Related papers: Genomic Informational Field Theory (GIFT) to chara…
We show how field- and information theory can be used to quantify the relationship between genotype and phenotype in cases where phenotype is a continuous variable. Given a sample population of phenotype measurements, from various known…
The Fisher-Rao metric from Information Geometry is related to phase transition phenomena in classical statistical mechanics. Several studies propose to extend the use of Information Geometry to study more general phase transitions in…
Generating executable CAD programs from images requires alignment between visual geometry and symbolic program representations, a capability that current methods fail to learn reliably as design complexity increases. Existing fine-tuning…
Given multi-platform genome data with prior knowledge of functional gene sets, how can we extract interpretable latent relationships between patients and genes? More specifically, how can we devise a tensor factorization method which…
Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The number of…
Finding local correspondences between images with different viewpoints requires local descriptors that are robust against geometric transformations. An approach for transformation invariance is to integrate out the transformations by…
Motivation: Methods are needed to test pre-defined genomic regions such as promoters for differential methylation in genome-wide association studies, where the number of samples is limited and the data have large amounts of measurement…
In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let $x$ denote today's frequency of the beneficial type, and given $x$, let $h(x)$ be the probability that, among all individuals of today's…
The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…
Information field theory (IFT) is the application of probabilistic reasoning to fields. Physical fields are mathematical functions over continuous spaces that exhibit certain properties of regularity, such as limited variance and finite…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However,…
With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new…
Many machine learning methods assume that the training and test data follow the same distribution. However, in the real world, this assumption is very often violated. In particular, the phenomenon that the marginal distribution of the data…
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…
At the present time reliably established that probability density functions of gene expression of microarray experiments possess a number of universal properties. First of all these distributions have power asymptotic and secondly the shape…
Fisher's fundamental theorem of natural selection states that the rate of change in a population's mean fitness equals its additive genetic variance in fitness. This implies that mean fitness should not decline in a constant environment,…
We advocate the use of a notion of entropy that reflects the relative abundances of the symbols in an alphabet, as well as the similarities between them. This concept was originally introduced in theoretical ecology to study the diversity…
The Gaussian function (GF) is widely used to explain the behavior or statistical distribution of many natural phenomena as well as industrial processes in different disciplines of engineering and applied science. For example, the GF can be…
Wright-Fisher diffusions and their dual ancestral graphs occupy a central role in the study of allele frequency change and genealogical structure, and they provide expressions, explicit in some special cases but generally implicit, for the…