Related papers: A stitch in time: Efficient computation of genomic…
DBSCAN is a popular density-based clustering algorithm. It computes the $\epsilon$-neighborhood graph of a dataset and uses the connected components of the high-degree nodes to decide the clusters. However, the full neighborhood graph may…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure…
A core challenge in the interpretation of deep neural networks is identifying commonalities between the underlying algorithms implemented by distinct networks trained for the same task. Motivated by this problem, we introduce DYNAMO, an…
We present an algorithm for the fast computation of the general $N$-point spatial correlation functions of any discrete point set embedded within an Euclidean space of $\mathbb{R}^n$. Utilizing the concepts of kd-trees and graph databases,…
This paper presents a graph bundling algorithm that agglomerates edges taking into account both spatial proximity as well as user-defined criteria in order to reveal patterns that were not perceivable with previous bundling techniques. Each…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
The 0/1 knapsack problem is weakly NP-hard in that there exist pseudo-polynomial time algorithms based on dynamic programming that can solve it exactly. There are also the core branch and bound algorithms that can solve large randomly…
Storing information in DNA molecules is of great interest because of its advantages in longevity, high storage density, and low maintenance cost. A key step in the DNA storage pipeline is to efficiently cluster the retrieved DNA sequences…
We present a fast general-purpose algorithm for high-throughput clustering of data "with a two dimensional organization". The algorithm is designed to be implemented with FPGAs or custom electronics. The key feature is a processing time…
We present a robust approach to incorporating models for the time-variable broadening of the pulse profile due to scattering in the ionized interstellar medium into profile-domain pulsar timing analysis. We use this approach to…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…
Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from…
Today, machine learning tools, particularly artificial neural networks, have become crucial for diverse applications. However, current digital computing tools to train and deploy artificial neural networks often struggle with massive data…
Dust properties, such as mass and porosity, impact planet formation directly. Understanding the time evolution of dust distribution across multiple properties requires numerical computation. However, available ways to calculate the…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Understanding the singular value spectrum of a matrix $A \in \mathbb{R}^{n \times n}$ is a fundamental task in countless applications. In matrix multiplication time, it is possible to perform a full SVD and directly compute the singular…
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…
We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA…