Author Correction: Improving the accuracy of medical diagnosis with causal machine learning.
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ABSTRACT:
SUBMITTER: Richens JG
PROVIDER: S-EPMC8012648 | biostudies-literature | 2021 Mar
REPOSITORIES: biostudies-literature
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Author Correction: Improving the accuracy of medical diagnosis with causal machine learning.
Richens Jonathan G JG Lee Ciarán M CM Johri Saurabh S
Nature communications 20210331 1
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Project description:Machine learning promises to revolutionize clinical decision making and diagnosis. In medical diagnosis a doctor aims to explain a patient's symptoms by determining the diseases causing them. However, existing machine learning approaches to diagnosis are purely associative, identifying diseases that are strongly correlated with a patients symptoms. We show that this inability to disentangle correlation from causation can result in sub-optimal or dangerous diagnoses. To overcome this, we reformulate diagnosis as a counterfactual inference task and derive counterfactual diagnostic algorithms. We compare our counterfactual algorithms to the standard associative algorithm and 44 doctors using a test set of clinical vignettes. While the associative algorithm achieves an accuracy placing in the top 48% of doctors in our cohort, our counterfactual algorithm places in the top 25% of doctors, achieving expert clinical accuracy. Our results show that causal reasoning is a vital missing ingredient for applying machine learning to medical diagnosis.
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Project description:An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Project description:Advances in high-throughput sequencing technologies have reduced the cost of genotyping dramatically and led to genomic prediction being widely used in animal and plant breeding, and increasingly in human genetics. Inspired by the efficient computing of linear mixed model and the accurate prediction of Bayesian methods, we propose a machine learning-based method incorporating cross-validation, multiple regression, grid search, and bisection algorithms named KAML that aims to combine the advantages of prediction accuracy with computing efficiency. KAML exhibits higher prediction accuracy than existing methods, and it is available at https://github.com/YinLiLin/KAML.
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Project description:Samples of primary tumors collected from 23 ovarian cancer patients
2018-04-07 | GSE112798 | GEO
Project description:ObjectivesTo explore an intelligent detection technology based on deep learning algorithms to assist the clinical diagnosis of distal radius fractures (DRFs), and further compare it with human performance to verify the feasibility of this method.MethodsA total of 3,240 patients (fracture: n = 1,620, normal: n = 1,620) were included in this study, with a total of 3,276 wrist joint anteroposterior (AP) X-ray films (1,639 fractured, 1,637 normal) and 3,260 wrist joint lateral X-ray films (1,623 fractured, 1,637 normal). We divided the patients into training set, validation set and test set in a ratio of 7:1.5:1.5. The deep learning models were developed using the data from the training and validation sets, and then their effectiveness were evaluated using the data from the test set. Evaluate the diagnostic performance of deep learning models using receiver operating characteristic (ROC) curves and area under the curve (AUC), accuracy, sensitivity, and specificity, and compare them with medical professionals.ResultsThe deep learning ensemble model had excellent accuracy (97.03%), sensitivity (95.70%), and specificity (98.37%) in detecting DRFs. Among them, the accuracy of the AP view was 97.75%, the sensitivity 97.13%, and the specificity 98.37%; the accuracy of the lateral view was 96.32%, the sensitivity 94.26%, and the specificity 98.37%. When the wrist joint is counted, the accuracy was 97.55%, the sensitivity 98.36%, and the specificity 96.73%. In terms of these variables, the performance of the ensemble model is superior to that of both the orthopedic attending physician group and the radiology attending physician group.ConclusionThis deep learning ensemble model has excellent performance in detecting DRFs on plain X-ray films. Using this artificial intelligence model as a second expert to assist clinical diagnosis is expected to improve the accuracy of diagnosing DRFs and enhance clinical work efficiency.
