Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate identification of lncRNAs in RNA-seq datasets is crucial for exploring their char…
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48 results for “non-coding RNA”
Machine learning improves RNA secondary structure prediction.
problem Stagnant performance of RNA secondary structure prediction methods.
method Machine learning, especially deep learning, is used to predict RNA secondary structures.
result Machine learning methods have improved the prediction of RNA secondary structures.
Non-coding RNA (ncRNA) are RNA sequences which don't code for a gene but instead carry important biological functions. The task of ncRNA classification consists in classifying a given ncRNA sequence into its family. While it has been shown that the graph structure of an ncRNA sequence folding is of great importance for…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms fo…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and translation. Since an RNA's function depends on its structural properties, the RN…
RNA-binding proteins (RBPs) play crucial roles in many biological processes, e.g. gene regulation. Computational identification of RBP binding sites on RNAs are urgently needed. In particular, RBPs bind to RNAs by recognizing sequence motifs. Thus, fast locating those motifs on RNA sequences is crucial and time-efficie…
Graph network predicts circRNA-disease associations using multi-source similarity features.
problem Identifying circRNA-disease associations is challenging and time-consuming.
method Proposes a graph convolution network framework using multi-source similarity information.
result Framework predicts circRNA-disease associations with promising results and outperforms existing methods.
New method learns complex cell networks from millions of cells.
problem Existing methods fail to scale to large datasets.
method Multi-axis Gaussian graphical models.
result Method scales to millions of cells in minutes.
Generalized Quandle Polynomials and Their Applications to Stuquandles, Stuck Links, and RNA Foldingmath.GT
Generalized quandle polynomial used for stuquandles, stuck links, and RNA folding.
problem Defining polynomial invariants for stuquandles, stuck links, and RNA foldings.
method Introduced a generalized quandle polynomial and proved its invariance for stuquandles. Used this invariant to define polynomials for stuck links and RNA foldings.
result Polynomial invariants for stuquandles, stuck links, and RNA foldings.
Deep learning predicts RNA degradation from crowdsourced data.
problem Predicting RNA degradation to improve thermostability.
method Crowdsourced machine learning competition on Kaggle.
result 41% of predictions matched experimental data, and models generalized to longer RNA molecules.
Predicting RNA base distances using a large language model.
problem Accurately predicting RNA structural information, especially distance maps.
method Using a large pretrained RNA language model coupled with a transformer.
result The model can accurately infer RNA base distances from sequence data.
SentRNA: Improving computational RNA design by incorporating a prior of human design strategiesq-bio.QM
Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made in developing machine-based inverse RNA folding algorithms, current approaches s…
A deep learning model organizes RNA graphs to reveal folding patterns and properties.
problem Organizing and understanding the complex folding patterns of RNA secondary structures.
method Geometric scattering autoencoder (GSAE) network for learning graph embeddings.
result GSAE accurately reflects bistable RNA structures and can sample new folding trajectories.
New benchmarks for RNA 3D structure-function modeling.
problem Lack of standardized benchmarks for RNA deep learning.
method Developed seven benchmark datasets, provided tools for data handling, and offered a user-friendly environment for model comparison.
result Demonstrated utility with baseline results using a relational graph neural network.
Review of Single-cell RNA-seq Data Clustering for Cell Type Identification and Characterizationq-bio.GN
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become the central component to identify and characterize novel cell types and gene exp…
The Regularized Nonlinear Acceleration (RNA) algorithm is an acceleration method capable of improving the rate of convergence of many optimization schemes such as gradient descend, SAGA or SVRG. Until now, its analysis is limited to convex problems, but empirical observations shows that RNA may be extended to wider set…
New method detects RNA modifications without prior training, revealing novel sites.
problem Detecting RNA modifications with high accuracy and sensitivity.
method Anomaly detection using nanopore raw ionic current signals and nearest neighbor comparison.
result Detects diverse RNA modifications without prior training, including a novel 2'-O-methylated site in DENV.
New invariants for RNA foldings and stuck links defined.
problem Defining invariants for RNA foldings and stuck links.
method Assigning Boltzmann weights at classical and stuck crossings.
result Explicit computations of new invariants provided.
