8 citations · 24 across the 14 of their papers we have counts for
16 papers
Generating the Unheard: Phylogeny-Guided Latent Generation for Ancestral Sound Reconstruction
Tianyi Xu, Shrinaath Narasimhan, Evan Gorstein +3
What did an ancestral bird species sound like? Existing ancestral state reconstruction methods can infer low-dimensional traits such as morphological characters at internal nodes o…
Matrix representations and distance metrics for unlabeled ranked phylogenetic networks
Jiayang Wang, Julia A. Palacios, Claudia Solís-Lemus
Phylogenetic networks are graphs inferred from molecular sequence data that represent ancestral histories shaped by reticulate processes such as recombination, hybridization, and h…
CMiNet: R package for learning the Consensus Microbiome Network
Rosa Aghdam, Claudia Solis-Lemus
Understanding complex interactions within microbiomes is essential for exploring their roles in health and disease. However, constructing reliable microbiome networks often poses a…
Unsupervised Learning of Phylogenetic Trees via Split-Weight Embedding
Yibo Kong, George P. Tiley, Claudia Solis-Lemus
Unsupervised learning has become a staple in classical machine learning, successfully identifying clustering patterns in data across a broad range of domain applications. Surprisin…
MiNAA: Microbiome Network Alignment Algorithm
Reed Nelson, Rosa Aghdam, Claudia Solis-Lemus
Our Microbiome Network Alignment Algorithm (MiNAA) aligns two microbial networks using a combination of the GRAph ALigner (GRAAL) algorithm and the Hungarian algorithm. Network ali…
Ultrafast learning of 4-node hybridization cycles in phylogenetic networks using algebraic invariants
Zhaoxing Wu, Claudia Solis-Lemus
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture…
Detectability of Varied Hybridization Scenarios using Genome-Scale Hybrid Detection Methods
Marianne Bjorner, Erin K. Molloy, Colin N. Dewey +1
Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating mode…
BioKlustering: a web app for semi-supervised learning of maximally imbalanced genomic data
Samuel Ozminkowski, Yuke Wu, Hailey Bruzzone +6
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate predicti…
Identifying microbial drivers in biological phenotypes with a Bayesian Network Regression model
Samuel Ozminkowski, Claudia Solis-Lemus
1. In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify reg…
Novel Symmetry-preserving Neural Network Model for Phylogenetic Inference
Xudong Tang, Leonardo Zepeda-Nunez, Shengwen Yang +2
Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this…
CARlasso: An R package for the estimation of sparse microbial networks with predictors
Yunyi Shen, Claudia Solis-Lemus
Microbiome data analyses require statistical tools that can simultaneously decode microbes' reactions to the environment and interactions among microbes. We introduce CARlasso, the…
The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models
Yunyi Shen, Claudia Solis-Lemus
Here, we investigate whether (and how) experimental design could aid in the estimation of the precision matrix in a Gaussian chain graph model, especially the interplay between the…
WI Fast Stats: a collection of web apps for the visualization and analysis of WI Fast Plants data
Yizhou Liu, Claudia Solis-Lemus
WI Fast Stats is the first and only dedicated tool tailored to the WI Fast Plants educational objectives. WI Fast Stats is an integrated animated web page with a collection of R-de…
Bayesian Chain Graph LASSO Models to Learn Sparse Microbial Networks with Predictors
Yunyi Shen, Claudia Solis-Lemus
Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regres…
On the Identifiability of Phylogenetic Networks under a Pseudolikelihood model
Claudia Solis-Lemus, Arrigo Coen, Cecile Ane
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconst…
Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting
Claudia Solís-Lemus, Cécile Ané
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all spec…