Dataset Information

Phyddle: software for phylogenetic model exploration with deep learning.

ABSTRACT: Many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, a pipeline-based toolkit for performing phylogenetic modeling tasks using likelihood-free deep learning approaches. phyddle coordinates modeling tasks through five analysis steps ( Simulate, Format, Train, Estimate , and Plot ) that transform raw phylogenetic datasets as input into numerical and visualized model-based output. Benchmarks show that phyddle accurately performs a range of inference tasks, such as estimating macroevolutionary parameters, selecting among continuous trait evolution models, and passing coverage tests for epidemiological models, even for models that lack tractable likelihoods. phyddle has a flexible command-line interface, making it easy to integrate deep learning approaches for phylogenetics into research workflows. Learn more about phyddle at https://phyddle.org .

SUBMITTER: Landis MJ

PROVIDER: S-EPMC11326143 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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phyddle: software for exploring phylogenetic models with deep learning.

Landis Michael J MJ Thompson Ammon A

bioRxiv : the preprint server for biology 20250228

Phylogenies contain a wealth of information about the evolutionary history and process that gave rise to the diversity of life. This information can be extracted by fitting phylogenetic models to trees. However, many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, pipeline-based software for performing phylogenetic modeling tasks on trees using likelihood-free deep learning approaches. phyddle has a fle ...[more]

PMID: 39149349

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Project description:BackgroundDuring the ongoing COVID-19 pandemic, we are being exposed to large amounts of information each day. This "infodemic" is defined by the World Health Organization as the mass spread of misleading or false information during a pandemic. This spread of misinformation during the infodemic ultimately leads to misunderstandings of public health orders or direct opposition against public policies. Although there have been efforts to combat misinformation spread, current manual fact-checking methods are insufficient to combat the infodemic.ObjectiveWe propose the use of natural language processing (NLP) and machine learning (ML) techniques to build a model that can be used to identify unreliable news articles online.MethodsFirst, we preprocessed the ReCOVery data set to obtain 2029 English news articles tagged with COVID-19 keywords from January to May 2020, which are labeled as reliable or unreliable. Data exploration was conducted to determine major differences between reliable and unreliable articles. We built an ensemble deep learning model using the body text, as well as features, such as sentiment, Empath-derived lexical categories, and readability, to classify the reliability.ResultsWe found that reliable news articles have a higher proportion of neutral sentiment, while unreliable articles have a higher proportion of negative sentiment. Additionally, our analysis demonstrated that reliable articles are easier to read than unreliable articles, in addition to having different lexical categories and keywords. Our new model was evaluated to achieve the following performance metrics: 0.906 area under the curve (AUC), 0.835 specificity, and 0.945 sensitivity. These values are above the baseline performance of the original ReCOVery model.ConclusionsThis paper identified novel differences between reliable and unreliable news articles; moreover, the model was trained using state-of-the-art deep learning techniques. We aim to be able to use our findings to help researchers and the public audience more easily identify false information and unreliable media in their everyday lives.

Dataset Information

Phyddle: software for phylogenetic model exploration with deep learning.

Publications

phyddle: software for exploring phylogenetic models with deep learning.

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