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20 result(s) for "Beyond Big Data to new Biomedical and Health Data Science: moving to next century precision health"
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Key challenges for delivering clinical impact with artificial intelligence
Background Artificial intelligence (AI) research in healthcare is accelerating rapidly, with potential applications being demonstrated across various domains of medicine. However, there are currently limited examples of such techniques being successfully deployed into clinical practice. This article explores the main challenges and limitations of AI in healthcare, and considers the steps required to translate these potentially transformative technologies from research to clinical practice. Main body Key challenges for the translation of AI systems in healthcare include those intrinsic to the science of machine learning, logistical difficulties in implementation, and consideration of the barriers to adoption as well as of the necessary sociocultural or pathway changes. Robust peer-reviewed clinical evaluation as part of randomised controlled trials should be viewed as the gold standard for evidence generation, but conducting these in practice may not always be appropriate or feasible. Performance metrics should aim to capture real clinical applicability and be understandable to intended users. Regulation that balances the pace of innovation with the potential for harm, alongside thoughtful post-market surveillance, is required to ensure that patients are not exposed to dangerous interventions nor deprived of access to beneficial innovations. Mechanisms to enable direct comparisons of AI systems must be developed, including the use of independent, local and representative test sets. Developers of AI algorithms must be vigilant to potential dangers, including dataset shift, accidental fitting of confounders, unintended discriminatory bias, the challenges of generalisation to new populations, and the unintended negative consequences of new algorithms on health outcomes. Conclusion The safe and timely translation of AI research into clinically validated and appropriately regulated systems that can benefit everyone is challenging. Robust clinical evaluation, using metrics that are intuitive to clinicians and ideally go beyond measures of technical accuracy to include quality of care and patient outcomes, is essential. Further work is required (1) to identify themes of algorithmic bias and unfairness while developing mitigations to address these, (2) to reduce brittleness and improve generalisability, and (3) to develop methods for improved interpretability of machine learning predictions. If these goals can be achieved, the benefits for patients are likely to be transformational.
‘Fit-for-purpose?’ – challenges and opportunities for applications of blockchain technology in the future of healthcare
Blockchain is a shared distributed digital ledger technology that can better facilitate data management, provenance and security, and has the potential to transform healthcare. Importantly, blockchain represents a data architecture, whose application goes far beyond Bitcoin – the cryptocurrency that relies on blockchain and has popularized the technology. In the health sector, blockchain is being aggressively explored by various stakeholders to optimize business processes, lower costs, improve patient outcomes, enhance compliance, and enable better use of healthcare-related data. However, critical in assessing whether blockchain can fulfill the hype of a technology characterized as ‘revolutionary’ and ‘disruptive’, is the need to ensure that blockchain design elements consider actual healthcare needs from the diverse perspectives of consumers, patients, providers, and regulators. In addition, answering the real needs of healthcare stakeholders, blockchain approaches must also be responsive to the unique challenges faced in healthcare compared to other sectors of the economy. In this sense, ensuring that a health blockchain is ‘fit-for-purpose’ is pivotal. This concept forms the basis for this article, where we share views from a multidisciplinary group of practitioners at the forefront of blockchain conceptualization, development, and deployment.
Why we need a small data paradigm
Background There is great interest in and excitement about the concept of personalized or precision medicine and, in particular, advancing this vision via various ‘big data’ efforts. While these methods are necessary, they are insufficient to achieve the full personalized medicine promise. A rigorous, complementary ‘small data’ paradigm that can function both autonomously from and in collaboration with big data is also needed. By ‘small data’ we build on Estrin’s formulation and refer to the rigorous use of data by and for a specific N-of-1 unit (i.e., a single person, clinic, hospital, healthcare system, community, city, etc.) to facilitate improved individual-level description, prediction and, ultimately, control for that specific unit. Main body The purpose of this piece is to articulate why a small data paradigm is needed and is valuable in itself, and to provide initial directions for future work that can advance study designs and data analytic techniques for a small data approach to precision health. Scientifically, the central value of a small data approach is that it can uniquely manage complex, dynamic, multi-causal, idiosyncratically manifesting phenomena, such as chronic diseases, in comparison to big data. Beyond this, a small data approach better aligns the goals of science and practice, which can result in more rapid agile learning with less data. There is also, feasibly, a unique pathway towards transportable knowledge from a small data approach, which is complementary to a big data approach. Future work should (1) further refine appropriate methods for a small data approach; (2) advance strategies for better integrating a small data approach into real-world practices; and (3) advance ways of actively integrating the strengths and limitations from both small and big data approaches into a unified scientific knowledge base that is linked via a robust science of causality. Conclusion Small data is valuable in its own right. That said, small and big data paradigms can and should be combined via a foundational science of causality. With these approaches combined, the vision of precision health can be achieved.
