Related papers: A Combinatorial Framework for Designing (Pseudokno…
Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of…
The motivation of this work is to define cohomology classes in the space of knots that are both easy to find and to evaluate, by reducing the problem to simple linear algebra. We achieve this goal by defining a combinatorial graded cochain…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
We extend our work for compression of currents and varifolds to a compression algorithm for the embedded normal cycles representation of shape, restricted to the constant normal kernel case, using the Nystrom approximation in Reproducing…
Representation learning on graphs has emerged as a powerful mechanism to automate feature vector generation for downstream machine learning tasks. The advances in representation on graphs have centered on both homogeneous and heterogeneous…
We introduce a quantum dynamic programming framework that allows us to directly extend to the quantum realm a large body of classical dynamic programming algorithms. The corresponding quantum dynamic programming algorithms retain the same…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
Many models have been proposed for vision and language tasks, especially the image-text retrieval task. All state-of-the-art (SOTA) models in this challenge contained hundreds of millions of parameters. They also were pretrained on a large…
We study dynamic graph algorithms in the Massively Parallel Computation model, which was inspired by practical data processing systems. Our goal is to provide algorithms that can efficiently handle large batches of edge insertions and…
The integration of Spiking Neural Networks (SNNs) and Graph Neural Networks (GNNs) is gradually attracting attention due to the low power consumption and high efficiency in processing the non-Euclidean data represented by graphs. However,…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Many complex systems involve interactions between more than two agents. Hypergraphs capture these higher-order interactions through hyperedges that may link more than two nodes. We consider the problem of embedding a hypergraph into…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
Graphs are a fundamental representation of complex, nonlinear structured data across various domains, including social networks and quantum systems. Quantum Graph Recurrent Neural Networks (QGRNNs) have been proposed to model quantum…
Recent advances in protein function prediction exploit graph-based deep learning approaches to correlate the structural and topological features of proteins with their molecular functions. However, proteins in vivo are not static but…
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…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
For a required payload, the existing reversible data hiding (RDH) methods always expect to reduce the embedding distortion as much as possible, such as by utilizing a well-designed predictor, taking into account the carrier-content…
A hypergraph spectral sparsifier of a hypergraph $G$ is a weighted subgraph $H$ that approximates the Laplacian of $G$ to a specified precision. Recent work has shown that similar to ordinary graphs, there exist $\widetilde{O}(n)$-size…
Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically…