Comprehensive Review and Comparison for Anticancer Peptides Identification Models.

Anticancer peptides (ACPs) eliminate pathogenic bacteria and kill tumor cells, showing no hemolysis and no damages to normal human cells. This unique ability explores the possibility of ACPs as therapeutic delivery and its potential applications in clinical therapy. Identifying ACPs is one of the most fundamental and central problems in new antitumor drug research. During the past decades, a number of machine learning-based prediction tools have been developed to solve this important task. However, the predictions produced by various tools are difficult to quantify and compare. Therefore, in this article, we provide a comprehensive review of existing machine learning methods for ACPs prediction and fair comparison of the predictors. To evaluate current prediction tools, we conducted a comparative study and analyzed the existing ACPs predictor from 10 public literatures. The comparative results obtained suggest that Support Vector Machine-based model with features combination provided significant improvement in the overall performance, when compared to the other machine learning method-based prediction models.

Ergonomic Assessment of the Mental Workload Confronted by Surgeons during Laparoscopic Surgery.

Although the mental workload confronted by laparoscopic surgeons is rather high, there is presently no reliable, established method for evaluating this workload. In the present study, four evaluation indices of eye movement metrics were applied to evaluate surgeons' mental workload. Correlations between these indices and National Aeronautics and Space Administration Task Load Index (NASA-TLX) scores were also explored. Sixteen participants were recruited to complete four laparoscopic procedures. Eye movement was recorded during the tasks, and NASA-TLX scales were also introduced for subjective evaluation. The data were analyzed using R 3.3.2. Significant differences in the mental workload of each task were observed. Statistically significant correlations between mean pupil diameter change and NASA-TLX scores were also observed. The correlation coefficients were 0.763, 0.675, 0.405, and 0.547, and the P values correspondingly were 0.001, 0.004, 0.12, and 0.028, respectively. The results clarify that the mental workload of laparoscopic surgeons is dependent on the specific demands of the operation. Appropriate objective physiological indices can be used to identify the mental workload state of the surgeon.

Inverse planning optimization method for intensity modulated radiation therapy.

In order to facilitate the leaf sequencing process in intensity modulated radiation therapy (IMRT), and design of a practical leaf sequencing algorithm, it is an important issue to smooth the planned fluence maps. The objective is to achieve both high-efficiency and high-precision dose delivering by considering characteristics of leaf sequencing process. The key factor which affects total number of monitor units for the leaf sequencing optimization process is the max flow value of the digraph which formulated from the fluence maps. Therefore, we believe that one strategy for compromising dose conformity and total number of monitor units in dose delivery is to balance the dose distribution function and the max flow value mentioned above. However, there are too many paths in the digraph, and we don't know the flow value of which path is the maximum. The maximum flow value among the horizontal paths was selected and used in the objective function of the fluence map optimization to formulate the model. The model is a traditional linear constrained quadratic optimization model which can be solved by interior point method easily. We believe that the smoothed maps from this model are more suitable for leaf sequencing optimization process than other smoothing models. A clinical head-neck case and a prostate case were tested and compared using our proposed model and the smoothing model which is based on the minimization of total variance. The optimization results with the same level of total number of monitor units (TNMU) show that the fluence maps obtained from our model have much better dose performance for the target/non-target region than the maps from total variance based on the smoothing model. This indicates that our model achieves better dose distribution when the algorithm suppresses the TNMU at the same level. Although we have just used the max flow value of the horizontal paths in the diagraph in the objective function, a good balance has been achieved between the dose conformity and the total number of monitor units. This idea can be extended to other fluence map optimization model, and we believe it can also achieve good performance.

Fluence map optimization (FMO) with dose-volume constraints in IMRT using the geometric distance sorting method.

A new heuristic algorithm based on the so-called geometric distance sorting technique is proposed for solving the fluence map optimization with dose-volume constraints which is one of the most essential tasks for inverse planning in IMRT. The framework of the proposed method is basically an iterative process which begins with a simple linear constrained quadratic optimization model without considering any dose-volume constraints, and then the dose constraints for the voxels violating the dose-volume constraints are gradually added into the quadratic optimization model step by step until all the dose-volume constraints are satisfied. In each iteration step, an interior point method is adopted to solve each new linear constrained quadratic programming. For choosing the proper candidate voxels for the current dose constraint adding, a so-called geometric distance defined in the transformed standard quadratic form of the fluence map optimization model was used to guide the selection of the voxels. The new geometric distance sorting technique can mostly reduce the unexpected increase of the objective function value caused inevitably by the constraint adding. It can be regarded as an upgrading to the traditional dose sorting technique. The geometry explanation for the proposed method is also given and a proposition is proved to support our heuristic idea. In addition, a smart constraint adding/deleting strategy is designed to ensure a stable iteration convergence. The new algorithm is tested on four cases including head-neck, a prostate, a lung and an oropharyngeal, and compared with the algorithm based on the traditional dose sorting technique. Experimental results showed that the proposed method is more suitable for guiding the selection of new constraints than the traditional dose sorting method, especially for the cases whose target regions are in non-convex shapes. It is a more efficient optimization technique to some extent for choosing constraints than the dose sorting method. By integrating a smart constraint adding/deleting scheme within the iteration framework, the new technique builds up an improved algorithm for solving the fluence map optimization with dose-volume constraints.

