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Diao H, Lu G, Wang Z, Zhang Y, Liu X, Ma Q, Yu H, Li Y. Risk factors and predictors of venous thromboembolism in patients with acute spontaneous intracerebral hemorrhage: A systematic review and meta-analysis. Clin Neurol Neurosurg 2024; 244:108430. [PMID: 39032425 DOI: 10.1016/j.clineuro.2024.108430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE), is a common and preventable complication of patients with acute spontaneous intracerebral hemorrhages (ICH). Knowledge of VTE risk factors in patients with acute spontaneous ICH continues to evolve while remains controversial. Therefore, this study aims to summarize the risk factors and predictors of VTE in patients with acute spontaneous ICH. METHODS EMBASE, PubMed, Web of Science and Cochrane databases were searched for articles containing Mesh words "Cerebral hemorrhage" and "Venous thromboembolism." Eligibility screening, data extraction, and quality assessment of the retrieved articles were conducted independently by two reviewers. We performed meta-analysis to determine risk factors for the development of VTE in acute spontaneous ICH patients. Sensitivity analysis were performed to explore the sources of heterogeneity. RESULTS Of the 12,362 articles retrieved, 17 cohort studies were included.Meta-analysis showed that longer hospital stay [OR=15.46, 95 % CI (12.54, 18.39), P<0.00001], infection [OR=5.59, 95 % CI (1.53, 20.42), P=0.009], intubation [OR=4.32, 95 % CI (2.79, 6.69), P<0.00001] and presence of intraventricular hemorrhage (IVH) [OR=1.89, 95 % CI (1.50, 2.38), P<0.00001] were significant risk factors for VTE in acute spontaneous ICH patients. Of the 17 studies included, five studies reported six prediction models, including 15 predictors. The area under the receiver operating curve (AUC) ranged from 0.71 to 0.95. One of the models was externally validated. CONCLUSION Infection, the intubation, presence of IVH and longer hospital stay were risk factors for the development of VTE in acute spontaneous ICH patients. Prediction models of VTE based on acute spontaneous ICH patients have been poorly reported and more research will be needed before such models can be applied in clinical settings.
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Affiliation(s)
- Haiqing Diao
- School of Nursing, Yangzhou University, Yangzhou, Jiangsu, China
| | - Guangyu Lu
- School of Public Health, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiyao Wang
- School of Clinical Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Neuro-Intensive Care Unit, Department of Neurosurgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Yang Zhang
- School of Nursing, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoguang Liu
- Neuro-Intensive Care Unit, Department of Neurosurgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Qiang Ma
- Neuro-Intensive Care Unit, Department of Neurosurgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Hailong Yu
- Neuro-Intensive Care Unit, Department of Neurosurgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Yuping Li
- Neuro-Intensive Care Unit, Department of Neurosurgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China; Department of Neurosurgery, Yangzhou Clinical Medical College of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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Ghosh S, Burger P, Simeunovic-Ostojic M, Maas J, Petković M. Review of machine learning solutions for eating disorders. Int J Med Inform 2024; 189:105526. [PMID: 38935998 DOI: 10.1016/j.ijmedinf.2024.105526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Eating Disorders (EDs) are one of the most complex psychiatric disorders, with significant impairment of psychological and physical health, and psychosocial functioning, and are associated with low rates of early detection, low recovery and high relapse rates. This underscores the need for better diagnostic and treatment methods. OBJECTIVE This narrative review explores current Machine Learning (ML) and Artificial Intelligence (AI) applications in the domain of EDs, with a specific emphasis on clinical management in treatment settings. The primary objective are to (i) decrease the knowledge gap between ED researchers and AI-practitioners, by presenting the current state-of-the-art AI applications (including models for causality) in different ED use-cases; (ii) identify limitations of these existing AI interventions and how to address them. RESULTS AI/ML methods have been applied in different ED use-cases, including ED risk factor identification and incidence prediction (including the analysis of social media content in the general population), diagnosis, monitoring patients and treatment response and prognosis in clinical populations. A comparative analysis of AI-techniques deployed in these use-cases have been performed, considering factors such as complexity, flexibility, functionality, explainability and adaptability to healthcare constraints. CONCLUSION Multiple restrictions have been identified in the existing methods in ML and Causality in terms of achieving actionable healthcare for ED, like lack of good quality and quantity of data for models to train on, while requiring models to be flexible, high-performing, yet being explainable and producing counterfactual explanations, for ensuring the fairness and trustworthiness of its decisions. We conclude that to overcome these limitations and for future AI research and application in clinical management of ED, (i) careful considerations are required with regards to AI-model selection, and (ii) joint efforts from ED researcher and patient community are essential in building better quality and quantity of dedicated ED datasets and secure AI-solution framework.
