Prediction of conversion from mild cognitive impairment to Alzheimer disease based on bayesian data mining with ensemble learning

Investigation of the Differential Power of Young’s Internet Addiction Questionnaire Using the Decision Stump Tree

Background. Internet addiction is one of the serious consequences of recent advances in the use of social media. Early detection of Internet addiction is essential because of its harms and is necessary for timely and effective treatment. Aim. The aim of this study was to use data mining and an artificial intelligence algorithm to estimate the differential power of each question in the Young Internet Addiction Test and build a decision stump model to predict which item in the questionnaire can be representative of the whole questionnaire. Methods. This is a descriptive study conducted at the University of Tabriz, in which 256 undergraduate students were selected in randomized cluster sampling, and they completed Young’s IAT (Internet Addiction Test) questionnaire and some demographic questions. The data were statistically analyzed with SPSS and were divided into two groups, normal and addicted, by using a cut-off point. Also, the data of the subjects was used to model the decision stump tree in WEKA. The clustering item was the normal and addicted specifier. Results. The study shows that Cronbach’s alpha of the IAT is 0.88, which shows good internal integration of subjects that are used to develop the model in WEKA (the Waikato Environment for Knowledge Analysis). Data analysis showed that by using the second question of this questionnaire as the root of the decision stump tree model, it is possible to distinguish between Internet addicts and healthy users with 82% accuracy using this model. Conclusion. The study shows innovative ways in which decision stump trees and data mining can help to improve methods used in Clinical Psychotherapy and Human Science. Regarding this, the study showed that early detection of Internet addiction would be possible by using the 2nd question of the IAT. Also, early detection can result in cost-effectiveness for the whole healthcare system.

Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees

Identifying potential protein-ligand interactions is central to the field of drug discovery as it facilitates the identification of potential novel drug leads, contributes to advancement from hits to leads, predicts potential off-target explanations for side effects of approved drugs or candidates, as well as de-orphans phenotypic hits. For the rapid identification of protein-ligand interactions, we here present a novel chemogenomics algorithm for the prediction of protein-ligand interactions using a new machine learning approach and novel class of descriptor. The algorithm applies Bayesian Additive Regression Trees (BART) on a newly proposed proteochemical space, termed the bow-pharmacological space. The space spans three distinctive sub-spaces that cover the protein space, the ligand space, and the interaction space. Thereby, the model extends the scope of classical target prediction or chemogenomic modelling that relies on one or two of these subspaces. Our model demonstrated excellent prediction power, reaching accuracies of up to 94.5–98.4% when evaluated on four human target datasets constituting enzymes, nuclear receptors, ion channels, and G-protein-coupled receptors . BART provided a reliable probabilistic description of the likelihood of interaction between proteins and ligands, which can be used in the prioritization of assays to be performed in both discovery and vigilance phases of small molecule development.

Random support vector machine cluster analysis of resting-state fMRI in Alzheimer's disease

Early diagnosis is critical for individuals with Alzheimer's disease (AD) in clinical practice because its progress is irreversible. In the existing literature, support vector machine (SVM) has always been applied to distinguish between AD and healthy controls (HC) based on neuroimaging data. But previous studies have only used a single SVM to classify AD and HC, and the accuracy is not very high and generally less than 90%. The method of random support vector machine cluster was proposed to classify AD and HC in this paper. From the Alzheimer's Disease Neuroimaging Initiative database, the subjects including 25 AD individuals and 35 HC individuals were obtained. The classification accuracy could reach to 94.44% in the results. Furthermore, the method could also be used for feature selection and the accuracy could be maintained at the level of 94.44%. In addition, we could also find out abnormal brain regions (inferior frontal gyrus, superior frontal gyrus, precentral gyrus and cingulate cortex). It is worth noting that the proposed random support vector machine cluster could be a new insight to help the diagnosis of AD.

Advancing Alzheimer's research: A review of big data promises

OBJECTIVE

To review the current state of science using big data to advance Alzheimer's disease (AD) research and practice. In particular, we analyzed the types of research foci addressed, corresponding methods employed and study findings reported using big data in AD.

METHOD

Systematic review was conducted for articles published in PubMed from January 1, 2010 through December 31, 2015. Keywords with AD and big data analytics were used for literature retrieval. Articles were reviewed and included if they met the eligibility criteria.

RESULTS

Thirty-eight articles were included in this review. They can be categorized into seven research foci: diagnosing AD or mild cognitive impairment (MCI) (n=10), predicting MCI to AD conversion (n=13), stratifying risks for AD (n=5), mining the literature for knowledge discovery (n=4), predicting AD progression (n=2), describing clinical care for persons with AD (n=3), and understanding the relationship between cognition and AD (n=3). The most commonly used datasets are AD Neuroimaging Initiative (ADNI) (n=16), electronic health records (EHR) (n=11), MEDLINE (n=3), and other research datasets (n=8). Logistic regression (n=9) and support vector machine (n=8) are the most used methods for data analysis.