Fissures segmentation using surface features: content-based retrieval for mammographic mass using ensemble classifier.

RATIONALE AND OBJECTIVES: Accurate classification is critical in mammography computer-aided diagnosis using content-based image retrieval approaches (CBIR CAD). The objectives of this study were to: 1) develop an accurate ensemble classifier based on domain knowledge and a robust feature selection method for CBIR CAD; 2) propose three new features; and 3) assess the performance of the proposed method and new features by using a relatively large imaging data set. MATERIALS AND METHODS: The data set used in this study consisted of 2114 regions of interest (ROI) extracted from a publicly available image database. The proposed ensemble classifier method we called E-DGA-KNN included four steps. In the first step, 804 ROIs depict masses were divided into five classes according to their boundary types. Then, each class of ROI with an equal number of negative ROIs were put together to create a sub-database. Second, a dual-stage genetic algorithm, which was called DGA, was applied on those five sub-databases for feature selection and weights determination respectively. In the third step, five base K-nearest neighbor (KNN) classifiers were created by using the results of the second step on 2114 ROIs, and five detection scores for a given queried ROI were obtained. Finally, these classifiers are combined to yield a final classification. The performances of the proposed methods were evaluated by using receiver operating characteristic (ROC) analysis. A comparison with eight different methods on the data set was provided which include the stepwise linear discriminative analysis algorithm (SLDA) and particle swarm optimization (PSO) algorithm with KNN classifier. RESULTS: When four hybrid feature selection methods were applied with single KNN classifier (ie, DGA-KNN, SLDA-WGA-KNN, SLDA-PSO-KNN, GA-PSO-KNN) and the proposed E-DGA-KNN method to the data set, the computed areas under the ROC curve (Az) were 0.8782 ± 0.0080, 0.8675 ± 0.0081, 0.8623 ± 0.0083, 0.8725 ± 0.0079, and 0.8927 ± 0.0073, respectively. If all features and single KNN classifier were used, the Az value was 0.8478 ± 0.0088. Az values were 0.8592 ± 0.0083 and 0.8632 ± 0.0081 when SLDA or GA algorithm used alone. CONCLUSIONS: In this study, an ensemble classifier based on domain knowledge and a dual-stage feature selection method was proposed. Evaluation results indicated that the proposed method achieved largest value of ROC compared to other algorithms. The proposed method shows better performance and has the potential to improve the performance of CBIR CAD in interpreting and analyzing mammograms.

Hybrid segmentation of mass in mammograms using template matching and dynamic programming.

RATIONALE AND OBJECTIVES: Accurate image segmentation for breast lesions is a critical step in computer-aided diagnosis systems. The objective of this study was to develop a robust method for the automatic segmentation of breast masses on mammograms to extract feasible features for computer-aided diagnosis systems. MATERIALS AND METHODS: The data set used in this study consisted of 483 regions of interest extracted from 328 patients. A hybrid method for segmenting breast masses was proposed on the basis of the template-matching and dynamic programming techniques. First, a template-matching technique was used to locate and obtain the rough region of masses. Then, on the basis of this rough region, a local cost function for dynamic programming was defined. Finally, the optimal contour was derived by applying dynamic programming as an optimization technique. The performance of this proposed segmentation method was evaluated using area-based and boundary distance-based similarity measures based on radiologists' manually marked annotations. A comparison with three different segmentation algorithms on the data set was provided. RESULTS: The mean overlap percentage for our proposed hybrid method was 0.727 ± 0.127, whereas those for Timp and Karssemeijer's dynamic programming method, Song et al's plane-fitting and dynamic programming method, and the normalized cut segmentation method were 0.657 ± 0.216, 0.636 ± 0.190, and 0.562 ± 0.199, respectively. All P values for the measure distribution of our proposed method and the other three algorithms were <.001. CONCLUSIONS: A hybrid method based on the template-matching and dynamic programming techniques was proposed to segment breast masses on mammograms. Evaluation results indicate that the proposed segmentation method can improve the accuracy of mass segmentation compared to three other algorithms. The proposed segmentation method shows better performance and has great potential in improving the accuracy of computer-aided diagnosis systems in interpreting mammograms.