Cube Kohonen self-organizing map (CKSOM) model with new equations in organizing unstructured data

Probabilistic nested model selection in pharmacokinetic analysis of DCE-MRI data in animal model of cerebral tumor

Best current practice in the analysis of dynamic contrast enhanced (DCE)-MRI is to employ a voxel-by-voxel model selection from a hierarchy of nested models. This nested model selection (NMS) assumes that the observed time-trace of contrast-agent (CA) concentration within a voxel, corresponds to a singular physiologically nested model. However, admixtures of different models may exist within a voxel's CA time-trace. This study introduces an unsupervised feature engineering technique (Kohonen-Self-Organizing-Map (K-SOM)) to estimate the voxel-wise probability of each nested model. Sixty-six immune-compromised-RNU rats were implanted with human U-251 N cancer cells, and DCE-MRI data were acquired from all the rat brains. The time-trace of change in the longitudinal-relaxivity (ΔR1) for all animals' brain voxels was calculated. DCE-MRI pharmacokinetic (PK) analysis was performed using NMS to estimate three model regions: Model-1: normal vasculature without leakage, Model-2: tumor tissues with leakage without back-flux to the vasculature, Model-3: tumor vessels with leakage and back-flux. Approximately two hundred thirty thousand (229,314) normalized ΔR1 profiles of animals' brain voxels along with their NMS results were used to build a K-SOM (topology-size: 8 × 8, with competitive-learning algorithm) and probability map of each model. K-fold nested-cross-validation (NCV, k = 10) was used to evaluate the performance of the K-SOM probabilistic-NMS (PNMS) technique against the NMS technique. The K-SOM PNMS's estimation for the leaky tumor regions were strongly similar (Dice-Similarity-Coefficient, DSC = 0.774 [CI: 0.731-0.823], and 0.866 [CI: 0.828-0.912] for Models 2 and 3, respectively) to their respective NMS regions. The mean-percent-differences (MPDs, NCV, k = 10) for the estimated permeability parameters by the two techniques were: -28%, + 18%, and + 24%, for vp, Ktrans, and ve, respectively. The KSOM-PNMS technique produced microvasculature parameters and NMS regions less impacted by the arterial-input-function dispersion effect. This study introduces an unsupervised model-averaging technique (K-SOM) to estimate the contribution of different nested-models in PK analysis and provides a faster estimate of permeability parameters.

PlaneSeg: Building a Plug-In for Boosting Planar Region Segmentation

Existing methods in planar region segmentation suffer the problems of vague boundaries and failure to detect small-sized regions. To address these, this study presents an end-to-end framework, named PlaneSeg, which can be easily integrated into various plane segmentation models. Specifically, PlaneSeg contains three modules, namely, the edge feature extraction module, the multiscale module, and the resolution-adaptation module. First, the edge feature extraction module produces edge-aware feature maps for finer segmentation boundaries. The learned edge information acts as a constraint to mitigate inaccurate boundaries. Second, the multiscale module combines feature maps of different layers to harvest spatial and semantic information from planar objects. The multiformity of object information can help recognize small-sized objects to produce more accurate segmentation results. Third, the resolution-adaptation module fuses the feature maps produced by the two aforementioned modules. For this module, a pairwise feature fusion is adopted to resample the dropped pixels and extract more detailed features. Extensive experiments demonstrate that PlaneSeg outperforms other state-of-the-art approaches on three downstream tasks, including plane segmentation, 3-D plane reconstruction, and depth prediction. Code is available at https://github.com/nku-zhichengzhang/PlaneSeg.

Probabilistic Nested Model Selection in Pharmacokinetic Analysis of DCE-MRI Data in Animal Model of Cerebral Tumor

Purpose

Best current practice in the analysis of dynamic contrast enhanced (DCE)-MRI is to employ a voxel-by-voxel model selection from a hierarchy of nested models. This nested model selection (NMS) assumes that the observed time-trace of contrast-agent (CA) concentration within a voxel, corresponds to a singular physiologically nested model. However, admixtures of different models may exist within a voxel's CA time-trace. This study introduces an unsupervised feature engineering technique (Kohonen-Self-Organizing-Map (K-SOM)) to estimate the voxel-wise probability of each nested model.

Methods

Sixty-six immune-compromised-RNU rats were implanted with human U-251N cancer cells, and DCE-MRI data were acquired from all the rat brains. The time-trace of change in the longitudinalrelaxivityΔ R 1 for all animals' brain voxels was calculated. DCE-MRI pharmacokinetic (PK) analysis was performed using NMS to estimate three model regions: Model-1: normal vasculature without leakage, Model-2: tumor tissues with leakage without back-flux to the vasculature, Model-3: tumor vessels with leakage and back-flux. Approximately two hundred thirty thousand (229,314) normalized Δ R 1 profiles of animals' brain voxels along with their NMS results were used to build a K-SOM (topology-size: 8×8, with competitive-learning algorithm) and probability map of each model. K-fold nested-cross-validation (NCV, k=10) was used to evaluate the performance of the K-SOM probabilistic-NMS (PNMS) technique against the NMS technique.

