Predicting rice diseases across diverse agro-meteorological conditions using an artificial intelligence approach.
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ABSTRACT:
SUBMITTER: Patil RR
PROVIDER: S-EPMC8444092 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Hybrid breeding is fast becoming a key instrument in plants' crop productivity. Grain yield performance of hybrids (F1) under different parental genetic features has consequently received considerable attention in the literature. The main objective of this study was to introduce a new method, known as AI_HIB under different parental genetic features using artificial intelligence (AI) techniques. In so doing, the rice cultivars TAM, KHZ, SPD, GHB, IR28, AHM, SHP and their F1 hybrid were used. Having recorded Grain Yield (GY), Unfertile Panicle Number (UFP), Plant Height (HE), Days to Flowering (DF), Panicle Exertion (PE), Panicle Length (PL), Filled Grain Number (FG), Primary Branches Number (PBN), Flag Leaf Length (FLL), Flag Leaf Width (FLW), Flag Leaf Area (FLA), and Plant Biomass (BI) in the field, we include these features in our proposed model. When using the GA and PSO algorithm to select the features, grain yield had the highest frequency at the input of the Artificial Neural Network (ANN), Adaptive Neuro-Fuzzy Inference System (ANFIS) and Support Vector Machine (SVM) structure. The AI_HIB_ANN result revealed that the trained neural network with parental data enjoyed a good ability to predict the response of hybrid performance. Findings also reflected that the obtained MSE was low and R2 value was greater than 96%. AI_HIB_SVM and AI_HIB_ANFIS showed that measuring attributes could predict number of primary branches, plant height, days to flowering and grain yield per plant with accuracies of 99%. These findings have significant implications as it presents a new promising prediction method for hybrid rice yield based on the characteristics of the parent lines by AI. These findings contribute to provide a basis for designing a smartphone application in terms of the AI_HIB_SVM and AI_HIB_ANFIS methods to easily predict hybrid performance with a high accuracy rate.
| S-EPMC9188612 | biostudies-literature
Project description:Three-quarters of lifetime mental illness occurs by the age of 24, but relatively little is known about how to robustly identify youth at risk to target intervention efforts known to improve outcomes. Barriers to knowledge have included obtaining robust predictions while simultaneously analyzing large numbers of different types of candidate predictors. In a new, large, transdiagnostic youth sample and multidomain high-dimension data, we used 160 candidate predictors encompassing neural, prenatal, developmental, physiologic, sociocultural, environmental, emotional and cognitive features and leveraged three different machine learning algorithms optimized with a novel artificial intelligence meta-learning technique to predict individual cases of anxiety, depression, attention deficit, disruptive behaviors and post-traumatic stress. Our models tested well in unseen, held-out data (AUC ≥ 0.94). By utilizing a large-scale design and advanced computational approaches, we were able to compare the relative predictive ability of neural versus psychosocial features in a principled manner and found that psychosocial features consistently outperformed neural metrics in their relative ability to deliver robust predictions of individual cases. We found that deep learning with artificial neural networks and tree-based learning with XGBoost outperformed logistic regression with ElasticNet, supporting the conceptualization of mental illnesses as multifactorial disease processes with non-linear relationships among predictors that can be robustly modeled with computational psychiatry techniques. To our knowledge, this is the first study to test the relative predictive ability of these gold-standard algorithms from different classes across multiple mental health conditions in youth within the same study design in multidomain data utilizing >100 candidate predictors. Further research is suggested to explore these findings in longitudinal data and validate results in an external dataset.
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Project description:Artificial Intelligence (AI) analytics has been used to predict, classify, and aid clinical management of multiple eye diseases. Its robust performances have prompted researchers to expand the use of AI into predicting systemic, non-ocular diseases and parameters based on ocular images. Herein, we discuss the reasons why the eye is well-suited for systemic applications, and review the applications of deep learning on ophthalmic images in the prediction of demographic parameters, body composition factors, and diseases of the cardiovascular, hematological, neurodegenerative, metabolic, renal, and hepatobiliary systems. Three main imaging modalities are included-retinal fundus photographs, optical coherence tomographs and external ophthalmic images. We examine the range of systemic factors studied from ophthalmic imaging in current literature and discuss areas of future research, while acknowledging current limitations of AI systems based on ophthalmic images.