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Affiliation(s)
- Sreejita Ghosh
- Dept. M & CS, Technical University of Eindhoven, Groene Loper 5, 5612 AZ Eindhoven, the Netherlands.
| | - Pia Burger
- Center of Eating Disorders, GGZ Oost-Brabant, Wesselmanlaan 25a, 5707 HA Helmond, the Netherlands.
| | | | - Joyce Maas
- Center of Eating Disorders, GGZ Oost-Brabant, Wesselmanlaan 25a, 5707 HA Helmond, the Netherlands; Dept. Medical and Clinical Psychology, Tilburg University, Prof. Cobbenhagenlaan, 5037 AB Tilburg, the Netherlands
| | - Milan Petković
- Dept. M & CS, Technical University of Eindhoven, Groene Loper 5, 5612 AZ Eindhoven, the Netherlands; Philips Hospital Patient Monitoring, High Tech Campus 34, 5656 AE Eindhoven, the Netherlands
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Aljarallah NA, Dutta AK, Sait ARW. A Systematic Review of Genetics- and Molecular-Pathway-Based Machine Learning Models for Neurological Disorder Diagnosis. Int J Mol Sci 2024; 25:6422. [PMID: 38928128 PMCID: PMC11203850 DOI: 10.3390/ijms25126422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/29/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The process of identification and management of neurological disorder conditions faces challenges, prompting the investigation of novel methods in order to improve diagnostic accuracy. In this study, we conducted a systematic literature review to identify the significance of genetics- and molecular-pathway-based machine learning (ML) models in treating neurological disorder conditions. According to the study's objectives, search strategies were developed to extract the research studies using digital libraries. We followed rigorous study selection criteria. A total of 24 studies met the inclusion criteria and were included in the review. We classified the studies based on neurological disorders. The included studies highlighted multiple methodologies and exceptional results in treating neurological disorders. The study findings underscore the potential of the existing models, presenting personalized interventions based on the individual's conditions. The findings offer better-performing approaches that handle genetics and molecular data to generate effective outcomes. Moreover, we discuss the future research directions and challenges, emphasizing the demand for generalizing existing models in real-world clinical settings. This study contributes to advancing knowledge in the field of diagnosis and management of neurological disorders.
