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General General

Data-Driven Models for Objective Grading Improvement of Parkinson's Disease.

In Annals of biomedical engineering ; h5-index 52.0

Parkinson's disease (PD) is a progressive disorder of the central nervous system that causes motor dysfunctions in affected patients. Objective assessment of symptoms can support neurologists in fine evaluations, improving patients' quality of care. Herein, this study aimed to develop data-driven models based on regression algorithms to investigate the potential of kinematic features to predict PD severity levels. Sixty-four patients with PD (PwPD) and 50 healthy subjects of control (HC) were asked to perform 13 motor tasks from the MDS-UPDRS III while wearing wearable inertial sensors. Simultaneously, the clinician provided the evaluation of the tasks based on the MDS-UPDRS scores. One hundred-ninety kinematic features were extracted from the inertial motor data. Data processing and statistical analysis identified a set of parameters able to distinguish between HC and PwPD. Then, multiple feature selection methods allowed selecting the best subset of parameters for obtaining the greatest accuracy when used as input for several predicting regression algorithms. The maximum correlation coefficient, equal to 0.814, was obtained with the adaptive neuro-fuzzy inference system (ANFIS). Therefore, this predictive model could be useful as a decision support system for a reliable objective assessment of PD severity levels based on motion performance, improving patients monitoring over time.

Butt Abdul Haleem, Rovini Erika, Fujita Hamido, Maremmani Carlo, Cavallo Filippo


ANFIS, Artificial intelligence, Parkinson disease severity, Predictive methods, Regression models

Pathology Pathology

Towards the Probabilistic Analysis of Small Bowel Capsule Endoscopy Features to Predict Severity of Duodenal Histology in Patients with Villous Atrophy.

In Journal of medical systems ; h5-index 48.0

Small bowel capsule endoscopy (SBCE) can be complementary to histological assessment of celiac disease (CD) and serology negative villous atrophy (SNVA). Determining the severity of disease on SBCE using statistical machine learning methods can be useful in the follow up of patients. SBCE can play an additional role in differentiating between CD and SNVA. De-identified SBCEs of patients with CD and SNVA were included. Probabilistic analysis of features on SBCE were used to predict severity of duodenal histology and to distinguish between CD and SNVA. Patients with higher Marsh scores were more likely to have a positive SBCE and a continuous distribution of macroscopic features of disease than those with lower Marsh scores. The same pattern was also true for patients with CD when compared to patients with SNVA. The validation accuracy when predicting the severity of Marsh scores and when distinguishing between CD and SNVA was 69.1% in both cases. When the proportions of each SBCE class group within the dataset were included in the classification model, to distinguish between the two pathologies, the validation accuracy increased to 75.3%. The findings of this work suggest that by using features of CD and SNVA on SBCE, predictions can be made of the type of pathology and the severity of disease.

Chetcuti Zammit Stefania, Bull Lawrence A, Sanders David S, Galvin Jessica, Dervilis Nikolaos, Sidhu Reena, Worden Keith


Celiac disease, Duodenal histology, Probabilistic analysis, Seronegative villous atrophy, Small bowel capsule endoscopy

General General

A survey on deep learning in DNA/RNA motif mining.

In Briefings in bioinformatics

DNA/RNA motif mining is the foundation of gene function research. The DNA/RNA motif mining plays an extremely important role in identifying the DNA- or RNA-protein binding site, which helps to understand the mechanism of gene regulation and management. For the past few decades, researchers have been working on designing new efficient and accurate algorithms for mining motif. These algorithms can be roughly divided into two categories: the enumeration approach and the probabilistic method. In recent years, machine learning methods had made great progress, especially the algorithm represented by deep learning had achieved good performance. Existing deep learning methods in motif mining can be roughly divided into three types of models: convolutional neural network (CNN) based models, recurrent neural network (RNN) based models, and hybrid CNN-RNN based models. We introduce the application of deep learning in the field of motif mining in terms of data preprocessing, features of existing deep learning architectures and comparing the differences between the basic deep learning models. Through the analysis and comparison of existing deep learning methods, we found that the more complex models tend to perform better than simple ones when data are sufficient, and the current methods are relatively simple compared with other fields such as computer vision, language processing (NLP), computer games, etc. Therefore, it is necessary to conduct a summary in motif mining by deep learning, which can help researchers understand this field.

