• Journal of Korea Multimedia Society
• /
• v.23 no.8
• /
• pp.940-952
• /
• 2020

The Alzheimer's disease (AD) is a neurodegenerative disease commonly found in the elderly individuals. It is one of the most common forms of dementia; patients with AD suffer from a degradation of cognitive abilities over time. To correctly diagnose AD, compuated-aided system equipped with automatic classification algorithm is of great importance. In this paper, we propose a novel deep learning based classification algorithm that takes advantage of MRI biomarker images including brain areas of hippocampus and cerebrospinal fluid for the purpose of improving the AD classification performance. In particular, we develop a new approach that effectively applies MRI biomarker patch images as input to 3D Deep Convolution Neural Network. To integrate multiple classification results from multiple biomarker patch images, we proposed the effective confidence score fusion that combine classification scores generated from soft-max layer. Experimental results show that AD classification performance can be considerably enhanced by using our proposed approach. Compared to the conventional AD classification approach relying on entire MRI input, our proposed method can improve AD classification performance of up to 10.57% thanks to using biomarker patch images. Moreover, the proposed method can attain better or comparable AD classification performances, compared to state-of-the-art methods.

• Journal of the Korea Institute of Military Science and Technology
• /
• v.14 no.4
• /
• pp.719-725
• /
• 2011

To apply TMAH-based Py-MS to a field biological detection system for real-time classification of cell-type, reproducible patterns of the TMAH-based Py-MS spectra was known as a critical factor for classification but was seriously disturbed by quantity of cells injected into pyro-tube. This factor is an exterior variable that could not be complemented by improving the performance of the TMAH-based Py-MS instrument. One of idea to solve the knotty problem has been flashed from "Top-down proteomics for identification of intact microoganisms". That is, biomarker peaks are selected from complicate Py-MS spectra for intact microoganisms by tracing out their origins, based on Py-MS spectra for the featured components of different cell-types, in Top-down approach. This idea has been tested in classification of different Gram-type microoganisms. Through the analyses of spectra for the featured components - peptidoglycan and lipoteichoic acid for Gram-positive cells and lipopolysaccharide and lipid A for Gram-negative cells - with comparing to the spectra the corresponding Gram-type cells in the Top-down approach, biomarker peaks were selected to carry out PCA(Principal Component Analysis) in order to see classification of different Gram-types, resulting in significant improvement of their classification. Furthermore, weighting biomarker peaks on intact cell's spectra, based on the data for the featured components of the Gram-types, contributed to elevate classification performance.

• Journal of Gastric Cancer
• /
• v.22 no.4
• /
• pp.273-305
• /
• 2022

Gastric cancer (GC) is one of the most common lethal malignant neoplasms worldwide, with limited treatment options for both locally advanced and/or metastatic conditions, resulting in a dismal prognosis. Although the widely used morphological classifications may be helpful for endoscopic or surgical treatment choices, they are still insufficient to guide precise and/or personalized therapy for individual patients. Recent advances in genomic technology and high-throughput analysis may improve the understanding of molecular pathways associated with GC pathogenesis and aid in the classification of GC at the molecular level. Advances in next-generation sequencing have enabled the identification of several genetic alterations through single experiments. Thus, understanding the driver alterations involved in gastric carcinogenesis has become increasingly important because it can aid in the discovery of potential biomarkers and therapeutic targets. In this article, we review the molecular classifications of GC, focusing on The Cancer Genome Atlas (TCGA) classification. We further describe the currently available biomarker-targeted therapies and potential biomarker-guided therapies. This review will help clinicians by providing an inclusive understanding of the molecular pathology of GC and may assist in selecting the best treatment approaches for patients with GC.

• Journal of Biomedical Engineering Research
• /
• v.38 no.5
• /
• pp.271-276
• /
• 2017

Cancer biomarkers are using in the diagnosis, staging, prognosis and prediction of disease progression. But, there are not sufficiently profiled and validated in early detection and risk classification of prostate cancer. In this study, we have devoted to finding a panel of serum biomarkers that are able to detect the diagnosis of prostate cancer. The serum samples were consisted of 111 prostate cancer and 343 control samples and examined. Eleven biomarkers were constructed in this study, and then nine biomarkers were relevant to candidate biomarkers by using t test. Finally, four biomarkers, PSA, ApoA2, CYFRA21.1 and TTR, were selected as the prostate cancer biomarker panel, logistic regression was used to identify algorithms for diagnostic biomarker combinations(AUC = 0.9697). A panel of combination biomarkers is less invasive and could supplement clinical diagnostic accuracy.

• BMB Reports
• /
• v.53 no.12
• /
• pp.664-669
• /
• 2020

Breast cancer is one of the most frequently diagnosed cancers. Although biomarkers are continuously being discovered, few specific markers, rather than classification markers, representing the aggressiveness and invasiveness of breast cancer are known. In this study, we used samples from canine mammary tumors in a comparative approach. We subjected 36 fractions of both canine normal and mammary tumor plasmas to high-performance quantitative proteomics analysis. Among the identified proteins, LCAT was selectively expressed in mixed tumor samples. With further MRM and Western blot validation, we discovered that the LCAT protein is an indicator of aggressive mammary tumors, an advanced stage of cancer, possibly highly metastatic. Interestingly, we also found that LCAT is overexpressed in high-grade and lymph-node-positive breast cancer in silico data. We also demonstrated that LCAT is highly expressed in the sera of advanced-stage human breast cancers within the same classification. In conclusion, we identified a possible common plasma protein biomarker, LCAT, that is highly expressed in aggressive human breast cancer and canine mammary tumor.