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Affiliation(s)
- Nasser Ali Aljarallah
- Department of Computer Science and Information Systems, College of Applied Sciences, AlMaarefa University, Ad Diriyah, Riyadh 13713, Saudi Arabia;
| | - Ashit Kumar Dutta
- Department of Computer Science and Information Systems, College of Applied Sciences, AlMaarefa University, Ad Diriyah, Riyadh 13713, Saudi Arabia;
| | - Abdul Rahaman Wahab Sait
- Department of Documents and Archive, Center of Documents and Administrative Communication, King Faisal University, Al-Ahsa, Al Hofuf 31982, Saudi Arabia
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Ramsay S, Allison K, Temples HS, Boccuto L, Sarasua SM. Inclusion of the severe and enduring anorexia nervosa phenotype in genetics research: a scoping review. J Eat Disord 2024; 12:53. [PMID: 38685102 PMCID: PMC11059621 DOI: 10.1186/s40337-024-01009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Anorexia nervosa has one of the highest mortality rates of all mental illnesses. For those who survive, less than 70% fully recover, with many going on to develop a more severe and enduring phenotype. Research now suggests that genetics plays a role in the development and persistence of anorexia nervosa. Inclusion of participants with more severe and enduring illness in genetics studies of anorexia nervosa is critical. OBJECTIVE The primary goal of this review was to assess the inclusion of participants meeting the criteria for the severe enduring anorexia nervosa phenotype in genetics research by (1) identifying the most widely used defining criteria for severe enduring anorexia nervosa and (2) performing a review of the genetics literature to assess the inclusion of participants meeting the identified criteria. METHODS Searches of the genetics literature from 2012 to 2023 were performed in the PubMed, PsycINFO, and Web of Science databases. Publications were selected per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The criteria used to define the severe and enduring anorexia nervosa phenotype were derived by how often they were used in the literature since 2017. The publications identified through the literature search were then assessed for inclusion of participants meeting these criteria. RESULTS most prevalent criteria used to define severe enduring anorexia nervosa in the literature were an illness duration of ≥ 7 years, lack of positive response to at least two previous evidence-based treatments, a body mass index meeting the Diagnostic and Statistical Manual of Mental Disorders-5 for extreme anorexia nervosa, and an assessment of psychological and/or behavioral severity indicating a significant impact on quality of life. There was a lack of consistent identification and inclusion of those meeting the criteria for severe enduring anorexia nervosa in the genetics literature. DISCUSSION This lack of consistent identification and inclusion of patients with severe enduring anorexia nervosa in genetics research has the potential to hamper the isolation of risk loci and the development of new, more effective treatment options for patients with anorexia nervosa.
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Affiliation(s)
- Sarah Ramsay
- Healthcare Genetics and Genomics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA.
| | - Kendra Allison
- School of Nursing, Clemson University , Clemson, SC 29634, USA
| | - Heide S Temples
- School of Nursing, Clemson University , Clemson, SC 29634, USA
| | - Luigi Boccuto
- Healthcare Genetics and Genomics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA
| | - Sara M Sarasua
- Healthcare Genetics and Genomics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA
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Barnett EJ, Onete DG, Salekin A, Faraone SV. Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:169-177. [PMID: 38109236 DOI: 10.1109/tcbb.2023.3343808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Many studies have been conducted with the goal of correctly predicting diagnostic status of a disorder using the combination of genomic data and machine learning. It is often hard to judge which components of a study led to better results and whether better reported results represent a true improvement or an uncorrected bias inflating performance. We extracted information about the methods used and other differentiating features in genomic machine learning models. We used these features in linear regressions predicting model performance. We tested for univariate and multivariate associations as well as interactions between features. Of the models reviewed, 46% used feature selection methods that can lead to data leakage. Across our models, the number of hyperparameter optimizations reported, data leakage due to feature selection, model type, and modeling an autoimmune disorder were significantly associated with an increase in reported model performance. We found a significant, negative interaction between data leakage and training size. Our results suggest that methods susceptible to data leakage are prevalent among genomic machine learning research, resulting in inflated reported performance. Best practice guidelines that promote the avoidance and recognition of data leakage may help the field avoid biased results.
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Alzoubi H, Alzubi R, Ramzan N. Deep Learning Framework for Complex Disease Risk Prediction Using Genomic Variations. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23094439. [PMID: 37177642 PMCID: PMC10181706 DOI: 10.3390/s23094439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/05/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Genome-wide association studies have proven their ability to improve human health outcomes by identifying genotypes associated with phenotypes. Various works have attempted to predict the risk of diseases for individuals based on genotype data. This prediction can either be considered as an analysis model that can lead to a better understanding of gene functions that underlie human disease or as a black box in order to be used in decision support systems and in early disease detection. Deep learning techniques have gained more popularity recently. In this work, we propose a deep-learning framework for disease risk prediction. The proposed framework employs a multilayer perceptron (MLP) in order to predict individuals' disease status. The proposed framework was applied to the Wellcome Trust Case-Control Consortium (WTCCC), the UK National Blood Service (NBS) Control Group, and the 1958 British Birth Cohort (58C) datasets. The performance comparison of the proposed framework showed that the proposed approach outperformed the other methods in predicting disease risk, achieving an area under the curve (AUC) up to 0.94.
