Related papers: LinearPartition: Linear-Time Approximation of RNA …
In this paper we experiment with using neural network structures to predict a protein's secondary structure ({\alpha} helix positions) from only its primary structure (amino acid sequence). We implement a fully connected neural network…
We present classical and quantum algorithms for approximating partition functions of classical Hamiltonians at a given temperature. Our work has two main contributions: first, we modify the classical algorithm of \v{S}tefankovi\v{c},…
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
This paper proposes an easy-to-use method for one-class classification: Repeated Element-wise Folding (REF). The algorithm consists of repeatedly standardizing and applying an element-wise folding operation on the one-class training data.…
We present a novel quantum algorithm for estimating Gibbs partition functions in sublinear time with respect to the logarithm of the size of the state space. This is the first speed-up of this type to be obtained over the seminal…
We propose a novel and efficient method for link prediction in bipartite networks, using \textit{formal concept analysis} (FCA) and the Transformer encoder. Link prediction in bipartite networks finds practical applications in various…
Link prediction is an elemental challenge in network science, which has already found applications in guiding laboratorial experiments, digging out drug targets, recommending friends in social networks, probing mechanisms in network…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
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…
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…
Monte Carlo methods are widely used in particle physics to integrate and sample probability distributions (differential cross sections or decay rates) on multi-dimensional phase spaces. We present a Neural Network (NN) algorithm optimized…
The RNA Inverse Folding problem comes from computational biology. The goal is to find a molecule that has a given folding. It is important for scientific fields such as bioengineering, pharmaceutical research, biochemistry, synthetic…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
The preformation factor quantifies the probability of {\alpha} particles preforming on the surface of the parent nucleus in decay theory and is closely related to the study of {\alpha} clustering structure. In this work, a multilayer…
We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy…
Hybrid Bayesian networks (HBN) contain complex conditional probabilistic distributions (CPD) specified as partitioned expressions over discrete and continuous variables. The size of these CPDs grows exponentially with the number of parent…
This paper seeks an efficient algorithm for stochastic precoding to maximize the long-term average weighted sum rates throughout a multiple-input multiple-output (MIMO) network. Unlike many existing works that assume a particular…
Computing the LZ factorization (or LZ77 parsing) of a string is a computational bottleneck in many diverse applications, including data compression, text indexing, and pattern discovery. We describe new linear time LZ factorization…