Deep Belief Network predicts lncRNA-disease associations with high accuracy.
problem Accurately identifying lncRNA-disease associations to understand lncRNA functionality and disease mechanism.
method Proposes a DBN-based model using heterogeneous networks and DBN for feature learning.
result Obtained AUC of 0.96 and AUPR of 0.967 on standard dataset.
RNA foldings and Stuck Knotsmath.GT
Study uses knot theory to model RNA foldings, emphasizing both entanglement and intrachain interactions.
problem Modeling RNA foldings considering both entanglement and intrachain interactions.
method Combines knot theory with embedded rigid vertex graphs to emphasize both entanglement and intrachain interactions of RNA foldings.
result Defines and computes a coloring counting invariant for stuck links, providing explicit computations for arc diagrams of RNA foldings.
Improved GPLVM model for single-cell RNA-seq data.
problem Lack of effective scalable models for clustering cell types in large-scale single-cell RNA-seq data.
method Introduces amortized stochastic variational Bayesian GPLVM (BGPLVM) tailored for single-cell RNA-seq.
result Matches the performance of scVI on synthetic and real-world datasets and reveals more interpretable latent structures.
HSSE framework embeds single-cell RNA-seq data at multiple scales.
problem Capturing heterogeneous local structure in single-cell RNA-seq data.
method Hierarchical sheaf spectral embedding (HSSE) framework.
result HSSE achieves competitive or improved performance in single-cell RNA-seq data representation learning.
Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate computational tools for transcript reconstruction, this technology may also become us…
In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly predict the RNA base-pairing matrix, and use an unrolled algorithm for constrained p…
New methods improve analysis of single cell RNA sequencing data.
problem High dimensionality and complexity of scRNA-seq data.
method Topological Nonnegative Matrix Factorization (TNMF) and Robust Topological NMF (rTNMF).
result TNMF and rTNMF significantly outperform other NMF-based methods.
RNA structures show that a significant portion of bases do not form hydrogen bonds.
problem Understanding the unpaired bases in RNA secondary structures.
method Comparing random words in free groups to RNA sequences, analyzing word lengths.
result The expected fraction of unpaired bases converges to a constant .
We study the secondary structure of RNA determined by Watson-Crick pairing without pseudo-knots using Milnor invariants of links. We focus on the first non-trivial invariant, which we call the Heisenberg invariant. The Heisenberg invariant, which is an integer, can be interpreted in terms of the Heisenberg group as wel…
Graph neural networks improve with edge similarity constraints in RNA structure analysis.
problem Lack of edge similarity constraints in graph neural networks.
method Introduced a graph neural network layer that leverages prior information about edge similarities.
result Edge similarity constraints do not enhance performance in graph neural networks.
Symmetric CNNs improve sequential recommendation and protein structure prediction.
problem Improving prediction accuracy in sequential recommendation and protein structure inference.
method Developed a CNN architecture that preserves symmetry in convolutional layers, using parameterized convolutional kernels.
result Symmetric structured CNNs achieve better performance with fewer parameters.
Finite Mixtures of Multivariate Poisson-Log Normal Factor Analyzers for Clustering Count Datastat.ME
Flexible models cluster RNA sequencing data.
problem Clustering discrete data from RNA sequencing studies.
method Finite mixtures of multivariate Poisson-log normal factor analyzers with constraints.
result Models give favorable clustering performance on real and simulated data.
Regularized nonlinear acceleration (RNA) estimates the minimum of a function by post-processing iterates from an algorithm such as the gradient method. It can be seen as a regularized version of Anderson acceleration, a classical acceleration scheme from numerical analysis. The new scheme provably improves the rate of …
Towards the Latent Transcriptomeq-bio.GN
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional representation that is used to predict abundance of each kmer. We report that our…
MarkerMap selects key genes for cell type analysis in single-cell RNA-seq.
problem Selecting informative genes from large single-cell RNA-seq datasets is challenging and computationally intensive.
method MarkerMap is a generative model that identifies minimal gene sets explaining cell type variability.
result MarkerMap outperforms existing methods in both supervised and unsupervised marker selection.
