Related papers: Transcription and noise in negative feedback loops

The propagation of noise through parallel regulatory pathways is a characteristic feature of feed-forward loops in genetic networks. Although the contributions of the direct and indirect regulatory pathways of feed-forward loops to output…

Random label noises (or observational noises) widely exist in practical machine learning settings. While previous studies primarily focus on the affects of label noises to the performance of learning, our work intends to investigate the…

Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising…

In this work we study the detection of weak stimuli by spiking neurons in the presence of certain level of noisy background neural activity. Our study has focused in the realistic assumption that the synapses in the network present…

It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a…

Some systems cannot be predicted by classical theories and it is required the development of combined deterministic and stochastic theories that make used of noise for dynamical prediction. Noise is not always an interfering signal which…

Motivation: Recent studies of genomic-scale regulatory networks suggested that a feed-forward loop (FFL) circuitry is a key component of many such networks. This led to a study of the functional properties of different FFL types, where the…

The inherent stochasticity of cellular processes leads to significant cell-to-cell variation in protein abundance. Although this noise has already been characterized and modeled, its broader implications and significance remain unclear. In…

Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this…

Deep learning with noisy labels presents significant challenges. In this work, we theoretically characterize the role of label noise from a feature learning perspective. Specifically, we consider a signal-noise data distribution, where each…

Learning from Preferences in Reinforcement Learning (PbRL) has gained attention recently, as it serves as a natural fit for complicated tasks where the reward function is not easily available. However, preferences often come with…

Stochastic oscillations in individual cells are usually characterized by a non-monotonic power spectrum with an oscillatory autocorrelation function. Here we develop an analytical approach of stochastic oscillations in a minimal hybrid…

Cortical sensory neurons are known to be highly variable, in the sense that responses evoked by identical stimuli often change dramatically from trial to trial. The origin of this variability is uncertain, but it is usually interpreted as…

While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…

Stochasticity in gene expression can result in fluctuations in gene product levels. Recent experiments indicated that feedback regulation plays an important role in controlling the noise in gene expression. A quantitative understanding of…

NF-{\kappa}B is a pleiotropic protein whose nucleo-cytoplasmic trafficking is tightly regulated by multiple negative feedback loops embedded in the NF-{\kappa}B signaling network and contributes to diverse gene expression profiles important…

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…

Transcriptional pulsing has been observed in both prokaryotes and eukaryotes and plays a crucial role in cell to cell variability of protein and mRNA numbers. The issue is how the time constants associated with episodes of transcriptional…

We study the effects of multiple binding sites in the promoter of a genetic oscillator. We evaluate the regulatory function of a promoter with multiple binding sites in the absence of cooperative binding, and consider different hypotheses…

Speech recognition system performance degrades in noisy environments. If the acoustic models are built using features of clean utterances, the features of a noisy test utterance would be acoustically mismatched with the trained model. This…