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Abstract It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.

ABSTRACTTauopathies as one of the typical neurodegenerative diseases are characterized by pathologically aggregated tau in neuron and glia, which causes dysfunction, synapse loss, and cognitive impairments. There are more than 26 cases that are classified according to major tau isoform aggregates production or abnormal tau generation processes. Although the various concepts for targeting tau mechanisms have been investigated, the obvious limitations still remain and consequently, hindering their applicability. Therefore, additional strategies are required in the therapeutics and diagnosis. Here, we briefly summarized the etiological tau in the hyperphosphorylation, and the present concepts of tau-targeted disease therapies and diagnosis. We suggest the potential of approaches from deep learning-based single-cell transcriptome to microbiome and discuss the encountered challenges for the applicability and practicality.

Abstract Digital pathology coupled with advanced machine learning (e.g., deep learning) has been changing the paradigm of whole-slide histopathological images (WSIs) analysis. Major applications in digital pathology using machine learning include automatic cancer classification, survival analysis, and subtyping from pathological images. While most pathological image analyses are based on patch-wise processing due to the extremely large size of histopathology images, there are several applications that predict a single clinical outcome or perform pathological diagnosis per slide (e.g., cancer classification, survival analysis). However, current slide-based analyses are task-dependent, and a general framework of slide-based analysis in WSI has been seldom investigated. We propose a novel slide-based histopathology analysis framework that creates a WSI representation map, called HipoMap, that can be applied to any slide-based problems, coupled with convolutional neural networks. HipoMap converts a WSI of various shapes and sizes to structured image-type representation. Our proposed HipoMap outperformed existing methods in intensive experiments with various settings and datasets. HipoMap showed the Area Under the Curve (AUC) of 0.96±0.026 (5% improved) in the experiments for lung cancer classification, and c-index of 0.787±0.013 (3.5% improved) and coefficient of determination ( $$R^2$$ R 2 ) of 0.978±0.032 (24% improved) in survival analysis and survival prediction with TCGA lung cancer data respectively, as a general framework of slide-based analysis with a flexible capability. The results showed significant improvement comparing to the current state-of-the-art methods on each task. We further discussed experimental results of HipoMap as pathological viewpoints and verified the performance using publicly available TCGA datasets. A Python package is available at https://pypi.org/project/hipomap , and the package can be easily installed using Python PIP. The open-source codes in Python are available at: https://github.com/datax-lab/HipoMap .

Telehealth has been widely accepted as an alternative to in-person primary care. This study examines whether the quality of primary care delivered via telehealth is equitable for older adults across racial and ethnic boundaries in provider-shortage urban settings. The study analyzed documentation of the 4Ms components (What Matters, Mobility, Medication, and Mentation) in relation to self-reported racial and ethnic backgrounds of 254 Medicare Advantage enrollees who used telehealth as their primary care modality in Southern Nevada from July 2021 through June 2022. Results revealed that Asian/Hawaiian/Pacific Islanders had significantly less documentation in What Matters (OR = 0.39, 95%, p = .04) and Blacks had significantly less documentation in Mobility (OR = 0.35, p

One critical vulnerability of stream ciphers is the reuse of an encryption key. Since most stream ciphers consist of only a key scheduling algorithm and an Exclusive OR (XOR) operation, an adversary may break the cipher by XORing two captured ciphertexts generated under the same key. Various cryptanalysis techniques based on this property have been introduced in order to recover plaintexts or encryption keys; in contrast, this research reinterprets the vulnerability as a method of detecting stream ciphers from the ciphertexts it generates. Patterns found in the values (characters) expressed across the bytes of a ciphertext make the ciphertext distinguishable from random and are unique to each combination of ciphers and encryption keys. We propose a scheme that uses these patterns as a fingerprint, which is capable of detecting all ciphertexts of a given length generated by an encryption pair. The scheme can be utilized to detect a specific type of malware that exploits a stream cipher with a stored key such as the DarkComet Remote Access Trojan (RAT). We show that our scheme achieves 100% accuracy for messages longer than 13 bytes in about 17 μsec, providing a fast and highly accurate tool to aid in encrypted malware detection.

