Related papers: StemP: A fast and deterministic Stem-graph approac…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
In a previous paper [CSIAM Trans. Appl. Math. 2 (2021), 1-55], the authors proposed a theoretical framework for the analysis of RNA velocity, which is a promising concept in scRNA-seq data analysis to reveal the cell state-transition…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
This paper explores the automated process of determining stem compatibility by identifying audio recordings of single instruments that blend well with a given musical context. To tackle this challenge, we present Stem-JEPA, a novel…
Poor bucking decisions made by forest harvesters can have a negative effect on the products that are generated from the logs. Making the right bucking decisions is not an easy task because harvesters must rely on predictions of the stem…
One algorithm to predict protein structure is the residual dipolar coupling based residue assembly and filter tool (REDCRAFT). This algorithm exploits an exponential reduction of the search space of all possible structures to find a…
Inferring missing links or detecting spurious ones based on observed graphs, known as link prediction, is a long-standing challenge in graph data analysis. With the recent advances in deep learning, graph neural networks have been used for…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
Accurate estimation of plant skeletal structure (e.g., branching structure) from images is essential for smart agriculture and plant science. Unlike human skeletons with fixed topology, plant skeleton estimation presents a unique challenge,…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Link prediction is a crucial task in many downstream applications of graph machine learning. To this end, Graph Neural Network (GNN) is a widely used technique for link prediction, mainly in transductive settings, where the goal is to…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
D. Wilson~\cite{[Wi]} in the 1990's described a simple and efficient algorithm based on loop-erased random walks to sample uniform spanning trees and more generally weighted trees or forests spanning a given graph. This algorithm provides a…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…