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Affiliation(s)
- Hadeel Alzoubi
- Department of Computer Science, College of Computer Science and Information Technology, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Raid Alzubi
- Department of Computer Science, College of Computer Science and Information Technology, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Naeem Ramzan
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, High Street, Paisley PA1 2BE, UK
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A Review of Machine Learning and Deep Learning Approaches on Mental Health Diagnosis. Healthcare (Basel) 2023; 11:healthcare11030285. [PMID: 36766860 PMCID: PMC9914523 DOI: 10.3390/healthcare11030285] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Combating mental illnesses such as depression and anxiety has become a global concern. As a result of the necessity for finding effective ways to battle these problems, machine learning approaches have been included in healthcare systems for the diagnosis and probable prediction of the treatment outcomes of mental health conditions. With the growing interest in machine and deep learning methods, analysis of existing work to guide future research directions is necessary. In this study, 33 articles on the diagnosis of schizophrenia, depression, anxiety, bipolar disorder, post-traumatic stress disorder (PTSD), anorexia nervosa, and attention deficit hyperactivity disorder (ADHD) were retrieved from various search databases using the preferred reporting items for systematic reviews and meta-analysis (PRISMA) review methodology. These publications were chosen based on their use of machine learning and deep learning technologies, individually assessed, and their recommended methodologies were then classified into the various disorders included in this study. In addition, the difficulties encountered by the researchers are discussed, and a list of some public datasets is provided.
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8
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Uhlenberg L, Derungs A, Amft O. Co-simulation of human digital twins and wearable inertial sensors to analyse gait event estimation. Front Bioeng Biotechnol 2023; 11:1104000. [PMID: 37122859 PMCID: PMC10132030 DOI: 10.3389/fbioe.2023.1104000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/29/2023] [Indexed: 05/02/2023] Open
Abstract
We propose a co-simulation framework comprising biomechanical human body models and wearable inertial sensor models to analyse gait events dynamically, depending on inertial sensor type, sensor positioning, and processing algorithms. A total of 960 inertial sensors were virtually attached to the lower extremities of a validated biomechanical model and shoe model. Walking of hemiparetic patients was simulated using motion capture data (kinematic simulation). Accelerations and angular velocities were synthesised according to the inertial sensor models. A comprehensive error analysis of detected gait events versus reference gait events of each simulated sensor position across all segments was performed. For gait event detection, we considered 1-, 2-, and 4-phase gait models. Results of hemiparetic patients showed superior gait event estimation performance for a sensor fusion of angular velocity and acceleration data with lower nMAEs (9%) across all sensor positions compared to error estimation with acceleration data only. Depending on algorithm choice and parameterisation, gait event detection performance increased up to 65%. Our results suggest that user personalisation of IMU placement should be pursued as a first priority for gait phase detection, while sensor position variation may be a secondary adaptation target. When comparing rotatory and translatory error components per body segment, larger interquartile ranges of rotatory errors were observed for all phase models i.e., repositioning the sensor around the body segment axis was more harmful than along the limb axis for gait phase detection. The proposed co-simulation framework is suitable for evaluating different sensor modalities, as well as gait event detection algorithms for different gait phase models. The results of our analysis open a new path for utilising biomechanical human digital twins in wearable system design and performance estimation before physical device prototypes are deployed.
