Related papers: Improving Gene Trees without more data
In this article the results of Waddell and Azad (2009) are extended. In particular, the geometric percentage mean standard deviation measure of the fit of distances to a phylogenetic tree is adjusted for the number of parameters fitted to…
Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for…
Gradient Boosting Machines (GBM) are hugely popular for solving tabular data problems. However, practitioners are not only interested in point predictions, but also in probabilistic predictions in order to quantify the uncertainty of the…
This paper presents a brand new nonparametric density estimation strategy named the best-scored random forest density estimation whose effectiveness is supported by both solid theoretical analysis and significant experimental performance.…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
In this second paper in a series of papers based on the most-up-to-date catalogue of symbiotic stars (SySts), we present a new approach for identifying and distinguishing SySts from other Halpha emitters in photometric surveys using machine…
Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Determining subgroups that respond especially well (or poorly) to specific interventions (medical or policy) requires new supervised learning methods tailored specifically for causal inference. Bayesian Causal Forest (BCF) is a recent…
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted…
We evaluate the performance of various text embedding models and pipeline configurations for AI-driven search systems. We compare sentence-transformer and generative embedding models (e.g., All-MPNet, BGE, GTE, and Qwen) at different…
ASTRAL is a method for reconstructing species trees after inferring a set of gene trees and is increasingly used in phylogenomic analyses. It is statistically consistent under the multi-species coalescent model, is scalable, and has shown…
Error detection (ED), which aims to identify incorrect or inconsistent cell values in tabular data, is important for ensuring data quality. Recent state-of-the-art ED methods leverage the pre-trained knowledge and semantic capability…
The best-performing models in ML are not interpretable. If we can explain why they outperform, we may be able to replicate these mechanisms and obtain both interpretability and performance. One example are decision trees and their…
A widely used approach for extracting information from gene expression data employ the construction of a gene co-expression network and the subsequent application of algorithms that discover network structure. In particular, a common goal…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
Rapid advancements in genome sequencing have led to the collection of vast amounts of genomics data. Researchers may be interested in using machine learning models on such data to predict the pathogenicity or clinical significance of a…
The Winograd Schema Challenge (WSC) serves as a prominent benchmark for evaluating machine understanding. While Large Language Models (LLMs) excel at answering WSC questions, their ability to generate such questions remains less explored.…
Although tree species classification from Moderate Resolution Imaging Spectroradiometer (MODIS) time series data is critical for supporting various environmental applications, it is a challenging task due to several key difficulties: the…
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…