2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)最新文献_第8页

Interictal Spike Classification in Pharmacoresistant Epilepsy using Combined EEG and MEG 脑电图与脑磁图联合应用于抗药癫痫的间期尖峰分类

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635501

Glykeria Sdoukopoulou, M. Antonakakis, Gabriel Modde, C. Wolters, M. Zervakis

{"title":"Interictal Spike Classification in Pharmacoresistant Epilepsy using Combined EEG and MEG","authors":"Glykeria Sdoukopoulou, M. Antonakakis, Gabriel Modde, C. Wolters, M. Zervakis","doi":"10.1109/BIBE52308.2021.9635501","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635501","url":null,"abstract":"Epilepsy is one of the most common brain disorders worldwide. The basic principle in epilepsy is to resect the epileptogenic zone (EZ) when the medicaments are inadequate to suppress epileptic seizures. Epilepsy is accompanied by interictal spikes, a surrogate marker serving as an identifier of seizures. The automatic temporal detection of these spikes is of major importance due to the demanding time consumption of the manual annotation. Electro- and magneto- encephalography (EEG and MEG) are the most usual measurement modalities for the recording of brain activity. EEG and MEG are ideal modalities for the non-invasive monitoring of drug-resistant epilepsy. Many approaches have been proposed for the temporal detection of interictal spikes. However, only single measurement modality (EEG or MEG) has been used up to now, neglecting their complementary content. In this study, we develop a multi-feature and iterative classification scheme with input from either single modality (EEG or MEG) or combined EEG/MEG (EMEG). The inputs include statistical (kurtosis and Renyi Entropy) and spectral (Energy) features as well as the functional connectivity metrics, global and local efficiency from imaginary phase lag index networks. The classification performance for all modalities ranges from 89% to 92.8%, with the maximum performance being observed for EMEG. Overall, the complementarity of EEG and MEG on the detection of interictal spikes is promising, opening new considerations on the development of automatic epileptic spike detection approaches.","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125094606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Brain-Heart Electromechanical Modeling 脑心机电建模

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635450

N. Filipovic, Christian Helmich, Jasmina Isaković

{"title":"Brain-Heart Electromechanical Modeling","authors":"N. Filipovic, Christian Helmich, Jasmina Isaković","doi":"10.1109/BIBE52308.2021.9635450","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635450","url":null,"abstract":"The brain controls the heart through the sympathetic and parasympathetic branches of the autonomic nervous system. It consists of multisynaptic pathways from myocardial cells back to peripheral ganglionic neurons and further to central preganglionic and premotor neurons. Still, there are no reliable cardiovascular markers of the sympathetic tone and of the sympathetic-parasympathetic balance. It is necessary to understand the interaction between the brain and the heart in order to make early detection and treatment of pathological changes in the brain-heart interaction. In this study we present a detailed electro-chemo-mechanical model of heart and torso, so as to simulate the three principal modes of actions of drugs for cardiomyopathy: (i) modulating calcium transients, (ii) changing kinetics of contractile proteins, (iii) changing the macroscopic structure or its boundary conditions. Heart model geometry included seven different regions. Monodomain model of modified FitzHugh-Nagumo model of the cardiac cell was used. Six electrodes were positioned on the chest to model the precordial leads and the results were compared with real clinical measurements. Inverse ECG method was used to optimize potential on the heart. A whole heart was embedded in the electrical activity throughout the torso environment, with spontaneous initiation of activation in the sinoatrial node, incorporating a specialized conduction system with heterogeneous action potential morphologies throughout the heart. We included body surface potential maps in a healthy subject during progression of ventricular activation in nine sequences. The electrical model was coupled with a mechanical model with orthotropic material properties obtained from the experiments of Holzapfel. In future research we will be more focused on in silico clinical trials with the aim to compare some clinical pathology findings on the body surface with standard 12 ECG electrode measurements.","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126722477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A subspace clustering method for satisfying stoimetric constraints in scRNA -seq scRNA -seq中满足计量约束的子空间聚类方法

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635324

Angela Huang, Junhyong Kim

{"title":"A subspace clustering method for satisfying stoimetric constraints in scRNA -seq","authors":"Angela Huang, Junhyong Kim","doi":"10.1109/BIBE52308.2021.9635324","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635324","url":null,"abstract":"With the advent of single-cell RNA-sequencing, researchers now have the ability to define cell types from large amounts of transcriptome information. Over the years, various clustering algorithms have been designed. Currently, most clustering algorithms measure cell-to-cell similarities using distance metrics based on the assumption that each cluster is comprised of “nearby” neighbors. In effect, clusters are a collection of similar cells in the embedded metric. Here, we propose that biological clusters should be comprised of sets of cells that satisfy a set of stochiometric constraints, whose intersections define a cell type. We propose to model each cell population with a single affine subspace, where all cells of the same type share a common set of linear constraints. We present an algorithm that leverages this subspace structure and learns a cell-to-cell affinity matrix based on notions of subspace similarity. We simulate scRNA-seq data according to the subspace model and benchmark our algorithm against preexisting methods. We further test our algorithm on an in-house C. elegans dataset and show recovery of information on both cell type and developmental time.","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126084873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Design and evaluation of a noninvasive tongue-computer interface for individuals with severe disabilities 重度残障人士非侵入性舌-电脑介面设计与评估

