Biodata Mining最新文献

DNA N6-adenine methylation (N6-methyladenine, 6mA) plays a key regulating role in the cellular processes. Precisely recognizing 6mA sites is of importance to further explore its biological functions. Although there are many developed computational methods for 6mA site prediction over the past decades, there is a large root left to improve. We presented a cross validation-based stacking ensemble model for 6mA site prediction, called 6mA-StackingCV. The 6mA-StackingCV is a type of meta-learning algorithm, which uses output of cross validation as input to the final classifier. The 6mA-StackingCV reached the state of the art performances in the Rosaceae independent test. Extensive tests demonstrated the stability and the flexibility of the 6mA-StackingCV. We implemented the 6mA-StackingCV as a user-friendly web application, which allows one to restrictively choose representations or learning algorithms. This application is freely available at http://www.biolscience.cn/6mA-stackingCV/ . The source code and experimental data is available at https://github.com/Xiaohong-source/6mA-stackingCV .

Background: Discrimination between patients affected by inflammatory bowel diseases and healthy controls on the basis of endoscopic imaging is an challenging problem for machine learning models. Such task is used here as the testbed for a novel deep learning classification pipeline, powered by a set of solutions enhancing characterising elements such as reproducibility, interpretability, reduced computational workload, bias-free modeling and careful image preprocessing.

Results: First, an automatic preprocessing procedure is devised, aimed to remove artifacts from clinical data, feeding then the resulting images to an aggregated per-patient model to mimic the clinicians decision process. The predictions are based on multiple snapshots obtained through resampling, reducing the risk of misleading outcomes by removing the low confidence predictions. Each patient's outcome is explained by returning the images the prediction is based upon, supporting clinicians in verifying diagnoses without the need for evaluating the full set of endoscopic images. As a major theoretical contribution, quantization is employed to reduce the complexity and the computational cost of the model, allowing its deployment on small power devices with an almost negligible 3% performance degradation. Such quantization procedure holds relevance not only in the context of per-patient models but also for assessing its feasibility in providing real-time support to clinicians even in low-resources environments. The pipeline is demonstrated on a private dataset of endoscopic images of 758 IBD patients and 601 healthy controls, achieving Matthews Correlation Coefficient 0.9 as top performance on test set.

Conclusion: We highlighted how a comprehensive pre-processing pipeline plays a crucial role in identifying and removing artifacts from data, solving one of the principal challenges encountered when working with clinical data. Furthermore, we constructively showed how it is possible to emulate clinicians decision process and how it offers significant advantages, particularly in terms of explainability and trust within the healthcare context. Last but not least, we proved that quantization can be a useful tool to reduce the time and resources consumption with an acceptable degradation of the model performs. The quantization study proposed in this work points up the potential development of real-time quantized algorithms as valuable tools to support clinicians during endoscopy procedures.

Background and objective: The classification of glioma subtypes is essential for precision therapy. Due to the heterogeneity of gliomas, the subtype-specific molecular pattern can be captured by integrating and analyzing high-throughput omics data from different genomic layers. The development of a deep-learning framework enables the integration of multi-omics data to classify the glioma subtypes to support the clinical diagnosis.

Results: Transcriptome and methylome data of glioma patients were preprocessed, and differentially expressed features from both datasets were identified. Subsequently, a Cox regression analysis determined genes and CpGs associated with survival. Gene set enrichment analysis was carried out to examine the biological significance of the features. Further, we identified CpG and gene pairs by mapping them in the promoter region of corresponding genes. The methylation and gene expression levels of these CpGs and genes were embedded in a lower-dimensional space with an autoencoder. Next, ANN and CNN were used to classify subtypes using the latent features from embedding space. CNN performs better than ANN for subtyping lower-grade gliomas (LGG) and glioblastoma multiforme (GBM). The subtyping accuracy of CNN was 98.03% (± 0.06) and 94.07% (± 0.01) in LGG and GBM, respectively. The precision of the models was 97.67% in LGG and 90.40% in GBM. The model sensitivity was 96.96% in LGG and 91.18% in GBM. Additionally, we observed the superior performance of CNN with external datasets. The genes and CpGs pairs used to develop the model showed better performance than the random CpGs-gene pairs, preprocessed data, and single omics data.

Conclusions: The current study showed that a novel feature selection and data integration strategy led to the development of DeepAutoGlioma, an effective framework for diagnosing glioma subtypes.

Background: The governance of health systems is complex in nature due to several intertwined and multi-dimensional factors contributing to it. Recent challenges of health systems reflect the need for innovative approaches that can minimize adverse consequences of policies. Hence, there is compelling evidence of a distinct outlook on the health ecosystem using artificial intelligence (AI). Therefore, this study aimed to investigate the roles of AI and its applications in health system governance through an interpretive scoping review of current evidence.

Method: This study intended to offer a research agenda and framework for the applications of AI in health systems governance. To include shreds of evidence with a greater focus on the application of AI in health governance from different perspectives, we searched the published literature from 2000 to 2023 through PubMed, Scopus, and Web of Science Databases.

Results: Our findings showed that integrating AI capabilities into health systems governance has the potential to influence three cardinal dimensions of health. These include social determinants of health, elements of governance, and health system tasks and goals. AI paves the way for strengthening the health system's governance through various aspects, i.e., intelligence innovations, flexible boundaries, multidimensional analysis, new insights, and cognition modifications to the health ecosystem area.

