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2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)最新文献

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Repeatability Study on a Classifier for Gastric Cancer Detection from Breath Sensor Data 基于呼吸传感器数据的胃癌检测分类器的重复性研究
Emmi Turppa, I. Poļaka, Edgars Vasiljevs, J. Kortelainen, Gidi Shani, M. Leja, H. Haick
The SNIFFPHONE device is a portable multichannel gas sensor, aiming to detect gastric cancer (GC) from breath samples. It employs gold nanoparticle (GNP) sensors reacting to volatile organic compounds (VOCs) in the exhaled breath, a non-invasive technique to support early diagnosis. This study evaluates the repeatability of the SNIFFPHONE classification result for measurements conducted on healthy subjects over a short period of time of less than 10 minutes. Due to the portable nature of the device, repeatability is studied with respect to varying measurement location. We find the classification results repeatable with a statistically significant 81 % Pearson correlation coefficient, even though the raw sensor responses are not concluded repeatable.
SNIFFPHONE设备是一种便携式多通道气体传感器,旨在从呼吸样本中检测胃癌(GC)。它采用金纳米粒子(GNP)传感器对呼出气体中的挥发性有机化合物(VOCs)作出反应,这是一种支持早期诊断的非侵入性技术。本研究评估了在不到10分钟的短时间内对健康受试者进行的SNIFFPHONE分类结果的可重复性。由于设备的便携性,可重复性研究相对于不同的测量位置。我们发现分类结果可重复与统计显著81%的Pearson相关系数,即使原始传感器的反应是不可重复的结论。
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引用次数: 3
Combined Statistics for Differential Expression Analysis of RNA-Sequencing Data rna测序数据差异表达分析的联合统计
Dionysios Fanidis, P. Moulos
Nowadays, genome-wide expression differences between various experimental conditions are mainly monitored using RNA-sequencing. Albeit in active use for over a decade and great progress in RNA-Seq analytics, experts have not been yet able to eliminate its technical and systematic biases, inherent to every high-throughput experimental technique. The vast majority of the attempts made towards confronting RNA-sequencing data analysis challenges are primarily focusing on the development of new analysis methods. However, less effort has been devoted in combined statistical analysis approaches. Here, we present the latest developments in PANDORA, a p-value combination algorithm, implemented in the metaseqR Bioconductor package. PANDORA was proved to successfully combine results of differential expression analysis algorithms. Its power is further enhanced by more recent and powerful algorithms in order enhance clarity of the reported differentially expressed gene lists.
目前,不同实验条件下的全基因组表达差异监测主要采用rna测序技术。尽管RNA-Seq分析已经活跃使用了十多年,取得了很大进展,但专家们还没有能够消除每一种高通量实验技术固有的技术和系统偏差。面对rna测序数据分析挑战的绝大多数尝试主要集中在开发新的分析方法上。然而,在综合统计分析方法方面投入的努力较少。在这里,我们介绍了在metaseqR Bioconductor包中实现的p值组合算法PANDORA的最新进展。PANDORA被证明可以成功地结合差分表达分析算法的结果。它的力量进一步增强了最新的和强大的算法,以提高报道的差异表达基因列表的清晰度。
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引用次数: 0
Banded Pair-HMM Algorithm for DNA Variant Calling and Its Hardware Accelerator Design DNA变异召唤的带状对hmm算法及其硬件加速器设计
Ming-Hung Chen, Mao-Jan Lin, Yu-Cheng Li, Yi-Chang Lu
In this paper, we propose a new pair hidden Markov model (Pair-HMM) algorithm, namely Banded Pair-HMM, which is a heuristic approach for variant calling applications. When compared to the conventional Pair-HMM, our Banded Pair-HMM can reduce the execution time at a minor cost in accuracy. In addition, a hardware accelerator is implemented using TSMC 40nm technology based on the proposed algorithm. As demonstrated later in the paper, the proposed hardware accelerator runs 4× faster than the conventional Pair-HMM hardware, and over 17,000× faster than the original Pair-HMM software.
