Biodata Mining最新文献

Background: The rapid growth of deep learning, as well as the vast and ever-growing amount of available data, have provided ample opportunity for advances in fusion and analysis of complex and heterogeneous data types. Different data modalities provide complementary information that can be leveraged to gain a more complete understanding of each subject. In the biomedical domain, multi-omics data includes molecular (genomics, transcriptomics, proteomics, epigenomics, metabolomics, etc.) and imaging (radiomics, pathomics) modalities which, when combined, have the potential to improve performance on prediction, classification, clustering and other tasks. Deep learning encompasses a wide variety of methods, each of which have certain strengths and weaknesses for multi-omics integration.

Method: In this review, we categorize recent deep learning-based approaches by their basic architectures and discuss their unique capabilities in relation to one another. We also discuss some emerging themes advancing the field of multi-omics integration.

Results: Deep learning-based multi-omics integration methods were categorized broadly into non-generative (feedforward neural networks, graph convolutional neural networks, and autoencoders) and generative (variational methods, generative adversarial models, and a generative pretrained model). Generative methods have the advantage of being able to impose constraints on the shared representations to enforce certain properties or incorporate prior knowledge. They can also be used to generate or impute missing modalities. Recent advances achieved by these methods include the ability to handle incomplete data as well as going beyond the traditional molecular omics data types to integrate other modalities such as imaging data.

Conclusion: We expect to see further growth in methods that can handle missingness, as this is a common challenge in working with complex and heterogeneous data. Additionally, methods that integrate more data types are expected to improve performance on downstream tasks by capturing a comprehensive view of each sample.

Background: Epistasis, the interaction between genetic loci where the effect of one locus is influenced by one or more other loci, plays a crucial role in the genetic architecture of complex traits. However, as the number of loci considered increases, the investigation of epistasis becomes exponentially more complex, making the selection of key features vital for effective downstream analyses. Relief-Based Algorithms (RBAs) are often employed for this purpose due to their reputation as "interaction-sensitive" algorithms and uniquely non-exhaustive approach. However, the limitations of RBAs in detecting interactions, particularly those involving multiple loci, have not been thoroughly defined. This study seeks to address this gap by evaluating the efficiency of RBAs in detecting higher-order epistatic interactions. Motivated by previous findings that suggest some RBAs may rank predictive features involved in higher-order epistasis negatively, we explore the potential of absolute value ranking of RBA feature weights as an alternative approach for capturing complex interactions. In this study, we assess the performance of ReliefF, MultiSURF, and MultiSURFstar on simulated genetic datasets that model various patterns of genotype-phenotype associations, including 2-way to 5-way genetic interactions, and compare their performance to two control methods: a random shuffle and mutual information.

Results: Our findings indicate that while RBAs effectively identify lower-order (2 to 3-way) interactions, their capability to detect higher-order interactions is significantly limited, primarily by large feature count but also by signal noise. Specifically, we observe that RBAs are successful in detecting fully penetrant 4-way XOR interactions using an absolute value ranking approach, but this is restricted to datasets with only 20 total features.

Conclusions: These results highlight the inherent limitations of current RBAs and underscore the need for the development of Relief-based approaches with enhanced detection capabilities for the investigation of epistasis, particularly in datasets with large feature counts and complex higher-order interactions.

Objectives: This study aims to develop an innovative approach for monitoring and assessing labor pain through ECG waveform analysis, utilizing machine learning techniques to monitor pain resulting from uterine contractions.

Methods: The study was conducted at National Taiwan University Hospital between January and July 2020. We collected a dataset of 6010 ECG samples from women preparing for natural spontaneous delivery (NSD). The ECG data was used to develop an ECG waveform-based Nociception Monitoring Index (NoM). The dataset was divided into training (80%) and validation (20%) sets. Multiple machine learning models, including LightGBM, XGBoost, SnapLogisticRegression, and SnapDecisionTree, were developed and evaluated. Hyperparameter optimization was performed using grid search and five-fold cross-validation to enhance model performance.

Results: The LightGBM model demonstrated superior performance with an AUC of 0.96 and an accuracy of 90%, making it the optimal model for monitoring labor pain based on ECG data. Other models, such as XGBoost and SnapLogisticRegression, also showed strong performance, with AUC values ranging from 0.88 to 0.95.

Conclusions: This study demonstrates that the integration of machine learning algorithms with ECG data significantly enhances the accuracy and reliability of labor pain monitoring. Specifically, the LightGBM model exhibits exceptional precision and robustness in continuous pain monitoring during labor, with potential applicability extending to broader healthcare settings.

