design and analysis of algorithms that generate and deal with taxonomies for the construction of compact and robust classifiers. In many applications of the data-driven knowledge discovery process, taxonomies have been shown to be useful in constructing compact, robust, and comprehensible classifiers. However, in many application domains, human-designed taxonomies are unavailable. We introduce algorithms for automated construction of taxonomies inductively from both structured (such as UCI Repository) and unstructured (such as text and biological sequences) data. We introduce AVT-Learner, an algorithm for automated construction of attribute value taxonomies (AVT) from data, and Word Taxonomy Learner (WTL), an algorithm for automated construction of word taxonomy from text and sequence data. We describe experiments on the UCI data sets and compare the performance of AVT-NBL (an AVT-guided Naive Bayes Learner) with that of the standard Naive Bayes Learner (NBL). Our results show that the AVTs generated by AVT-Learner are compeitive with human-generated AVTs (in cases where such AVTs are available). AVT-NBL using AVTs generated by AVT-Learner achieves classification accuracies that are comparable to or higher than those obtained by NBL; and the resulting classifiers are significantly more compact than those generated by NBL. Similarly, our experimental results of WTL and WTNBL on protein localization sequences and Reuters newswire text categorization data sets show that the proposed algorithms can generate Naive Bayes classifiers that are more compact and often more accurate than those produced by standard Naive Bayes learner for the Multinomial Model;Secondly, we apply aggregation to construct features as a multiset of values for the intrusion detection task. For this task, we propose a bag of system calls representation for system call traces and describe misuse and anomaly detection results on the University of New Mexico (UNM) and MIT Lincoln Lab (MIT LL) system call sequences with the proposed representation. With the feature representation as input, we compare the performance of several machine learning techniques for misuse detection and show experimental results on anomaly detection. The results show that standard machine learning and clustering techniques using the simple bag of system calls representation based on the system call traces generated by the operating system\u27s kernel is effective and often performs better than approaches that use foreign contiguous sequences in detecting intrusive behaviors of compromised processes;Finally, we construct a set of classifiers by recursive application of the Naive Bayes learning algorithms. Naive Bayes (NB) classifier relies on the assumption that the instances in each class can be described by a single generative model. This assumption can be restrictive in many real world classification tasks. We describe recursive Naive Bayes learner (RNBL), which relaxes this assumption by constructing a tree of Naive Bayes classifiers for sequence classification, where each individual NB classifier in the tree is based on an event model (one model for each class at each node in the tree). In our experiments on protein sequences, Reuters newswire documents and UC-Irvine benchmark data sets, we observe that RNBL substantially outperforms NB classifier. Furthermore, our experiments on the protein sequences and the text documents show that RNBL outperforms C4.5 decision tree learner (using tests on sequence composition statistics as the splitting criterion) and yields accuracies that are comparable to those of support vector machines (SVM) using similar information

Analyzing the Trade-offs between Runtime and Accuracy in Classification Algorithms for Natural Language Processing

This research aims to analyze the trade-offs between runtime and accuracy in classification algorithms for Natural Language Processing (NLP) and propose an optimization framework for balancing these trade-offs. The study employs a quantitative approach and evaluates the performance of different classification algorithms using metrics such as precision, recall, F1-score, and AUC. The population for this study is all publicly available datasets for NLP classification, and the data is collected using open-source NLP tools. The study shows that certain classification algorithms such as Random Forest, Decision Trees, Naive Bayes, SVM, or Neural Networks perform better than others in terms of both runtime and accuracy. However, some algorithms are faster but less accurate, while others are slower but more accurate. The analysis provided insights into how the choice of algorithm affects the trade-offs between runtime and accuracy in NLP. Based on the results, an optimization framework is proposed that can assist researchers and practitioners in NLP to choose the optimal algorithm for a given task and dataset, considering the desired balance between runtime and accuracy. This research provides valuable insights into the trade-offs between runtime and accuracy in NLP classification algorithms and proposes a framework that can help researchers make informed decisions about which algorithm to choose