相关论文: Three dimensional chaos game representation of pro…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
We review the properties of fractals, the Mandelbrot set and how deterministic chaos ties to the picture. A detailed study on three body systems, one of the major applications of chaos theory was undertaken. Systems belonging to different…
Signaling game problems investigate communication scenarios where encoder(s) and decoder(s) have misaligned objectives due to the fact that they either employ different cost functions or have inconsistent priors. This problem has been…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is…
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…
This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional…
The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event…
It remains a challenge to efficiently extract spatialtemporal information from skeleton sequences for 3D human action recognition. Although most recent action recognition methods are based on Recurrent Neural Networks which present…
We propose a computational framework to jointly parse a single RGB image and reconstruct a holistic 3D configuration composed by a set of CAD models using a stochastic grammar model. Specifically, we introduce a Holistic Scene Grammar (HSG)…
Poker is a family of card games that includes many variations. We hypothesize that most poker games can be solved as a pattern matching problem, and propose creating a strong poker playing system based on a unified poker representation. Our…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…
High dimensional data analysis for exploration and discovery includes three fundamental tasks: dimensionality reduction, clustering, and visualization. When the three associated tasks are done separately, as is often the case thus far,…
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…
3D Gaussian Splatting has recently emerged as a highly promising technique for modeling of static 3D scenes. In contrast to Neural Radiance Fields, it utilizes efficient rasterization allowing for very fast rendering at high-quality.…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
Chaotic systems which are due to nonlinearity have attracted a great concern in the current world and chaotic models. Systems for a wide range of operation conditions have their application in almost all branches of engineering and science.…
Much scientific enquiry across disciplines is founded upon a mechanistic treatment of dynamic systems that ties form to function. A highly visible instance of this is in molecular biology, where an important goal is to determine…