| S-EPMC9190759 | biostudies-literature
Project description:BackgroundInflammatory Bowel Diseases with its complexity and heterogeneity could benefit from the increased application of Artificial Intelligence in clinical management.AimTo accurately predict adverse outcomes in patients with IBD using advanced computational models in a nationally representative dataset for potential use in clinical practice.MethodsWe built a training model cohort and validated our result in a separate cohort. We used LASSO and Ridge regressions, Support Vector Machines, Random Forests and Neural Networks to balance between complexity and interpretability and analyzed their relative performances and reported the strongest predictors to the respective models. The participants in our study were patients with IBD selected from The OptumLabs® Data Warehouse (OLDW), a longitudinal, real-world data asset with de-identified administrative claims and electronic health record (EHR) data.ResultsWe included 72,178 and 69,165 patients in the training and validation set, respectively. In total, 4.1% of patients in the validation set were hospitalized, 2.9% needed IBD-related surgeries, 17% used long-term steroids and 13% of patients were initiated with biological therapy. Of the AI models we tested, the Random Forest and LASSO resulted in high accuracies (AUCs 0.70-0.92). Our artificial neural network performed similarly well in most of the models (AUCs 0.61-0.90).ConclusionsThis study demonstrates feasibility of accurately predicting adverse outcomes using complex and novel AI models on large longitudinal data sets of patients with IBD. These models could be applied for risk stratification and implementation of preemptive measures to avoid adverse outcomes in a clinical setting.
| S-EPMC9515047 | biostudies-literature
Project description:Understanding the conditionally-dependent clinical variables that drive cardiovascular health outcomes is a major challenge for precision medicine. Here, we deploy a recently developed massively scalable comorbidity discovery method called Poisson Binomial based Comorbidity discovery (PBC), to analyze Electronic Health Records (EHRs) from the University of Utah and Primary Children's Hospital (over 1.6 million patients and 77 million visits) for comorbid diagnoses, procedures, and medications. Using explainable Artificial Intelligence (AI) methodologies, we then tease apart the intertwined, conditionally-dependent impacts of comorbid conditions and demography upon cardiovascular health, focusing on the key areas of heart transplant, sinoatrial node dysfunction and various forms of congenital heart disease. The resulting multimorbidity networks make possible wide-ranging explorations of the comorbid and demographic landscapes surrounding these cardiovascular outcomes, and can be distributed as web-based tools for further community-based outcomes research. The ability to transform enormous collections of EHRs into compact, portable tools devoid of Protected Health Information solves many of the legal, technological, and data-scientific challenges associated with large-scale EHR analyses.
| S-EPMC8975108 | biostudies-literature
Project description:To better combat the expansion of antibiotic resistance in pathogens, new compounds, particularly those with novel mechanisms-of-action [MOA], represent a major research priority in biomedical science. However, rediscovery of known antibiotics demonstrates a need for approaches that accurately identify potential novelty with higher throughput and reduced labor. Here we describe an explainable artificial intelligence classification methodology that emphasizes prediction performance and human interpretability by using a Hierarchical Ensemble of Classifiers model optimized with a novel feature selection algorithm called Clairvoyance; collectively referred to as a CoHEC model. We evaluated our methods using whole transcriptome responses from Escherichia coli challenged with 41 known antibiotics and 9 crude extracts while depositing 122 transcriptomes unique to this study. Our CoHEC model can properly predict the primary MOA of previously unobserved compounds in both purified forms and crude extracts at an accuracy above 99%, while also correctly identifying darobactin, a newly discovered antibiotic, as having a novel MOA. In addition, we deploy our methods on a recent E. coli transcriptomics dataset from a different strain and a Mycobacterium smegmatis metabolomics timeseries dataset showcasing exceptionally high performance; improving upon the performance metrics of the original publications. We not only provide insight into the biological interpretation of our model but also that the concept of MOA is a non-discrete heuristic with diverse effects for different compounds within the same MOA, suggesting substantial antibiotic diversity awaiting discovery within existing MOA.
| S-EPMC8031737 | biostudies-literature
Project description:Failure to attend scheduled hospital appointments disrupts clinical management and consumes resource estimated at £1 billion annually in the United Kingdom National Health Service alone. Accurate stratification of absence risk can maximize the yield of preventative interventions. The wide multiplicity of potential causes, and the poor performance of systems based on simple, linear, low-dimensional models, suggests complex predictive models of attendance are needed. Here, we quantify the effect of using complex, non-linear, high-dimensional models enabled by machine learning. Models systematically varying in complexity based on logistic regression, support vector machines, random forests, AdaBoost, or gradient boosting machines were trained and evaluated on an unselected set of 22,318 consecutive scheduled magnetic resonance imaging appointments at two UCL hospitals. High-dimensional Gradient Boosting Machine-based models achieved the best performance reported in the literature, exhibiting an area under the receiver operating characteristic curve of 0.852 and average precision of 0.511. Optimal predictive performance required 81 variables. Simulations showed net potential benefit across a wide range of attendance characteristics, peaking at £3.15 per appointment at current prevalence and call efficiency. Optimal attendance prediction requires more complex models than have hitherto been applied in the field, reflecting the complex interplay of patient, environmental, and operational causal factors. Far from an exotic luxury, high-dimensional models based on machine learning are likely essential to optimal scheduling amongst other operational aspects of hospital care. High predictive performance is achievable with data from a single institution, obviating the need for aggregating large-scale sensitive data across governance boundaries.
