Related papers: Transcription factor clusters as information trans…
In genetic networks, information of relevance to the organism is represented by the concentrations of transcription factor molecules. In order to extract this information the cell must effectively "measure"' these concentrations, but there…
The presence of synchronized clusters in neuron networks is a hallmark of information transmission and processing. The methods commonly used to study cluster synchronization in networks of coupled oscillators ground on simplifying…
Positional encodings enable Transformers to incorporate sequential information, yet their theoretical understanding remains limited to two properties: distance attenuation and translation invariance. Because natural language lacks purely…
Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
As machine learning models are increasingly deployed in sensitive application areas, the demand for interpretable and trustworthy decision-making has increased. Random Forests (RF), despite their widespread use and strong performance on…
The mean time required by a transcription factor (TF) or an enzyme to find a target in the nucleus is of prime importance for the initialization of transcription, gene activation or the start of DNA repair. We obtain new estimates for the…
Transformers have emerged as a powerful neural network architecture capable of tackling a wide range of learning tasks. In this work, we provide a theoretical analysis of their ability to automatically extract structure from data in an…
Monitoring flowers over time is essential for precision robotic pollination in agriculture. To accomplish this, a continuous spatial-temporal observation of plant growth can be done using stationary RGB-D cameras. However, image…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
Encoder transformer models compress information from all tokens in a sequence into a single [CLS] token to represent global context. This approach risks diluting fine-grained or hierarchical features, leading to information loss in…
We study by simulation the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels in the case of a repressed gene. We find that spatial fluctuations due to diffusion can drastically enhance the noise…
Deep learning has shown remarkable success in the field of clustering recently. However, how to transfer a trained clustering model on a source domain to a target domain by leveraging the acquired knowledge to guide the clustering process…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
Transcription factors (TFs) are proteins that bind to specific sites on the DNA and regulate gene activity. Identifying where TF molecules bind and how much time they spend on their target sites is key for understanding transcriptional…
The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller…
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…
Assessing where and how information is stored in biological networks (such as neuronal and genetic networks) is a central task both in neuroscience and in molecular genetics, but most available tools focus on the network's structure as…
Cancer is a number of related yet highly heterogeneous diseases. Correct identification of cancer subtypes is critical for clinical decisions. The advance in sequencing technologies has made it possible to study cancer based on abundant…
In many cellular signaling pathways, key components form clusters at the cell membrane. Although much work has focused on the mechanisms behind such cluster formation, the implications for downstream signaling remain poorly understood.…