Related papers: Stochastics of DNA Quantification
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
DNA computing is an unconventional approach to computing that harnesses the parallelism and information storage capabilities of DNA molecules. It has emerged as a promising field with potential applications in solving a variety of…
Neural network quantization is becoming an industry standard to efficiently deploy deep learning models on hardware platforms, such as CPU, GPU, TPU, and FPGAs. However, we observe that the conventional quantization approaches are…
Generative data-free quantization emerges as a practical compression approach that quantizes deep neural networks to low bit-width without accessing the real data. This approach generates data utilizing batch normalization (BN) statistics…
Imperfect molecular detection in single-cell experiments introduces technical noise that obscures the true stochastic dynamics of gene regulatory networks. While binomial models of molecular capture provide a principled description of…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…
Quantum error correction can reduce the effects of noise in quantum systems, e.g. in metrology or most notably in quantum computing. Typically, this requires making measurements that provide information about the errors that have occurred…
Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques,…
We investigate the measurement of DNA supercoiling density ($\sigma$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in…
Unlike classification, whose goal is to estimate the class of each data point in a dataset, prevalence estimation or quantification is a task that aims to estimate the distribution of classes in a dataset. The two main tasks in prevalence…
Stochastic spectral methods have become a popular technique to quantify the uncertainties of nano-scale devices and circuits. They are much more efficient than Monte Carlo for certain design cases with a small number of random parameters.…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…
Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the…
Several of the next generation sequencers are limited in their sample preparation process by the need to make an absolute measurement of the number of template molecules in the library to be sequenced. As currently practiced, the practical…
Diffusion models have achieved cutting-edge performance in image generation. However, their lengthy denoising process and computationally intensive score estimation network impede their scalability in low-latency and resource-constrained…
DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the…