Peter Kokol

Decision Trees: An Overview and Their Use in Medicine

In medical decision making (classification, diagnosing, etc.) there are many situations where decision must be made effectively and reliably. Conceptual simple decision making models with the possibility of automatic learning are the most appropriate for performing such tasks. Decision trees are a reliable and effective decision making technique that provide high classification accuracy with a simple representation of gathered knowledge and they have been used in different areas of medical decision making. In the paper we present the basic characteristics of decision trees and the successful alternatives to the traditional induction approach with the emphasis on existing and possible future applications in medicine.

Genetic Algorithm Based System for Patient Scheduling in Highly Constrained Situations

In medicine and health care there are a lot of situations when patients have to be scheduled on different devices and/or with different physicians or therapists. It may concern preventive examinations, laboratory tests or convalescent therapies, therefore we are always looking for an optimal schedule that would result in finishing all the activities scheduled as soon as possible, with the least patient waiting time and maximum device utilization. Since patient scheduling is a highly complex problem, it is impossible to make a qualitative schedule by hand or even with exact heuristic methods. Therefore we developed a powerful automated scheduling method for highly constrained situations based on genetic algorithms and machine learning. In this paper we present the method, together with the whole process of schedule generation, the important parameters to direct the evolution and how the algorithm is guaranteed to produce only feasible solutions, not breaking any of the required constraints. We applied the described method to a problem of scheduling patients with different therapy needs to a limited number of therapeutic devices, but the algorithm can be easily modified for use in similar situations. The results are quite encouraging and since all the solutions are feasible, the method can be easily incorporated into an interactive user interface, which can be of major importance when scheduling patients, and human resources in general, is considered.

Decision trees based on automatic learning and their use in cardiology

Computerized information systems, especially decision support systems, have become an increasingly important role in medical applications, particularly in those where important decision must be made effectively and reliably. But the possibility of using computers in medical decision making is limited by many difficulties, including the complexity of conventional computer languages, methodologies and tools. Thus a conceptual simple decision making model with the possibility of automating learning should be used. In this paper we introduce a cardiological knowledge-based system based on the decision tree approach supporting the mitral valve prolapse determination. Prolapse is defined as the displacement of a bodily part from its normal position. The term mitral valve prolaps (PMV), therefore, implies that the mitral leaflets are displaced relative to some structure, generally taken to be the mitral annulus. The implications of the PMV are the following: disturbed normal laminar blood flow, turbulence of the blood flow, injury of the chordae tendinae, the possibility of thrombuss composition, bacterial endocarditis, and finally hemodynamic changes defined as mitral insufficiency and mitral regurgitation. Uncertainty persists about how it should be diagnosed and about its clinical importance. It is our deep belief that the echocardiography enables properly trained experts armed with proper criteria to evaluate PMV almost 100%. But unfortunately, there are some problems concerned with the use of echocardiography. In that manner we have decided to start a research project aimed at finding new criteria and enabling the general practitioner to evaluate PMV using conventional methods and to select potential patients from the general population. To empower one to perform needed activities we have developed a computer tool called ROSE (computeRised prOlaps Syndrom dEtermination) based on algorithms of automatic learning. This tool supports the definition of new criteria and the selection of potential PMV-patients.

Comprehensive Decision Tree Models in Bioinformatics

Purpose Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. Methods This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. Results The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. Conclusions The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly redundant attributes that are very common in bioinformatics.

Knowledge discovery with classification rules in a cardiovascular dataset

In this paper we study an evolutionary machine learning approach to data mining and knowledge discovery based on the induction of classification rules. A method for automatic rules induction called AREX using evolutionary induction of decision trees and automatic programming is introduced. The proposed algorithm is applied to a cardiovascular dataset consisting of different groups of attributes which should possibly reveal the presence of some specific cardiovascular problems in young patients. A case study is presented that shows the use of AREX for the classification of patients and for discovering possible new medical knowledge from the dataset. The defined knowledge discovery loop comprises a medical experts assessment of induced rules to drive the evolution of rule sets towards more appropriate solutions. The final result is the discovery of a possible new medical knowledge in the field of pediatric cardiology.

