Related papers: Genetic Analysis of Transformed Phenotypes

Generalized linear models (GLMs) are fundamental tools for statistical modeling, with maximum likelihood estimation (MLE) serving as the classical approach for parameter inference. While MLE performs well for canonical GLMs, it can become…

The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel…

State of the art large language models (LLMs) have shown impressive performance on a variety of benchmark tasks and are increasingly used as components in larger applications, where LLM-based predictions serve as proxies for human…

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

Despite strong advisory against it, large generative models (LMs) are already being used for decision making tasks that were previously done by predictive models or humans. We put popular LMs to the test in a high-stakes decision making…

The Gene-pool Optimal Mixing Evolutionary Algorithm (GOMEA) is a model-based EA framework that has been shown to perform well in several domains, including Genetic Programming (GP). Differently from traditional EAs where variation acts…

Large language models (LLMs) have recently been proposed as general-purpose agents for experimental design, with claims that they can perform in-context experimental design. We evaluate this hypothesis using both open- and closed-source…

Transformer-based language models (LMs) continue to advance state-of-the-art performance on NLP benchmark tasks, including tasks designed to mimic human-inspired "commonsense" competencies. To better understand the degree to which LMs can…

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE),…

Genetic Algorithms (GAs) are explored as a tool for probing new physics with high dimensionality. We study the 19-dimensional pMSSM, including experimental constraints from all sources and assessing the consistency of potential signals of…

Linear mixed models (LMMs) are suitable for clustered data and are common in biometrics, medicine, survey statistics and many other fields. In those applications, it is essential to carry out valid inference after selecting a subset of the…

Linear Mixed Effects (LME) models have been widely applied in clustered data analysis in many areas including marketing research, clinical trials, and biomedical studies. Inference can be conducted using maximum likelihood approach if…

Motivated by genome-wide association studies, we consider a standard linear model with one additional random effect in situations where many predictors have been collected on the same subjects and each predictor is analyzed separately.…

Generalized linear models (GLMs) have been used quite effectively in the modeling of a mean response under nonstandard conditions, where discrete as well as continuous data distributions can be accommodated. The choice of design for a GLM…

Gaussian process-based latent variable models are flexible and theoretically grounded tools for nonlinear dimension reduction, but generalizing to non-Gaussian data likelihoods within this nonlinear framework is statistically challenging.…

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs…

Mixtures of Linear Regressions (MLR) is an important mixture model with many applications. In this model, each observation is generated from one of the several unknown linear regression components, where the identity of the generated…

Convolutional neural networks (CNNs) provide flexible function approximations for a wide variety of applications when the input variables are in the form of images or spatial data. Although CNNs often outperform traditional statistical…

We present the Mixed Likelihood Gaussian process latent variable model (GP-LVM), capable of modeling data with attributes of different types. The standard formulation of GP-LVM assumes that each observation is drawn from a Gaussian…