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A relatively new set of transport-based transforms (CDT, R-CDT, LOT) have shown their strength and great potential in various image and data processing tasks such as parametric signal estimation, classification, cancer detection among many…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…
Introducing genetic algorithms as a reliable and efficient tool to find ordered equilibrium structures, we predict minimum energy configurations of the square shoulder system for different values of corona width $\lambda$. Varying…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
This paper studies the minimax detection of a small submatrix of elevated mean in a large matrix contaminated by additive Gaussian noise. To investigate the tradeoff between statistical performance and computational cost from a…
Side channels have become an essential component of many modern information-theoretic schemes. The emerging field of cross technology communications (CTC) provides practical methods for creating intentional side channels between existing…
We propose matrix commutator based stability characterization for discrete-time switched linear systems under restricted switching. Given an admissible minimum dwell time, we identify sufficient conditions on subsystems such that a switched…
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit…
The dose delivered to the planning target volume by proton beams is highly conformal, sparing organs at risk and normal tissues. New treatment planning systems adapted to spot scanning techniques have been recently proposed to…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
Randomized controlled trials (RCTs) can be used to generate guarantees on treatment effects. However, RCTs often spend unnecessary resources exploring sub-optimal treatments, which can reduce the power of treatment guarantees. To address…
The Crack Topology Score (CTS) is a recently proposed metric that focuses on evaluating the topological correctness of crack segmentation outputs. While pixel-wise metrics such as IoU or F1-score fail to capture structural validity, CTS…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective,…
The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the unbinding of a repressor (negative control).…
We present a new method for proving lower bounds on the expected running time of evolutionary algorithms. It is based on fitness-level partitions and an additional condition on transition probabilities between fitness levels. The method is…
Gradient clipping is a commonly used technique to stabilize the training process of neural networks. A growing body of studies has shown that gradient clipping is a promising technique for dealing with the heavy-tailed behavior that emerged…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
Some clinical and pre-clinical data suggests that treating some tumors at a mild, patient-specific dose might delay resistance to treatment and increase survival time. A recent mathematical model with sensitive and resistant tumor cells…