Related papers: Genetic Paralog Analysis and Simulations
Important objectives in cancer research are the prediction of a patient's risk based on molecular measurements such as gene expression data and the identification of new prognostic biomarkers (e.g. genes). In clinical practice, this is…
This paper derives a population sizing relationship for genetic programming (GP). Following the population-sizing derivation for genetic algorithms in Goldberg, Deb, and Clark (1992), it considers building block decision making as a key…
We present new sampling methods in finite population that allow to control the joint inclusion probabilities of units and especially the spreading of sampled units in the population. They are based on the use of renewal chains and…
The size of pretrained models is increasing, and so is their performance on a variety of NLP tasks. However, as their memorization capacity grows, they might pick up more social biases. In this work, we examine the connection between model…
A large offspring number diploid biparental multilocus population model of Moran type is our object of study. At each timestep, a pair of diploid individuals drawn uniformly at random contribute offspring to the population. The number of…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC)…
We study the fundamental question of how likely it is that two randomly chosen trees are isomorphic to each other for different models of random trees. We show that the probability decays exponentially for rooted labeled trees as well as…
An ongoing "reproducibility crisis" calls into question scientific discoveries across a variety of disciplines ranging from life to social sciences. Replication studies aim to investigate the validity of findings in published research, and…
A density-dependent branching process is a particle system in which individuals reproduce independently, but in a way that depends on the current population size. This feature can model a wide range of ecological interactions at the cost of…
Given samples (x_1,...,x_m) and (z_1,...,z_n) which we believe are independent realizations of random variables X and Z respectively, where we further believe that Z=X+Y with Y independent of X, the problem is to estimate the distribution…
In the design of clinical trials, it is essential to assess the design operating characteristics (e.g., power and the type I error rate). Common practice for the evaluation of operating characteristics in Bayesian clinical trials relies on…
We construct a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species posses genetic information, which is inherited according to the rules of the Penna model of genetic evolution.…
We consider the model of random sequential adsorption, with depositing objects, as well as those already at the surface, decreasing in size according to a specified time dependence, from a larger initial value to a finite value in the large…
For various two dimensional non linear $\sigma$ models, we present a direct comparison between the $\beta$ functions computed with the $2+\epsilon$ renormalization group and the $\beta$ functions measured by Monte Carlo simulations. The…
Monte Carlo simulations alone could not clarify the corrections to scaling for the size-dependent p_c(L) above the upper critical dimension. Including the previous series estimate for the bulk threshold $p_c(\infty)$ gives preference for…
A learned generative model often produces biased statistics relative to the underlying data distribution. A standard technique to correct this bias is importance sampling, where samples from the model are weighted by the likelihood ratio…
Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
Synthetic lethality, the finding that the simultaneous knockout of two or more individually non-essential genes leads to cell or organism death, has offered a systematic framework to explore cellular function, and also offered therapeutic…