Related papers: RNA-RNA interaction prediction: partition function…
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
We study computational aspects of repulsive Gibbs point processes, which are probabilistic models of interacting particles in a finite-volume region of space. We introduce an approach for reducing a Gibbs point process to the hard-core…
In this paper we relate the partition function to the max-statistics of random variables. In particular, we provide a novel framework for approximating and bounding the partition function using MAP inference on randomly perturbed models. As…
We show that the folding rates (k_F) of RNA are determined by N, the number of nucleotides. By assuming that the distribution of free energy barriers separating the folded and the unfolded states is Gaussian, which follows from central…
The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more…
We study the statistical complexity of estimating partition functions given sample access to a proposal distribution and an unnormalized density ratio for a target distribution. While partition function estimation is a classical problem,…
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…
We develop Random Batch Methods for interacting particle systems with large number of particles. These methods use small but random batches for particle interactions, thus the computational cost is reduced from $O(N^2)$ per time step to…
In this paper the relation between nonanticipative rate distortion function (RDF) and Bayesian filtering theory is further investigated on general Polish spaces. The relation is established via an optimization on the space of conditional…
Many scientific problems require identifying a small set of covariates that are associated with a target response and estimating their effects. Often, these effects are nonlinear and include interactions, so linear and additive methods can…
We present a polynomial-time Markov chain Monte Carlo algorithm for estimating the partition function of the antiferromagnetic Ising model on any line graph. The analysis of the algorithm exploits the "winding" technology devised by…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…
For many complex diseases, prognosis is of essential importance. It has been shown that, beyond the main effects of genetic (G) and environmental (E) risk factors, the gene-environment (G$\times$E) interactions also play a critical role. In…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
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…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
We model fission at barrier-top energies in a simplified model space that permits comparison of different components of the residual nucleon-nucleon interaction. The model space is built on particle-hole excitations of reference…
Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…