The paper proposes a method to infer differentiation trees from RNA velocity data.
problem Reconstructing dynamic cellular processes from sequencing data.
method Defining varifold distances between RNA velocity curves to approximate shortest-path distances in a tree.
result The varifold distance method approximates the shortest-path distance in a tree isomorphic to the target differentiation tree.
A new algorithm reconstructs population dynamics from coarse samples.
problem Reconstructing population dynamics from unlabeled samples at coarse time intervals.
method Deep Momentum Multi-Marginal Schrödinger Bridge (DMSB) framework.
result Significantly outperforms baselines in synthetic and real-world datasets.
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.
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…
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.
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.
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…
New method preserves topology in Hodge decomposition for scalar and vector fields.
problem Topology-preserving Hodge decomposition on manifolds with boundaries.
method Comprehensive 5-component decomposition in Eulerian representation.
result Effective numerical experiments validate the method's accuracy and orthogonality.
E2Efold predicts RNA secondary structures better than previous methods.
problem RNA secondary structure prediction with constraints.
method End-to-end deep learning model using unrolled algorithms to enforce constraints.
result E2Efold predicts significantly better structures, especially for pseudoknotted structures.
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.
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…
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.
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.
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…
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…
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 λ2. 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.
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 …
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…
We discuss some aspects about the computation of kinematic, spectroscopic, Fermi and astrometric relative velocities that are geometrically defined in general relativity. Mainly, we state that kinematic and spectroscopic relative velocities only depend on the 4-velocities of the observer and the test particle, unlike F…
DSNE visualizes data velocity in lower dimensions.
problem Understanding movement patterns in high-dimensional data.
method DSNE is a variation of Stochastic Neighbor Embedding that learns velocity embeddings using Euclidean distances on a unit sphere.
result DSNE enables visualization of data movement in lower dimensions.
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.
RFM improves CNFs by adding a boundary constraint term and matching velocity fields.
problem Flow matching on constrained domains leads to unnatural samples.
method RFM adds a boundary constraint term and matches velocity fields in a simulation-free manner.
result RFM achieves comparable or better results on standard image benchmarks and produces high-quality samples.
Log-ergodic model improves velocity of money prediction.
problem Improving velocity of money prediction for economic control.
method Log-ergodic processes to simulate monetary velocity.
result Log-ergodic model offers superior predictive power.
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.
Optimal self-distillation improves generative models' velocity risk and mode recovery.
problem Improving generative models' velocity risk and mode recovery.
method Proved optimal self-distillation for rectified flow via linear probing, derived mixing coefficient, and provided validation tuning.
result Optimal self-distillation improves velocity risk and mode recovery.
New method estimates velocity fields for minimizing f-divergences without overfitting.
problem Minimizing statistical discrepancies between target and particle distributions.
method Directly estimate velocity fields using interpolation techniques, proving consistency under mild conditions.
result Consistent estimators of velocity fields improve accuracy in applications like domain adaptation and missing data imputation.
We prove that, in a space-time of dimension n>3 with a velocity field that is shear-free, vorticity-free and acceleration-free, the covariant divergence of the Weyl tensor is zero if the contraction of the Weyl tensor with the velocity is zero. The other way, if the covariant divergence of the Weyl tensor is zero, then…
Proves strong solutions for graphical Brakke flows with L2 normal velocity.
problem Proving strong solutions for graphical Brakke flows with specific velocity conditions.
method Combining L2 normal velocity with parabolic regularity theory. result Graphical Brakke flows with forcing term in Lp,q and C0,α are strong and classical solutions. 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.
CCVFM uses coreset to improve generative models by refining residual flows.
problem Generating multimodal distributions from scratch is challenging.
method Augments hierarchical rectified flow with a data-informed source distribution using a coreset.
result CCVFM achieves competitive few-step generation without a learned noise-to-data map.
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.
SAGE generates subsurface velocity models from sparse well logs and seismic images.
problem Lack of high-quality subsurface velocity models due to limited data availability.
method Subsurface AI-driven geostatistical extraction using proxy posterior.
result SAGE produces geologically plausible and statistically accurate velocity realizations.
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.
New method distinguishes cause from effect using causal velocity.
problem Inferring causal direction from bivariate data.
method Parametrization of bivariate SCMs in terms of causal velocity, using tools from measure transport.
result Method extends beyond known model classes and requires no assumptions on noise distributions.