CONCLUSION

Big data are increasingly used to address AD-related research questions. While existing research datasets are frequently used, other datasets such as EHR data provide a unique, yet under-utilized opportunity for advancing AD research.

Machine learning and microsimulation techniques on the prognosis of dementia: A systematic literature review

Background

Dementia is a complex disorder characterized by poor outcomes for the patients and high costs of care. After decades of research little is known about its mechanisms. Having prognostic estimates about dementia can help researchers, patients and public entities in dealing with this disorder. Thus, health data, machine learning and microsimulation techniques could be employed in developing prognostic estimates for dementia.

Objective

The goal of this paper is to present evidence on the state of the art of studies investigating and the prognosis of dementia using machine learning and microsimulation techniques.

Method

To achieve our goal we carried out a systematic literature review, in which three large databases—Pubmed, Socups and Web of Science were searched to select studies that employed machine learning or microsimulation techniques for the prognosis of dementia. A single backward snowballing was done to identify further studies. A quality checklist was also employed to assess the quality of the evidence presented by the selected studies, and low quality studies were removed. Finally, data from the final set of studies were extracted in summary tables.

Results

In total 37 papers were included. The data summary results showed that the current research is focused on the investigation of the patients with mild cognitive impairment that will evolve to Alzheimer’s disease, using machine learning techniques. Microsimulation studies were concerned with cost estimation and had a populational focus. Neuroimaging was the most commonly used variable.

Conclusions

Prediction of conversion from MCI to AD is the dominant theme in the selected studies. Most studies used ML techniques on Neuroimaging data. Only a few data sources have been recruited by most studies and the ADNI database is the one most commonly used. Only two studies have investigated the prediction of epidemiological aspects of Dementia using either ML or MS techniques. Finally, care should be taken when interpreting the reported accuracy of ML techniques, given studies’ different contexts.

Brain morphometric analysis predicts decline of intelligence quotient in children with sickle cell disease: A preliminary study

PURPOSE

For children with sickle cell disease (SCD) and at low risk category of stroke, we aim to build a predictive model to differentiate those with decline of intelligence-quotient (IQ) from counterparts without decline, based on structural magnetic-resonance (MR) imaging volumetric analysis.

MATERIALS AND METHODS

This preliminary prospective cohort study included 25 children with SCD, homozygous for hemoglobin S, with no history of stroke and transcranial Doppler mean velocities below 170cm/s at baseline. We administered the Kaufman Brief Intelligence Test (K-BIT) to each child at yearly intervals for 2-4 years. Each child underwent MR examination within 30 days of the baseline K-BIT evaluation date. We calculated K-BIT change rates, and used rate of change in K-BIT to classify children into two groups: a decline group and a non-decline group. We then generated predictive models to predict K-BIT decline/non-decline based on regional gray-matter (GM) volumes computed from structural MR images.

RESULTS

We identified six structures (the left median cingulate gyrus, the right middle occipital gyrus, the left inferior occipital gyrus, the right fusiform gyrus, the right middle temporal gyrus, the right inferior temporal gyrus) that, when assessed for volume at baseline, are jointly predictive of whether a child would suffer subsequent K-BIT decline. Based on these six regional GM volumes and the baseline K-BIT, we built a prognostic model using the K^* algorithm. The accuracy, sensitivity and specificity were 0.84, 0.78 and 0.86, respectively.

CONCLUSIONS

GM volumetric analysis predicts subsequent IQ decline for children with SCD.

Bayesian networks in neuroscience: a survey

Bayesian networks are a type of probabilistic graphical models lie at the intersection between statistics and machine learning. They have been shown to be powerful tools to encode dependence relationships among the variables of a domain under uncertainty. Thanks to their generality, Bayesian networks can accommodate continuous and discrete variables, as well as temporal processes. In this paper we review Bayesian networks and how they can be learned automatically from data by means of structure learning algorithms. Also, we examine how a user can take advantage of these networks for reasoning by exact or approximate inference algorithms that propagate the given evidence through the graphical structure. Despite their applicability in many fields, they have been little used in neuroscience, where they have focused on specific problems, like functional connectivity analysis from neuroimaging data. Here we survey key research in neuroscience where Bayesian networks have been used with different aims: discover associations between variables, perform probabilistic reasoning over the model, and classify new observations with and without supervision. The networks are learned from data of any kind-morphological, electrophysiological, -omics and neuroimaging-, thereby broadening the scope-molecular, cellular, structural, functional, cognitive and medical- of the brain aspects to be studied.