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Following the advance of style transfer with Convolutional Neural Networks (CNNs), the role of styles in CNNs has drawn growing attention from a broader perspective. In this paper, we aim to fully leverage the potential of styles to improve…

The genome-wide recombination rate ($RR$) of a species is often described by one parameter, the ratio between total genetic map length ($G$) and physical map length ($P$), measured in centiMorgans per Megabase (cM/Mb). The value of this…

We consider a new model which consists of a DNA together with a RNA. Here we assume that DNA is from a mammal or bird but RNA comes from a virus. To study thermodynamic properties of this model we use methods of statistical mechanics,…

We derive a new margin-based regularization formulation, termed multi-margin regularization (MMR), for deep neural networks (DNNs). The MMR is inspired by principles that were applied in margin analysis of shallow linear classifiers, e.g.,…

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…

The emergence of a predominant phenotype within a cell population is often triggered by a rare accumulation of DNA mutations in a single cell. For example, tumors may be initiated by a single cell in which multiple mutations cooperate to…

A modulated icosahedral shell with an inclusion is a concise description of many viruses, including recently-discovered large double-stranded DNA ones. Many X-ray scattering patterns of such viruses show major polygonal fringes, which can…

Epidemics on complex networks is a widely investigated topic in the last few years, mainly due to the last pandemic events. Usually, real contact networks are dynamic, hence much effort has been invested in studying epidemics on evolving…

We consider a Markovian model for the kinetics of RNA Polymerase (RNAP) which provides a physical explanation for the phenomenon of cooperative pushing during transcription elongation observed in biochemical experiments on Escherichia coli…

Stochastic resonance (SR) is a well known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic noise. Here we carry out the first experimental study of SR in…

Accelerated Cardiovascular Magnetic Resonance (CMR) image reconstruction remains a critical challenge due to the trade-off between scan time and image quality, particularly when generalizing across diverse acquisition settings. We propose…

The Caspar-Klug classification of viruses whose protein shell, called viral capsid, exhibits icosahedral symmetry, has recently been extended to incorporate viruses whose capsid proteins are exclusively organised in pentamers. The approach,…

Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the…

The statistical mechanics of a treelike polymer in a confining volume is relevant to the packaging of the genome in RNA viruses. Making use of the mapping of the grand partition function of this system onto the statistical mechanics of a…

Traditional studies about disease dynamics have focused on global stability issues, due to their epidemiological importance. We study a classical SIR-SI model for arboviruses in two different directions: we begin by describing an…

The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…

We study a susceptible-infected-recovered (SIR) epidemic model on a network of $n$ interacting subpopulations. We analyze the transient and asymptotic behavior of the infection dynamics in each node of the network. In contrast to the…

Masked diffusion models (MDMs) offer a promising non-autoregressive alternative for large language modeling. Standard decoding methods for MDMs, such as confidence-based sampling, select tokens independently based on individual token…

Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…

Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural…