Related papers: Optimal decoding of information from a genetic net…
Multi Expression Programming (MEP) is a Genetic Programming variant that uses a linear representation of chromosomes. MEP individuals are strings of genes encoding complex computer programs. When MEP individuals encode expressions, their…
Rapid information (energy) propagation in deep feature extractors is crucial to balance computational complexity versus expressiveness as a representation of the input. We prove an upper bound for the speed of energy propagation in a…
Morphogens are proteins, often produced in a localised region, whose concentrations spatially demarcate regions of differing gene expression in developing embryos. The boundaries of expression must be set accurately and in proportion to the…
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions…
This work contains two main contributions concerning the asymmetric broadcast channel. The first is an analysis of the exact random coding error exponents for both users, and the second is the derivation of universal decoders for both…
The three-dimensional data-driven Allen Gene Expression Atlas of the adult mouse brain consists of numerized in-situ hybridization data for thousands of genes, co-registered to the Allen Reference Atlas. We propose quantitative criteria to…
We study the problem of decoding classical information encoded on quantum states at the output of a quantum channel, with particular focus on increasing the communication rates towards the maximum allowed by Quantum Mechanics. After a brief…
Grid cells in the entorhinal cortex encode the position of an animal in its environment using spatially periodic tuning curves of varying periodicity. Recent experiments established that these cells are functionally organized in discrete…
The processes occurring in climatic change evolution and their variations play a major role in environmental engineering. Different techniques are used to model the relationship between temperatures, dew point and relative humidity. Gene…
Consider the problem of identifying a massive number of bees, uniquely labeled with barcodes, using noisy measurements. We formally introduce this `bee-identification problem', define its error exponent, and derive efficiently computable…
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
We consider the problem of erasure/list decoding using certain classes of simplified decoders. Specifically, we assume a class of erasure/list decoders, such that a codeword is in the list if its likelihood is larger than a threshold. This…
This paper presents encoding and decoding algorithms for several families of optimal rank metric codes whose codes are in restricted forms of symmetric, alternating and Hermitian matrices. First, we show the evaluation encoding is the right…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing…
The data processing inequality is an information-theoretic principle stating that the information content of a signal cannot be increased by processing the observations. In particular, it suggests that there is no benefit in enhancing the…
Language, as an information medium created by advanced organisms, has always been a concern of neuroscience regarding how it is represented in the brain. Decoding linguistic representations in the evoked brain has shown groundbreaking…
The digital nature of genes combined with the associated low copy numbers of proteins regulating them is a significant source of stochasticity, which affects the phase of biochemical oscillations. We provide a theoretical framework for…