Distinguishing time-delayed causal interactions using convergent cross mapping.
Ontology highlight
ABSTRACT:
SUBMITTER: Ye H
PROVIDER: S-EPMC4592974 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The hydrologic connectivity of non-floodplain wetlands (NFWs) with downstream water (DW) has gained increased importance, but connectivity via groundwater (GW) is largely unknown owing to the high complexity of hydrological processes and climatic seasonality. In this study, a causal inference method, convergent cross mapping (CCM), was applied to detect the hydrologic causality between upland NFW and DW through GW. CCM is a nonlinear inference method for detecting causal relationships among environmental variables with weak or moderate coupling in nonlinear dynamical systems. We assumed that causation would exist when the following conditions were observed: (1) the presence of two direct causal (NFW → GW and GW → DW) and one indirect causal (NFW → DW) relationship; (2) a nonexistent opposite causal relationship (DW → NFW); (3) the two direct causations with shorter lag times relative to indirect causation; and (4) similar patterns not observed with pseudo DW. The water levels monitored by a well and piezometer represented NFW and GW measurements, respectively, and the DW was indicated by the baseflow at the outlet of the drainage area, including NFW. To elucidate causality, the DW taken at the adjacent drainage area with similar climatic seasonality was also tested as pseudo DW. The CCM results showed that the water flow from NFW to GW and then DW was only present, and any opposite flows did not exist. In addition, direct causations had shorter lag time than indirect causation, and 3-day lag time was shown between NFW and DW. Interestingly, the results with pseudo DW did not show any lagged interactions, indicating non-causation. These results provide the signals for the hydrologic connectivity of NFW and DW with GW. Therefore, this study would support the importance of NFW protection and management.
| S-EPMC10567775 | biostudies-literature
Project description:Understanding the causality between energy consumption, carbon emissions and economic growth is helpful for policymakers to formulate energy, environmental and economic policies. For the first time, based on nonlinear dynamics, this paper employs multispatial convergent cross mapping (CCM) to revisit the energy-carbon-economy causation for China, India and the G7 countries using both aggregate data and per capita data. The findings indicate that there are significant differences between developing countries and developed countries. A bidirectional nexus between energy consumption, carbon emissions and economic growth is found in China and India, but various causal relationships are identified in the G7 countries, including bidirectional, unidirectional and neutral nexus. The results confirm that the decoupling phenomenon is common in most G7 countries. By leveraging a variety of samples and a new approach, this study provides new evidence for policy authorities to formulate country-specific policies to obtain better environmental quality while achieving sustainable economic growth.
| S-EPMC6532921 | biostudies-literature
Project description:Geographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene flow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes. To understand the impact of convergent positive selection on neutral diversity at linked loci, we make use of the fact that hitchhiking can be modeled as an increase in the variance in neutral allele frequencies around a selected site within a population. We build on coalescent theory to show how shared hitchhiking events between subpopulations act to increase covariance in allele frequencies between subpopulations at loci near the selected site, and extend this theory under different models of migration and selection on the same standing variation. We incorporate this hitchhiking effect into a multivariate normal model of allele frequencies that also accounts for population structure. Based on this theory, we present a composite-likelihood-based approach that utilizes genomic data to identify loci involved in convergence, and distinguishes among alternate modes of convergent adaptation. We illustrate our method on genome-wide polymorphism data from two distinct cases of convergent adaptation. First, we investigate the adaptation for copper toxicity tolerance in two populations of the common yellow monkey flower, Mimulus guttatus We show that selection has occurred on an allele that has been standing in these populations prior to the onset of copper mining in this region. Lastly, we apply our method to data from four populations of the killifish, Fundulus heteroclitus, that show very rapid convergent adaptation for tolerance to industrial pollutants. Here, we identify a single locus at which both independent mutation events and selection on an allele shared via gene flow, either slightly before or during selection, play a role in adaptation across the species' range.