Trial registration: ClinicalTrials.gov Identifier: NCT04461704.

Genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of complex traits and diseases. GWAS summary statistics have become essential tools for various genetic analyses, including meta-analysis, fine-mapping, and risk prediction. However, the increasing number of GWAS summary statistics and the diversity of software tools available for their analysis can make it challenging for researchers to select the most appropriate tools for their specific needs. This systematic review aims to provide a comprehensive overview of the currently available software tools and databases for GWAS summary statistics analysis. We conducted a comprehensive literature search to identify relevant software tools and databases. We categorized the tools and databases by their functionality, including data management, quality control, single-trait analysis, and multiple-trait analysis. We also compared the tools and databases based on their features, limitations, and user-friendliness. Our review identified a total of 305 functioning software tools and databases dedicated to GWAS summary statistics, each with unique strengths and limitations. We provide descriptions of the key features of each tool and database, including their input/output formats, data types, and computational requirements. We also discuss the overall usability and applicability of each tool for different research scenarios. This comprehensive review will serve as a valuable resource for researchers who are interested in using GWAS summary statistics to investigate the genetic basis of complex traits and diseases. By providing a detailed overview of the available tools and databases, we aim to facilitate informed tool selection and maximize the effectiveness of GWAS summary statistics analysis.

Objective: Data imbalance is a pervasive issue in medical data mining, often leading to biased and unreliable predictive models. This study aims to address the urgent need for effective strategies to mitigate the impact of data imbalance on classification models. We focus on quantifying the effects of different imbalance degrees and sample sizes on model performance, identifying optimal cut-off values, and evaluating the efficacy of various methods to enhance model accuracy in highly imbalanced and small sample size scenarios.

Methods: We collected medical records of patients receiving assisted reproductive treatment in a reproductive medicine center. Random forest was used to screen the key variables for the prediction target. Various datasets with different imbalance degrees and sample sizes were constructed to compare the classification performance of logistic regression models. Metrics such as AUC, G-mean, F1-Score, Accuracy, Recall, and Precision were used for evaluation. Four imbalance treatment methods (SMOTE, ADASYN, OSS, and CNN) were applied to datasets with low positive rates and small sample sizes to assess their effectiveness.

Results: The logistic model's performance was low when the positive rate was below 10% but stabilized beyond this threshold. Similarly, sample sizes below 1200 yielded poor results, with improvement seen above this threshold. For robustness, the optimal cut-offs for positive rate and sample size were identified as 15% and 1500, respectively. SMOTE and ADASYN oversampling significantly improved classification performance in datasets with low positive rates and small sample sizes.

Conclusions: The study identifies a positive rate of 15% and a sample size of 1500 as optimal cut-offs for stable logistic model performance. For datasets with low positive rates and small sample sizes, SMOTE and ADASYN are recommended to improve balance and model accuracy.

Background: Identifying critical genes is important for understanding the pathogenesis of complex diseases. Traditional studies typically comparing the change of biomecules between normal and disease samples or detecting important vertices from a single static biomolecular network, which often overlook the dynamic changes that occur between different disease stages. However, investigating temporal changes in biomolecular networks and identifying critical genes is critical for understanding the occurrence and development of diseases.

Methods: A novel method called Quantifying Importance of Genes with Tensor Decomposition (QIGTD) was proposed in this study. It first constructs a time series network by integrating both the intra and inter temporal network information, which preserving connections between networks at adjacent stages according to the local similarities. A tensor is employed to describe the connections of this time series network, and a 3-order tensor decomposition method was proposed to capture both the topological information of each network snapshot and the time series characteristics of the whole network. QIGTD is also a learning-free and efficient method that can be applied to datasets with a small number of samples.

Results: The effectiveness of QIGTD was evaluated using lung adenocarcinoma (LUAD) datasets and three state-of-the-art methods: T-degree, T-closeness, and T-betweenness were employed as benchmark methods. Numerical experimental results demonstrate that QIGTD outperforms these methods in terms of the indices of both precision and mAP. Notably, out of the top 50 genes, 29 have been verified to be highly related to LUAD according to the DisGeNET Database, and 36 are significantly enriched in LUAD related Gene Ontology (GO) terms, including nuclear division, mitotic nuclear division, chromosome segregation, organelle fission, and mitotic sister chromatid segregation.

Conclusion: In conclusion, QIGTD effectively captures the temporal changes in gene networks and identifies critical genes. It provides a valuable tool for studying temporal dynamics in biological networks and can aid in understanding the underlying mechanisms of diseases such as LUAD.