Related papers: Strong Purifying Selection at Synonymous Sites in …
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
The evolutionary fitness landscape of biological molecules is extremely sparse and heterogeneous, with functional sequences forming isolated dense ``islands'' within a vast combinatorial space of largely non-functional variants. Protein…
Genetic Programming yields interpretable programs, but small syntactic mutations can induce large, unpredictable behavioral shifts, degrading locality and sample efficiency. We frame this as an operator-design problem: learn a continuous…
Gene expression of social actions in Drosophilae has been attracting wide interest from biologists, medical scientists and psychologists. Gene-edited Drosophilae have been used as a test platform for experimental investigation. For example,…
Determinantal Point Processes (DPPs) are probabilistic models that arise in quantum physics and random matrix theory and have recently found numerous applications in computer science. DPPs define distributions over subsets of a given ground…
A selective sweep describes the reduction of linked genetic variation due to strong positive selection. If s is the fitness advantage of a homozygote for the beneficial allele and h its dominance coefficient, it is usually assumed that…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
We study a stochastic spatial model of biological competition in which two species have the same birth and death rates, but different diffusion constants. In the absence of this difference, the model can be considered as an off-lattice…
Flux-limited and volume-limited galaxy samples are constructed from SDSS data releases DR4, DR6 and DR7 for statistical analysis. The two-point correlation functions $\xi(s)$, monopole of three-point correlation functions $\zeta_0$,…
We consider a population subdivided into two demes connected by migration in which selection acts in opposite direction. We explore the effects of recombination and migration on the maintenance of multilocus polymorphism, on local…
We consider a discrete-time stochastic growth model on the $d$-dimensional lattice with non-negative real numbers as possible values per site. The growth model describes various interesting examples such as oriented site/bond percolation,…
The presence of phenomena analogous to phase transition in Statistical Mechanics, has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model…
The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements,…
We introduce a doubly stochastic marked point process model for supervised classification problems. Regardless of the number of classes or the dimension of the feature space, the model requires only 2--3 parameters for the covariance…
We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets…
The phenotypic consequences of individual mutations are modulated by the wild type genetic background in which they occur.Although such background dependence is widely observed, we do not know whether general patterns across species and…
Developmental processes in multicellular organisms occur far from equilibrium, yet produce complex patterns with astonishing reproducibility. We measure the precision and reproducibility of bilaterally symmetric fly wings across the natural…
Deep neural networks (DNNs), the agents of deep learning (DL), require a massive number of parallel/sequential operations, which makes it difficult to comprehend them and impedes proper diagnosis. Without better knowledge of DNNs' internal…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…