Biomedical subjects

Michael R Lyu

Publications and source records attributed to Michael R Lyu.

7 recordsLinked to original sources

PubMed2006

Maximizing sensitivity in medical diagnosis using biased minimax probability machine.

The challenging task of medical diagnosis based on machine learning techniques requires an inherent bias, i.e., the diagnosis should favor the "ill" class over the "healthy" class, since misdiagnosing a patient as a healthy person may delay the therapy and aggravate the illness. Therefore, the objective in this task is not to improve the overall accuracy of the classification, but to focus on improving the sensitivity (the accuracy of the "ill" class) while maintaining an acceptable specificity (the accuracy of the "healthy" class). Some current methods adopt roundabout ways to impose a certain bias toward the important class, i.e., they try to utilize some intermediate factors to influence the classification. However, it remains uncertain whether these methods can improve the classification performance systematically. In this paper, by engaging a novel learning tool, the biased minimax probability machine (BMPM), we deal with the issue in a more elegant way and directly achieve the objective of appropriate medical diagnosis. More specifically, the BMPM directly controls the worst case accuracies to incorporate a bias toward the "ill" class. Moreover, in a distribution-free way, the BMPM derives the decision rule in such a way as to maximize the worst case sensitivity while maintaining an acceptable worst case specificity. By directly controlling the accuracies, the BMPM provides a more rigorous way to handle medical diagnosis; by deriving a distribution-free decision rule, the BMPM distinguishes itself from a large family of classifiers, namely, the generative classifiers, where an assumption on the data distribution is necessary. We evaluate the performance of the model and compare it with three traditional classifiers: the k-nearest neighbor, the naive Bayesian, and the C4.5. The test results on two medical datasets, the breast-cancer dataset and the heart disease dataset, show that the BMPM outperforms the other three models.

Algorithms↗

PubMed2006

Extraction of line segments and circular arcs from freehand strokes based on segmental homogeneity features.

The extraction of component line segments and circular arcs from freehand strokes along with their relations is a prerequisite for sketch understanding. Existing approaches usually take three stages to segment a stroke: first identifying segmentation points, then classifying the substroke between each pair of adjacent segmentation points, and, finally, obtaining graphical representations of substrokes by fitting graphical primitives to them. Since a stroke inevitably contains noises, the first stage may produce wrong or inaccurate segmentation points, resulting in the wrong substroke classification in the second stage and inaccurately fitted parameters in the third stage. To overcome the noise sensitivity of the three-stage method, the segmental homogeneity feature is emphasized in this paper. We propose a novel approach, which first extracts graphical primitives from a stroke by a connected segment growing from a seed-segment and then utilizes relationships between the primitives to refine their control parameters. We have conducted experiments using real-life strokes and compared the proposed approach with others. Experimental results demonstrate that the proposed approach is effective and robust.

Algorithms↗

PubMed2006

Imbalanced learning with a biased minimax probability machine.

Imbalanced learning is a challenged task in machine learning. In this context, the data associated with one class are far fewer than those associated with the other class. Traditional machine learning methods seeking classification accuracy over a full range of instances are not suitable to deal with this problem, since they tend to classify all the data into a majority class, usually the less important class. In this correspondence, the authors describe a new approach named the biased minimax probability machine (BMPM) to deal with the problem of imbalanced learning. This BMPM model is demonstrated to provide an elegant and systematic way for imbalanced learning. More specifically, by controlling the accuracy of the majority class under all possible choices of class-conditional densities with a given mean and covariance matrix, this model can quantitatively and systematically incorporate a bias for the minority class. By establishing an explicit connection between the classification accuracy and the bias, this approach distinguishes itself from the many current imbalanced-learning methods; these methods often impose a certain bias on the minority data by adapting intermediate factors via the trial-and-error procedure. The authors detail the theoretical foundation, prove its solvability, propose an efficient optimization algorithm, and perform a series of experiments to evaluate the novel model. The comparison with other competitive methods demonstrates the effectiveness of this new model.

Algorithms↗

PubMed2006

Network analysis of the protein chain tertiary structures of heterocomplexes.

In this paper, the tertiary structures of protein chains of heterocomplexes were mapped to 2D networks; based on the mapping approach, statistical properties of these networks were systematically studied. Firstly, our experimental results confirmed that the networks derived from protein structures possess small-world properties. Secondly, an interesting relationship between network average degree and the network size was discovered, which was quantified as an empirical function enabling us to estimate the number of residue contacts of the protein chains accurately. Thirdly, by analyzing the average clustering coefficient for nodes having the same degree in the network, it was found that the architectures of the networks and protein structures analyzed are hierarchically organized. Finally, network motifs were detected in the networks which are believed to determine the family or superfamily the networks belong to. The study of protein structures with the new perspective might shed some light on understanding the underlying laws of evolution, function and structures of proteins, and therefore would be complementary to other currently existing methods.

Models, Molecular↗

PubMed2005

Predicting protein interaction sites from residue spatial sequence profile and evolution rate.

This paper proposes a novel method that can predict protein interaction sites in heterocomplexes using residue spatial sequence profile and evolution rate approaches. The former represents the information of multiple sequence alignments while the latter corresponds to a residue's evolutionary conservation score based on a phylogenetic tree. Three predictors using a support vector machines algorithm are constructed to predict whether a surface residue is a part of a protein-protein interface. The efficiency and the effectiveness of our proposed approach is verified by its better prediction performance compared with other models. The study is based on a non-redundant data set of heterodimers consisting of 69 protein chains.

Algorithms↗

PubMed2005

Recognition of merged characters based on forepart prediction, necessity-sufficiency matching, and character-adaptive masking.

Merged characters are the major cause of recognition errors. We classify the merging relationship between two involved characters into three types: "linear," "nonlinear," and "overlapped." Most segmentation methods handle the first type well, however, their capabilities of handling the other two types are limited. The weakness of handling the nonlinear and overlapped types results from character segmentation by linear, usually vertical, cuts assumed in these methods. This paper proposes a novel merged character segmentation and recognition method based on forepart prediction, necessity-sufficiency matching and character-adaptive masking. This method utilizes the information obtained from the forepart of merged characters to predict candidates for the leftmost character, and then applies character-adaptive masking and character recognition to verifying the prediction. Therefore, the arbitrary-shaped cutting path will follow the right shape of the leftmost character so as to preserve the shape of the next character. This method handles the first two types well and greatly improves the segmentation accuracy of the overlapped type. The experimental results and the performance comparisons with other methods demonstrate the effectiveness of the proposed method.

Algorithms↗

PubMed2004

Effective multiresolution arc segmentation: algorithms and performance evaluation.

Arc segmentation plays an important role in the process of graphics recognition from scanned images. The GREC arc segmentation contest shows there is a lot of room for improvement in this area. This paper proposes a multiresolution arc segmentation method based on our previous seeded circular tracking algorithm which largely depends on the OOPSV model. The newly-introduced multiresolution paradigm can handle arcs/circles with large radii well. We describe new approaches for arc seed detection, arc localization, and arc verification, making the proposed method self-contained and more efficient. Moreover, this paper also brings major improvement to the dynamic adjustment algorithm of circular tracking to make it more robust. A systematic performance evaluation of the proposed method has been conducted using the third-party evaluation tool and test images obtained from the GREC arc segmentation contests. The overall performance over various arc angles, arc lengths, line thickness, noises, arc-arc intersections, and arc-line intersections has been measured. The experimental results and time complexity analyses on real scanned images are also reported and compared with other approaches. The evaluation result demonstrates the stable performance and the significant improvement on processing large arcs/circles of the MAS method.

Algorithms↗