Related papers: RNAmountAlign: efficient software for local, globa…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
In this paper, we analyze and improve the adversarial robustness of a convolutional neural network (CNN) that assists crystal-collimator alignment at CERN's Large Hadron Collider (LHC) by classifying a beam-loss monitor (BLM) time series…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
The subcellular localization of RNAs, including long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and other smaller RNAs, plays a critical role in determining their biological functions. For instance, lncRNAs are…
With new accelerator hardware for DNN, the computing power for AI applications has increased rapidly. However, as DNN algorithms become more complex and optimized for specific applications, latency requirements remain challenging, and it is…
Large Artificial Neural Network (ANN) models have demonstrated success in various domains, including general text and image generation, drug discovery, and protein-RNA (ribonucleic acid) binding tasks. However, these models typically demand…
We present SentAlign, an accurate sentence alignment tool designed to handle very large parallel document pairs. Given user-defined parameters, the alignment algorithm evaluates all possible alignment paths in fairly large documents of…
Graph neural networks (GNNs) have achieved impressive performance in graph domain adaptation. However, extensive source graphs could be unavailable in real-world scenarios due to privacy and storage concerns. To this end, we investigate an…
The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA…
We introduce a manifold analysis technique for neural network representations. Normalized Space Alignment (NSA) compares pairwise distances between two point clouds derived from the same source and having the same size, while potentially…
In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus $g$, for arbitrary $g>0$. Furthermore…
Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the…
We study the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss…
Spatial transcriptomics (ST) profiles gene expression across a tissue section while preserving the spatial coordinates. Because current ST technologies typically profile two-dimensional tissue slices, integrating and aligning slices from…
Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although…
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…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
The problem of determining if an $r$-CNF boolean formula $F$ over $n$ variables is satisifiable reduces to the problem of determining if $F$ has a satisfying assignment with a Hamming distance of at most $d$ from a fixed assignment…