• Progress in Medical Physics
• /
• v.30 no.2
• /
• pp.39-48
• /
• 2019

Deep learning has been applied to various medical data. In particular, current deep learning models exhibit remarkable performance at specific tasks, sometimes offering higher accuracy than that of experts for discriminating specific diseases from medical images. The current status of deep learning applications to molecular imaging can be divided into a few subtypes in terms of their purposes: differential diagnostic classification, enhancement of image acquisition, and image-based quantification. As functional and pathophysiologic information is key to molecular imaging, this review will emphasize the need for accurate biomarker acquisition by deep learning in molecular imaging. Furthermore, this review addresses practical issues that include clinical validation, data distribution, labeling issues, and harmonization to achieve clinically feasible deep learning models. Eventually, deep learning will enhance the role of theranostics, which aims at precision targeting of pathophysiology by maximizing molecular imaging functional information.

• Genomics & Informatics
• /
• v.15 no.4
• /
• pp.156-161
• /
• 2017

Transcriptome analysis has been widely used to make biomarker panels to diagnose cancers. In breast cancer, the age of the patient has been known to be associated with clinical features. As clinical transcriptome data have accumulated significantly, we classified all human genes based on age-specific differential expression between normal and breast cancer cells using public data. We retrieved the values for gene expression levels in breast cancer and matched normal cells from The Cancer Genome Atlas. We divided genes into two classes by paired t test without considering age in the first classification. We carried out a secondary classification of genes for each class into eight groups, based on the patterns of the p-values, which were calculated for each of the three age groups we defined. Through this two-step classification, gene expression was eventually grouped into 16 classes. We showed that this classification method could be applied to establish a more accurate prediction model to diagnose breast cancer by comparing the performance of prediction models with different combinations of genes. We expect that our scheme of classification could be used for other types of cancer data.

• Journal of Korea Multimedia Society
• /
• v.22 no.10
• /
• pp.1168-1177
• /
• 2019

In order to diagnose and prevent Alzheimer's Disease (AD), it is becoming increasingly important to develop a CAD(Computer-aided Diagnosis) system for AD diagnosis, which provides effective treatment for patients by analyzing 3D MRI images. It is essential to apply powerful deep learning algorithms in order to automatically classify stages of Alzheimer's Disease and to develop a Alzheimer's Disease support diagnosis system that has the function of detecting hippocampus and CSF(Cerebrospinal fluid) which are important biomarkers in diagnosis of Alzheimer's Disease. In this paper, for AD diagnosis, we classify a given MRI data into three categories of AD, mild cognitive impairment, and normal control according by applying 3D brain MRI image to the Faster R-CNN model and detect hippocampus and CSF in MRI image. To do this, we use the 2D MRI slice images extracted from the 3D MRI data of the Faster R-CNN, and perform the widely used majority voting algorithm on the resulting bounding box labels for classification. To verify the proposed method, we used the public ADNI data set, which is the standard brain MRI database. Experimental results show that the proposed method achieves impressive classification performance compared with other state-of-the-art methods.

• Journal of Biomedical Engineering Research
• /
• v.42 no.3
• /
• pp.71-79
• /
• 2021

Currently, the naked eyes-based diagnosis of bone metastases on CT images relies on qualitative assessment. For this reason, there is a great need for a state-of-the-art approach that can assess and follow-up the bone metastases with quantitative biomarker. Radiomics can be used as a biomarker for objective lesion assessment by extracting quantitative numerical values from digital medical images. In this study, therefore, we evaluated the clinical applicability of non-invasive and objective bone metastases computer-aided diagnosis using radiomics-based biomarkers in CT. We employed a total of 21 approaches consist of three-classifiers and seven-feature selection methods to predict bone metastases and select biomarkers. We extracted three-dimensional features from the CT that three groups consisted of osteoblastic, osteolytic, and normal-healthy vertebral bodies. For evaluation, we compared the prediction results of the classifiers with the medical staff's diagnosis results. As a result of the three-class-classification performance evaluation, we demonstrated that the combination of the random forest classifier and the sequential backward selection feature selection approach reached AUC of 0.74 on average. Moreover, we confirmed that 90-percentile, kurtosis, and energy were the features that contributed high in the classification of bone metastases in this approach. We expect that selected quantitative features will be helpful as biomarkers in improving the patient's survival and quality of life.

• Journal of Life Science
• /
• v.32 no.10
• /
• pp.803-811
• /
• 2022

Despite the importance of traditional Korean fermented foods, little is known about the microbial communities and diversity of fermented soy products. To gain insight into the unexplored microbial communities of both Doenjang (DJ) and Ganjang (GJ) that may contribute to the fermentation in Korean traditional foods, we carried out next-generation sequencing (NGS) based on the V3-V4 region of 16S rDNA gene analysis. The alpha diversity analysis results revealed that both the Shannon and Simpson diversity indices were significantly different between the two groups, whereas the richness indices, including ACE, CHAO, and Jackknife, were not significant. Firmicutes were the most dominant phylum in both groups, but several taxa were found to be more abundant in DJ than in GJ. The proportions of Bacillus, Kroppenstedtia, Clostridium, and Pseudomonas and most halophiles and halotolerant bacteria, such as Tetragenococcus, Chromohalobacter, Lentibacillus, and Psychrobacter, were lower in DJ than in GJ. Linear discriminant effect size (LEfSe) analysis was carried out to discover discriminative functional biomarkers. Biomarker discovery results showed that Bacillus and Tetragenococcus were identified as the most important features for the classification of subjects to DJ and GJ. Paired-permutational multivariate analysis of variance (PERMANOVA) further revealed that the bacterial community structure between the two groups was statistically different (p=0.001).