Conclusion: AI is expected to be seen as a tool with new applications and capabilities, with the potential to change each component of governance in the health ecosystem, which can eventually help achieve health-related goals.

Background: Patients with Type 2 Diabetes Mellitus (T2DM) are at a higher risk of polypharmacy and more susceptible to irrational prescriptions; therefore, pharmacological therapy patterns are important to be monitored. The primary objective of this study was to highlight current prescription patterns in T2DM patients and compare them with existing Standards of Medical Care in Diabetes. The second objective was to analyze whether age and gender affect prescription patterns.

Method: This cross-sectional study was conducted using the Iran Health Insurance Organization (IHIO) prescription database. It was mined by an Association Rule Mining (ARM) technique, FP-Growth, in order to find co-prescribed drugs with anti-diabetic medications. The algorithm was implemented at different levels of the Anatomical Therapeutic Chemical (ATC) classification system, which assigns different codes to drugs based on their anatomy, pharmacological, therapeutic, and chemical properties to provide an in-depth analysis of co-prescription patterns.

Results: Altogether, the prescriptions of 914,652 patients were analyzed, of whom 91,505 were found to have diabetes. According to our results, prescribing Lipid Modifying Agents (C10) (56.3%), Agents Acting on The Renin-Angiotensin System (C09) (48.9%), Antithrombotic Agents (B01) (35.7%), and Beta Blocking Agents (C07) (30.1%) were meaningfully associated with the prescription of Drugs Used in Diabetes. Our study also revealed that female diabetic patients have a higher lift for taking Thyroid Preparations, and the older the patients were, the more they were prone to take neuropathy-related medications. Additionally, the results suggest that there are gender differences in the association between aspirin and diabetes drugs, with the differences becoming less pronounced in old age.

Conclusions: Almost all of the association rules found in this research were clinically meaningful, proving the potential of ARM for co-prescription pattern discovery. Moreover, implementing level-based ARM was effective in detecting difficult-to-spot rules. Additionally, the majority of drugs prescribed by physicians were consistent with the Standards of Medical Care in Diabetes.

Automatic segmentation of skin lesions is a critical step in Computer Aided Diagnosis (CAD) of melanoma. However, due to the blurring of the lesion boundary, uneven color distribution, and low image contrast, resulting in poor segmentation result. Aiming at the problem of difficult segmentation of skin lesions, this paper proposes an Attention-based Dual-path Feature Fusion Network (ADFFNet) for automatic skin lesion segmentation. Firstly, in the spatial path, a Boundary Refinement (BR) module is designed for the output of low-level features to filter out irrelevant background information and retain more boundary details of the lesion area. Secondly, in the context path, a Multi-scale Feature Selection (MFS) module is constructed for high-level feature output to capture multi-scale context information and use the attention mechanism to filter out redundant semantic information. Finally, we design a Dual-path Feature Fusion (DFF) module, which uses high-level global attention information to guide the step-by-step fusion of high-level semantic features and low-level detail features, which is beneficial to restore image detail information and further improve the pixel-level segmentation accuracy of skin lesion. In the experiment, the ISIC 2018 and PH2 datasets are employed to evaluate the effectiveness of the proposed method. It achieves a performance of 0.890/ 0.925 and 0.933 /0.954 on the F1-score and SE index, respectively. Comparative analysis with state-of-the-art segmentation methods reveals that the ADFFNet algorithm exhibits superior segmentation performance.

Squiggle data is the numerical output of DNA and RNA sequencing by the Nanopore next generation sequencing platform. Nanopore sequencing offers expanded applications compared to previous sequencing techniques but produces a large amount of data in the form of current measurements over time. The analysis of these segments of current measurements require more complex and computationally intensive algorithms than previous sequencing technologies. The purpose of this study is to investigate in principle the potential of using quantum computers to speed up Nanopore data analysis. Quantum circuits are designed to extract major features of squiggle current measurements. The circuits are analyzed theoretically in terms of size and performance. Practical experiments on IBM QX show the limitations of the state of the art quantum computer to tackle real life squiggle data problems. Nevertheless, pre-processing of the squiggle data using the inverse wavelet transform, as experimented and analyzed in this paper as well, reduces the dimensionality of the problem in order to fit a reasonable size quantum computer in the hopefully near future.

Gliomas are primary malignant brain tumors with poor survival and high resistance to available treatments. Improving the molecular understanding of glioma and disclosing novel biomarkers of tumor development and progression could help to find novel targeted therapies for this type of cancer. Public databases such as The Cancer Genome Atlas (TCGA) provide an invaluable source of molecular information on cancer tissues. Machine learning tools show promise in dealing with the high dimension of omics data and extracting relevant information from it. In this work, network inference and clustering methods, namely Joint Graphical lasso and Robust Sparse K-means Clustering, were applied to RNA-sequencing data from TCGA glioma patients to identify shared and distinct gene networks among different types of glioma (glioblastoma, astrocytoma, and oligodendroglioma) and disclose new patient groups and the relevant genes behind groups' separation. The results obtained suggest that astrocytoma and oligodendroglioma have more similarities compared with glioblastoma, highlighting the molecular differences between glioblastoma and the others glioma subtypes. After a comprehensive literature search on the relevant genes pointed our from our analysis, we identified potential candidates for biomarkers of glioma. Further molecular validation of these genes is encouraged to understand their potential role in diagnosis and in the design of novel therapies.