A review of intelligent systems for heart sound signal analysis

Intelligent computer-aided diagnosis (CAD) systems can enhance the diagnostic capabilities of physicians and reduce the time required for accurate diagnosis. CAD systems could provide physicians with a suggestion about the diagnostic of heart diseases. The objective of this paper is to review the recent published preprocessing, feature extraction and classification techniques and their state of the art of phonocardiogram (PCG) signal analysis. Published literature reviewed in this paper shows the potential of machine learning techniques as a design tool in PCG CAD systems and reveals that the CAD systems for PCG signal analysis are still an open problem. Related studies are compared to their datasets, feature extraction techniques and the classifiers they used. Current achievements and limitations in developing CAD systems for PCG signal analysis using machine learning techniques are presented and discussed. In the light of this review, a number of future research directions for PCG signal analysis are provided.     

基于深度学习的医学图像识别研究进展

近年来,随着医学影像技术的快速发展,医学图像分析步入大数据时代,如何从海量的医学图像数据中挖掘出有用信息,对医学图像识别带来巨大的挑战。深度学习是机器学习的一个新领域,传统的机器学习方法不能有效地挖掘到医学图像中蕴含的丰富信息,而深度学习通过模拟人脑建立分层模型,具有强大的自动特征提取、复杂模型构建以及高效的特征表达能力,更重要的是深度学习方法能从像素级的原始数据中逐级提取从底层到高层的特征,这为解决医学图像识别面临的新问题提供了新思路。首先阐述深度学习方法,列举深度学习方法的三种常见的实现模型,并介绍深度学习的训练过程;随后总结了深度学习方法在疾病检测与分类和病变识别两方面的应用情况,以及深度学习应用在医学图像识别中的两个共性问题;最后对深度学习在医学图像识别中存在的问题进行分析及展望.     

Text summarization in the biomedical domain: A systematic review of recent research

ObjectiveThe amount of information for clinicians and clinical researchers is growing exponentially. Text summarization reduces information as an attempt to enable users to find and understand relevant source texts more quickly and effortlessly. In recent years, substantial research has been conducted to develop and evaluate various summarization techniques in the biomedical domain. The goal of this study was to systematically review recent published research on summarization of textual documents in the biomedical domain.Materials and methodsMEDLINE (2000 to October 2013), IEEE Digital Library, and the ACM digital library were searched. Investigators independently screened and abstracted studies that examined text summarization techniques in the biomedical domain. Information is derived from selected articles on five dimensions: input, purpose, output, method and evaluation.ResultsOf 10,786 studies retrieved, 34 (0.3%) met the inclusion criteria. Natural language processing (17; 50%) and a hybrid technique comprising of statistical, Natural language processing and machine learning (15; 44%) were the most common summarization approaches. Most studies (28; 82%) conducted an intrinsic evaluation.DiscussionThis is the first systematic review of text summarization in the biomedical domain. The study identified research gaps and provides recommendations for guiding future research on biomedical text summarization.ConclusionRecent research has focused on a hybrid technique comprising statistical, language processing and machine learning techniques. Further research is needed on the application and evaluation of text summarization in real research or patient care settings.     

卷积神经网络在医学图像分割中的研究进展

卷积神经网络（CNN）是目前计算机视觉和模式识别中效果最为突出的算法。CNN拥有强大的空间识别能力,可以从图像中提取高阶的空间特征,同时通过共用卷积核的方式大幅减少参数量,从而在提升网络性能的同时保持总参数量在一个合理的、可运算的范畴。部分采用无监督学习的CNN算法可以在没有先验知识的条件下实现一定程度的图像语义分割,大幅减少人工读图的负担。本研究就CNN在医学图像分割中的研究进展和使用CNN时的具体技巧及其效果进行综述。以使用CNN为核心的深度学习工具解决医学图像分割的课题为中心,展示了CNN在有监督学习、半监督学习及无监督学习中的巨大潜力,分析比较了现有方案的优点与不足,探讨了未来CNN在医学图像领域的前进方向。     

Novel machine learning methods for ERP analysis: a validation from research on infants at risk for autism

Machine learning and other computer intensive pattern recognition methods are successfully applied to a variety of fields that deal with high-dimensional data and often small sample sizes such as genetic microarray, functional magnetic resonance imaging (fMRI) and, more recently, electroencephalogram (EEG) data. The aim of this article is to discuss the use of machine learning and discrimination methods and their possible application to the analysis of infant event-related potential (ERP) data. The usefulness of two methods, regularized discriminant function analyses and support vector machines, will be demonstrated by reanalyzing an ERP dataset from infants ( Elsabbagh et al., 2009 ). Using cross-validation, both methods successfully discriminated above chance between groups of infants at high and low risk of a later diagnosis of autism. The suitability of machine learning methods for the use of single trial or averaged ERP data is discussed.     

