arXiv research

Machine learning improves RNA secondary structure prediction.

Symmetric CNNs improve sequential recommendation and protein structure prediction.

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…

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…

RNA structures show that a significant portion of bases do not form hydrogen bonds.

A deep learning model organizes RNA graphs to reveal folding patterns and properties.

Deep learning predicts RNA degradation from crowdsourced data.

Predicting RNA base distances using a large language model.

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…

New benchmarks for RNA 3D structure-function modeling.

Many machine learning techniques have been proposed in the last few years to process data represented in graph-structured form. Graphs can be used to model several scenarios, from molecules and materials to RNA secondary structures. Several kernel functions have been defined on graphs that coupled with kernelized learn…

Study uses knot theory to model RNA foldings, emphasizing both entanglement and intrachain interactions.

HSSE framework embeds single-cell RNA-seq data at multiple scales.

In this study, we generalize double tangent bundles to double jet bundles. We present a secondary vector bundle structure on a 1-jet of a vector bundle. We show that 1-jet of a vector bundle carries two vector bundle structures, namely primary and secondary structures. We also show that the manifold charts induced by p…

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…

Improved GPLVM model for single-cell RNA-seq data.

PS8-Net improves eight-state protein secondary structure prediction accuracy.

Graph neural networks improve with edge similarity constraints in RNA structure analysis.

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…

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…

Generalized quandle polynomial used for stuquandles, stuck links, and RNA folding.

Tree data are ubiquitous because they model a large variety of situations, e.g., the architecture of plants, the secondary structure of RNA, or the hierarchy of XML files. Nevertheless, the analysis of these non-Euclidean data is difficult per se. In this paper, we focus on the subtree kernel that is a convolution kern…

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…

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.

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.

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…

Secondary Calculus formalizes PDEs using cohomology, simplifying their study.

CRF model improves protein secondary structure prediction.

Mathematician summarizes protein geometry and mutation effects.

We tackle the problem of protein secondary structure prediction using a common task framework. This lead to the introduction of multiple ideas for neural architectures based on state of the art building blocks, used in this task for the first time. We take a principled machine learning approach, which provides genuine,…

We give a survey of the approaches to classifying foliations, starting with the Haefliger classifying spaces and the various results and examples about the secondary classes of foliations. Various dynamical properties of foliations are introduced and discussed, including expansion rate, local entropy, and orbit growth …

Deep learning helps remove secondary $B$-mode polarization to detect primordial gravitational waves.

DiffKnock improves feature selection in neural networks with complex dependencies and non-linear associations.

New methods improve analysis of single cell RNA sequencing data.

In this paper we define K-theoretic secondary invariants attached to a Lie groupoid $G$. The K-theory of $C^*_r(G_{ad}^0)$ (where $G_{ad}^0$ is the adiabatic deformation $G$ restricted to the interval $[0,1)$) is the receptacle for K-theoretic secondary invariants. We give a Lie groupoid version of construction given b…

Let G be a simple Lie group of real rank one, and S the ideal boundary of the corresponding symmetric space of noncompact type (H^n_R, H^n_C, H^n_H or H^2_O). We show the finiteness of the possible values of the secondary characteristic classes of transversely homogeneous foliations on a fixed manifold whose transverse…

Constructs combinatorial 2D topological field theories from cyclic A-infinity algebras.

Graph Canonical Correlation Analysis improves CCA for multiomics datasets.

Study of spectral flow in symmetric Toeplitz operator families.

The knot invariant Upsilon, defined by Ozsvath, Stipsicz, and Szabo, induces a homomorphism from the smooth knot concordance group to the group of piecewise linear functions on the interval [0,2]. Here we define a set of related secondary invariants, each of which assigns to a knot a piecewise linear function on [0,2].…

The paper tackles online learning with two types of losses and shows it's impossible without certain assumptions.

We introduce the secondary Stiefel-Whitney class $\tilde w_2$ of homotopically trivial diffeomorphisms and show that a homotopically trivial symplectomorphism of a ruled 4-manifold is isotopic to identity if and only if the class $\tilde w_2$ vanishes. Using this, we give a detailed description of the combinatorial str…

The problem of distributed learning and channel access is considered in a cognitive network with multiple secondary users. The availability statistics of the channels are initially unknown to the secondary users and are estimated using sensing decisions. There is no explicit information exchange or prior agreement amon…

Fuses ITRs for primary and secondary outcomes to minimize harm.

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 …