Results

The K-SOM PNMS's estimation for the leaky tumor regions were strongly similar (Dice-Similarity-Coefficient, DSC=0.774 [CI: 0.731-0.823], and 0.866 [CI: 0.828-0.912] for Models 2 and 3, respectively) to their respective NMS regions. The mean-percent-differences (MPDs, NCV, k=10) for the estimated permeability parameters by the two techniques were: -28%, +18%, and +24%, forv p , K trans , andv e , respectively. The KSOM-PNMS technique produced microvasculature parameters and NMS regions less impacted by the arterial-input-function dispersion effect.

Conclusion

This study introduces an unsupervised model-averaging technique (K-SOM) to estimate the contribution of different nested-models in PK analysis and provides a faster estimate of permeability parameters.

Radiomics characterization of tissues in an animal brain tumor model imaged using dynamic contrast enhanced (DCE) MRI

Here, we investigate radiomics-based characterization of tumor vascular and microenvironmental properties in an orthotopic rat brain tumor model measured using dynamic-contrast-enhanced (DCE) MRI. Thirty-two immune compromised-RNU rats implanted with human U-251N cancer cells were imaged using DCE-MRI (7Tesla, Dual-Gradient-Echo). The aim was to perform pharmacokinetic analysis using a nested model (NM) selection technique to classify brain regions according to vasculature properties considered as the source of truth. A two-dimensional convolutional-based radiomics analysis was performed on the raw-DCE-MRI of the rat brains to generate dynamic radiomics maps. The raw-DCE-MRI and respective radiomics maps were used to build 28 unsupervised Kohonen self-organizing-maps (K-SOMs). A Silhouette-Coefficient (SC), k-fold Nested-Cross-Validation (k-fold-NCV), and feature engineering analyses were performed on the K-SOMs' feature spaces to quantify the distinction power of radiomics features compared to raw-DCE-MRI for classification of different Nested Models. Results showed that eight radiomics features outperformed respective raw-DCE-MRI in prediction of the three nested models. The average percent difference in SCs between radiomics features and raw-DCE-MRI was: 29.875% ± 12.922%, p < 0.001. This work establishes an important first step toward spatiotemporal characterization of brain regions using radiomics signatures, which is fundamental toward staging of tumors and evaluation of tumor response to different treatments.

Self-Organizing Neuroevolution for Solving Carpool Service Problem With Dynamic Capacity to Alternate Matches

Traffic congestion often incurs environmental problems. One of the most effective ways to mitigate this is carpooling transportation, which substantially reduces automobile demands. Due to the popularization of smartphones and mobile applications, a carpool service can be conveniently accessed via the intelligent carpool system. In this system, the service optimization required to intelligently and adaptively distribute the carpool participant resources is called the carpool service problem (CSP). Several previous studies have examined viable and preliminary solutions to the CSP by using exact and metaheuristic optimization approaches. For CSP-solving, evolutionary computation (e.g., metaheuristics) is a more promising option in comparison to exact-type approaches. However, all the previous state-of-the-art approaches use pure optimization to solve the CSP. In this paper, we employ the framework of neuroevolution to propose the self-organizing map-based neuroevolution (SOMNE) solver by which the SOM-like network represents the abstract CSP solution and is well-trained by using neural learning and evolutionary mechanism. The experimental section of this paper investigates the comparisons and analyses of two objective functions of the CSP and demonstrates that the proposed SOMNE solver achieves superior results when compared against those the other approaches produce, especially in regard to the optimization of the primary objective functions of the CSP. Finally, the visual results of the SOM are illustrated to show the effectiveness and efficiency of the evolutionary neural learning process.

Neurofuzzy c-Means Network-Based SCARA Robot for Head Gimbal Assembly (HGA) Circuit Inspection

Decision and control of SCARA robot in HGA (head gimbal assembly) inspection line is a very challenge issue in hard disk drive (HDD) manufacturing. The HGA circuit called slider FOS is a part of HDD which is used for reading and writing data inside the disk with a very small dimension, i.e., 45 × 64 µm. Accuracy plays an important role in this inspection, and classification of defects is very crucial to assign the action of the SCARA robot. The robot can move the inspected parts into the corresponding boxes, which are divided into 5 groups and those are “Good,” “Bridging,” “Missing,” “Burn,” and “No connection.” A general image processing technique, blob analysis, in conjunction with neurofuzzy c-means (NFC) clustering with branch and bound (BNB) technique to find the best structure in all possible candidates was proposed to increase the performance of the entire robotics system. The results from two clustering techniques which are K-means, Kohonen network, and neurofuzzy c-means were investigated to show the effectiveness of the proposed algorithm. Training results from the 30x microscope inspection with 300 samples show that the best accuracy for clustering is 99.67% achieved from the NFC clustering with the following features: area, moment of inertia, and perimeter, and the testing results show 92.21% accuracy for the conventional Kohonen network. The results exhibit the improvement on the clustering when the neural network was applied. This application is one of the progresses in neurorobotics in industrial applications. This system has been implemented successfully in the HDD production line at Seagate Technology (Thailand) Co. Ltd.

Grid topologies for the self-organizing map

The original Self-Organizing Feature Map (SOFM) has been extended in many ways to suit different goals and application domains. However, the topologies of the map lattice that we can found in literature are nearly always square or, more rarely, hexagonal. In this paper we study alternative grid topologies, which are derived from the geometrical theory of tessellations. Experimental results are presented for unsupervised clustering, color image segmentation and classification tasks, which show that the differences among the topologies are statistically significant in most cases, and that the optimal topology depends on the problem at hand. A theoretical interpretation of these results is also developed.