Related papers: A Conversation with Robert C. Elston
An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
This is the Proceedings of the Eighth Conference on Uncertainty in Artificial Intelligence, which was held in Stanford, CA, July 17-19, 1992
After completing their undergraduate studies, many computer science (CS) students apply for competitive graduate programs in North America. Their long-term goal is often to be hired by one of the big five tech companies or to become a…
Infectious diseases remain among the top contributors to human illness and death worldwide, among which many diseases produce epidemic waves of infection. The unavailability of specific drugs and ready-to-use vaccines to prevent most of…
There is now significant historical data available on decision making in organizations, consisting of the decision problem, what decisions were made, and how desirable the outcomes were. Using this data, it is possible to learn a surrogate…
A statistical framework we call CQUESST (Carbon Quantification and Uncertainty from Evolutionary Soil STochastics), which models carbon sequestration and cycling in soils, is applied to a long-running agricultural experiment that controls…
Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
Chlamydia trachomatis (Ct) is the most common bacterial sexually transmitted infection (STI) in the United States and is major cause of infertility, pelvic inflammatory disease, and ectopic pregnancy among women. Despite decades of…
Genetic Programming has been very successful in solving a large area of problems but its use as a machine learning algorithm has been limited so far. One of the reasons is the problem of overfitting which cannot be solved or suppresed as…
In the past ten years this author published some 15 highly mathematical papers about his new Evo-SETI (Evolution and SETI) Theory. He proved that key features of Evo-SETI are: 1) The Statistical Drake Equation is the extension of the…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
This work presents the development and evaluation of an NLP-enabled probabilistic classifier designed to estimate the probability of technical and regulatory success (pTRS) for clinical trials in the field of neuroscience. While…
I developed the lecture notes based on my ``Causal Inference'' course at the University of California Berkeley over the past seven years. Since half of the students were undergraduates, my lecture notes only required basic knowledge of…
A key goal in studies of ecology and evolution is understanding the causes of phenotypic diversity in nature. Most traits of interest, such as those relating to morphology, life-history, immunity and behaviour are quantitative, and…
The basic reproduction number ($R_0$) is a threshold parameter for disease extinction or survival in isolated populations. However no human population is fully isolated from other human or animal populations. We use compartmental models to…
In the face of an infectious disease, a key epidemiological measure is the basic reproduction number, which quantifies the average secondary infections caused by a single case in a susceptible population. In practice, the effective…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
In this study, we investigate the prey predator dynamics of the elk wolf system in northern Yellowstone National Park, USA, using a data driven modeling approach. We used yearly population data for elk and wolves from 1995 to 2022 to…