Related papers: An efficient algorithm to compute the minimum free…
The Kinfold and KFOLD programs for RNA folding kinetics implement the Gillespie algorithm to generate stochastic folding trajectories from an initial structure s to a target structure t, in which each intermediate secondary structure is…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
Magneto-static finite element (FE) simulations make numerical optimization of electrical machines very time-consuming and computationally intensive during the design stage. In this paper, we present the application of a hybrid data-and…
The Partitioning Min-Max Weighted Matching (PMMWM) problem is an NP-hard problem that combines the problem of partitioning a group of vertices of a bipartite graph into disjoint subsets with limited size and the classical Min-Max Weighted…
Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases,…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
In this paper, we study the interaction of an antisense RNA and its target mRNA, based on the model introduced by Alkan {\it et al.} (Alkan {\it et al.}, J. Comput. Biol., Vol:267--282, 2006). Our main results are the derivation of the…
We study an NP-hard problem motivated by energy-efficiently maintaining the connectivity of a symmetric wireless communication network: Given an edge-weighted $n$-vertex graph, find a connected spanning subgraph of minimum cost, where the…
Motivated by applications to sensor networks, as well as to many other areas, this paper studies the construction of minimum-degree spanning trees. We consider the classical node-register state model, with a weakly fair scheduler, and we…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
We give two fully dynamic algorithms that maintain a $(1+\varepsilon)$-approximation of the weight $M$ of a minimum spanning forest (MSF) of an $n$-node graph $G$ with edges weights in $[1,W]$, for any $\varepsilon>0$. (1) Our deterministic…
Partial Differential Equations (PDE) are fundamental to model different phenomena in science and engineering mathematically. Solving them is a crucial step towards a precise knowledge of the behaviour of natural and engineered systems. In…
The numerical modeling of thin shell structures is a challenge, which has been met by a variety of finite element (FE) and other formulations -- many of which give rise to new challenges, from complex implementations to artificial locking.…
New high-throughput sequencing technologies have made it possible to pursue the advent of genome-wide transcriptomics. That progress combined with the recent discovery of regulatory non-coding RNAs (ncRNAs) has necessitated fast and…
Recent advancements in quantum computing have opened new avenues for tackling long-standing complex combinatorial optimization problems that are intractable for classical computers. Predicting secondary structure of mRNA is one such…
Neural Architecture Search (NAS) is increasingly popular to automatically explore the accuracy versus computational complexity trade-off of Deep Learning (DL) architectures. When targeting tiny edge devices, the main challenge for DL…
Two kinds of approximation algorithms exist for the k-BALANCED PARTITIONING problem: those that are fast but compute unsatisfying approximation ratios, and those that guarantee high quality ratios but are slow. In this paper we prove that…
Neural operators (NOs) struggle with high-contrast multiscale partial differential equations (PDEs), where fine-scale heterogeneities cause large errors. To address this, we use the Generalized Multiscale Finite Element Method (GMsFEM) that…
Finding Minimum Energy Configurations (MECs) is essential in fields such as physics, chemistry, and materials science, as they represent the most stable states of the systems. In particular, identifying such MECs in multi-component alloys…