Related papers: Finding the center reliably: robust patterns of de…
The precise layout of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low expression domains requires a genetic mechanism which is both sensitive and robust to fluctuations, a demand…
Neural IR architectures, particularly cross-encoders, are highly effective models whose internal mechanisms are mostly unknown. Most works trying to explain their behavior focused on high-level processes (e.g., what in the input influences…
An important component in studying mathematical models in many biochemical systems, such as those found in developmental biology, is phase transition. The purpose of this work is to analyze the phase transition property of a…
The early fly embryo offers a relatively pure version of the problem of spatial scaling in biological pattern formation. Within three hours, a "blueprint" for the final segmented body plan of the animal is visible in striped patterns of…
This contribution is concerned with mathematical models for the dynamics of the genetic composition of populations evolving under recombination. Recombination is the genetic mechanism by which two parent individuals create the mixed type of…
Deploying reliable deep learning techniques in interdisciplinary applications needs learned models to output accurate and (even more importantly) explainable predictions. Existing approaches typically explicate network outputs in a post-hoc…
We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network inference and network topological analysis…
The performance of adaptive estimators that employ embedding in reproducing kernel Hilbert spaces (RKHS) depends on the choice of the location of basis kernel centers. Parameter convergence and error approximation rates depend on where and…
In multicellular organisms, patterns of gene expression are established in response to gradients of signaling molecules. During fly development in early Drosophila embryos, the Bicoid (Bcd) morphogen gradient is established within the first…
Mechanical stress plays an intricate role in gene expression in individual cells and sculpting of developing tissues. However, systematic methods of studying how mechanical stress and feedback help to harmonize cellular activities within a…
We consider networks with two types of nodes. The v-nodes, called centers, are hyperconnected and interact one to another via many u-nodes, called satellites. This centralized architecture, widespread in gene networks, realize a bow-tie…
Machine Learning models should ideally be compact and robust. Compactness provides efficiency and comprehensibility whereas robustness provides resilience. Both topics have been studied in recent years but in isolation. Here we present a…
Efficient pattern separation in dentate gyrus plays an important role in storing information in the hippocampus. Current knowledge of the structure and function of the hippocampus, entorhinal cortex and dentate gyrus, in pattern separation…
Axes of polarity (and primary morphogenetic gradients) are established in the oocyte - early embryo through active transport and localization of maternal factors. It is the oocyte - syncytial embryo of Drosophila (D. melanogaster) that is a…
Locating the sources of forced low-frequency oscillations in power systems is an important problem. A number of proposed methods demonstrate their practical usefulness, but many of them rely on strong modeling assumptions and provide poor…
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
In tumoral cells, gene regulation mechanisms are severely altered, and these modifications in the regulations may be characteristic of different subtypes of cancer. However, these alterations do not necessarily induce differential…
The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper,…
Consider a lossy compression system with $\ell$ distributed encoders and a centralized decoder. Each encoder compresses its observed source and forwards the compressed data to the decoder for joint reconstruction of the target signals under…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…