Related papers: On the combinatorics of sparsification

RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…

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…

Fully finetuning foundation language models (LMs) with billions of parameters is often impractical due to high computational costs, memory requirements, and the risk of overfitting. Although methods like low-rank adapters help address these…

Randomized matrix sparsification has proven to be a fruitful technique for producing faster algorithms in applications ranging from graph partitioning to semidefinite programming. In the decade or so of research into this technique, the…

In this work, we leverage advances in sparse coding techniques to reduce the number of trainable parameters in a fully connected neural network. While most of the works in literature impose $\ell_1$ regularization, DropOut or DropConnect…

Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…

In this paper a sublinear time algorithm is presented for the reconstruction of functions that can be represented by just few out of a potentially large candidate set of Fourier basis functions in high spatial dimensions, a so-called…

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…

Sparsity is a well-studied technique for compressing deep neural networks (DNNs) without compromising performance. In deep reinforcement learning (DRL), neural networks with up to 5% of their original weights can still be trained with…

This paper presents a Spatial Re-parameterization (SpRe) method for the N:M sparsity. SpRe stems from an observation regarding the restricted variety in spatial sparsity of convolution kernels presented in N:M sparsity compared with…

Although sparse neural networks have been studied extensively, the focus has been primarily on accuracy. In this work, we focus instead on network structure, and analyze three popular algorithms. We first measure performance when structure…

Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…

Many high dimensional classification techniques have been proposed in the literature based on sparse linear discriminant analysis (LDA). To efficiently use them, sparsity of linear classifiers is a prerequisite. However, this might not be…

Prior results for tRNA and 5S rRNA demonstrated that secondary structure prediction accuracy can be significantly improved by modifying the parameters in the multibranch loop entropic penalty function. However, for reasons not well…

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…

Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…

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…

Sparse tensor decomposition and completion are common in numerous applications, ranging from machine learning to computational quantum chemistry. Typically, the main bottleneck in optimization of these models are contractions of a single…

RNA secondary structures prediction is one of the main issues in bioinformatics. It seeks to elucidate structural conserved regions within a set of RNA sequences. Unfortunately, finding an accurate conserved structure is a very hard task to…

We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…