LEARNA uses deep reinforcement learning to design RNA sequences.
problem Designing RNA molecules to satisfy structural constraints.
method LEARNA employs deep reinforcement learning to train a policy network for RNA design.
result LEARNA achieves new state-of-the-art performance in RNA Design benchmarks.
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…
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.
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.
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…
PLIT identifies plant lncRNAs from RNA-seq data with high accuracy.
problem Inaccurate identification of lncRNAs in plant transcriptomic datasets.
method PLIT uses L1 regularization and iRF classification to select optimal features from sequence and codon-bias data.
result PLIT outperforms existing CPC tools in identifying lncRNAs in plant RNA-seq datasets.
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.
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.
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.
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.
This study reviews and evaluates clustering methods for single-cell RNA-seq data.
problem Identifying and characterizing novel cell types from single-cell RNA-seq data.
method Review and performance comparison of clustering methods.
result Performance comparison experiments on two datasets.
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.
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.
Paper introduces a new method for error estimation in classification tasks with limited data.
problem Challenges in designing accurate classifiers and evaluating their performance with limited training data.
method Introduces a novel Bayesian MMSE estimator for optimal Bayesian transfer learning (OBTL) using Monte Carlo importance sampling.
result Proposed OBTL error estimation scheme outperforms standard methods, especially in small-sample settings.
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.
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.
New method optimizes diffusion models without fine-tuning, integrating soft value functions.
problem Optimizing natural design spaces of images, molecules, DNA, RNA, and protein sequences.
method Iterative sampling method integrating soft value functions into diffusion model inference.
result Directly utilizes non-differentiable features/reward feedback, applies to discrete diffusion models.
Graph ConvNet improves ncRNA classification accuracy.
problem Classifying non-coding RNA sequences into families.
method Graph Convolutional Network model trained on raw RNA graphs.
result 85.73% accuracy and 85.61% F1-score over 13 classes.
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.
VSD efficiently learns conditional distributions for combinatorial designs.
problem Learning conditional distributions for rare combinatorial designs.
method Variational Search Distributions (VSD) using variational inference.
result VSD outperforms existing methods on real sequence-design problems.
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. MSBM extends SB for multi-marginal trajectory inference.
problem Trajectory inference from multiple discrete snapshots.
method Multi-Marginal Schrödinger Bridge Matching (MSBM) using iterative Markovian fitting (IMF).
result MSBM effectively captures complex trajectories and respects intermediate distributions.
Develops a model for RNA-seq data clustering.
problem Challenges in clustering RNA-seq count data with variable selection.
method Sparse negative binomial mixture model with lasso or fused lasso regularization.
result Superior performance in clustering accuracy, feature selection, and biological interpretation.
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.
The paper proposes a method to reliably select design algorithms for machine learning-guided design tasks.
problem Choosing the right design algorithm for machine learning-guided design tasks.
method Combining designs' predicted property values with held-out labeled data to reliably forecast characteristics of the label distributions produced by different design algorithms.
result The method is guaranteed to return design algorithms that yield successful label distributions.
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…
DeepRAM evaluates and selects the best deep learning architecture for DNA/RNA binding specificity prediction.
problem Selecting the best deep learning architecture for predicting DNA/RNA binding specificity.
method Systematic exploration of various deep learning architectures using deepRAM, an end-to-end deep learning tool.
result A k-mer embedding convolutional layer and recurrent layer architecture outperforms other methods.
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.
A scalable method to learn causal graphs from large data.
problem Learning causal graphs from large scale data is challenging.
method Differentiable Adjacency Test (DAT) to evaluate adjacency in causal graphs.
result DAT-Graph can learn graphs of 1000 variables with state-of-the-art accuracy.
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
problem Optimizing biological sequences for a black-box score function.
method Bootstrapped training of score-conditioned generator (BootGen) algorithm.
result Our method outperforms competitive baselines on biological sequential design tasks.
Generative Distribution Embeddings learn multiscale representations of distributions.
problem Learning representations of entire distributions for multiscale reasoning.
method Introducing GDE framework that lifts autoencoders to the space of distributions, using conditional generative models and distributional invariance.
result GDEs learn predictive sufficient statistics embedded in Wasserstein space, recovering distances and trajectories for Gaussian and Gaussian mixture distributions.
A new tree-Wasserstein distance for high-dimensional data with latent feature hierarchy.
problem Finding meaningful distances between high-dimensional data samples with latent feature hierarchy.
method Proposes a new tree-Wasserstein distance (TWD) for high-dimensional data with a latent feature hierarchy, using diffusion geometry and tree decoding.
result The proposed TWD effectively recovers the latent feature hierarchy and is efficient and scalable.
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.
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design architectures to suit it. As such, architectures that fit the structure of genomics should …
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.