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Likelihood Functions

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A machine-learning-based alternative to phylogenetic bootstrap.

Bioinformatics (Oxford, England)
MOTIVATION: Currently used methods for estimating branch support in phylogenetic analyses often rely on the classic Felsenstein's bootstrap, parametric tests, or their approximations. As these branch support scores are widely used in phylogenetic ana...

Boosting integral-based human pose estimation through implicit heatmap learning.

Neural networks : the official journal of the International Neural Network Society
Human pose estimation typically encompasses three categories: heatmap-, regression-, and integral-based methods. While integral-based methods possess advantages such as end-to-end learning, full-convolution learning, and being free from quantization ...

Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments.

Molecular phylogenetics and evolution
Phylogenetic tree reconstruction with molecular data is important in many fields of life science research. The gold standard in this discipline is the phylogenetic tree reconstruction based on the Maximum Likelihood method. In this study, we present ...

Non-Intrusive System for Honeybee Recognition Based on Audio Signals and Maximum Likelihood Classification by Autoencoder.

Sensors (Basel, Switzerland)
Artificial intelligence and Internet of Things are playing an increasingly important role in monitoring beehives. In this paper, we propose a method for automatic recognition of honeybee type by analyzing the sound generated by worker bees and drone ...

Reliable estimation of tree branch lengths using deep neural networks.

PLoS computational biology
A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the t...

Machine learning in causal inference for epidemiology.

European journal of epidemiology
In causal inference, parametric models are usually employed to address causal questions estimating the effect of interest. However, parametric models rely on the correct model specification assumption that, if not met, leads to biased effect estimate...

Ethical and security challenges in AI for forensic genetics: From bias to adversarial attacks.

Forensic science international. Genetics
Forensic scientists play a crucial role in assigning probabilities to evidence based on competing hypotheses, which is fundamental in legal contexts where propositions are presented usually by prosecution and defense. The likelihood ratio (LR) is a w...

An efficient deep learning method for amino acid substitution model selection.

Journal of evolutionary biology
Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundred...

Guidelines and Best Practices for the Use of Targeted Maximum Likelihood and Machine Learning When Estimating Causal Effects of Exposures on Time-To-Event Outcomes.

Statistics in medicine
Targeted maximum likelihood estimation (TMLE) is an increasingly popular framework for the estimation of causal effects. It requires modeling both the exposure and outcome but is doubly robust in the sense that it is valid if at least one of these mo...

Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks.

Molecular biology and evolution
Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art maximum likelihood and Bayesian inference methods limits their us...