Towards More Optimal Medical Diagnosing with Evolutionary Algorithms

Efficiency in hospital performance is becoming more and more important. Studies showed that diagnosis can considerably reduce the inefficiency, so one of the most important tasks in achieving greater hospital efficiency is to optimize the diagnostic process. For the best of the patient the diagnostic process has to be optimized regarding the number of the examinations and individualized in order to maximize accuracy, sensitivity and specificity. In addition the duration of the diagnostic process has to be minimized and the process has to be performed on the most reliable equipment. The main contribution of our paper is the introduction of the integrated computerized environment DIAPRO enabling the diagnostic process optimization. The DIAPRO is based on a single approach—evolutionary algorithms.

Metaparadigm: A soft and situation oriented MIS design approach

Every-day routine work performed by medical staff can be enormous, thus continuing education, diagnostic assistance, medical research or literature searches remains only an aspiration for them. The appearance of the computer-based information technology has initiated the possibility to significantly ease these routine activities and enable the medical staff to devote more time to enhanced creative work. However, only when medical staff can use computers reliably, effectively, democratically, easily, and in natural, intuitive fashion, medical information system (MIS) will be used enthusiastically and favourably. In that manner special attention must be dedicated to MIS design. The aim of our paper is to introduce the new (M)IS design approach called metaparadigm and show its applicability to MIS design. A metaparadigm is a holistic, participative and systemic approach, incorporating design activities needed to construct both the (M)IS design paradigm and the selected (M)IS. It is our deepest belief that metaparadigms employment can enhance many IS design weaknesses and result in the successful medical information systems design and use.

Evolutionary induced decision trees for dangerous software modules prediction

Abstract We study the possibility of constructing decision trees with evolutionary algorithms in order to increase their predictive accuracy. We present a self-adapting evolutionary algorithm for the induction of decision trees and describe the principle of decision making based on multiple evolutionary induced decision trees—decision forest. The developed model is used as a fault predictive approach to foresee dangerous software modules, which identification can largely enhance the reliability of software.

The Limitations of Decision Trees and Automatic Learning in Real World Medical Decision Making

The decision tree approach is one of the most common approaches in automatic learning and decision making. The automatic learning of decision trees and their use usually show very good results in various “ theoretical” environments. But in real life it is often impossible to find the desired number of representative training objects for various reasons. The lack of possibilities to measure attribute values, high cost and complexity of such measurements, and unavailability of all attributes at the same time are the typical representatives. For this reason we decided to use the decision trees not for their primary task—the decision making—but for outlining the most important attributes. This was possible by using a well-known property of the decision trees—their knowledge representation, which can be easily understood by humans. In a delicate field of medical decision making, we cannot allow ourselves to make any inaccurate decisions and the “tips,” provided by the decision trees, can be of a great assistance. Our main interest was to discover a predisposition to two forms of acidosis: themetabolic acidosis and respiratory acidosis, which can both have serious effects on childs health. We decided to construct different decision trees from a set of training objects. Instead of using a test set for evaluation of a decision tree, we asked medical experts to take a closer look at the generated trees. They examined and evaluated the decision trees branch by branch. Their comments show that trees generated from the available training set mainly have surprisingly good branches, but on the other hand, for some, no medical explanation could be found.

Stability of Ranked Gene Lists in Large Microarray Analysis Studies

This paper presents an empirical study that aims to explain the relationship between the number of samples and stability of different gene selection techniques for microarray datasets. Unlike other similar studies where number of genes in a ranked gene list is variable, this study uses an alternative approach where stability is observed at different number of samples that are used for gene selection. Three different metrics of stability, including a novel metric in bioinformatics, were used to estimate the stability of the ranked gene lists. Results of this study demonstrate that the univariate selection methods produce significantly more stable ranked gene lists than the multivariate selection methods used in this study. More specifically, thousands of samples are needed for these multivariate selection methods to achieve the same level of stability any given univariate selection method can achieve with only hundreds.