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635238

Oguzhan Kirtas, M. Mohammadi, B. Bentsen, P. Veltink, L. Struijk

{"title":"Design and evaluation of a noninvasive tongue-computer interface for individuals with severe disabilities","authors":"Oguzhan Kirtas, M. Mohammadi, B. Bentsen, P. Veltink, L. Struijk","doi":"10.1109/BIBE52308.2021.9635238","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635238","url":null,"abstract":"Tongue-computer interfaces have shown the potential to control assistive devices developed for individuals with severe disabilities. However, current efficient tongue-computer interfaces require invasive methods for attaching the sensor activation units to the tongue, such as piercing. In this study, we propose a noninvasive tongue-computer interface to avoid the requirement of invasive activation unit attachment methods. We developed the noninvasive tongue-computer interface by integrating an activation unit on a frame, and mounting the frame on an inductive tongue-computer interface (ITCI). Thus, the users are able to activate the inductive sensors on the interface by positioning the activation unit with their tongue. They also do not need to remount the activation unit before each use. We performed pointing tests for controlling a computer cursor and number typing tests with two able-bodied participants, where one of them was experienced with using invasive tongue-computer interfaces and other one had no experience. We measured throughput and movement error for pointing tasks, and speed and accuracy for number typing tasks for the evaluation of the feasibility and performance of the developed noninvasive system. Results show that the inexperienced participant achieved similar results with the developed noninvasive tongue-computer interface compared to the current invasive version of the ITCI, while the experienced participant performed better with the invasive tongue-computer interface.","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"59 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114517045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Estimation of Shear Stress Variation in Extracellular Matrix Caused by Duchenne Muscular Dystrophy 杜氏肌营养不良引起的细胞外基质剪切应力变化的估计

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635402

Momcilo Prodanovic, Danica Prodanovic, B. Stojanovic, N. Filipovic, Gordana R. Jovicic, S. Mijailovich

{"title":"Estimation of Shear Stress Variation in Extracellular Matrix Caused by Duchenne Muscular Dystrophy","authors":"Momcilo Prodanovic, Danica Prodanovic, B. Stojanovic, N. Filipovic, Gordana R. Jovicic, S. Mijailovich","doi":"10.1109/BIBE52308.2021.9635402","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635402","url":null,"abstract":"Continuous degeneration of muscle tissue, inflammatory processes and fibrosis characterized by a loss of muscle mass, formation of micro-scars, adipose tissue in the muscles and eventual muscle punctures are often signs of muscular dystrophies (dystrophinopathies). These neuromuscular diseases result from genetic mutations of a structural protein called dystrophin. The absence of functional dystrophin leads to the most common and severe form of muscular dystrophy, Duchenne muscular dystrophy (DMD). Typically, within one muscle bundle there are so-called fast and slow muscle fibers that shorten and lengthen at different speeds during muscle contraction. Using the multiscale muscle platform Mexie we evaluated how the lack of dystrophin affects the connective tissue deformation between these two types of muscle fibers. By adjusting the elasticity of extracellular matrix layer, we estimated the magnitude of the shear strain under unloaded and lightly loaded fiber contractions caused by differences in shortening velocities between fast and slow fibers. The simulations showed that without dystrophin large shear strains are generated causing local micro injury and inflammation leading to further muscle degeneration. The multiscale muscle modeling approach presented here could help accelerate understanding of DMD and lead to faster development of new drugs and treatments of patients.","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130775984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An investigation of the performances of simple gene selection methodologies for cancer classification 简单基因选择方法在癌症分类中的应用研究

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635167

Salim Sazzed

{"title":"An investigation of the performances of simple gene selection methodologies for cancer classification","authors":"Salim Sazzed","doi":"10.1109/BIBE52308.2021.9635167","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635167","url":null,"abstract":"Gene expression datasets usually contain a large number of genes which impose a computational burden and complexity on the classifier. Thus, feature selection plays an integral part in sophisticated cancer classification frameworks. In the existing literature, feature selections have been often performed by computationally expensive methods (e.g., wrapper-based methods, evolutionary algorithms). In this paper, we show that the combinations of various simple feature selection methods that require minimal computational cost are often effective for cancer classification. We utilize two sets of simple statistical methods to identify the topmost class-correlated genes (set 1) and eliminate redundant genes (set 2), respectively. Finally, the selected gene set is integrated with the support vector machine (SVM) classifier. The performances of these simple methodologies are compared with a number of existing methods on ten gene expression benchmark datasets. It is observed that in many datasets, these simple methodologies yield similar efficacy to the complex and computationally expensive approaches using only a small number of genes.","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"86 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115694174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Deep Learning and Transfer Learning for Skin Cancer Segmentation and Classification 皮肤癌分割与分类的深度学习与迁移学习