High-dimensional LASSO (Hi-LASSO) is a powerful feature selection tool for high-dimensional data. Our previous study showed that Hi-LASSO outperformed the other state-of-the-art LASSO methods. However, the substantial cost of bootstrapping and the lack of experiments for a parametric statistical test for feature selection have impeded to apply Hi-LASSO for practical applications. In this paper, the Python package and its Spark library are efficiently designed in a parallel manner for practice with real-world problems, as well as providing the capability of the parametric statistical tests for feature selection on high-dimensional data. We demonstrate Hi-LASSO's outperformance with various intensive experiments in a practical manner. Hi-LASSO will be efficiently and easily performed by using the packages for feature selection. Hi-LASSO packages are publicly available at https://github.com/datax-lab/Hi-LASSO under the MIT license. The packages can be easily installed by Python PIP, and additional documentation is available at https://pypi.org/project/hi-lasso and https://pypi.org/project/Hi-LASSO-spark.

Abstract Background Understanding the complex biological mechanisms of cancer patient survival using genomic and clinical data is vital, not only to develop new treatments for patients, but also to improve survival prediction. However, highly nonlinear and high-dimension, low-sample size (HDLSS) data cause computational challenges to applying conventional survival analysis. Results We propose a novel biologically interpretable pathway-based sparse deep neural network, named Cox-PASNet, which integrates high-dimensional gene expression data and clinical data on a simple neural network architecture for survival analysis. Cox-PASNet is biologically interpretable where nodes in the neural network correspond to biological genes and pathways, while capturing the nonlinear and hierarchical effects of biological pathways associated with cancer patient survival. We also propose a heuristic optimization solution to train Cox-PASNet with HDLSS data. Cox-PASNet was intensively evaluated by comparing the predictive performance of current state-of-the-art methods on glioblastoma multiforme (GBM) and ovarian serous cystadenocarcinoma (OV) cancer. In the experiments, Cox-PASNet showed out-performance, compared to the benchmarking methods. Moreover, the neural network architecture of Cox-PASNet was biologically interpreted, and several significant prognostic factors of genes and biological pathways were identified. Conclusions Cox-PASNet models biological mechanisms in the neural network by incorporating biological pathway databases and sparse coding. The neural network of Cox-PASNet can identify nonlinear and hierarchical associations of genomic and clinical data to cancer patient survival. The open-source code of Cox-PASNet in PyTorch implemented for training, evaluation, and model interpretation is available at: https://github.com/DataX-JieHao/Cox-PASNet.

High-throughput genomic technologies are leading to a paradigm shift in research of computational biology. Computational analysis with high-dimensional data and its interpretation are essential for the understanding of complex biological systems. Most biological data (e.g., gene expression and DNA sequence data) are high-dimensional, but consist of much fewer samples than predictors. Such high-dimension, low sample size (HDLSS) data often cause computational challenges in biological data analysis. A number of least absolute shrinkage and selection operator (LASSO) methods have been widely used for identifying biomarkers or prognostic factors in the field of bioinformatics. The LASSO solution has been improved through the development of the LASSO derivatives, including elastic-net, adaptive LASSO, relaxed LASSO, VISA, random LASSO, and recursive LASSO. However, there are several known limitations of the existing LASSO solutions: multicollinearity (particularly with different signs), subset size limitation, and the lack of the statistical test of significance. We propose a high-dimensional LASSO (Hi-LASSO) that theoretically improves a LASSO model providing better performance of both prediction and feature selection on extremely high-dimensional data. The Hi-LASSO alleviates bias introduced from bootstrapping, refines importance scores, improves the performance taking advantage of global oracle property, provides a statistical strategy to determine the number of bootstrapping, and allows tests of significance for feature selection with appropriate distribution. The performance of Hi-LASSO was assessed by comparing the existing state-of-the-art LASSO methods in extensive simulation experiments with multiple data settings. The Hi-LASSO was also applied for survival analysis with GBM gene expression data.