基于磁共振图像的帕金森病计算机辅助诊断研究进展

近年来,由于帕金森病(PD)的临床复杂性与多模态磁共振(MR)图像的高维性,如何有效挖掘图像中特异性标记PD的影像生物标志物、建立高效的PD计算机辅助诊断(CAD)模型是研究中极具挑战性的问题。综述目前国内外研究进展,进一步分析MR多模态特征提取、特征选择、分类器模型等传统机器学习方法建立CAD模型的关键技术,并简要概述基于深度学习方法在早期PD分类诊断中的应用。指出基于多模态MR图像,采用机器学习或深度学习方法构建CAD模型,能够客观、准确地识别PD患者,对提高早期PD诊断的准确性具有很大价值和应用前景。今后研究应更深入挖掘多模态MR图像中的潜在标记PD的影像生物指标,开发更高阶的CAD模型,以辅助早期PD的临床智能诊断。     

机器学习在电子病历中应用的可视化分析

为探讨机器学习方法在电子病历领域应用的研究现状、研究热点与前沿,以2000～2022年中国知网数据库和Web of Science核心合集数据库中关于机器学习在电子病历中应用的相关文献为数据来源,运用CiteSpace软件绘制国家/地区、作者、机构、关键词共现以及关键词突现5个方面科学知识图谱进行可视化对比分析,以便了解国内外研究的差异,为该领域的研究和发展提供参考。     

Learning to Translate Sequence and Structure to Function: Identifying DNA Binding and Membrane Binding Proteins

A protein's function depends in a large part on interactions with other molecules. With an increasing number of protein structures becoming available every year, a corresponding structural annotation approach identifying such interactions grows more expedient. At the same time, machine learning has gained popularity in bioinformatics providing robust annotation of genes and proteins without sequence homology. Here we have developed a general machine learning protocol to identify proteins that bind DNA and membrane. In general, there is no theory or even rule of thumb to pick the best machine learning algorithm. Thus, a systematic comparison of several classification algorithms known to perform well is investigated. Indeed, the boosted tree classifier is found to give the best performance, achieving 93% and 88% accuracy to discriminate non-homologous proteins that bind membrane and DNA, respectively, significantly outperforming all previously published works. We also attempted to address the importance of the attributes in function prediction and the relationships between relevant attributes. A graphical model based on boosted trees is applied to study the important features in discriminating DNA-binding proteins. In summary, the current protocol identified physical features important in DNA and membrane binding, rather than annotating function through sequence similarity.     

Optimization of infobutton design and Implementation: A systematic review

ObjectiveInfobuttons are clinical decision tools embedded in the electronic health record that attempt to link clinical data with context sensitive knowledge resources. We systematically reviewed technical approaches that contribute to improved infobutton design, implementation and functionality.MethodsWe searched databases including MEDLINE, EMBASE, and the Cochrane Library database from inception to March 1, 2016 for studies describing the use of infobuttons. We selected full review comparative studies, usability studies, and qualitative studies examining infobutton design and implementation. We abstracted usability measures such as user satisfaction, impact, and efficiency, as well as prediction accuracy of infobutton content retrieval algorithms and infobutton adoption/interoperability.ResultsWe found 82 original research studies on infobuttons. Twelve studies met criteria for detailed abstraction. These studies investigated infobutton interoperability (1 study); tools to help tailor infobutton functionality (1 study); interventions to improve user experience (7 studies); and interventions to improve content retrieval by improving prediction of relevant knowledge resources and information needs (3 studies). In-depth interviews with implementers showed the Health Level Seven (HL7) Infobutton standard to be simple and easy to implement. A usability study demonstrated the feasibility of a tool to help medical librarians tailor infobutton functionality. User experience studies showed that access to resources with which users are familiar increased user satisfaction ratings; and that links to specific subsections of drug monographs increased information seeking efficiency. However, none of the user experience improvements led to increased usage uptake. Recommender systems based on machine learning algorithms outperformed hand-crafted rules in the prediction of relevant resources and clinicians’ information needs in a laboratory setting, but no studies were found using these techniques in clinical settings. Improved content indexing in one study led to improved content retrieval across three health care organizations.ConclusionBest practice technical approaches to ensure optimal infobutton functionality, design and implementation remain understudied. The HL7 Infobutton standard has supported wide adoption of infobutton functionality among clinical information systems and knowledge resources. Limited evidence supports infobutton enhancements such as links to specific subtopics, configuration of optimal resources for specific tasks and users, and improved indexing and content coverage. Further research is needed to investigate user experience improvements to increase infobutton use and effectiveness.     