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Project description:Applying machine learning to clinical outcome prediction is challenging due to imbalanced datasets and sensitive tasks that contain rare yet critical outcomes and where equitable treatment across diverse patient groups is essential. Despite attempts, biases in predictions persist, driven by disparities in representation and exacerbated by the scarcity of positive labels, perpetuating health inequities. This paper introduces FairPlay, a synthetic data generation approach leveraging large language models, to address these issues. FairPlay enhances algorithmic performance and reduces bias by creating realistic, anonymous synthetic patient data that improves representation and augments dataset patterns while preserving privacy. Through experiments on multiple datasets, we demonstrate that FairPlay boosts mortality prediction performance across diverse subgroups, achieving up to a 21% improvement in F1 Score without requiring additional data or altering downstream training pipelines. Furthermore, FairPlay consistently reduces subgroup performance gaps, as shown by universal improvements in performance and fairness metrics across four experimental setups.
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Project description:[This corrects the article DOI: 10.1038/s41560-020-0662-1.].
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Project description:BackgroundWith the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and apply it to de novo sequencing of new organisms. As an example, this paper demonstrates how such extra information can be used to improve de novo assemblies by augmenting the overlapping step. Finding all pairs of overlapping reads is a key task in many genome assemblers, and to this end, highly efficient algorithms have been developed to find alignments in large collections of sequences. It is well known that due to repeated sequences, many aligned pairs of reads nevertheless do not overlap. But no overlapping algorithm to date takes a rigorous approach to separating aligned but non-overlapping read pairs from true overlaps.ResultsWe present an approach that extends the Minimus assembler by a data driven step to classify overlaps as true or false prior to contig construction. We trained several different classification models within the Weka framework using various statistics derived from overlaps of reads available from prior sequencing projects. These statistics included percent mismatch and k-mer frequencies within the overlaps as well as a comparative genomics score derived from mapping reads to multiple reference genomes. We show that in real whole-genome sequencing data from the E. coli and S. aureus genomes, by providing a curated set of overlaps to the contigging phase of the assembler, we nearly doubled the median contig length (N50) without sacrificing coverage of the genome or increasing the number of mis-assemblies.ConclusionsMachine learning methods that use comparative and non-comparative features to classify overlaps as true or false can be used to improve the quality of a sequence assembly.
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Project description:BackgroundPrehospital telemedicine triage systems combined with machine learning (ML) methods have the potential to improve triage accuracy and safely redirect low-acuity patients from attending the emergency department. However, research in prehospital settings is limited but needed; emergency department overcrowding and adverse patient outcomes are increasingly common.ObjectiveIn this scoping review, we sought to characterize the existing methods for ML-enhanced telemedicine emergency triage. In order to support future research, we aimed to delineate what data sources, predictors, labels, ML models, and performance metrics were used, and in which telemedicine triage systems these methods were applied.MethodsA scoping review was conducted, querying multiple databases (MEDLINE, PubMed, Scopus, and IEEE Xplore) through February 24, 2023, to identify potential ML-enhanced methods, and for those eligible, relevant study characteristics were extracted, including prehospital triage setting, types of predictors, ground truth labeling method, ML models used, and performance metrics. Inclusion criteria were restricted to the triage of emergency telemedicine services using ML methods on an undifferentiated (disease nonspecific) population. Only primary research studies in English were considered. Furthermore, only those studies using data collected remotely (as opposed to derived from physical assessments) were included. In order to limit bias, we exclusively included articles identified through our predefined search criteria and had 3 researchers (DR, JS, and KS) independently screen the resulting studies. We conducted a narrative synthesis of findings to establish a knowledge base in this domain and identify potential gaps to be addressed in forthcoming ML-enhanced methods.ResultsA total of 165 unique records were screened for eligibility and 15 were included in the review. Most studies applied ML methods during emergency medical dispatch (7/15, 47%) or used chatbot applications (5/15, 33%). Patient demographics and health status variables were the most common predictors, with a notable absence of social variables. Frequently used ML models included support vector machines and tree-based methods. ML-enhanced models typically outperformed conventional triage algorithms, and we found a wide range of methods used to establish ground truth labels.ConclusionsThis scoping review observed heterogeneity in dataset size, predictors, clinical setting (triage process), and reported performance metrics. Standard structured predictors, including age, sex, and comorbidities, across articles suggest the importance of these inputs; however, there was a notable absence of other potentially useful data, including medications, social variables, and health system exposure. Ground truth labeling practices should be reported in a standard fashion as the true model performance hinges on these labels. This review calls for future work to form a standardized framework, thereby supporting consistent reporting and performance comparisons across ML-enhanced prehospital triage systems.
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