| S-EPMC5714468 | biostudies-other
Project description:Causality detection likely misidentifies indirect causations as direct ones, due to the effect of causation transitivity. Although several methods in traditional frameworks have been proposed to avoid such misinterpretations, there still is a lack of feasible methods for identifying direct causations from indirect ones in the challenging situation where the variables of the underlying dynamical system are non-separable and weakly or moderately interacting. Here, we solve this problem by developing a data-based, model-independent method of partial cross mapping based on an articulated integration of three tools from nonlinear dynamics and statistics: phase-space reconstruction, mutual cross mapping, and partial correlation. We demonstrate our method by using data from different representative models and real-world systems. As direct causations are keys to the fundamental underpinnings of a variety of complex dynamics, we anticipate our method to be indispensable in unlocking and deciphering the inner mechanisms of real systems in diverse disciplines from data.
| S-EPMC7251131 | biostudies-literature
Project description:Inferring the gene regulatory network (GRN) is crucial to understanding the working of the cell. Many computational methods attempt to infer the GRN from time series expression data, instead of through expensive and time-consuming experiments. However, existing methods make the convenient but unrealistic assumption of causal sufficiency, i.e. all the relevant factors in the causal network have been observed and there are no unobserved common cause. In principle, in the real world, it is impossible to be certain that all relevant factors or common causes have been observed, because some factors may not have been conceived of, and therefore are impossible to measure. In view of this, we have developed a novel algorithm named HCC-CLINDE to infer an GRN from time series data allowing the presence of hidden common cause(s). We assume there is a sparse causal graph (possibly with cycles) of interest, where the variables are continuous and each causal link has a delay (possibly more than one time step). A small but unknown number of variables are not observed. Each unobserved variable has only observed variables as children and parents, with at least two children, and the children are not linked to each other. Since it is difficult to obtain very long time series, our algorithm is also capable of utilizing multiple short time series, which is more realistic. To our knowledge, our algorithm is far less restrictive than previous works. We have performed extensive experiments using synthetic data on GRNs of size up to 100, with up to 10 hidden nodes. The results show that our algorithm can adequately recover the true causal GRN and is robust to slight deviation from Gaussian distribution in the error terms. We have also demonstrated the potential of our algorithm on small YEASTRACT subnetworks using limited real data.
| S-EPMC4578777 | biostudies-literature
Project description:BackgroundUnderstanding gene interactions is a fundamental question in systems biology. Currently, modeling of gene regulations using the Bayesian Network (BN) formalism assumes that genes interact either instantaneously or with a certain amount of time delay. However in reality, biological regulations, both instantaneous and time-delayed, occur simultaneously. A framework that can detect and model both these two types of interactions simultaneously would represent gene regulatory networks more accurately.ResultsIn this paper, we introduce a framework based on the Bayesian Network (BN) formalism that can represent both instantaneous and time-delayed interactions between genes simultaneously. A novel scoring metric having firm mathematical underpinnings is also proposed that, unlike other recent methods, can score both interactions concurrently and takes into account the reality that multiple regulators can regulate a gene jointly, rather than in an isolated pair-wise manner. Further, a gene regulatory network (GRN) inference method employing an evolutionary search that makes use of the framework and the scoring metric is also presented.ConclusionBy taking into consideration the biological fact that both instantaneous and time-delayed regulations can occur among genes, our approach models gene interactions with greater accuracy. The proposed framework is efficient and can be used to infer gene networks having multiple orders of instantaneous and time-delayed regulations simultaneously. Experiments are carried out using three different synthetic networks (with three different mechanisms for generating synthetic data) as well as real life networks of Saccharomyces cerevisiae, E. coli and cyanobacteria gene expression data. The results show the effectiveness of our approach.