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Affiliation(s)
- Lena Uhlenberg
- Hahn-Schickard, Freiburg, Germany
- Intelligent Embedded Systems Lab, University of Freiburg, Freiburg, Germany
- *Correspondence: Lena Uhlenberg,
| | - Adrian Derungs
- F. Hoffmann–La Roche Ltd, pRED, Roche Innovation Center Basel, Basel, Switzerland
| | - Oliver Amft
- Hahn-Schickard, Freiburg, Germany
- Intelligent Embedded Systems Lab, University of Freiburg, Freiburg, Germany
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Potential benefits and limitations of machine learning in the field of eating disorders: current research and future directions. J Eat Disord 2022; 10:66. [PMID: 35527306 PMCID: PMC9080128 DOI: 10.1186/s40337-022-00581-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/17/2022] [Indexed: 12/02/2022] Open
Abstract
Advances in machine learning and digital data provide vast potential for mental health predictions. However, research using machine learning in the field of eating disorders is just beginning to emerge. This paper provides a narrative review of existing research and explores potential benefits, limitations, and ethical considerations of using machine learning to aid in the detection, prevention, and treatment of eating disorders. Current research primarily uses machine learning to predict eating disorder status from females' responses to validated surveys, social media posts, or neuroimaging data often with relatively high levels of accuracy. This early work provides evidence for the potential of machine learning to improve current eating disorder screening methods. However, the ability of these algorithms to generalise to other samples or be used on a mass scale is only beginning to be explored. One key benefit of machine learning over traditional statistical methods is the ability of machine learning to simultaneously examine large numbers (100s to 1000s) of multimodal predictors and their complex non-linear interactions, but few studies have explored this potential in the field of eating disorders. Machine learning is also being used to develop chatbots to provide psychoeducation and coping skills training around body image and eating disorders, with implications for early intervention. The use of machine learning to personalise treatment options, provide ecological momentary interventions, and aid the work of clinicians is also discussed. Machine learning provides vast potential for the accurate, rapid, and cost-effective detection, prevention, and treatment of eating disorders. More research is needed with large samples of diverse participants to ensure that machine learning models are accurate, unbiased, and generalisable to all people with eating disorders. There are important limitations and ethical considerations with utilising machine learning methods in practice. Thus, rather than a magical solution, machine learning should be seen as an important tool to aid the work of researchers, and eventually clinicians, in the early identification, prevention, and treatment of eating disorders.
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Liu Y, Lin D, Li L, Chen Y, Wen J, Lin Y, He X. Using machine-learning algorithms to identify patients at high risk of upper gastrointestinal lesions for endoscopy. J Gastroenterol Hepatol 2021; 36:2735-2744. [PMID: 33929063 DOI: 10.1111/jgh.15530] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/13/2021] [Accepted: 04/25/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND AIM Endoscopic screening for early detection of upper gastrointestinal (UGI) lesions is important. However, population-based endoscopic screening is difficult to implement in populous countries. By identifying high-risk individuals from the general population, the screening targets can be narrowed to individuals who are in most need of an endoscopy. This study was designed to develop an artificial intelligence (AI)-based model to predict patient risk of UGI lesions to identify high-risk individuals for endoscopy. METHODS A total of 620 patients (from 5300 participants) were equally allocated into 10 parts for 10-fold cross validation experiments. The machine-learning predictive models for UGI lesion risk were constructed using random forest, logistic regression, decision tree, and support vector machine (SVM) algorithms. A total of 48 variables covering lifestyles, social-economic status, clinical symptoms, serological results, and pathological data were used in the model construction. RESULTS The accuracies of the four models were between 79.3% and 93.4% in the training set and between 77.2% and 91.2% in the testing dataset (logistics regression: 77.2%; decision tree: 87.3%; random forest: 88.2%; SVM: 91.2%;). The AUCs of four models showed impressive predictive ability. Comparing the four models with the different algorithms, the SVM model featured the best sensitivity and specificity in all datasets tested. CONCLUSIONS Machine-learning algorithms can accurately and reliably predict the risk of UGI lesions based on readily available parameters. The predictive models have the potential to be used clinically for identifying patients with high risk of UGI lesions and stratifying patients for necessary endoscopic screening.
