Related papers: Facilitated diffusion buffers noise in gene expres…
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be…
Conditional image generation has paved the way for several breakthroughs in image editing, generating stock photos and 3-D object generation. This continues to be a significant area of interest with the rise of new state-of-the-art methods…
We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a…
We explore unsupervised speech enhancement using diffusion models as expressive generative priors for clean speech. Existing approaches guide the reverse diffusion process using noisy speech through an approximate, noise-perturbed…
The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
Generative diffusion models have emerged as leading models in speech and image generation. However, in order to perform well with a small number of denoising steps, a costly tuning of the set of noise parameters is needed. In this work, we…
Stochasticity in gene expression can give rise to fluctuations in protein levels and lead to phenotypic variation across a population of genetically identical cells. Recent experiments indicate that bursting and feedback mechanisms play…
Diffusion models are a class of generative models that have been recently used for speech enhancement with remarkable success but are computationally expensive at inference time. Therefore, these models are impractical for processing…
Automatic drum transcription (ADT) is traditionally formulated as a discriminative task to predict drum events from audio spectrograms. In this work, we redefine ADT as a conditional generative task and introduce Noise-to-Notes (N2N), a…
Online Speech Enhancement was mainly reserved for predictive models. A key advantage of these models is that for an incoming signal frame from a stream of data, the model is called only once for enhancement. In contrast, generative Speech…
Gene expression is inherently a noisy process which manifests as cell-to-cell variability in time evolution of proteins. Consequently, events that trigger at critical threshold levels of regulatory proteins exhibit stochasticity in their…
The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…
How diffusion models generalize beyond their training set is not known, and is somewhat mysterious given two facts: the optimum of the denoising score matching (DSM) objective usually used to train diffusion models is the score function of…
The denoising process of diffusion models can be interpreted as an approximate projection of noisy samples onto the data manifold. Moreover, the noise level in these samples approximates their distance to the underlying manifold. Building…
Can continuous diffusion models bring the same performance breakthrough on natural language they did for image generation? To circumvent the discrete nature of text data, we can simply project tokens in a continuous space of embeddings, as…
Probabilistic diffusion models have achieved state-of-the-art results for image synthesis, inpainting, and text-to-image tasks. However, they are still in the early stages of generating complex 3D shapes. This work proposes Diffusion-SDF, a…
Practically, training diffusion models typically requires explicit time conditioning to guide the network through the denoising sampling process. Especially in deterministic methods like DDIM, the absence of time conditioning leads to…
This paper introduces a novel speech enhancement (SE) approach based on a denoising diffusion probabilistic model (DDPM), termed Guided diffusion for speech enhancement (GDiffuSE). In contrast to conventional methods that directly map noisy…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…