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IntroductionBecause Alzheimer’s disease (AD) has significant heterogeneity in encephalatrophy and clinical manifestations, AD research faces two critical challenges: eliminating the impact of natural aging and extracting valuable clinical data for patients with AD.MethodsThis study attempted to address these challenges by developing a novel machine-learning model called tensorized contrastive principal component analysis (T-cPCA). The objectives of this study were to predict AD progression and identify clinical subtypes while minimizing the influence of natural aging.ResultsWe leveraged a clinical variable space of 872 features, including almost all AD clinical examinations, which is the most comprehensive AD feature description in current research. T-cPCA yielded the highest accuracy in predicting AD progression by effectively minimizing the confounding effects of natural aging.DiscussionThe representative features and pathogenic circuits of the four primary AD clinical subtypes were discovered. Confirmed by clinical doctors in Tangdu Hospital, the plaques (18F-AV45) distribution of typical patients in the four clinical subtypes are consistent with representative brain regions found in four AD subtypes, which further offers novel insights into the underlying mechanisms of AD pathogenesis.

TADfit is a computational method that can identify hierarchical or partially overlapping TADs from Hi-C data, in part by using information from multiple replicates to improve detection power.

Abstract Background The zone adjacent to a transcription start site (TSS), namely, the promoter, is primarily involved in the process of DNA transcription initiation and regulation. As a result, proper promoter identification is critical for further understanding the mechanism of the networks controlling genomic regulation. A number of methodologies for the identification of promoters have been proposed. Nonetheless, due to the great heterogeneity existing in promoters, the results of these procedures are still unsatisfactory. In order to establish additional discriminative characteristics and properly recognize promoters, we developed the hybrid model for promoter identification (HMPI), a hybrid deep learning model that can characterize both the native sequences of promoters and the morphological outline of promoters at the same time. We developed the HMPI to combine a method called the PSFN (promoter sequence features network), which characterizes native promoter sequences and deduces sequence features, with a technique referred to as the DSPN (deep structural profiles network), which is specially structured to model the promoters in terms of their structural profile and to deduce their structural attributes. Results The HMPI was applied to human, plant and Escherichia coli K-12 strain datasets, and the findings showed that the HMPI was successful at extracting the features of the promoter while greatly enhancing the promoter identification performance. In addition, after the improvements of synthetic sampling, transfer learning and label smoothing regularization, the improved HMPI models achieved good results in identifying subtypes of promoters on prokaryotic promoter datasets. Conclusions The results showed that the HMPI was successful at extracting the features of promoters while greatly enhancing the performance of identifying promoters on both eukaryotic and prokaryotic datasets, and the improved HMPI models are good at identifying subtypes of promoters on prokaryotic promoter datasets. The HMPI is additionally adaptable to different biological functional sequences, allowing for the addition of new features or models.

The successful application of fuzzy control depends to a large extent on the parameters of some subjective decisions, such as fuzzy membership function (MF). Fuzzy logic controller (FLC) implementing augmented output MFs as compare to input MFs is presented to improve the accuracy, robustness, and performance of the system. The best possible combination of input and output MFs is introduced to distribute the uniform input MFs and augmented output MFs in the treatise. The simulation of the 2-Inputs 1-Output Fuzzy Control System is performed in many nonlinear processes. Then, the experimental outcomes of the uniformly and augmented distributed output MFs are compared under similar circumstances. The experimental outcomes are in a virtuous covenant with the simulation outcomes. The experimental outcomes show that the root mean square error (RMSE) is reduced around 75.3% and bringing down the relative error to the acceptable range (≤±10%). The control accuracy is improved and the robustness is boosted by reducing the RMSE through the FLC with augmented-distributed output MFs. Moreover, the cost and energy efficiency in any fuzzy system will be improved by implementing the augmented-distributed output MFs using the best possible combination of input and output MFs.

Abstract Identifying genetic variants that are associated with methylation variation—an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping—is important for understanding the epigenetic mechanisms underlying genotype-trait associations. Here, we develop a statistical method, IMAGE, for mQTL mapping in sequencing-based methylation studies. IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery. We compare IMAGE with existing approaches through extensive simulation. We also apply IMAGE to analyze two bisulfite sequencing studies, in which IMAGE identifies more mQTL than existing approaches.

PageRank has been widely used for the problem of evaluating the importance of data in many applications, such as Web science, information systems, and social network analysis. As vast amounts of data generate, the development of efficient PageRank computation is a vibrant area of contemporary research. In this paper, we propose a fast PageRank computation method based on network decomposition and the structure of directed acyclic graph (DAG). A network decomposition technique is first introduced to decompose the original network into three parts, including a general sub-network and two sub-DAGs. Based on the acyclic characteristic, we demonstrate that these two sub-DAGs can be theoretically lumped into two single nodes by a similarity transformation. Then, the PageRank problem on the original network is transformed into a PageRank problem on a much smaller network, and the full PageRank vector can be easily recovered from the result of new problem. As the time taken by the estimation of PageRank is directly proportional to the network size, the proposed method achieves an improved time complexity and is more efficient as the size of two sub-DAGs increases. Experimental results on real data sets show that our method provides a significant speedup compared with existing alternatives.

High dimensionality and small sample sizes, and their inherent risk of overfitting, pose great challenges for constructing efficient classifiers in microarray data classification. Therefore a feature selection technique should be conducted prior to data classification to enhance prediction performance. In general, filter methods can be considered as principal or auxiliary selection mechanism because of their simplicity, scalability, and low computational complexity. However, a series of trivial examples show that filter methods result in less accurate performance because they ignore the dependencies of features. Although few publications have devoted their attention to reveal the relationship of features by multivariate-based methods, these methods describe relationships among features only by linear methods. While simple linear combination relationship restrict the improvement in performance. In this paper, we used kernel method to discover inherent nonlinear correlations among features as well as between feature and target. Moreover, the number of orthogonal components was determined by kernel Fishers linear discriminant analysis (FLDA) in a self-adaptive manner rather than by manual parameter settings. In order to reveal the effectiveness of our method we performed several experiments and compared the results between our method and other competitive multivariate-based features selectors. In our comparison, we used two classifiers (support vector machine, [Formula: see text]-nearest neighbor) on two group datasets, namely two-class and multi-class datasets. Experimental results demonstrate that the performance of our method is better than others, especially on three hard-classify datasets, namely Wang's Breast Cancer, Gordon's Lung Adenocarcinoma and Pomeroy's Medulloblastoma.