Related papers: Facilitated diffusion buffers noise in gene expres…

The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression…

Generative adversarial networks (GANs) are challenging to train stably, and a promising remedy of injecting instance noise into the discriminator input has not been very effective in practice. In this paper, we propose Diffusion-GAN, a…

During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signaling molecules - morphogens - guide this process. The continuous positional information…

The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…

Diffusion models are state-of-the-art generative models on data modalities such as images, audio, proteins and materials. These modalities share the property of exponentially decaying variance and magnitude in the Fourier domain. Under the…

We empirically study the effect of noise scheduling strategies for denoising diffusion generative models. There are three findings: (1) the noise scheduling is crucial for the performance, and the optimal one depends on the task (e.g.,…

Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…

Recently, conditional score-based diffusion models have gained significant attention in the field of supervised speech enhancement, yielding state-of-the-art performance. However, these methods may face challenges when generalising to…

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…

Recently, diffusion models have shown remarkable results in image synthesis by gradually removing noise and amplifying signals. Although the simple generative process surprisingly works well, is this the best way to generate image data? For…

In eukaryotic cell nuclei, a variety of DNA interactions with nuclear elements occur, which, in combination with intra- and inter- chromosomal cross-talks, shape a functional 3D architecture. In some cases they are organized by active, i.e.…

Score-based diffusion models are a highly effective method for generating samples from a distribution of images. We consider scenarios where the training data comes from a noisy version of the target distribution, and present an efficiently…

We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…

Diffusion models have demonstrated impressive capabilities in synthesizing diverse content. However, despite their high-quality outputs, these models often perpetuate social biases, including those related to gender and race. These biases…

Regulation of gene expression is the consequence of interactions between the promoter of the gene and the transcription factors (TFs). In this paper, we explore the features of a genetic network where the TFs (activators and repressors)…

Diffusion-based generative models have recently achieved remarkable results in speech and vocal enhancement due to their ability to model complex speech data distributions. While these models generalize well to unseen acoustic environments,…

We study the steady state properties of a genotype selection model in presence of correlated Gaussian white noise. The effect of the noise on the genotype selection model is discussed. It is found that correlated noise can break the balance…

Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events…

Singing voice synthesis (SVS) systems are built to synthesize high-quality and expressive singing voice, in which the acoustic model generates the acoustic features (e.g., mel-spectrogram) given a music score. Previous singing acoustic…

Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…