Graphical Models for Quasi-experimental Designs

Randomized controlled trials (RCTs) and quasi-experimental designs like regression discontinuity (RD) designs, instrumental variable (IV) designs, and matching and propensity score (PS) designs are frequently used for inferring causal effects. It is well known that the features of these designs facilitate the identification of a causal estimand and, thus, warrant a causal interpretation of the estimated effect. In this article, we discuss and compare the identifying assumptions of quasi-experiments using causal graphs. The increasing complexity of the causal graphs as one switches from an RCT to RD, IV, or PS designs reveals that the assumptions become stronger as the researcher's control over treatment selection diminishes. We introduce limiting graphs for the RD design and conditional graphs for the latent subgroups of com-pliers, always takers, and never takers of the IV design, and argue that the PS is a collider that offsets confounding bias via collider bias.

Confounding in Studies on Metacognition: A Preliminary Causal Analysis Framework

By definition, metacognitive processes may monitor or regulate various stages of first-order processing. By combining causal analysis with hypotheses expressed by other authors we derive the theoretical and methodological consequences of this special relation between metacognition and the underlying processes. In particular, we prove that because multiple processing stages may be monitored or regulated and because metacognition may form latent feedback loops, (1) without strong additional causal assumptions, typical measures of metacognitive monitoring or regulation are confounded; (2) without strong additional causal assumptions, typical methods of controlling for first-order task performance (i.e., calibration, staircase, including first-order task performance in a regression analysis, or analyzing correct and incorrect trials separately) not only do not deconfound measures of metacognition but may even introduce bias; (3) that the first two problems cannot be solved by using simple models of decision-making derived from Signal Detection Theory. We conclude the paper by advocating robust methods of discovering properties of latent mechanisms.

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This article proposes a general approach for querying a causal biological knowledge graph, and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. We demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm, and performing counterfactual inference to estimate the causal effect of medical countermeasures for severely ill patients.

Machine Learning-Aided Causal Inference Framework for Environmental Data Analysis: A COVID-19 Case Study

Links between environmental conditions (e.g., meteorological factors and air quality) and COVID-19 severity have been reported worldwide. However, the existing frameworks of data analysis are insufficient or inefficient to investigate the potential causality behind the associations involving multidimensional factors and complicated interrelationships. Thus, a causal inference framework equipped with the structural causal model aided by machine learning methods was proposed and applied to examine the potential causal relationships between COVID-19 severity and 10 environmental factors (NO₂, O₃, PM2.5, PM10, SO₂, CO, average air temperature, atmospheric pressure, relative humidity, and wind speed) in 166 Chinese cities. The cities were grouped into three clusters based on the socio-economic features. Time-series data from these cities in each cluster were analyzed in different pandemic phases. The robustness check refuted most potential causal relationships' estimations (89 out of 90). Only one potential relationship about air temperature passed the final test with a causal effect of 0.041 under a specific cluster-phase condition. The results indicate that the environmental factors are unlikely to cause noticeable aggravation of the COVID-19 pandemic. This study also demonstrated the high value and potential of the proposed method in investigating causal problems with observational data in environmental or other fields.

Causal inference under over-simplified longitudinal causal models

Many causal models of interest in epidemiology involve longitudinal exposures, confounders and mediators. However, repeated measurements are not always available or used in practice, leading analysts to overlook the time-varying nature of exposures and work under over-simplified causal models. Our objective is to assess whether - and how - causal effects identified under such misspecified causal models relates to true causal effects of interest. We derive sufficient conditions ensuring that the quantities estimated in practice under over-simplified causal models can be expressed as weighted averages of longitudinal causal effects of interest. Unsurprisingly, these sufficient conditions are very restrictive, and our results state that the quantities estimated in practice should be interpreted with caution in general, as they usually do not relate to any longitudinal causal effect of interest. Our simulations further illustrate that the bias between the quantities estimated in practice and the weighted averages of longitudinal causal effects of interest can be substantial. Overall, our results confirm the need for repeated measurements to conduct proper analyses and/or the development of sensitivity analyses when they are not available.

Algorithmic Accountability in Context. Socio-Technical Perspectives on Structural Causal Models

The increasing use of automated decision making (ADM) and machine learning sparked an ongoing discussion about algorithmic accountability. Within computer science, a new form of producing accountability has been discussed recently: causality as an expression of algorithmic accountability, formalized using structural causal models (SCMs). However, causality itself is a concept that needs further exploration. Therefore, in this contribution we confront ideas of SCMs with insights from social theory, more explicitly pragmatism, and argue that formal expressions of causality must always be seen in the context of the social system in which they are applied. This results in the formulation of further research questions and directions.