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Affiliation(s)
- Yongjia Liu
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Da Lin
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Lan Li
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yu Chen
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiayao Wen
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yiguang Lin
- School of Life Sciences, University of Technology Sydney, Broadway, New South Wales, Australia
| | - Xingxiang He
- Department of Gastroenterology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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Bracher-Smith M, Crawford K, Escott-Price V. Machine learning for genetic prediction of psychiatric disorders: a systematic review. Mol Psychiatry 2021; 26:70-79. [PMID: 32591634 PMCID: PMC7610853 DOI: 10.1038/s41380-020-0825-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 12/25/2022]
Abstract
Machine learning methods have been employed to make predictions in psychiatry from genotypes, with the potential to bring improved prediction of outcomes in psychiatric genetics; however, their current performance is unclear. We aim to systematically review machine learning methods for predicting psychiatric disorders from genetics alone and evaluate their discrimination, bias and implementation. Medline, PsycInfo, Web of Science and Scopus were searched for terms relating to genetics, psychiatric disorders and machine learning, including neural networks, random forests, support vector machines and boosting, on 10 September 2019. Following PRISMA guidelines, articles were screened for inclusion independently by two authors, extracted, and assessed for risk of bias. Overall, 63 full texts were assessed from a pool of 652 abstracts. Data were extracted for 77 models of schizophrenia, bipolar, autism or anorexia across 13 studies. Performance of machine learning methods was highly varied (0.48-0.95 AUC) and differed between schizophrenia (0.54-0.95 AUC), bipolar (0.48-0.65 AUC), autism (0.52-0.81 AUC) and anorexia (0.62-0.69 AUC). This is likely due to the high risk of bias identified in the study designs and analysis for reported results. Choices for predictor selection, hyperparameter search and validation methodology, and viewing of the test set during training were common causes of high risk of bias in analysis. Key steps in model development and validation were frequently not performed or unreported. Comparison of discrimination across studies was constrained by heterogeneity of predictors, outcome and measurement, in addition to sample overlap within and across studies. Given widespread high risk of bias and the small number of studies identified, it is important to ensure established analysis methods are adopted. We emphasise best practices in methodology and reporting for improving future studies.
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Affiliation(s)
- Matthew Bracher-Smith
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Karen Crawford
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
- Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
- Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
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Exploring the Eating Disorder Examination Questionnaire, Clinical Impairment Assessment, and Autism Quotient to Identify Eating Disorder Vulnerability: A Cluster Analysis. MACHINE LEARNING AND KNOWLEDGE EXTRACTION 2020. [DOI: 10.3390/make2030019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Eating disorders are very complicated and many factors play a role in their manifestation. Furthermore, due to the variability in diagnosis and symptoms, treatment for an eating disorder is unique to the individual. As a result, there are numerous assessment tools available, which range from brief survey questionnaires to in-depth interviews conducted by a professional. One of the many benefits to using machine learning is that it offers new insight into datasets that researchers may not previously have, particularly when compared to traditional statistical methods. The aim of this paper was to employ k-means clustering to explore the Eating Disorder Examination Questionnaire, Clinical Impairment Assessment, and Autism Quotient scores. The goal is to identify prevalent cluster topologies in the data, using the truth data as a means to validate identified groupings. Our results show that a model with k = 2 performs the best and clustered the dataset in the most appropriate way. This matches our truth data group labels, and we calculated our model’s accuracy at 78.125%, so we know that our model is working well. We see that the Eating Disorder Examination Questionnaire (EDE-Q) and Clinical Impairment Assessment (CIA) scores are, in fact, important discriminators of eating disorder behavior.
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13
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Fryett JJ, Morris AP, Cordell HJ. Investigation of prediction accuracy and the impact of sample size, ancestry, and tissue in transcriptome-wide association studies. Genet Epidemiol 2020; 44:425-441. [PMID: 32190932 PMCID: PMC8641384 DOI: 10.1002/gepi.22290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/05/2020] [Accepted: 03/06/2020] [Indexed: 01/14/2023]
Abstract
In transcriptome-wide association studies (TWAS), gene expression values are predicted using genotype data and tested for association with a phenotype. The power of this approach to detect associations relies, at least in part, on the accuracy of the prediction. Here we compare the prediction accuracy of six different methods-LASSO, Ridge regression, Elastic net, Best Linear Unbiased Predictor, Bayesian Sparse Linear Mixed Model, and Random Forests-by performing cross-validation using data from the Geuvadis Project. We also examine prediction accuracy (a) at different sample sizes, (b) when ancestry of the prediction model training and testing populations is different, and (c) when the tissue used to train the model is different from the tissue to be predicted. We find that, for most genes, the expression cannot be accurately predicted, but in general sparse statistical models tend to outperform polygenic models at prediction. Average prediction accuracy is reduced when the model training set size is reduced or when predicting across ancestries and is marginally reduced when predicting across tissues. We conclude that using sparse statistical models and the development of large reference panels across multiple ethnicities and tissues will lead to better prediction of gene expression, and thus may improve TWAS power.
