Related papers: Optimal decoding of information from a genetic net…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
There is growing consensus among neuroscientists that neural circuits critical for survival are the result of genomic decompression processes. We introduce SynaptoGen, a novel computational framework--member of the Connectome Models…
Based on Jaynes' maximum entropy principle, exponential random graphs provide a family of principled models that allow the prediction of network properties as constrained by empirical data (observables). However, their use is often hindered…
Raptor code ensembles with linear random outer codes in a fixed-rate setting are considered. An expression for the average distance spectrum is derived and this expression is used to obtain the asymptotic exponent of the weight…
In systems biology, attractor landscape analysis of gene regulatory networks is recognized as a powerful computational tool for studying various cellular states from proliferation and differentiation to senescence and apoptosis. Therefore,…
The state-of-the-art error correcting codes are based on large random constructions (random graphs, random permutations, ...) and are decoded by linear-time iterative algorithms. Because of these features, they are remarkable examples of…
This paper studies random-coding error exponents of randomised list decoding, in which the decoder randomly selects $L$ messages with probabilities proportional to the decoding metric of the codewords. The exponents (or bounds) are given…
Optimal transport has numerous applications, particularly in machine learning tasks involving generative models. In practice, the transportation process often encounters an information bottleneck, typically arising from the conversion of a…
We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…
We derive various error exponents for communication channels with random states, which are available non-causally at the encoder only. For both the finite-alphabet Gel'fand-Pinsker channel and its Gaussian counterpart, the dirty-paper…
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…
We consider the problem of predicting eye movement goals from local field potentials (LFP) recorded through a multielectrode array in the macaque prefrontal cortex. The monkey is tasked with performing memory-guided saccades to one of eight…
Understanding spatial location and relationships is a fundamental capability for modern artificial intelligence systems. Insights from human spatial cognition provide valuable guidance in this domain. Neuroscientific discoveries have…
During development, cell fates are determined through a combination of intracellular transcriptional regulations and extracellular signaling. As a result, spatial patterns of different cell types arise. We investigate the decision between…
Neural decoding may be formulated as dynamic state estimation (filtering) based on point process observations, a generally intractable problem. Numerical sampling techniques are often practically useful for the decoding of real neural data.…
In evolutionary policy search, neural networks are usually represented using a direct mapping: each gene encodes one network weight. Indirect encoding methods, where each gene can encode for multiple weights, shorten the genome to reduce…
The optimal decoder achieving the outage capacity under imperfect channel estimation is investigated. First, by searching into the family of nearest neighbor decoders, which can be easily implemented on most practical coded modulation…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
The release of large datasets and developments in AI have led to dramatic improvements in decoding methods that reconstruct seen images from human brain activity. We evaluate the prospect of further improving recent decoding methods by…
Gene transcription is a critical step in gene expression. The currently accepted physical model of transcription predicts the existence of a physical limit on the maximal rate of transcription, which does not depend on the transcribed gene.…