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635175

Lin Li, Wonseok Seo

{"title":"Deep Learning and Transfer Learning for Skin Cancer Segmentation and Classification","authors":"Lin Li, Wonseok Seo","doi":"10.1109/BIBE52308.2021.9635175","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635175","url":null,"abstract":"According to Skin Cancer Foundation, skin cancer is by far the most common type of cancer in the United States and worldwide. Early diagnosis of skin cancer is critical because proper treatment at early stages can increase the chance of cure and recovery. However, visual inspection of dermoscopic images by dermatologists is error-prone and time-consuming. To ensure accurate diagnosis and faster treatment of skin cancer, deep learning techniques have been utilized to conduct automated skin lesion segmentation and classification. In this paper, after image processing, a Mask R-CNN model is built for lesion segmentation, where transfer learning is utilized by using the pre-trained weights from Microsoft COCO dataset. The weights of the trained Mask R-CNN model are saved and transferred to the next task - skin lesion classification, to train a Mask R-CNN model for classification. Our experiments are conducted on the benchmark datasets from the International Skin Imaging Collaboration 2018 (ISIC 2018) and evaluated by the same metrics used in ISIC 2018. The lesion boundary segmentation and lesion classification have achieved an accuracy of 96% and a balanced multiclass accuracy of 80%, respectively.","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"62 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123052178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Automated Grading of Oral Squamous Cell Carcinoma into Multiple Classes Using Deep Learning Methods 基于深度学习方法的口腔鳞状细胞癌自动分级

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635261

J. Musulin, D. Štifanić, Ana Zulijani, Sandi Baressi Segota, I. Lorencin, N. Anđelić, Z. Car

引用次数: 2

Does the influence of hydroxychloroquine in a hypoxic ventricle differ from that of a non-hypoxic ventricle under congenital LQTS1 ? 羟氯喹对缺氧脑室的影响与先天性LQTS1下非缺氧脑室的影响不同吗?

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635330

P. Priya, Srinivasan Jayaraman

{"title":"Does the influence of hydroxychloroquine in a hypoxic ventricle differ from that of a non-hypoxic ventricle under congenital LQTS1 ?","authors":"P. Priya, Srinivasan Jayaraman","doi":"10.1109/BIBE52308.2021.9635330","DOIUrl":"https://doi.org/10.1109/BIBE52308.2021.9635330","url":null,"abstract":"Factors inducing Hydroxychloroquine (HCQ) car-diotoxicity are still unclear, and this paper attempts to understand whether the presence of hypoxia in a congenital long QT syndrome1 (LQTS1) ventricular tissue can affect the outcome of HCQ interaction. This is facilitated by analysing the combination of LQTS1, HCQ and, mild and severe hypoxic conditions in a) the three types of cardiomyocytes: endocardial, midmyocardial and epicardial, as well as b) by generating pseudo ECGs from a 2D transmural anisotropic ventricular tissue model that has been excited with premature beats (PBs) to understand the possibility of arrhythmic occurrence. Results show that inclusion of HCQ in LQTS1 conditions prolongs the action potential duration(APD) in all cell types, leading to early after depolarisations (EADs) in M-cells alone. In contrast, on including hypoxia, the APDs are shortened in all cell types. Pseudo ECGs show a QT interval prolongation on adding HCQ with LQTS1 condition. In addition to LQTS1, mild and severe hypoxia, induces QT interval reduction, with low amplitude notched or inverted T-wave respectively. In presence of PBs, premature ventricular complexes (PVCs) are generated only in presence of HCQ with LQTS1. However, no significant effect of HCQ is observed in both hypoxia severities. Clinical relevance-This in-silico ventricular model indicates that although LQTS1 patients might be contraindicated for HCQ treatment, the combination of mild hypoxia and LQTS1 doesn't pose a risk factor and could help guide HCQ therapy","PeriodicalId":343724,"journal":{"name":"2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132820498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparison of mechanical response of knee joint with healthy and damaged femoral cartilage 股骨软骨损伤与健康膝关节力学反应的比较

2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2021-10-25 DOI: 10.1109/BIBE52308.2021.9635319

Aleksandra Vulovic, G. Filardo, N. Filipovic

引用次数: 0