He Ying, Shen Zhen, Zhang Qinhu, Wang Siguo, Huang De-Shuang


convolutional neural network, deep learning, motif mining, protein binding site, recurrent neural networks

Surgery Surgery

Systems Biology of Gastric Cancer: Perspectives on the Omics-Based Diagnosis and Treatment.

In Frontiers in molecular biosciences

Gastric cancer is the fifth most diagnosed cancer in the world, affecting more than a million people and causing nearly 783,000 deaths each year. The prognosis of advanced gastric cancer remains extremely poor despite the use of surgery and adjuvant therapy. Therefore, understanding the mechanism of gastric cancer development, and the discovery of novel diagnostic biomarkers and therapeutics are major goals in gastric cancer research. Here, we review recent progress in application of omics technologies in gastric cancer research, with special focus on the utilization of systems biology approaches to integrate multi-omics data. In addition, the association between gastrointestinal microbiota and gastric cancer are discussed, which may offer insights in exploring the novel microbiota-targeted therapeutics. Finally, the application of data-driven systems biology and machine learning approaches could provide a predictive understanding of gastric cancer, and pave the way to the development of novel biomarkers and rational design of cancer therapeutics.

Shi Xiao-Jing, Wei Yongjun, Ji Boyang


data integration, gastric cancer, omics, personalized medicine, systems biology

Radiology Radiology

Evaluation of the clinical efficacy of a TW3-based fully automated bone age assessment system using deep neural networks.

In Imaging science in dentistry ; h5-index 21.0

Purpose : The aim of this study was to evaluate the clinical efficacy of a Tanner-Whitehouse 3 (TW3)-based fully automated bone age assessment system on hand-wrist radiographs of Korean children and adolescents.

Materials and Methods : Hand-wrist radiographs of 80 subjects (40 boys and 40 girls, 7-15 years of age) were collected. The clinical efficacy was evaluated by comparing the bone ages that were determined using the system with those from the reference standard produced by 2 oral and maxillofacial radiologists. Comparisons were conducted using the paired t-test and simple regression analysis.

Results : The bone ages estimated with this bone age assessment system were not significantly different from those obtained with the reference standard (P>0.05) and satisfied the equivalence criterion of 0.6 years within the 95% confidence interval (- 0.07 to 0.22), demonstrating excellent performance of the system. Similarly, in the comparisons of gender subgroups, no significant difference in bone age between the values produced by the system and the reference standard was observed (P>0.05 for both boys and girls). The determination coefficients obtained via regression analysis were 0.962, 0.945, and 0.952 for boys, girls, and overall, respectively (P=0.000); hence, the radiologist-determined bone ages and the system-determined bone ages were strongly correlated.

Conclusion : This TW3-based system can be effectively used for bone age assessment based on hand-wrist radiographs of Korean children and adolescents.

Shin Nan-Young, Lee Byoung-Dai, Kang Ju-Hee, Kim Hye-Rin, Oh Dong Hyo, Lee Byung Il, Kim Sung Hyun, Lee Mu Sook, Heo Min-Suk


Age Determination by Skeleton, Artificial Intelligence, Deep Learning, Radiography

General General

Mixture Optimization of Recycled Aggregate Concrete Using Hybrid Machine Learning Model.

In Materials (Basel, Switzerland)

Recycled aggregate concrete (RAC) contributes to mitigating the depletion of natural aggregates, alleviating the carbon footprint of concrete construction, and averting the landfilling of colossal amounts of construction and demolition waste. However, complexities in the mixture optimization of RAC due to the variability of recycled aggregates and lack of accuracy in estimating its compressive strength require novel and sophisticated techniques. This paper aims at developing state-of-the-art machine learning models to predict the RAC compressive strength and optimize its mixture design. Results show that the developed models including Gaussian processes, deep learning, and gradient boosting regression achieved robust predictive performance, with the gradient boosting regression trees yielding highest prediction accuracy. Furthermore, a particle swarm optimization coupled with gradient boosting regression trees model was developed to optimize the mixture design of RAC for various compressive strength classes. The hybrid model achieved cost-saving RAC mixture designs with lower environmental footprint for different target compressive strength classes. The model could be further harvested to achieve sustainable concrete with optimal recycled aggregate content, least cost, and least environmental footprint.

Nunez Itzel, Marani Afshin, Nehdi Moncef L


Gaussian process, deep learning, gated recurrent unit, gradient boosting, machine learning, model, recycled aggregate concrete, regression trees