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Machine learning in medicine: a practical introduction
by
Sidey-Gibbons, Jenni A. M.
,
Sidey-Gibbons, Chris J.
in
Accuracy
,
Algorithms
,
Archives & records
2019
Background
Following visible successes on a wide range of predictive tasks, machine learning techniques are attracting substantial interest from medical researchers and clinicians. We address the need for capacity development in this area by providing a conceptual introduction to machine learning alongside a practical guide to developing and evaluating predictive algorithms using freely-available open source software and public domain data.
Methods
We demonstrate the use of machine learning techniques by developing three predictive models for cancer diagnosis using descriptions of nuclei sampled from breast masses. These algorithms include regularized General Linear Model regression (GLMs), Support Vector Machines (SVMs) with a radial basis function kernel, and single-layer Artificial Neural Networks. The publicly-available dataset describing the breast mass samples (
N
=683) was randomly split into evaluation (
n
=456) and validation (
n
=227) samples.
We trained algorithms on data from the evaluation sample before they were used to predict the diagnostic outcome in the validation dataset. We compared the predictions made on the validation datasets with the real-world diagnostic decisions to calculate the accuracy, sensitivity, and specificity of the three models. We explored the use of averaging and voting ensembles to improve predictive performance. We provide a step-by-step guide to developing algorithms using the open-source
R
statistical programming environment.
Results
The trained algorithms were able to classify cell nuclei with high accuracy (.94 -.96), sensitivity (.97 -.99), and specificity (.85 -.94). Maximum accuracy (.96) and area under the curve (.97) was achieved using the SVM algorithm. Prediction performance increased marginally (accuracy =.97, sensitivity =.99, specificity =.95) when algorithms were arranged into a voting ensemble.
Conclusions
We use a straightforward example to demonstrate the theory and practice of machine learning for clinicians and medical researchers. The principals which we demonstrate here can be readily applied to other complex tasks including natural language processing and image recognition.
Journal Article
MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction
2021
Background
Unsupervised learning can discover various unseen abnormalities, relying on large-scale unannotated medical images of healthy subjects. Towards this, unsupervised methods reconstruct a 2D/3D single medical image to detect outliers either in the learned feature space or from high reconstruction loss. However, without considering continuity between multiple adjacent slices, they cannot directly discriminate diseases composed of the accumulation of subtle anatomical anomalies, such as Alzheimer’s disease (AD). Moreover, no study has shown how unsupervised anomaly detection is associated with either disease stages, various (i.e., more than two types of) diseases, or multi-sequence magnetic resonance imaging (MRI) scans.
Results
We propose unsupervised medical anomaly detection generative adversarial network (MADGAN), a novel two-step method using GAN-based multiple adjacent brain MRI slice reconstruction to detect brain anomalies at different stages on multi-sequence structural MRI: (
Reconstruction
) Wasserstein loss with Gradient Penalty + 100
ℓ
1
loss—trained on 3 healthy brain axial MRI slices to reconstruct the next 3 ones—reconstructs unseen healthy/abnormal scans; (
Diagnosis
) Average
ℓ
2
loss per scan discriminates them, comparing the ground truth/reconstructed slices. For training, we use two different datasets composed of 1133 healthy T1-weighted (T1) and 135 healthy contrast-enhanced T1 (T1c) brain MRI scans for detecting AD and brain metastases/various diseases, respectively. Our self-attention MADGAN can detect AD on T1 scans at a very early stage, mild cognitive impairment (MCI), with area under the curve (AUC) 0.727, and AD at a late stage with AUC 0.894, while detecting brain metastases on T1c scans with AUC 0.921.
Conclusions
Similar to physicians’ way of performing a diagnosis, using massive healthy training data, our first multiple MRI slice reconstruction approach, MADGAN, can reliably predict the next 3 slices from the previous 3 ones only for unseen healthy images. As the first unsupervised various disease diagnosis, MADGAN can reliably detect the accumulation of subtle anatomical anomalies and hyper-intense enhancing lesions, such as (especially late-stage) AD and brain metastases on multi-sequence MRI scans.
Journal Article
Saint Anthony's Fire from Antiquity to the Eighteenth Century
by
Foscati, Alessandra
in
Ergotism
2019
After the discovery of the ergotism epidemics and its etiology, 18th-century physicians interpreted medieval chronicles in their medical texts in order to recognize the occurrences of ergotic diseases through retrospective diagnosis. This book examines this historical prejudice through textual analysis, comparing medieval and early modern sources.