| S-EPMC3529704 | biostudies-literature
Project description:Physical interaction of regulatory elements in three-dimensional space poses a challenge for studies of disease because non-coding risk variants may be great distances from the genes they regulate. Experimental methods to capture these interactions, such as chromosome conformation capture, usually cannot assign causal direction of effect between regulatory elements, an important component of fine-mapping studies. We developed a Bayesian hierarchical approach that uses two-stage least squares and applied it to an ATAC-seq (assay for transposase-accessible chromatin using sequencing) data set from 100 individuals, to identify over 15,000 high-confidence causal interactions. Most (60%) interactions occurred over <20?kb, where chromosome conformation capture-based methods perform poorly. For a fraction of loci, we identified a single variant that alters accessibility across multiple regions, and experimentally validated the BLK locus, which is associated with multiple autoimmune diseases, using CRISPR genome editing. Our study highlights how association genetics of chromatin state is a powerful approach for identifying interactions between regulatory elements.
| S-EPMC6330062 | biostudies-literature
Project description:Cognitive control plays an important role in goal-directed behavior, but dynamic brain mechanisms underlying it are poorly understood. Here, using multisite fMRI data from over 100 participants, we investigate causal interactions in three cognitive control tasks within a core Frontal-Cingulate-Parietal network. We found significant causal influences from anterior insula (AI) to dorsal anterior cingulate cortex (dACC) in all three tasks. The AI exhibited greater net causal outflow than any other node in the network. Importantly, a similar pattern of causal interactions was uncovered by two different computational methods for causal analysis. Furthermore, the strength of causal interaction from AI to dACC was greater on high, compared with low, cognitive control trials and was significantly correlated with individual differences in cognitive control abilities. These results emphasize the importance of the AI in cognitive control and highlight its role as a causal hub in the Frontal-Cingulate-Parietal network. Our results further suggest that causal signaling between the AI and dACC plays a fundamental role in implementing cognitive control and are consistent with a two-stage cognitive control model in which the AI first detects events requiring greater access to cognitive control resources and then signals the dACC to execute load-specific cognitive control processes.
| S-EPMC4830290 | biostudies-literature
Project description:COVID-19 pandemic is fueling digital health transformation-accelerating innovations of digital health services, surveillance, and interventions, whereas hastening social contagion of deliberate infodemic. The USA and many other countries are experiencing a resurgent wave of the COVID-19 pandemic with vaccination rate slowdown, making policymaking fraught with challenges. Political leaders and scientists have publicly warned of a "pandemic of the unvaccinated," reinforcing their calls for citizens to get jabs. However, some scientists accused elites of stigmatizing the unvaccinated people and undermining the moral pillars of public health. Following the PRISMA-ScR guidelines, we first reviewed the nuances of stakeholders involved in the ongoing debates and revealed the potential consequences of divisive pronouncements to provide perspectives to reframe extensible discussions. Then, we employed the convergent cross mapping (CCM) model to reveal the uncharted knock-on effects of the contentious tsunami in a stakeholders-oriented policymaking framework, coupled with rich metadata from the GDELT project and Google Trends. Our experimental findings suggest that current news coverage may shape the mindsets of the vaccines against the unvaccinated, thereby exacerbating the risk of dualistic antagonism in algorithmically infused societies. Finally, we briefly summarized how open debates are conducive to increasing vaccination rates and bolstering the outcomes of impending policies for pandemic preparedness.
| S-EPMC9047174 | biostudies-literature
Project description:Re-parameterized regression models may enable tests of crucial theoretical predictions involving interactive effects of predictors that cannot be tested directly using standard approaches. First, we present a re-parameterized regression model for the Linear × Linear interaction of 2 quantitative predictors that yields point and interval estimates of 1 key parameter-the crossover point of predicted values-and leaves certain other parameters unchanged. We explain how resulting parameter estimates provide direct evidence for distinguishing ordinal from disordinal interactions. We generalize the re-parameterized model to Linear × Qualitative interactions, where the qualitative variable may have 2 or 3 categories, and then describe how to modify the re-parameterized model to test moderating effects. To illustrate our new approach, we fit alternate models to social skills data on 438 participants in the National Institute of Child Health and Human Development Study of Early Child Care. The re-parameterized regression model had point and interval estimates of the crossover point that fell near the mean on the continuous environment measure. The disordinal form of the interaction supported 1 theoretical model-differential-susceptibility-over a competing model that predicted an ordinal interaction.
| S-EPMC3553243 | biostudies-literature