Building the case for actionable ethics in digital health research supported by artificial intelligence
The digital revolution is disrupting the ways in which health research is conducted, and subsequently, changing healthcare. Direct-to-consumer wellness products and mobile apps, pervasive sensor technologies and access to social network data offer exciting opportunities for researchers to passively observe and/or track patients ‘in the wild’ and 24/7. The volume of granular personal health data gathered using these technologies is unprecedented, and is increasingly leveraged to inform personalized health promotion and disease treatment interventions. The use of artificial intelligence in the health sector is also increasing. Although rich with potential, the digital health ecosystem presents new ethical challenges for those making decisions about the selection, testing, implementation and evaluation of technologies for use in healthcare. As the ‘Wild West’ of digital health research unfolds, it is important to recognize who is involved, and identify how each party can and should take responsibility to advance the ethical practices of this work. While not a comprehensive review, we describe the landscape, identify gaps to be addressed, and offer recommendations as to how stakeholders can and should take responsibility to advance socially responsible digital health research.
Beyond the hype of big data and artificial intelligence: building foundations for knowledge and wisdom
Big data, coupled with the use of advanced analytical approaches, such as artificial intelligence (AI), have the potential to improve medical outcomes and population health. Data that are routinely generated from, for example, electronic medical records and smart devices have become progressively easier and cheaper to collect, process, and analyze. In recent decades, this has prompted a substantial increase in biomedical research efforts outside traditional clinical trial settings. Despite the apparent enthusiasm of researchers, funders, and the media, evidence is scarce for successful implementation of products, algorithms, and services arising that make a real difference to clinical care. This article collection provides concrete examples of how “big data” can be used to advance healthcare and discusses some of the limitations and challenges encountered with this type of research. It primarily focuses on real-world data, such as electronic medical records and genomic medicine, considers new developments in AI and digital health, and discusses ethical considerations and issues related to data sharing. Overall, we remain positive that big data studies and associated new technologies will continue to guide novel, exciting research that will ultimately improve healthcare and medicine—but we are also realistic that concerns remain about privacy, equity, security, and benefit to all.
The challenges of colposcopy for cervical cancer screening in LMICs and solutions by artificial intelligence
Background The World Health Organization (WHO) called for global action towards the elimination of cervical cancer. One of the main strategies is to screen 70% of women at the age between 35 and 45 years and 90% of women managed appropriately by 2030. So far, approximately 85% of cervical cancers occur in low- and middle-income countries (LMICs). The colposcopy-guided biopsy is crucial for detecting cervical intraepithelial neoplasia (CIN) and becomes the main bottleneck limiting screening performance. Unprecedented advances in artificial intelligence (AI) enable the synergy of deep learning and digital colposcopy, which offers opportunities for automatic image-based diagnosis. To this end, we discuss the main challenges of traditional colposcopy and the solutions applying AI-guided digital colposcopy as an auxiliary diagnostic tool in low- and middle- income countries (LMICs). Main body Existing challenges for the application of colposcopy in LMICs include strong dependence on the subjective experience of operators, substantial inter- and intra-operator variabilities, shortage of experienced colposcopists, consummate colposcopy training courses, and uniform diagnostic standard and strict quality control that are hard to be followed by colposcopists with limited diagnostic ability, resulting in discrepant reporting and documentation of colposcopy impressions. Organized colposcopy training courses should be viewed as an effective way to enhance the diagnostic ability of colposcopists, but implementing these courses in practice may not always be feasible to improve the overall diagnostic performance in a short period of time. Fortunately, AI has the potential to address colposcopic bottleneck, which could assist colposcopists in colposcopy imaging judgment, detection of underlying CINs, and guidance of biopsy sites. The automated workflow of colposcopy examination could create a novel cervical cancer screening model, reduce potentially false negatives and false positives, and improve the accuracy of colposcopy diagnosis and cervical biopsy. Conclusion We believe that a practical and accurate AI-guided digital colposcopy has the potential to strengthen the diagnostic ability in guiding cervical biopsy, thereby improves cervical cancer screening performance in LMICs and accelerates the process of global cervical cancer elimination eventually.
GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network
Background Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver illness with a genetically heterogeneous background that can be accompanied by considerable morbidity and attendant health care costs. The pathogenesis and progression of NAFLD is complex with many unanswered questions. We conducted genome-wide association studies (GWASs) using both adult and pediatric participants from the Electronic Medical Records and Genomics (eMERGE) Network to identify novel genetic contributors to this condition. Methods First, a natural language processing (NLP) algorithm was developed, tested, and deployed at each site to identify 1106 NAFLD cases and 8571 controls and histological data from liver tissue in 235 available participants. These include 1242 pediatric participants (396 cases, 846 controls). The algorithm included billing codes, text queries, laboratory values, and medication records. Next, GWASs were performed on NAFLD cases and controls and case-only analyses using histologic scores and liver function tests adjusting for age, sex, site, ancestry, PC, and body mass index (BMI). Results Consistent with previous results, a robust association was detected for the PNPLA3 gene cluster in participants with European ancestry. At the PNPLA3-SAMM50 region, three SNPs, rs738409, rs738408, and rs3747207, showed strongest association (best SNP rs738409 p  = 1.70 × 10 − 20 ). This effect was consistent in both pediatric ( p  = 9.92 × 10 − 6 ) and adult ( p  = 9.73 × 10 − 15 ) cohorts. Additionally, this variant was also associated with disease severity and NAFLD Activity Score (NAS) ( p  = 3.94 × 10 − 8 , beta = 0.85). PheWAS analysis link this locus to a spectrum of liver diseases beyond NAFLD with a novel negative correlation with gout ( p  = 1.09 × 10 − 4 ). We also identified novel loci for NAFLD disease severity, including one novel locus for NAS score near IL17RA (rs5748926, p  = 3.80 × 10 − 8 ), and another near ZFP90-CDH1 for fibrosis (rs698718, p  = 2.74 × 10 − 11 ). Post-GWAS and gene-based analyses identified more than 300 genes that were used for functional and pathway enrichment analyses. Conclusions In summary, this study demonstrates clear confirmation of a previously described NAFLD risk locus and several novel associations. Further collaborative studies including an ethnically diverse population with well-characterized liver histologic features of NAFLD are needed to further validate the novel findings.
Suicide prevention and depression apps’ suicide risk assessment and management: a systematic assessment of adherence to clinical guidelines
Background There are an estimated 800,000 suicides per year globally, and approximately 16,000,000 suicide attempts. Mobile apps may help address the unmet needs of people at risk. We assessed adherence of suicide prevention advice in depression management and suicide prevention apps to six evidence-based clinical guideline recommendations: mood and suicidal thought tracking, safety plan development, recommendation of activities to deter suicidal thoughts, information and education, access to support networks, and access to emergency counseling. Methods A systematic assessment of depression and suicide prevention apps available in Google Play and Apple’s App Store was conducted. Apps were identified by searching 42matters in January 2019 for apps launched or updated since January 2017 using the terms “depression,” “depressed,” “depress,” “mood disorders,” “suicide,” and “self-harm.” General characteristics of apps, adherence with six suicide prevention strategies identified in evidence-based clinical guidelines using a 50-question checklist developed by the study team, and trustworthiness of the app based on HONcode principles were appraised and reported as a narrative review, using descriptive statistics. Results The initial search yielded 2690 potentially relevant apps. Sixty-nine apps met inclusion criteria and were systematically assessed. There were 20 depression management apps (29%), 3 (4%) depression management and suicide prevention apps, and 46 (67%) suicide prevention apps. Eight (12%) depression management apps were chatbots. Only 5/69 apps (7%) incorporated all six suicide prevention strategies. Six apps (6/69, 9%), including two apps available in both app stores and downloaded more than one million times each, provided an erroneous crisis helpline number. Most apps included emergency contact information (65/69 apps, 94%) and direct access to a crisis helpline through the app (46/69 apps, 67%). Conclusions Non-existent or inaccurate suicide crisis helpline phone numbers were provided by mental health apps downloaded more than 2 million times. Only five out of 69 depression and suicide prevention apps offered all six evidence-based suicide prevention strategies. This demonstrates a failure of Apple and Google app stores, and the health app industry in self-governance, and quality and safety assurance. Governance levels should be stratified by the risks and benefits to users of the app, such as when suicide prevention advice is provided.