本文提出了一种新的对隐马尔可夫模型(pair - hmm)算法,即带状对隐马尔可夫算法,它是一种针对变量调用应用的启发式方法。与传统的Pair-HMM相比,我们的带状Pair-HMM可以在较小的精度成本下减少执行时间。在此基础上,采用台积电40nm工艺实现了硬件加速器。正如本文后面所展示的,所提出的硬件加速器比传统的Pair-HMM硬件快4倍,比原始的Pair-HMM软件快17000倍以上。
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引用次数: 1
Abnormal Behavior Detection for Elderly People Living Alone Leveraging IoT Sensors 利用物联网传感器检测独居老人异常行为
M. Koutli, Natalia Theologou, Athanasios Tryferidis, D. Tzovaras
E-health home based solutions reduce healthcare costs and allow aging population to continue their daily life independently. Our objective, is to combine simple IoT sensors and machine learning techniques, in order to provide a home based solution that is able to detect behavioral changes of elderly people who live alone. For this purpose, we introduce a non-intrusive, spatio-temporal abnormal behavior detection approach. In this approach, motion and door sensor signals are elaborated to produce contextual metrics, which are filtered from any deviant observations, after performing a silhouette analysis on five outlier detection algorithms. Next, the combination of a classification and a regression based approach is proposed for detecting abnormalities in the metrics, both in the contexts of space and time. IoT sensor data from ten elderly people houses have been collected and seven different machine learning algorithms have been analyzed in order to evaluate the performance of the individual as well as the combined approach.
基于家庭的电子健康解决方案降低了医疗保健成本,并允许老年人独立地继续他们的日常生活。我们的目标是结合简单的物联网传感器和机器学习技术,以提供一个基于家庭的解决方案,能够检测独居老人的行为变化。为此,我们引入了一种非侵入式的时空异常行为检测方法。在这种方法中,运动和门传感器信号被精心设计,以产生上下文指标,在对五种异常值检测算法进行轮廓分析后,从任何异常观察中过滤出来。接下来,提出了基于分类和回归的方法的组合,用于在空间和时间上下文中检测度量中的异常。收集了来自10个养老院的物联网传感器数据,并分析了7种不同的机器学习算法,以评估个人和组合方法的表现。
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引用次数: 13
Imaging with Ultra Fast Light Pulse in Scattering Media using the DRTS Method 超快光脉冲在散射介质中的DRTS成像方法
A. Georgakopoulos, K. Politopoulos, E. Georgiou
We demonstrate 3D-view imaging in strongly scattering media, with embedded absorbing objects, illuminated with ultra-fast photon pulse. The time-resolved photon propagation process was simulated using the Dynamic Radiative Transfer System (DRTS). Three-dimensional views were obtained at various camera positions using scattered photons. By judiciously selecting time-frame imaging and single-angle directional detection, we extract clean images of the embedded objects. Our modeling method, optical media parameters and image extraction techniques can be useful in biological imaging applications in tissues, where scattering is the dominant optical propagation process. These results have the potential of accomplishing a full 3D reconstruction of the volume of interest.
我们展示了在强散射介质中,嵌入吸收物体,用超快光子脉冲照射的3d视图成像。利用动态辐射传输系统(DRTS)模拟了时间分辨光子的传播过程。利用散射光子在不同的相机位置获得三维视图。通过合理选择时间帧成像和单角度方向检测,提取出被嵌入目标的清晰图像。我们的建模方法、光学介质参数和图像提取技术可用于组织中的生物成像应用,其中散射是主要的光学传播过程。这些结果有可能完成感兴趣的体积的完整3D重建。
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引用次数: 0
Surgical Audio Guidance SurAG: Extracting Non-Invasively Meaningful Guidance Information During Minimally Invasive Procedures 外科音频引导SurAG:在微创手术中提取无创有意义的指导信息
A. Illanes, T. Sühn, N. Esmaeili, I. Maldonado, Anna Schaufler, Chien-Hsi Chen, Axel Boese, M. Friebe
In this work we summarize applications of a novel approach for providing complementary information for guiding medical interventional devices (MID) and that have been recently published by our research team. This approach consist of using an audio sensor located in the proximal end of the MID in order to extract meaningful information concerning the interaction between the tip of the instrument and the tissue. The approach was successfully evaluated with different setups and MIDs.