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Affiliation(s)
- James J. Fryett
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew P. Morris
- Division of Musculoskeletal and Dermatological SciencesUniversity of ManchesterManchesterUK
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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Rodas G, Osaba L, Arteta D, Pruna R, Fernández D, Lucia A. Genomic Prediction of Tendinopathy Risk in Elite Team Sports. Int J Sports Physiol Perform 2020; 15:489-495. [PMID: 31615970 DOI: 10.1123/ijspp.2019-0431] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/24/2019] [Accepted: 07/11/2019] [Indexed: 11/18/2022]
Abstract
PURPOSE The authors investigated the association between risk of tendinopathies and genetic markers in professional team sports. METHODS The authors studied 363 (mean [SD]; 25 [6] y, 89% male) elite players (soccer, futsal, basketball, handball, and roller hockey) from a top-level European team (FC Barcelona, Spain). Of 363, 55% (cases) had experienced 1+ episodes of tendinopathy during 2008-2018 and 45% (controls) remained injury free. The authors first examined the association between single-nucleotide polymorphisms (SNPs) and tendinopathy risk in a hypothesis-free case-control genome-wide association study (495,837 SNPs) with additional target analysis of 58 SNPs that are potential candidates to influence tendinopathy risk based on the literature. Thereafter, the authors augmented the SNP set by performing synthetic variant imputation (1,419,369 SNPs) and then used machine learning-based multivariate modeling (support vector machine and random forest) to build a reliable predictive model. RESULTS Suggestive association (P < 10-5) was found for rs11154027 (gap junction alpha 1), rs4362400 (vesicle amine transport 1-like), and rs10263021 (contactin-associated protein-like 2). Carriage of 1+ variant alleles for rs11154027 (odds ratio = 2.11; 95% confidence interval, 1.07-4.19, P = 1.01 × 10-6) or rs4362400 (odds ratio = 1.98; 95% confidence interval, 1.05-3.73, P = 9.6 × 10-6) was associated with a higher risk of tendinopathy, whereas an opposite effect was found for rs10263021 (odds ratio = 0.42; 95% confidence interval, 0.20-0.91], P = 4.5 × 10-6). In the modeling approach, one of the most robust SNPs was rs10477683 in the fibrillin 2 gene encoding fibrillin 2, a component of connective tissue microfibrils involved in elastic fiber assembly. CONCLUSIONS The authors have identified previously undescribed genetic predictors of tendinopathy in elite team sports athletes, notably rs11154027, rs4362400, and rs10263021.
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Modeling anorexia nervosa: transcriptional insights from human iPSC-derived neurons. Transl Psychiatry 2017; 7:e1060. [PMID: 28291261 PMCID: PMC5416680 DOI: 10.1038/tp.2017.37] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 12/20/2022] Open
Abstract
Anorexia nervosa (AN) is a complex and multifactorial disorder occurring predominantly in women. Despite having the highest mortality among psychiatric conditions, it still lacks robust and effective treatment. Disorders such as AN are most likely syndromes with multiple genetic contributions, however, genome-wide studies have been underpowered to reveal associations with this uncommon illness. Here, we generated induced pluripotent stem cells (iPSCs) from adolescent females with AN and unaffected controls. These iPSCs were differentiated into neural cultures and subjected to extensive transcriptome analysis. Within a small cohort of patients who presented for treatment, we identified a novel gene that appears to contribute to AN pathophysiology, TACR1 (tachykinin 1 receptor). The participation of tachykinins in a variety of biological processes and their interactions with other neurotransmitters suggest novel mechanisms for how a disrupted tachykinin system might contribute to AN symptoms. Although TACR1 has been associated with psychiatric conditions, especially anxiety disorders, we believe this report is its first association with AN. Moreover, our human iPSC approach is a proof-of-concept that AN can be modeled in vitro with a full human genetic complement, and represents a new tool for understanding the elusive molecular and cellular mechanisms underlying the disease.
