Related papers: Shrinkage Effect in Ancestral Maximum Likelihood

The dynamical phenomena of complex networks are very difficult to predict from local information due to the rich microstructures and corresponding complex dynamics. On the other hands, it is a horrible job to compute some stochastic…

Efficient estimation methods for simultaneous autoregressive (SAR) models with missing data in the response variable have been well-explored in the literature. A common practice is to introduce measurement error into SAR models to separate…

Training deep neural networks (DNNs) is an important and challenging optimization problem in machine learning due to its non-convexity and non-separable structure. The alternating minimization (AM) approaches split the composition structure…

The normalized maximized likelihood (NML) provides the minimax regret solution in universal data compression, gambling, and prediction, and it plays an essential role in the minimum description length (MDL) method of statistical modeling…

Empirical economic research frequently applies maximum likelihood estimation in cases where the likelihood function is analytically intractable. Most of the theoretical literature focuses on maximum simulated likelihood (MSL) estimators,…

The saddlepoint approximation gives an approximation to the density of a random variable in terms of its moment generating function. When the underlying random variable is itself the sum of $n$ unobserved i.i.d. terms, the basic classical…

We present an Evolutionary Placement Algorithm (EPA) for the rapid assignment of sequence fragments (short reads) to branches of a given phylogenetic tree under the Maximum Likelihood (ML) model. The accuracy of the algorithm is evaluated…

Neural networks trained on real-world datasets with long-tailed label distributions are biased towards frequent classes and perform poorly on infrequent classes. The imbalance in the ratio of positive and negative samples for each class…

Inference of the marginal likelihood of sample allele configurations using backward algorithms yields identical results with the Kingman coalescent, the Moran model, and the diffusion model (up to a scaling of time). For inference of…

Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such…

Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

Machine learning (ML) has emerged as a powerful tool for tackling complex regression and classification tasks, yet its success often hinges on the quality of training data. This study introduces an ML paradigm inspired by domain knowledge…

We compare an autoencoder convolutional neural network (AE-CNN) with a conventional maximum-likelihood estimator (MLE) for inferring cluster virial masses, $M_v$, directly from the galaxy distribution around clusters, without identifying…

Automated Machine Learning (AutoML) approaches encompass traditional methods that optimize fixed pipelines for model selection and ensembling, as well as newer LLM-based frameworks that autonomously build pipelines. While LLM-based agents…

Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…

Survival analysis studies and predicts the time of death, or other singular unrepeated events, based on historical data, while the true time of death for some instances is unknown. Survival trees enable the discovery of complex nonlinear…

The AMP Markov property is a recently proposed alternative Markov property for chain graphs. In the case of continuous variables with a joint multivariate Gaussian distribution, it is the AMP rather than the earlier introduced LWF Markov…

In Bayesian phylogenetics, our goal is to estimate the posterior distribution over phylogenetic trees. Markov chain Monte Carlo methods are widely used to approximate the phylogenetic posterior distributions. For large-scale sequence data,…

There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…