在这项工作中,我们总结了一种新方法的应用,为指导医疗介入设备(MID)提供补充信息,并已由我们的研究小组最近发表。该方法包括使用位于MID近端的音频传感器,以提取有关仪器尖端与组织之间相互作用的有意义的信息。通过不同的设置和mid成功地评估了该方法。
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引用次数: 10
Wavelet Singularity Analysis for CAP Sleep Delineation 小波奇异性分析在CAP睡眠描述中的应用
David Israel Medina, M. Méndez, J. S. Murguía, I. Chouvarda
Sleep is an essential process in our life, which covers 1/3 of our lifetime. But this process can be affected by disorders producing serious consequences at physiological and behavioral level. One of the major indexes connected to the sleep disorders is the dynamic of the sleep macrostructure that is used for the assessment of sleep quality. Beyond sleep macrostructure, recently attention is also given to a finer structure of sleep called Cyclic Alternating Pattern (CAP). CAP is composed by short cortical events (A-phases), where some transition processes can be observed. With the aim to unveil properties of this transition phenomenon, in this work, we present a wavelet singularity analysis of the EEG signal during the onset and offset of A-phases. The results showed that EEG signal presents significant differences between A-phases and activity of background when the average singularity is considered. This finding can help both in better delineating the A-phases of CAP sleep and in understanding the mechanisms behind the CAP dynamics.
睡眠是我们生命中必不可少的过程,它占了我们生命的三分之一。但这一过程可能会受到生理和行为水平上产生严重后果的疾病的影响。睡眠宏观结构的动态是与睡眠障碍相关的主要指标之一,用于评估睡眠质量。除了睡眠宏观结构外,最近人们还关注一种更精细的睡眠结构,即循环交替模式(CAP)。CAP由短皮层事件(a期)组成,其中可以观察到一些过渡过程。为了揭示这种过渡现象的性质,在这项工作中,我们提出了a相开始和偏移时脑电信号的小波奇异性分析。结果表明,考虑平均奇异性时,脑电信号a相与背景活动存在显著差异。这一发现有助于更好地描述CAP睡眠的a期,并有助于理解CAP动态背后的机制。
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引用次数: 2
Automated Sleep Spindle Detection System using Period-Amplitude Analysis 基于周期-振幅分析的自动睡眠主轴检测系统
Panagiotis Rizogiannis, P. Ktonas, H. Tsekou, T. Paparrigopoulos, D. Dikeos, E. Ventouras
Sleep spindles are rhythmic transient waveforms present in the electroencephalogram (EEG) of non-rapid eye movement (NREM) sleep. In the present study a period-amplitude analysis method was applied for the automated detection of sleep spindles in all-night sleep EEG recordings of young healthy subjects. The method relies on the characterization of individual half-waves of the EEG data, by estimating electrographic parameters such as amplitude and duration and by assigning a grade to each half-wave depending on where it lies in the amplitude-frequency plane. The grading is followed by the detection system, checking consecutive half-wave characteristics and implementing a set of rules for determining the start and the end of spindle bursts and for retaining or rejecting sleep spindle indications provided during the various stages of the detection system. The sensitivity and false positive rate across subjects was 78.9% and 10.9%, respectively, providing indication that the method could be successfully applied to larger sets of healthy subjects of various age groups, as well as to patient populations.
