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General General

Machine learning assistive rapid, label-free molecular phenotyping of blood with two-dimensional NMR correlational spectroscopy.

In Communications biology

Translation of the findings in basic science and clinical research into routine practice is hampered by large variations in human phenotype. Developments in genotyping and phenotyping, such as proteomics and lipidomics, are beginning to address these limitations. In this work, we developed a new methodology for rapid, label-free molecular phenotyping of biological fluids (e.g., blood) by exploiting the recent advances in fast and highly efficient multidimensional inverse Laplace decomposition technique. We demonstrated that using two-dimensional T1-T2 correlational spectroscopy on a single drop of blood (<5 μL), a highly time- and patient-specific 'molecular fingerprint' can be obtained in minutes. Machine learning techniques were introduced to transform the NMR correlational map into user-friendly information for point-of-care disease diagnostic and monitoring. The clinical utilities of this technique were demonstrated through the direct analysis of human whole blood in various physiological (e.g., oxygenated/deoxygenated states) and pathological (e.g., blood oxidation, hemoglobinopathies) conditions.

Peng Weng Kung, Ng Tian-Tsong, Loh Tze Ping


General General

Pattern recognition of the fluid flow in a 3D domain by combination of Lattice Boltzmann and ANFIS methods.

In Scientific reports ; h5-index 158.0

Many numerical methods have been used to simulate the fluid flow pattern in different industrial devices. However, they are limited with modeling of complex geometries, numerical stability and expensive computational time for computing, and large hard drive. The evolution of artificial intelligence (AI) methods in learning large datasets with massive inputs and outputs of CFD results enables us to present completely artificial CFD results without existing numerical method problems. As AI methods can not feel barriers in numerical methods, they can be used as an assistance tool beside numerical methods to predict the process in complex geometries and unstable numerical regions within the short computational time. In this study, we use an adaptive neuro-fuzzy inference system (ANFIS) in the prediction of fluid flow pattern recognition in the 3D cavity. This prediction overview can reduce the computational time for visualization of fluid in the 3D domain. The method of ANFIS is used to predict the flow in the cavity and illustrates some artificial cavities for a different time. This method is also compared with the genetic algorithm fuzzy inference system (GAFIS) method for the assessment of numerical accuracy and prediction capability. The result shows that the ANFIS method is very successful in the estimation of flow compared with the GAFIS method. However, the GAFIS can provide faster training and prediction platform compared with the ANFIS method.

Babanezhad Meisam, Nakhjiri Ali Taghvaie, Marjani Azam, Shirazian Saeed


General General

Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation.

In Journal of proteome research

Liquid chromatography tandem mass spectrometry (LC-MS/MS) has been the most widely used technology for phosphoproteomics studies. As an alternative to database searching and probability-based phosphorylation site localization approaches, spectral library searching has been proved to be effective in the identification of phosphopeptides. However, incompletion of experimental spectral libraries limits the identification capability. Herein, we utilize MS/MS spectrum prediction coupled with spectral matching for site localization of phosphopeptides. In silico MS/MS spectra are generated from peptide sequences by deep learning/machine learning models trained with non-phosphopeptides. Then mass shift according to phosphorylation sites, phosphoric acid neutral loss and a "budding" strategy are adopted to adjust the in silico mass spectra. In silico MS/MS spectra can also be generated in one step for phosphopeptides using models trained with phosphopeptides. The method is benchmarked on data sets of synthetic phosphopeptides and is used to process real biological samples. It is demonstrated to be a method requiring only computational resources that supplements the probability-based approaches for phosphorylation site localization of singly and multiply phosphorylated peptides.

Yang Yi, Horvatovich Péter, Qiao Liang


General General

Artificial Intelligence Approaches to Social Determinants of Cognitive Impairment and Its Associated Conditions.

In Dementia and neurocognitive disorders

BACKGROUND AND PURPOSE : This study uses an artificial-intelligence model (recurrent neural network) for evaluating the following hypothesis: social determinants of disease association in a middle-aged or old population are different across gender and age groups. Here, the disease association indicates an association among cerebrovascular disease, hearing loss and cognitive impairment.

METHODS : Data came from the Korean Longitudinal Study of Ageing (2014-2016), with 6,060 participants aged 53 years or more, that is, 2,556 men, 3,504 women, 3,640 aged 70 years or less (70-), 2,420 aged 71 years or more (71+). The disease association was divided into 8 categories: 1 category for having no disease, 3 categories for having 1, 3 categories for having 2, and 1 category for having 3. Variable importance, the effect of a variable on model performance, was used for finding important social determinants of the disease association in a particular gender/age group, and evaluating the hypothesis above.