Investigating the impacting factors for the healthcare professionals to adopt artificial intelligence-based medical diagnosis support system (AIMDSS)
by
Fan, Wenjuan
,
Liu, Jingnan
,
Pardalos, Panos M
in
Artificial intelligence
,
Health care
,
Intelligent systems
2020
Compared to the booming industry of AIMDSS, the usage of AIMDSS among healthcare professionals is relatively low in the hospital. Thus, a research on the acceptance and adoption intention of AIMDSS by health professionals is imperative. In this study, an integration of Unified theory of user acceptance of technology and trust theory is proposed for exploring the adoption of AIMDSS. Besides, two groups of additional factors, related to AIMDSS (task complexity, technology characteristics, and perceived substitution crisis) and health professionals’ characteristics (propensity to trust and personal innovativeness in IT) are considered in the integrated model. The data set of proposed research model is collected through paper survey and Internet survey in China. The empirical examination demonstrates a high predictive power of this proposed model in explaining AIMDSS adoption. Finally, the theoretical contribution and practical implications of this research are discussed.
Journal Article
New machine learning method for image-based diagnosis of COVID-19
2020
COVID-19 is a worldwide epidemic, as announced by the World Health Organization (WHO) in March 2020. Machine learning (ML) methods can play vital roles in identifying COVID-19 patients by visually analyzing their chest x-ray images. In this paper, a new ML-method proposed to classify the chest x-ray images into two classes, COVID-19 patient or non-COVID-19 person. The features extracted from the chest x-ray images using new Fractional Multichannel Exponent Moments (FrMEMs). A parallel multi-core computational framework utilized to accelerate the computational process. Then, a modified Manta-Ray Foraging Optimization based on differential evolution used to select the most significant features. The proposed method evaluated using two COVID-19 x-ray datasets. The proposed method achieved accuracy rates of 96.09% and 98.09% for the first and second datasets, respectively.
Journal Article
The Ethics of Precision Medicine
2024
Paul Scherz explores the ethical challenges raised by precision medicine and its focus on medical risk as opposed to current disease.
Genetic technologies and artificial intelligence are rapidly changing the landscape of medical practice and patient care. In the emerging field of precision medicine, a patient's risk factors—especially genetic risk factors—are incorporated into an all-encompassing plan to prevent future disease. But identifying at-risk individuals through technologies such as wearable devices and direct-to-consumer genetic sequencing can undermine the overall experience of health. The potential for overdiagnosis and overtreatment grows as patients are prescribed medications and receive prophylactic surgeries that carry inherent risks. Also, as the medical industry shifts its attention from individuals to trends in the general population, the one-to-one practitioner-patient relationship becomes strained.
Using the lens of virtue ethics and theological bioethics, The Ethics of Precision Medicine offers suggestions for better implementing precision medicine to treat those currently suffering from or at high risk of disease, while also recognizing that effectively preventing disease depends, ultimately, on addressing the social determinants of health. The book provides a new perspective on the problems of contemporary healthcare, proposing practical steps that individuals and institutions can take to ensure that the advanced technologies of precision medicine can be used to promote human flourishing.
A deep learning approach for Parkinson’s disease diagnosis from EEG signals
by
Oh, Shu Lih
,
Hagiwara, Yuki
,
Yuvaraj, Rajamanickam
in
Artificial Intelligence
,
Artificial neural networks
,
Automation
2020
An automated detection system for Parkinson’s disease (PD) employing the convolutional neural network (CNN) is proposed in this study. PD is characterized by the gradual degradation of motor function in the brain. Since it is related to the brain abnormality, electroencephalogram (EEG) signals are usually considered for the early diagnosis. In this work, we have used the EEG signals of twenty PD and
twenty
normal subjects in this study. A
thirteen
-layer CNN architecture which can overcome the need for the conventional feature representation stages is implemented. The developed model has achieved a promising performance of 88.25% accuracy, 84.71% sensitivity, and 91.77% specificity. The developed classification model is ready to be used on large population before installation of clinical usage.
Journal Article
Computer-aided X-ray screening for tuberculosis and HIV testing among adults with cough in Malawi (the PROSPECT study): A randomised trial and cost-effectiveness analysis
2021
Suboptimal tuberculosis (TB) diagnostics and HIV contribute to the high global burden of TB. We investigated costs and yield from systematic HIV-TB screening, including computer-aided digital chest X-ray (DCXR-CAD).