睡眠纺锤波是在非快速眼动(NREM)睡眠的脑电图(EEG)中出现的有节奏的瞬态波形。本研究采用周期-振幅分析方法对健康青年的睡眠脑电图记录中的睡眠纺锤波进行自动检测。该方法依赖于脑电图数据中单个半波的特征,通过估计振幅和持续时间等电参数,并根据每个半波在幅频平面中的位置为其分配等级。分级之后是检测系统,检查连续的半波特征,并实施一套规则,以确定纺锤波爆发的开始和结束,并保留或拒绝在检测系统的各个阶段提供的睡眠纺锤波指示。受试者的敏感性和假阳性率分别为78.9%和10.9%,表明该方法可以成功地应用于更大范围的不同年龄组的健康受试者以及患者群体。
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引用次数: 0
Parkinson's Disease Mid-Brain Assessment using MR T2 Images 使用MR T2图像评估帕金森病中脑
S. Soltaninejad, Pengda Xu, I. Cheng
The reduction of dopamine generating neurons in the brain regions known as substantia nigra (SN) is the reason for Parkinson's Disease (PD). To detect such symptom, for each subject, our algorithm only needs to analyze 3 slices around the center of a MRI DICOM volume, i.e., mid-brain area. In each slice, a window covering the SN becomes the region of interest (ROI) for further analysis. The ROIs are pre-processed by denoising and removing intensity non-uniformity. Local Binary Pattern (LBP) and Histogram Oriented Gradient (HOG) are used for feature extraction. Random Forest (RF) and Support Vector Machine (SVM) are used as classifiers with Principle Component Analysis (PCA) as feature reduction method. For evaluation, we use MRI T2 scans from the Parkinson's Progression Markers Initiative (PPMI) data set. We conducted experiments to illustrate the different classification capabilities of LBP, HOG and the fusion of these features for PD prognosis. Analysis shows that the SVM classifier with fusion feature descriptors has the most accurate classification outcome for PD assessment.
在被称为黑质(SN)的大脑区域中产生多巴胺的神经元减少是帕金森病(PD)的原因。为了检测这种症状,对于每个受试者,我们的算法只需要分析MRI DICOM体积中心周围的3个切片,即中脑区域。在每个切片中,覆盖SN的窗口成为进一步分析的感兴趣区域(ROI)。对roi进行去噪和去除强度不均匀性预处理。采用局部二值模式(LBP)和直方图梯度(HOG)进行特征提取。采用随机森林(Random Forest, RF)和支持向量机(Support Vector Machine, SVM)作为分类器,主成分分析(principal Component Analysis, PCA)作为特征约简方法。为了评估,我们使用了帕金森病进展标志物倡议(PPMI)数据集的MRI T2扫描。我们通过实验来说明LBP、HOG的不同分类能力以及这些特征的融合对PD预后的影响。分析表明,融合特征描述子的SVM分类器对PD评估的分类结果最准确。
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引用次数: 3
Computational Modeling of Psychological Resilience Trajectories During Breast Cancer Treatment 乳腺癌治疗过程中心理弹性轨迹的计算模型
Georgios C. Manikis, R. Pat-Horenczyk, D. Fotiadis, M. Tsiknakis, P. Simos, Konstantina D. Kourou, P. Poikonen-Saksela, H. Kondylakis, E. Karademas, K. Marias, Dimitrios G. Katehakis, L. Koumakis, A. Kouroubali
Coping with breast cancer and its consequences has now become a major socioeconomic challenge. The BOUNCE EU H2020 project aims at building a quantitative mathematical model of factors associated with optimal adjustment capacity to cancer. This paper gives an overview of the project targets and on the algorithmic methods focusing on modeling the psychological resilience trajectories during breast cancer treatment.
应对乳腺癌及其后果现已成为一项重大的社会经济挑战。BOUNCE EU H2020项目旨在建立与癌症最佳调节能力相关因素的定量数学模型。本文概述了项目目标和算法方法,重点是建模乳腺癌治疗期间的心理弹性轨迹。
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引用次数: 4
期刊
2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)
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