Emotion recognition via facial expression and affective prosody in schizophrenia: a methodological review

Disturbances in affect recognition may be one of the most pervasive and serious aspects of the schizophrenic patient's interpersonal problems. Interest in the decoding of emotional information in schizophrenia has focused on facial affect recognition with 29 experimental papers on that topic published since 1987. A smaller literature exists on the topic of recognition of affect in speech and there are at least seven studies, which have examined both face and voice perception in the same individuals with schizophrenia. This paper includes a comprehensive analysis of the schizophrenia facial affect recognition research over the past decade and the schizophrenia literature on affective prosody, and provides the first review of the schizophrenia literature on multichannel emotion recognition research. The weight of evidence would suggest that individuals with schizophrenia experience problems in the perception of emotional material; however, the specificity, extent, and nature of the deficits are unclear. Emotion recognition research in schizophrenia should be informed by the general literature on emotion recognition with serious attention paid to methodological issues.     

Filter versus wrapper gene selection approaches in DNA microarray domains

DNA microarray experiments generating thousands of gene expression measurements, are used to collect information from tissue and cell samples regarding gene expression differences that could be useful for diagnosis disease, distinction of the specific tumor type, etc. One important application of gene expression microarray data is the classification of samples into known categories. As DNA microarray technology measures the gene expression en masse, this has resulted in data with the number of features (genes) far exceeding the number of samples. As the predictive accuracy of supervised classifiers that try to discriminate between the classes of the problem decays with the existence of irrelevant and redundant features, the necessity of a dimensionality reduction process is essential. We propose the application of a gene selection process, which also enables the biology researcher to focus on promising gene candidates that actively contribute to classification in these large scale microarrays. Two basic approaches for feature selection appear in machine learning and pattern recognition literature: the filter and wrapper techniques. Filter procedures are used in most of the works in the area of DNA microarrays. In this work, a comparison between a group of different filter metrics and a wrapper sequential search procedure is carried out. The comparison is performed in two well-known DNA microarray datasets by the use of four classic supervised classifiers. The study is carried out over the original-continuous and three-intervals discretized gene expression data. While two well-known filter metrics are proposed for continuous data, four classic filter measures are used over discretized data. The same wrapper approach is used for both continuous and discretized data. The application of filter and wrapper gene selection procedures leads to considerably better accuracy results in comparison to the non-gene selection approach, coupled with interesting and notable dimensionality reductions. Although the wrapper approach mainly shows a more accurate behavior than filter metrics, this improvement is coupled with considerable computer-load necessities. We note that most of the genes selected by proposed filter and wrapper procedures in discrete and continuous microarray data appear in the lists of relevant-informative genes detected by previous studies over these datasets. The aim of this work is to make contributions in the field of the gene selection task in DNA microarray datasets. By an extensive comparison with more popular filter techniques, we would like to make contributions in the expansion and study of the wrapper approach in this type of domains.     

Epilepsy detection from EEG signals: a review

Abstract

Over many decades, research is being attempted for the detection of epileptic seizure to support for automatic diagnosis system to help clinicians from burdensome work. In this respect, an enormous number of research papers is published for identification of epileptic seizure. It is difficult to present a detailed review of all these literature. Therefore, in this paper, an attempt has been made to review the detection of an epileptic seizure. More than 100 research papers have been discussed to discern the techniques for detecting the epileptic seizure. Further, the literature survey shows that the pattern recognition required to detect epileptic seizure varies with different conditions of EEG datasets. This is mainly due to the fact that EEG detected under different conditions has different characteristics. This is, in turn, necessitates the identification of pattern recognition technique to effectively distinguish EEG epileptic data from a various condition of EEG data.     