Develops a method to infer cell trajectories from RNA sequencing data.
problem Inferring cell trajectories from single cell RNA-sequencing data.
method Entropy-regularized optimal transport for global optimization.
result Proves and implements a method to recover ground truth trajectories from limited samples.
ChemCPA predicts cellular responses to novel drugs using transfer learning.
problem Scaling high-throughput screens to measure cellular responses for many drugs is costly and challenging.
method ChemCPA, a new encoder-decoder architecture combined with transfer learning.
result Training on existing bulk RNA HTS datasets improves generalization performance, reducing the need for extensive single-cell screens.
DiffKnock improves feature selection in neural networks with complex dependencies and non-linear associations.
problem Selecting important features in neural networks with complex dependencies and non-linear associations.
method DiffKnock uses diffusion models to generate knockoffs and neural network statistics to measure feature importance.
result DiffKnock outperforms existing methods in detecting non-linear associations and preserving feature dependencies.
sgdGMF efficiently estimates generalized matrix factorization models for single-cell RNA sequencing data.
problem Challenges in dimensionality reduction for large single-cell RNA sequencing datasets.
method Scalable adaptive stochastic gradient descent algorithm for generalized matrix factorization models.
result sgdGMF outperforms existing methods in scalability and accuracy for large datasets.
Paper proposes a new method for sparse spectral clustering on Stiefel manifold.
problem Sparse spectral clustering on Stiefel manifold with nonsmooth and nonconvex objective.
method Proposes a manifold proximal linear method (ManPL) to solve the original SSC formulation.
result Demonstrates the advantage of ManPL over existing methods on single-cell RNA sequencing data.
Super-OT combines GANs and optimal transport for lineage tracing.
problem Lineage tracing in single-cell RNA-seq data.
method Supervised learning framework with GANs for optimal transport.
result Super-OT outperforms Waddington-OT in predicting cell differentiation outcomes.
Study compares single vs ensemble feature selection for cancer diagnosis.
problem Identifying relevant variables for cancer diagnosis and prognosis.
method Comparison of single feature selection algorithms and ensemble of diverse algorithms.
result Ensemble approach did not improve predictive performance over individual algorithms.
Extrapolation Guarantees for Perturbation Modeling Under the Additive Latent Shift Assumptionstat.ML
The paper tackles extrapolation of gene knockouts effects on RNA counts.
problem Modeling effects of gene knockouts on RNA counts for new perturbations.
method Formulated as a latent variable model with additive perturbation effects, proved identifiability, proposed PDAE for estimation.
result PDAE can accurately predict effects of unseen but identifiable perturbations.
Sources of variability in experimentally derived data include measurement error in addition to the physical phenomena of interest. This measurement error is a combination of systematic components, originating from the measuring instrument, and random measurement errors. Several novel biological technologies, such as ma…
Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq dataq-bio.QM
Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has …
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical investigations. In the study, we will be using the dataset collected by the authors of Sys…
The paper develops methods for causal inference from single-cell RNA sequencing data with multiple outcomes.
problem Causal inference from single-cell RNA sequencing data with multiple heterogeneous outcomes.
method Generic semiparametric inference framework for doubly robust estimation with multiple derived outcomes.
result Demonstrates the use of semiparametric inferential results for estimating causal effects in genomics.
Machine learning accurately diagnoses cancer from whole genome sequencing data.
problem Accurate cancer diagnosis at all stages.
method Novel MLAC (Machine Learning Against Cancer) method using next-gen RNA sequencing.
result Perfect precision, sensitivity, and specificity achieved for most tumor types.
We introduce and study the Hermitian matrix model with potential V(x)=x^2/2-stx/(1-tx), which enumerates the number of linear chord diagrams of fixed genus with specified numbers of backbones generated by s and chords generated by t. For the one-cut solution, the partition function, correlators and free energies are co…
We present a sparse knowledge gradient (SpKG) algorithm for adaptively selecting the targeted regions within a large RNA molecule to identify which regions are most amenable to interactions with other molecules. Experimentally, such regions can be inferred from fluorescence measurements obtained by binding a complement…