| S-EPMC6550247 | biostudies-literature
Project description:Purpose:Next-generation sequencing technologies are actively applied in clinical oncology. Bioinformatics pipeline analysis is an integral part of this process; however, humans cannot yet realize the full potential of the highly complex pipeline output. As a result, the decision to include a variant in the final report during routine clinical sign-out remains challenging. Methods:We used an artificial intelligence approach to capture the collective clinical sign-out experience of six board-certified molecular pathologists to build and validate a decision support tool for variant reporting. We extracted all reviewed and reported variants from our clinical database and tested several machine learning models. We used 10-fold cross-validation for our variant call prediction model, which derives a contiguous prediction score from 0 to 1 (no to yes) for clinical reporting. Results:For each of the 19,594 initial training variants, our pipeline generates approximately 500 features, which results in a matrix of > 9 million data points. From a comparison of naive Bayes, decision trees, random forests, and logistic regression models, we selected models that allow human interpretability of the prediction score. The logistic regression model demonstrated 1% false negativity and 2% false positivity. The final models' Youden indices were 0.87 and 0.77 for screening and confirmatory cutoffs, respectively. Retraining on a new assay and performance assessment in 16,123 independent variants validated our approach (Youden index, 0.93). We also derived individual pathologist-centric models (virtual consensus conference function), and a visual drill-down functionality allows assessment of how underlying features contributed to a particular score or decision branch for clinical implementation. Conclusion:Our decision support tool for variant reporting is a practically relevant artificial intelligence approach to harness the next-generation sequencing bioinformatics pipeline output when the complexity of data interpretation exceeds human capabilities.
| S-EPMC6198661 | biostudies-literature
Project description:BackgroundCardiac arrest is a life-threatening cessation of activity in the heart. Early prediction of cardiac arrest is important, as it allows for the necessary measures to be taken to prevent or intervene during the onset. Artificial intelligence (AI) technologies and big data have been increasingly used to enhance the ability to predict and prepare for the patients at risk.ObjectiveThis study aims to explore the use of AI technology in predicting cardiac arrest as reported in the literature.MethodsA scoping review was conducted in line with the guidelines of the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) extension for scoping reviews. Scopus, ScienceDirect, Embase, the Institute of Electrical and Electronics Engineers, and Google Scholar were searched to identify relevant studies. Backward reference list checks of the included studies were also conducted. Study selection and data extraction were independently conducted by 2 reviewers. Data extracted from the included studies were synthesized narratively.ResultsOut of 697 citations retrieved, 41 studies were included in the review, and 6 were added after backward citation checking. The included studies reported the use of AI in the prediction of cardiac arrest. Of the 47 studies, we were able to classify the approaches taken by the studies into 3 different categories: 26 (55%) studies predicted cardiac arrest by analyzing specific parameters or variables of the patients, whereas 16 (34%) studies developed an AI-based warning system. The remaining 11% (5/47) of studies focused on distinguishing patients at high risk of cardiac arrest from patients who were not at risk. Two studies focused on the pediatric population, and the rest focused on adults (45/47, 96%). Most of the studies used data sets with a size of <10,000 samples (32/47, 68%). Machine learning models were the most prominent branch of AI used in the prediction of cardiac arrest in the studies (38/47, 81%), and the most used algorithm was the neural network (23/47, 49%). K-fold cross-validation was the most used algorithm evaluation tool reported in the studies (24/47, 51%).ConclusionsAI is extensively used to predict cardiac arrest in different patient settings. Technology is expected to play an integral role in improving cardiac medicine. There is a need for more reviews to learn the obstacles to the implementation of AI technologies in clinical settings. Moreover, research focusing on how to best provide clinicians with support to understand, adapt, and implement this technology in their practice is also necessary.
| S-EPMC8726033 | biostudies-literature
Project description:Dry eye disease is one of the most common ophthalmological complaints and is defined by a loss of tear film homeostasis. Establishing a diagnosis can be time-consuming, resource demanding and unpleasant for the patient. In this pilot study, we retrospectively included clinical data from 431 patients with dry eye disease examined in the Norwegian Dry Eye Clinic to evaluate how artificial intelligence algorithms perform on clinical data related to dry eye disease. The data was processed and subjected to numerous machine learning classification algorithms with the aim to predict decreased tear film break-up time. Moreover, feature selection techniques (information gain and information gain ratio) were applied to determine which clinical factors contribute most to an unstable tear film. The applied machine learning algorithms outperformed baseline classifications performed with ZeroR according to included evaluation metrics. Clinical features such as ocular surface staining, meibomian gland expressibility and dropout, blink frequency, osmolarity, meibum quality and symptom score were recognized as important predictors for tear film instability. We identify and discuss potential limitations and pitfalls.
| S-EPMC9741582 | biostudies-literature