In this open, three-arm randomised trial, adults (≥18 years) with cough attending acute primary services in Malawi were randomised (1:1:1) to standard of care (SOC); oral HIV testing (HIV screening) and linkage to care; or HIV testing and linkage to care plus DCXR-CAD with sputum Xpert for high CAD4TBv5 scores (HIV-TB screening). Participants and study staff were not blinded to intervention allocation, but investigator blinding was maintained until final analysis. The primary outcome was time to TB treatment. Secondary outcomes included proportion with same-day TB treatment; prevalence of undiagnosed/untreated bacteriologically confirmed TB on day 56; and undiagnosed/untreated HIV. Analysis was done on an intention-to-treat basis. Cost-effectiveness analysis used a health-provider perspective. Between 15 November 2018 and 27 November 2019, 8,236 were screened for eligibility, with 473, 492, and 497 randomly allocated to SOC, HIV, and HIV-TB screening arms; 53 (11%), 52 (9%), and 47 (9%) were lost to follow-up, respectively. At 56 days, TB treatment had been started in 5 (1.1%) SOC, 8 (1.6%) HIV screening, and 15 (3.0%) HIV-TB screening participants. Median (IQR) time to TB treatment was 11 (6.5 to 38), 6 (1 to 22), and 1 (0 to 3) days (hazard ratio for HIV-TB versus SOC: 2.86, 1.04 to 7.87), with same-day treatment of 0/5 (0%) SOC, 1/8 (12.5%) HIV, and 6/15 (40.0%) HIV-TB screening arm TB patients (p = 0.03). At day 56, 2 SOC (0.5%), 4 HIV (1.0%), and 2 HIV-TB (0.5%) participants had undiagnosed microbiologically confirmed TB. HIV screening reduced the proportion with undiagnosed or untreated HIV from 10 (2.7%) in the SOC arm to 2 (0.5%) in the HIV screening arm (risk ratio [RR]: 0.18, 0.04 to 0.83), and 1 (0.2%) in the HIV-TB screening arm (RR: 0.09, 0.01 to 0.71). Incremental costs were US$3.58 and US$19.92 per participant screened for HIV and HIV-TB; the probability of cost-effectiveness at a US$1,200/quality-adjusted life year (QALY) threshold was 83.9% and 0%. Main limitations were the lower than anticipated prevalence of TB and short participant follow-up period; cost and quality of life benefits of this screening approach may accrue over a longer time horizon.
DCXR-CAD with universal HIV screening significantly increased the timeliness and completeness of HIV and TB diagnosis. If implemented at scale, this has potential to rapidly and efficiently improve TB and HIV diagnosis and treatment.
clinicaltrials.gov NCT03519425.
Journal Article
Putting a Name to It
2024
Outlines how the social dimensions of medical diagnosis can deepen our understanding of health.
Diagnosis is central to medicine. It creates order, explains illness, identifies treatments, and predicts outcomes. In Putting a Name to It, Annemarie Jutel presents medical diagnosis as more than a mere clinical tool, but as a social phenomenon with the potential to deepen our understanding of health, illness, and disease.
Jutel outlines how the sociology of diagnosis should function by situating it within the broader discipline, laying out the directions it should explore, and discussing how the classification of illness and the framing of diagnosis relate to social status and order. This second edition provides important updates to the groundbreaking first edition by incorporating new research that demonstrates how the social nature of diagnosis is just as important as the clinical. It includes new perspectives on diagnostic recognition, diagnostic coding, lay diagnosis, crowdsourced diagnosis, algorithmic diagnosis, diagnostic exploitation, diagnostic systems, stigmatizing diagnosis, and contested diagnosis. The new edition also features a case study of COVID-19 from a critical sociological perspective and a new conclusion.
Both a challenge and a call to arms, Putting a Name to It is a lucid, persuasive argument for formalizing, professionalizing, and advancing long-standing practice. Jutel's innovative, open approach and engaging arguments illustrate how diagnoses have the power to legitimize our medical ailments—and stigmatize them.
Deep learning for detection of radiographic sacroiliitis: achieving expert-level performance
by
Hermann, Kay-Geert
,
Bressem, Keno K.
,
Rademacher, Judith
in
Application programming interface
,
Arthritis
,
Artificial intelligence
2021
Background
Radiographs of the sacroiliac joints are commonly used for the diagnosis and classification of axial spondyloarthritis. The aim of this study was to develop and validate an artificial neural network for the detection of definite radiographic sacroiliitis as a manifestation of axial spondyloarthritis (axSpA).
Methods
Conventional radiographs of the sacroiliac joints obtained in two independent studies of patients with axSpA were used. The first cohort comprised 1553 radiographs and was split into training (
n
= 1324) and validation (
n
= 229) sets. The second cohort comprised 458 radiographs and was used as an independent test dataset. All radiographs were assessed in a central reading session, and the final decision on the presence or absence of definite radiographic sacroiliitis was used as a reference. The performance of the neural network was evaluated by calculating areas under the receiver operating characteristic curves (AUCs) as well as sensitivity and specificity. Cohen’s kappa and the absolute agreement were used to assess the agreement between the neural network and the human readers.
Results
The neural network achieved an excellent performance in the detection of definite radiographic sacroiliitis with an AUC of 0.97 and 0.94 for the validation and test datasets, respectively. Sensitivity and specificity for the cut-off weighting both measurements equally were 88% and 95% for the validation and 92% and 81% for the test set. The Cohen’s kappa between the neural network and the reference judgements were 0.79 and 0.72 for the validation and test sets with an absolute agreement of 90% and 88%, respectively.
Conclusion
Deep artificial neural networks enable the accurate detection of definite radiographic sacroiliitis relevant for the diagnosis and classification of axSpA.
Journal Article