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The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo…
Similarity plays a fundamental role in many areas, including data mining, machine learning, statistics and various applied domains. Inspired by the success of ensemble methods and the flexibility of trees, we propose to learn a similarity…
1. Understanding the mechanisms underlying biological systems, and ultimately, predicting their behaviours in a changing environment requires overcoming the gap between mathematical models and experimental or observational 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…
Probabilistic Regression Trees (PRTrees) generalize traditional decision trees by incorporating probability functions that associate each data point with different regions of the tree, providing smooth decisions and continuous responses.…
Time series classification (TSC) is a challenging task due to the diversity of types of feature that may be relevant for different classification tasks, including trends, variance, frequency, magnitude, and various patterns. To address this…
Retrieval-augmented generation (RAG) combines document retrieval with large language models to produce responses grounded in external evidence. While several R packages support core components of RAG workflows, integrated evaluation of RAG…
Accurate software effort estimation has been a challenge for many software practitioners and project managers. Underestimation leads to disruption in the projects estimated cost and delivery. On the other hand, overestimation causes…
We establish a general framework using a diffusion approximation to simulate forward-in-time state counts or frequencies for cladogenetic state-dependent speciation-extinction (ClaSSE) models. We apply the framework to various two- and…
We introduce bloomRF as a unified method for approximate membership testing that supports both point- and range-queries on a single data structure. bloomRF extends Bloom-Filters with range query support and may replace them. The core idea…
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…
Traditional applications of latent class models (LCMs) often focus on scenarios where a set of unobserved classes are well-defined and easily distinguishable. However, in numerous real-world applications, these classes are weakly separated…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Age estimation from facial images is typically cast as a label distribution learning or regression problem, since aging is a gradual progress. Its main challenge is the facial feature space w.r.t. ages is inhomogeneous, due to the large…
In this work, we present a modified fuzzy decision forest for real-time 3D object pose estimation based on typical template representation. We employ an extra preemptive background rejector node in the decision forest framework to terminate…
Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells. Traditional tree construction methods, while instrumental in…
Decision-tree ensembles are a cornerstone of predictive modeling, and SHAP is a standard framework for interpreting their predictions. Among its variants, Background SHAP offers high accuracy by modeling missing features using a background…