A biologist's guide to model selection and causal inference.

Proc Biol Sci

Department of Epidemiology, Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA.

Published: January 2021

A goal of many research programmes in biology is to extract meaningful insights from large, complex datasets. Researchers in ecology, evolution and behavior (EEB) often grapple with long-term, observational datasets from which they construct models to test causal hypotheses about biological processes. Similarly, epidemiologists analyse large, complex observational datasets to understand the distribution and determinants of human health. A key difference in the analytical workflows for these two distinct areas of biology is the delineation of data analysis tasks and explicit use of causal directed acyclic graphs (DAGs), widely adopted by epidemiologists. Here, we review the most recent causal inference literature and describe an analytical workflow that has direct applications for EEB. We start this commentary by defining four distinct analytical tasks (description, prediction, association, causal inference). The remainder of the text is dedicated to causal inference, specifically focusing on the use of DAGs to inform the modelling strategy. Given the increasing interest in causal inference and misperceptions regarding this task, we seek to facilitate an exchange of ideas between disciplinary silos and provide an analytical framework that is particularly relevant for making causal inference from observational data.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893255PMC
http://dx.doi.org/10.1098/rspb.2020.2815DOI Listing

Publication Analysis

Top Keywords

causal inference
24
causal
8
large complex
8
observational datasets
8
inference
6
biologist's guide
4
guide model
4
model selection
4
selection causal
4
inference goal
4

Similar Publications

Background: The 2019 Canada's Food Guide provides universal recommendations to individuals aged ≥2 years. However, the extent to which these recommendations are appropriate for older adults is unknown. Although ideal, conducting a large randomized controlled trial is unrealistic in the short term.

View Article and Find Full Text PDF

Spatially resolved transcriptomics technologies potentially provide the extra spatial position information and tissue image to better infer spatial cell-cell interactions (CCIs) in processes such as tissue homeostasis, development, and disease progression. However, methods for effectively integrating spatial multimodal data to infer CCIs are still lacking. Here, the authors propose a deep learning method for integrating features through co-convolution, called SpaGraphCCI, to effectively integrate data from different modalities of SRT by projecting gene expression and image feature into a low-dimensional space.

View Article and Find Full Text PDF

Our commentary proposes the application of directed acyclic graphs (DAGs) in the design of decision-analytic models, offering researchers a valuable and structured tool to enhance transparency and accuracy by bridging the gap between causal inference and model design in medical decision making.The practical examples in this article showcase the transformative effect DAGs can have on model structure, parameter selection, and the resulting conclusions on effectiveness and cost-effectiveness.This methodological article invites a broader conversation on decision-modeling choices grounded in causal assumptions.

View Article and Find Full Text PDF

Background: Previous observational studies have shown that Hypothyroidism is associated with Von Willebrand Disease (VWD), but the causal relationship has not been confirmed because of conflicting findings and confounding by mixing factors. There are also some studies suggesting that polyunsaturated fatty acids (PUFA) may be one of the potential mediators. In this study, we used a Mendelian randomization study to analyze the causal relationship between Hypothyroidism and VWD and to investigate whether polyunsaturated fatty acids mediate the effects of Hypothyroidism on VWD.

View Article and Find Full Text PDF

Predictive models are indeed useful for causal inference.

Ecology

January 2025

Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA.

The subject of investigating causation in ecology has been widely discussed in recent years, especially by advocates of a structural causal model (SCM) approach. Some of these advocates have criticized the use of predictive models and model selection for drawing inferences about causation. We argue that the comparison of model-based predictions with observations is a key step in hypothetico-deductive (H-D) science and remains a valid approach for assessing causation.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!