RESULTS : Based on variable importance from the recurrent neural network, important social determinants of the disease association were different across gender and age groups: 1) leisure activity for men; 2) parents alive, income and economic activity for women; 3) children alive, education and family activity for 70-; and 4) brothers/sisters cohabiting, religious activity and leisure activity for 70+.

CONCLUSIONS : The findings of this study support the hypothesis, suggesting the development of new guidelines reflecting different social determinants of the disease association across gender and age groups.

Lee Kwang Sig, Park Kun Woo


Age, Cerebrovascular Disease, Cognitive Impairment, Gender, Hearing Loss, Social Determinant

General General

Application of artificial intelligence models and optimization algorithms in plant cell and tissue culture.

In Applied microbiology and biotechnology

Artificial intelligence (AI) models and optimization algorithms (OA) are broadly employed in different fields of technology and science and have recently been applied to improve different stages of plant tissue culture. The usefulness of the application of AI-OA has been demonstrated in the prediction and optimization of length and number of microshoots or roots, biomass in plant cell cultures or hairy root culture, and optimization of environmental conditions to achieve maximum productivity and efficiency, as well as classification of microshoots and somatic embryos. Despite its potential, the use of AI and OA in this field has been limited due to complex definition terms and computational algorithms. Therefore, a systematic review to unravel modeling and optimizing methods is important for plant researchers and has been acknowledged in this study. First, the main steps for AI-OA development (from data selection to evaluation of prediction and classification models), as well as several AI models such as artificial neural networks (ANNs), neurofuzzy logic, support vector machines (SVMs), decision trees, random forest (FR), and genetic algorithms (GA), have been represented. Then, the application of AI-OA models in different steps of plant tissue culture has been discussed and highlighted. This review also points out limitations in the application of AI-OA in different plant tissue culture processes and provides a new view for future study objectives. KEY POINTS: • Artificial intelligence models and optimization algorithms can be considered a novel and reliable computational method in plant tissue culture. • This review provides the main steps and concepts for model development. • The application of machine learning algorithms in different steps of plant tissue culture has been discussed and highlighted.

Hesami Mohsen, Jones Andrew Maxwell Phineas


Androgenesis, Computational approach, Data-driven model, Embryogenesis, In vitro culture, Machine learning algorithm, Organogenesis, Plant biotechnology, Rhizogenesis, Shoot proliferation

General General

A machine learning-based clinical decision support system to identify prescriptions with a high risk of medication error.

In Journal of the American Medical Informatics Association : JAMIA

OBJECTIVE : To improve patient safety and clinical outcomes by reducing the risk of prescribing errors, we tested the accuracy of a hybrid clinical decision support system in prioritizing prescription checks.

MATERIALS AND METHODS : Data from electronic health records were collated over a period of 18 months. Inferred scores at a patient level (probability of a patient's set of active orders to require a pharmacist review) were calculated using a hybrid approach (machine learning and a rule-based expert system). A clinical pharmacist analyzed randomly selected prescription orders over a 2-week period to corroborate our findings. Predicted scores were compared with the pharmacist's review using the area under the receiving-operating characteristic curve and area under the precision-recall curve. These metrics were compared with existing tools: computerized alerts generated by a clinical decision support (CDS) system and a literature-based multicriteria query prioritization technique. Data from 10 716 individual patients (133 179 prescription orders) were used to train the algorithm on the basis of 25 features in a development dataset.

RESULTS : While the pharmacist analyzed 412 individual patients (3364 prescription orders) in an independent validation dataset, the areas under the receiving-operating characteristic and precision-recall curves of our digital system were 0.81 and 0.75, respectively, thus demonstrating greater accuracy than the CDS system (0.65 and 0.56, respectively) and multicriteria query techniques (0.68 and 0.56, respectively).

DISCUSSION : Our innovative digital tool was notably more accurate than existing techniques (CDS system and multicriteria query) at intercepting potential prescription errors.

CONCLUSIONS : By primarily targeting high-risk patients, this novel hybrid decision support system improved the accuracy and reliability of prescription checks in a hospital setting.

Corny Jennifer, Rajkumar Asok, Martin Olivier, Dode Xavier, Lajonchère Jean-Patrick, Billuart Olivier, Bézie Yvonnick, Buronfosse Anne


clinical, clinical pharmacy information systems, decision support systems, electronic prescribing, medication errors, supervised machine learning