Causal Inference With Observational Data and Unobserved Confounding Variables

Experiments have long been the gold standard for causal inference in Ecology. As Ecology tackles progressively larger problems, however, we are moving beyond the scales at which randomised controlled experiments are feasible. To answer causal questions at scale, we need to also use observational data -something Ecologists tend to view with great scepticism. The major challenge using observational data for causal inference is confounding variables: variables affecting both a causal variable and response of interest. Unmeasured confounders-known or unknown-lead to statistical bias, creating spurious correlations and masking true causal relationships. To combat this omitted variable bias, other disciplines have developed rigorous approaches for causal inference from observational data that flexibly control for broad suites of confounding variables. We show how ecologists can harness some of these methods-causal diagrams to identify confounders coupled with nested sampling and statistical designs-to reduce risks of omitted variable bias. Using an example of estimating warming effects on snails, we show how current methods in Ecology (e.g., mixed models) produce incorrect inferences due to omitted variable bias and how alternative methods can eliminate it, improving causal inferences with weaker assumptions. Our goal is to expand tools for causal inference using observational and imperfect experimental data in Ecology.

Changes in Vertical Stratification of Neotropical Nymphalid Butterflies at Forest Edges Are Not Directly Caused by Light and Temperature Conditions

Habitat fragmentation and land use changes threaten neotropical habitats and alter patterns of diversity at forest edges. Like other arthropod assemblages, neotropical fruit-feeding butterfly communities show strong vertical stratification within forests, with some recent work showing its potential role in speciation. At forest edges, species considered to be forest canopy specialists have been observed descending to the forest understory, with the similarity in light conditions between the canopy and understory strata at edges hypothesized to be responsible for this phenomenon. We conducted a study using standardized sampling to document and quantify this edge effect, characterize edge and forest strata, and estimate the relative contributions of temperature and light conditions to changes in nymphalid butterfly stratification at forest edges. We found strong evidence of an edge effect in these butterflies and confirmed strong differences in light and temperature, showing that the edge understory differs little from forest canopy conditions. Of 41 species common to both forests and edges, 28 shifted to have a lower canopy probability at the edge, and our model detected a decrease in canopy probability of 0.165. Furthermore, our analysis indicated the relative abundance of canopy taxa increased at the edge, and the tribes Haeterini and Morphini were especially sensitive to edge effects. However, the analyses here did not clearly implicate temperature or light magnitude in causing changes in neotropical nymphalid vertical stratification at forest edges. Instead, our results point to other mediator variables as being important for changes at tropical forest edges. From our data, edge-responsive species can be separated into two different categories, which likely relates to their resilience to anthropogenic disturbance. We also note that structural causal models have a potential place in future work on tropical conservation, given they can provide causal estimates with observational data.

Refining the Allostatic Self-Efficacy Theory of Fatigue and Depression Using Causal Inference

Allostatic self-efficacy (ASE) represents a computational theory of fatigue and depression. In brief, it postulates that (i) fatigue is a feeling state triggered by a metacognitive diagnosis of loss of control over bodily states (persistently elevated interoceptive surprise); and that (ii) generalization of low self-efficacy beliefs beyond bodily control induces depression. Here, we converted ASE theory into a structural causal model (SCM). This allowed identification of empirically testable hypotheses regarding causal relationships between the variables of interest. Applying conditional independence tests to questionnaire data from healthy volunteers, we sought to identify contradictions to the proposed SCM. Moreover, we estimated two causal effects proposed by ASE theory using three different methods. Our analyses identified specific aspects of the proposed SCM that were inconsistent with the available data. This enabled formulation of an updated SCM that can be tested against future data. Second, we confirmed the predicted negative average causal effect from metacognition of allostatic control to fatigue across all three different methods of estimation. Our study represents an initial attempt to refine and formalize ASE theory using methods from causal inference. Our results confirm key predictions from ASE theory but also suggest revisions which require empirical verification in future studies.

Foundations and Future Directions for Causal Inference in Ecological Research

Ecology often seeks to answer causal questions, and while ecologists have a rich history of experimental approaches, novel observational data streams and the need to apply insights across naturally occurring conditions pose opportunities and challenges. Other fields have developed causal inference approaches that can enhance and expand our ability to answer ecological causal questions using observational or experimental data. However, the lack of comprehensive resources applying causal inference to ecological settings and jargon from multiple disciplines creates barriers. We introduce approaches for causal inference, discussing the main frameworks for counterfactual causal inference, how causal inference differs from other research aims and key challenges; the application of causal inference in experimental and quasi-experimental study designs; appropriate interpretation of the results of causal inference approaches given their assumptions and biases; foundational papers; and the data requirements and trade-offs between internal and external validity posed by different designs. We highlight that these designs generally prioritise internal validity over generalisability. Finally, we identify opportunities and considerations for ecologists to further integrate causal inference with synthesis science and meta-analysis and expand the spatiotemporal scales at which causal inference is possible. We advocate for ecology as a field to collectively define best practices for causal inference.