A new hybrid method based on fuzzy-artificial immune system and k-nn algorithm for breast cancer diagnosis

The use of machine learning tools in medical diagnosis is increasing gradually. This is mainly because the effectiveness of classification and recognition systems has improved in a great deal to help medical experts in diagnosing diseases. Such a disease is breast cancer, which is a very common type of cancer among woman. As the incidence of this disease has increased significantly in the recent years, machine learning applications to this problem have also took a great attention as well as medical consideration. This study aims at diagnosing breast cancer with a new hybrid machine learning method. By hybridizing a fuzzy-artificial immune system with k-nearest neighbour algorithm, a method was obtained to solve this diagnosis problem via classifying Wisconsin Breast Cancer Dataset (WBCD). This data set is a very commonly used data set in the literature relating the use of classification systems for breast cancer diagnosis and it was used in this study to compare the classification performance of our proposed method with regard to other studies. We obtained a classification accuracy of 99.14%, which is the highest one reached so far. The classification accuracy was obtained via 10-fold cross validation. This result is for WBCD but it states that this method can be used confidently for other breast cancer diagnosis problems, too.     

Machine learning of clinical performance in a pancreatic cancer database

ObjectiveWe consider predictive models for clinical performance of pancreatic cancer patients based on machine learning techniques. The predictive performance of machine learning is compared with that of the linear and logistic regression techniques that dominate the medical oncology literature.Methods and materialsWe construct predictive models over a clinical database that we have developed for the University of Massachusetts Memorial Hospital in Worcester, Massachusetts, USA. The database contains retrospective records of 91 patient treatments for pancreatic tumors. Classification and regression targets include patient survival time, Eastern Cooperative Oncology Group (ECOG) quality of life scores, surgical outcomes, and tumor characteristics. The predictive performance of several techniques is described, and specific models are presented.ResultsWe show that machine learning techniques attain a predictive performance that is as good as, or better than, that of linear and logistic regression, for target attributes that include tumor N and T stage, survival time, and ECOG quality of life scores. Bayesian techniques are found to provide the best performance overall. For tumor size as the target attribute, however, logistic regression (respectively linear regression in the case of a numerical as opposed to discrete target) performs best. Preprocessing in the form of attribute selection and supervised attribute discretization improves predictive performance for most of the predictive techniques and target attributes considered.ConclusionMachine learning provides techniques for improved prediction of clinical performance. These techniques therefore merit consideration as valuable alternatives to traditional multivariate regression techniques in clinical medical studies.     

医学图像深度学习处理方法的研究进展

由于医学图像数据爆炸式增长,传统依靠医生人工对医学图像进行分析诊断,不仅工作效率低下,工作量大,还容易误诊、漏诊。随着人工智能(artificial intelligence,AI)技术的发展与应用,机器学习(machine learning,ML),尤其是深度学习(deep learning,DL)在医学图像分析领域发挥着越来越重要的作用。本文对DL在医学图像自动分割和分类识别中的研究进展进行综述,为DL在解决医学图像分析诊断方面提供有益参考。     

一种对混养细胞基于形态的细胞分选方法

目的通过对采集的细胞图像的定量识别,并结合基于机器学习的聚类分析,实现对混合培养的多种细胞基于形态的快速识别分选。方法对体外混合培养的A549和3T3两种细胞进行免疫荧光染色以表征其形态轮廓,利用CellProfiler对采集的荧光图片进行细胞形态特征的提取,再通过CellProfiler Analyst对提取的数据进行机器学习,训练出一种规则,形成一种泛化能力,以达到对混合培养的两种细胞进行识别分选的目的。结果训练分类器准确率为81.24%,可以实现A549和3T3细胞的二分类。结论机器学习有助于提升数据聚类分析的准确率,将其应用于细胞图像的识别,可为临床对组织切片进行快速病理检测提供预判断,从而减轻医生的工作量,提高诊断的准确率。     

Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review

BackgroundThe matrix assisted laser desorption/ionization and time-of-flight mass spectrometry (MALDI-TOF MS) technology has revolutionized the field of microbiology by facilitating precise and rapid species identification. Recently, machine learning techniques have been leveraged to maximally exploit the information contained in MALDI-TOF MS, with the ultimate goal to refine species identification and streamline antimicrobial resistance determination.ObjectivesThe aim was to systematically review and evaluate studies employing machine learning for the analysis of MALDI-TOF mass spectra.Data sourcesUsing PubMed/Medline, Scopus and Web of Science, we searched the existing literature for machine learning-supported applications of MALDI-TOF mass spectra for microbial species and antimicrobial susceptibility identification.Study eligibility criteriaOriginal research studies using machine learning to exploit MALDI-TOF mass spectra for microbial specie and antimicrobial susceptibility identification were included. Studies focusing on single proteins and peptides, case studies and review articles were excluded.MethodsA systematic review according to the PRISMA guidelines was performed and a quality assessment of the machine learning models conducted.ResultsFrom the 36 studies that met our inclusion criteria, 27 employed machine learning for species identification and nine for antimicrobial susceptibility testing. Support Vector Machines, Genetic Algorithms, Artificial Neural Networks and Quick Classifiers were the most frequently used machine learning algorithms. The quality of the studies ranged between poor and very good. The majority of the studies reported how to interpret the predictors (88.89%) and suggested possible clinical applications of the developed algorithm (100%), but only four studies (11.11%) validated machine learning algorithms on external datasets.ConclusionsA growing number of studies utilize machine learning to optimize the analysis of MALDI-TOF mass spectra. This review, however, demonstrates that there are certain shortcomings of current machine learning-supported approaches that have to be addressed to make them widely available and incorporated them in the clinical routine.     

Research hurdles complicating the analysis of infertility treatment and child health

Research aimed at the empirical evaluation of infertility treatment including assisted reproductive technologies (ART) on child health and development is hampered by investigators' inability to methodologically separate possible treatment effects from underlying fecundity impairments. While the literature continues to identify ART as a risk factor for many child health outcomes, less attention has been paid to the methodologic rigor needed to answer this question. We identify aspects of fecundity and the nuances of medical practice that need to be considered and captured when designing epidemiologic investigations aimed at assessing ART and child health. These include: (i) the use of prospective study designs in which the unit of analysis (cycle versus individual versus couple) is defined; (ii) data collection on relevant time-varying covariates at, before and during treatment; and (iii) the use of statistical techniques appropriate for hierarchical data and correlated exposures. While none of these issues in and by itself is unique to ART research, attention to these issues has been lacking in much of the published research limiting our ability to evaluate health consequences for children. Longitudinal studies of children conceived with ART will benefit from attention to these issues and, hopefully, produce answers to lingering questions about safety.     

A primer on gene expression and microarrays for machine learning researchers

Data originating from biomedical experiments has provided machine learning researchers with an important source of motivation for developing and evaluating new algorithms. A new wave of algorithmic development has been initiated with the publication of gene expression data derived from microarrays. Microarray data analysis is particularly challenging given the large number of measurements (typically in the order of thousands) that are reported for relatively few samples (typically in the order of dozens). Many data sets are now available on the web. It is important that machine learning researchers understand how data are obtained and which assumptions are necessary in the analysis. Microarray data have the potential to cause significant impact in machine learning research, not just as a rich and realistic source of cases for testing new algorithms, as has been the UCI machine learning repository in the past decades, but also as a main motivation for their development. In this article, we briefly review the biology underlying microarrays, the process of obtaining gene expression measurements, and the rationale behind the common types of analyses involved in a microarray experiment. We outline the main challenges and reiterate critical considerations regarding the construction of supervised learning models that use this type of data. The goal of this article is to familiarize machine learning researchers with data originated from gene expression microarrays.     

电子病历中命名实体的智能识别

电子病历中命名实体的识别对于构建和挖掘大型临床数据库以服务于临床决策具有重要意义,而我国目前对此的研究相对较少。在比较现有的实体识别方法和模型后,采用条件随机场模型(CRF)机器学习的方法,对疾病、临床症状、手术操作3类中文病历中常见的命名实体进行智能识别。首先,通过分析电子病历的数据特征,选择以语言符号、词性、构词特征、词边界、上下文为特征集。然后,基于随机抽取的来自临床医院多个科室的电子病历数据,构建小规模语料库并进行标注。最后,利用条件随机场算法执行工具CRF++进行3次对照实验。通过逐步分析特征集中的多种特征对CRF自动识别的影响,提出在中文病历环境下CRF特征选择和模板设计的一些基本规则。在对照实验中,本方法取得了良好效果,3类实体的最佳F值分别达到了92.67%、93.76%和95.06%。