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Damen JAAG, Hooft L, Schuit E, Debray TPA, Collins GS, Tzoulaki I, Lassale CM, Siontis GCM, Chiocchia V, Roberts C, Schlüssel MM, Gerry S, Black JA, Heus P, van der Schouw YT, Peelen LM, Moons KGM. Prediction models for cardiovascular disease risk in the general population: systematic review. BMJ 2016; 353:i2416. [PMID: 27184143 PMCID: PMC4868251 DOI: 10.1136/bmj.i2416] [Citation(s) in RCA: 465] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2016] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To provide an overview of prediction models for risk of cardiovascular disease (CVD) in the general population. DESIGN Systematic review. DATA SOURCES Medline and Embase until June 2013. ELIGIBILITY CRITERIA FOR STUDY SELECTION Studies describing the development or external validation of a multivariable model for predicting CVD risk in the general population. RESULTS 9965 references were screened, of which 212 articles were included in the review, describing the development of 363 prediction models and 473 external validations. Most models were developed in Europe (n=167, 46%), predicted risk of fatal or non-fatal coronary heart disease (n=118, 33%) over a 10 year period (n=209, 58%). The most common predictors were smoking (n=325, 90%) and age (n=321, 88%), and most models were sex specific (n=250, 69%). Substantial heterogeneity in predictor and outcome definitions was observed between models, and important clinical and methodological information were often missing. The prediction horizon was not specified for 49 models (13%), and for 92 (25%) crucial information was missing to enable the model to be used for individual risk prediction. Only 132 developed models (36%) were externally validated and only 70 (19%) by independent investigators. Model performance was heterogeneous and measures such as discrimination and calibration were reported for only 65% and 58% of the external validations, respectively. CONCLUSIONS There is an excess of models predicting incident CVD in the general population. The usefulness of most of the models remains unclear owing to methodological shortcomings, incomplete presentation, and lack of external validation and model impact studies. Rather than developing yet another similar CVD risk prediction model, in this era of large datasets, future research should focus on externally validating and comparing head-to-head promising CVD risk models that already exist, on tailoring or even combining these models to local settings, and investigating whether these models can be extended by addition of new predictors.
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Affiliation(s)
- Johanna A A G Damen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands Cochrane Netherlands, University Medical Center Utrecht, PO Box 85500, Str 6.131, 3508 GA Utrecht, Netherlands
| | - Lotty Hooft
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands Cochrane Netherlands, University Medical Center Utrecht, PO Box 85500, Str 6.131, 3508 GA Utrecht, Netherlands
| | - Ewoud Schuit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands Cochrane Netherlands, University Medical Center Utrecht, PO Box 85500, Str 6.131, 3508 GA Utrecht, Netherlands Stanford Prevention Research Center, Stanford University, Stanford, CA, USA
| | - Thomas P A Debray
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands Cochrane Netherlands, University Medical Center Utrecht, PO Box 85500, Str 6.131, 3508 GA Utrecht, Netherlands
| | - Gary S Collins
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Camille M Lassale
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - George C M Siontis
- Department of Cardiology, Bern University Hospital, 3010 Bern, Switzerland
| | - Virginia Chiocchia
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK Surgical Intervention Trials Unit, University of Oxford, Oxford, UK
| | - Corran Roberts
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Michael Maia Schlüssel
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Stephen Gerry
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - James A Black
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Pauline Heus
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands Cochrane Netherlands, University Medical Center Utrecht, PO Box 85500, Str 6.131, 3508 GA Utrecht, Netherlands
| | - Yvonne T van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Linda M Peelen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Karel G M Moons
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands Cochrane Netherlands, University Medical Center Utrecht, PO Box 85500, Str 6.131, 3508 GA Utrecht, Netherlands
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