High-risk multimorbidity patterns on the road to cardiovascular mortality
Background Multimorbidity, the co-occurrence of two or more diseases in one patient, is a frequent phenomenon. Understanding how different diseases condition each other over the lifetime of a patient could significantly contribute to personalised prevention efforts. However, most of our current knowledge on the long-term development of the health of patients (their disease trajectories) is either confined to narrow time spans or specific (sets of) diseases. Here, we aim to identify decisive events that potentially determine the future disease progression of patients. Methods Health states of patients are described by algorithmically identified multimorbidity patterns (groups of included or excluded diseases) in a population-wide analysis of 9,000,000 patient histories of hospital diagnoses observed over 17 years. Over time, patients might acquire new diagnoses that change their health state; they describe a disease trajectory. We measure the age- and sex-specific risks for patients that they will acquire certain sets of diseases in the future depending on their current health state. Results In the present analysis, the population is described by a set of 132 different multimorbidity patterns. For elderly patients, we find 3 groups of multimorbidity patterns associated with low (yearly in-hospital mortality of 0.2–0.3%), medium (0.3–1%) and high in-hospital mortality (2–11%). We identify combinations of diseases that significantly increase the risk to reach the high-mortality health states in later life. For instance, in men (women) aged 50–59 diagnosed with diabetes and hypertension, the risk for moving into the high-mortality region within 1 year is increased by the factor of 1.96 ± 0.11 (2.60 ± 0.18) compared with all patients of the same age and sex, respectively, and by the factor of 2.09 ± 0.12 (3.04 ± 0.18) if additionally diagnosed with metabolic disorders. Conclusions Our approach can be used both to forecast future disease burdens, as well as to identify the critical events in the careers of patients which strongly determine their disease progression, therefore constituting targets for efficient prevention measures. We show that the risk for cardiovascular diseases increases significantly more in females than in males when diagnosed with diabetes, hypertension and metabolic disorders.
Investigation of the impact of the NICE guidelines regarding antibiotic prophylaxis during invasive dental procedures on the incidence of infective endocarditis in England: an electronic health records study
Background Infective endocarditis is an uncommon but serious infection, where evidence for giving antibiotic prophylaxis before invasive dental procedures is inconclusive. In England, antibiotic prophylaxis was offered routinely to patients at risk of infective endocarditis until March 2008, when new guidelines aimed at reducing unnecessary antibiotic use were issued. We investigated whether changes in infective endocarditis incidence could be detected using electronic health records, assessing the impact of inclusion criteria/statistical model choice on inferences about the timing/type of any change. Methods Using national data from Hospital Episode Statistics covering 1998–2017, we modelled trends in infective endocarditis incidence using three different sets of inclusion criteria plus a range of regression models, identifying the most likely date for a change in trends if evidence for one existed. We also modelled trends in the proportions of different organism groups identified during infection episodes, using secondary diagnosis codes and data from national laboratory records. Lastly, we applied non-parametric local smoothing to visually inspect any changes in trend around the guideline change date. Results Infective endocarditis incidence increased markedly over the study (22.2–41.3 per million population in 1998 to 42.0–67.7 in 2017 depending on inclusion criteria). The most likely dates for a change in incidence trends ranged from September 2001 (uncertainty interval August 2000–May 2003) to May 2015 (March 1999–January 2016), depending on inclusion criteria and statistical model used. For the proportion of infective endocarditis cases associated with streptococci, the most likely change points ranged from October 2008 (March 2006–April 2010) to August 2015 (September 2013–November 2015), with those associated with oral streptococci decreasing in proportion after the change point. Smoothed trends showed no notable changes in trend around the guideline date. Conclusions Infective endocarditis incidence has increased rapidly in England, though we did not detect any change in trends directly following the updated guidelines for antibiotic prophylaxis, either overall or in cases associated with oral streptococci. Estimates of when changes occurred were sensitive to inclusion criteria and statistical model choice, demonstrating the need for caution in interpreting single models when using large datasets. More research is needed to explore the factors behind this increase.