In recent years, deep learning has emerged as a highly active research field, achieving great success in various machine learning areas, including image processing, speech recognition, and natural language processing, and now rapidly becoming a dominant tool in biomedicine [...]

Abstract Background Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis may be caused by high complexity of biological systems, where multiple biological components and their hierarchical relationships are involved. Moreover, it is challenging to develop robust computational solutions with high-dimension, low-sample size data. Results In this study, we propose a Pathway-Associated Sparse Deep Neural Network (PASNet) that not only predicts patients’ prognoses but also describes complex biological processes regarding biological pathways for prognosis. PASNet models a multilayered, hierarchical biological system of genes and pathways to predict clinical outcomes by leveraging deep learning. The sparse solution of PASNet provides the capability of model interpretability that most conventional fully-connected neural networks lack. We applied PASNet for long-term survival prediction in Glioblastoma multiforme (GBM), which is a primary brain cancer that shows poor prognostic performance. The predictive performance of PASNet was evaluated with multiple cross-validation experiments. PASNet showed a higher Area Under the Curve (AUC) and F1-score than previous long-term survival prediction classifiers, and the significance of PASNet’s performance was assessed by Wilcoxon signed-rank test. Furthermore, the biological pathways, found in PASNet, were referred to as significant pathways in GBM in previous biology and medicine research. Conclusions PASNet can describe the different biological systems of clinical outcomes for prognostic prediction as well as predicting prognosis more accurately than the current state-of-the-art methods. PASNet is the first pathway-based deep neural network that represents hierarchical representations of genes and pathways and their nonlinear effects, to the best of our knowledge. Additionally, PASNet would be promising due to its flexible model representation and interpretability, embodying the strengths of deep learning. The open-source code of PASNet is available at https://github.com/DataX-JieHao/PASNet.

Abstract Backgrounds A large number of long intergenic non-coding RNAs (lincRNAs) are linked to a broad spectrum of human diseases. The disease association with many other lincRNAs still remain as puzzle. Validation of such links between the two entities through biological experiments are expensive. However, a plethora lincRNA-data are available now, thanks to the High Throughput Sequencing (HTS) platforms, Genome Wide Association Studies (GWAS), etc, which opens the opportunity for cutting-edge machine learning and data mining approaches to extract meaningful relationships among lincRNAs and diseases. However, there are only a few in silico lincRNA-disease association inference tools available to date, and none of them utilizes side information of both the entities simultaneously in a single framework. Methods The recently developed Inductive Matrix Completion (IMC) technique provides a recommendation platform among two entities considering respective side information about them. However, the formulation of IMC is incapable of handling noise and outliers that may be present in the datasets, while data sparsity consideration is another issue with the standard IMC method. Thus, a robust version of IMC is needed that can solve the two issues. As a remedy, in this paper, we propose Stable Robust Inductive Matrix Completion (SRIMC) that utilizes the l 2,1 norm based regularization to optimize the objective function with a unique 2-step stable solution approach. Results We applied SRIMC to the available association data between human lincRNAs and OMIM disease phenotypes as well as a diverse set of side information about the lincRNAs and the diseases. The method performs better than the state-of-the-art methods in terms of p r e c i s i o n @ k and r e c a l l @ k at the top-k disease prioritization to the subject lincRNAs. We also demonstrate that SRIMC is equally effective for querying about novel lincRNAs, as well as predicting rank of a newly known disease for a set of well-characterized lincRNAs. Conclusions With the experimental results and computational evaluation, we show that SRIMC is robust in handling datasets with noise and outliers as well as dealing with novel lincRNAs and disease phenotypes.