9,744 research outputs found
Identifying Nonlinear 1-Step Causal Influences in Presence of Latent Variables
We propose an approach for learning the causal structure in stochastic
dynamical systems with a -step functional dependency in the presence of
latent variables. We propose an information-theoretic approach that allows us
to recover the causal relations among the observed variables as long as the
latent variables evolve without exogenous noise. We further propose an
efficient learning method based on linear regression for the special sub-case
when the dynamics are restricted to be linear. We validate the performance of
our approach via numerical simulations
Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches
In the past two decades, functional Magnetic Resonance Imaging has been used
to relate neuronal network activity to cognitive processing and behaviour.
Recently this approach has been augmented by algorithms that allow us to infer
causal links between component populations of neuronal networks. Multiple
inference procedures have been proposed to approach this research question but
so far, each method has limitations when it comes to establishing whole-brain
connectivity patterns. In this work, we discuss eight ways to infer causality
in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality,
Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and
Transfer Entropy. We finish with formulating some recommendations for the
future directions in this area
Impact of environmental inputs on reverse-engineering approach to network structures
Background: Uncovering complex network structures from a biological system is one of the main topic in system biology. The network structures can be inferred by the dynamical Bayesian network or Granger causality, but neither techniques have seriously taken into account the impact of environmental inputs.
Results: With considerations of natural rhythmic dynamics of biological data, we propose a system biology approach to reveal the impact of environmental inputs on network structures. We first represent the environmental inputs by a harmonic oscillator and combine them with Granger causality to identify environmental inputs and then uncover the causal network structures. We also generalize it to multiple harmonic oscillators to represent various exogenous influences. This system approach is extensively tested with toy models and successfully applied to a real biological network of microarray data of the flowering genes of the model plant Arabidopsis Thaliana. The aim is to identify those genes that are directly affected by the presence of the sunlight and uncover the interactive network structures associating with flowering metabolism.
Conclusion: We demonstrate that environmental inputs are crucial for correctly inferring network structures. Harmonic causal method is proved to be a powerful technique to detect environment inputs and uncover network structures, especially when the biological data exhibit periodic oscillations
Multivariate Granger Causality and Generalized Variance
Granger causality analysis is a popular method for inference on directed
interactions in complex systems of many variables. A shortcoming of the
standard framework for Granger causality is that it only allows for examination
of interactions between single (univariate) variables within a system, perhaps
conditioned on other variables. However, interactions do not necessarily take
place between single variables, but may occur among groups, or "ensembles", of
variables. In this study we establish a principled framework for Granger
causality in the context of causal interactions among two or more multivariate
sets of variables. Building on Geweke's seminal 1982 work, we offer new
justifications for one particular form of multivariate Granger causality based
on the generalized variances of residual errors. Taken together, our results
support a comprehensive and theoretically consistent extension of Granger
causality to the multivariate case. Treated individually, they highlight
several specific advantages of the generalized variance measure, which we
illustrate using applications in neuroscience as an example. We further show
how the measure can be used to define "partial" Granger causality in the
multivariate context and we also motivate reformulations of "causal density"
and "Granger autonomy". Our results are directly applicable to experimental
data and promise to reveal new types of functional relations in complex
systems, neural and otherwise.Comment: added 1 reference, minor change to discussion, typos corrected; 28
pages, 3 figures, 1 table, LaTe
Identifiable Latent Polynomial Causal Models Through the Lens of Change
Causal representation learning aims to unveil latent high-level causal
representations from observed low-level data. One of its primary tasks is to
provide reliable assurance of identifying these latent causal models, known as
identifiability. A recent breakthrough explores identifiability by leveraging
the change of causal influences among latent causal variables across multiple
environments \citep{liu2022identifying}. However, this progress rests on the
assumption that the causal relationships among latent causal variables adhere
strictly to linear Gaussian models. In this paper, we extend the scope of
latent causal models to involve nonlinear causal relationships, represented by
polynomial models, and general noise distributions conforming to the
exponential family. Additionally, we investigate the necessity of imposing
changes on all causal parameters and present partial identifiability results
when part of them remains unchanged. Further, we propose a novel empirical
estimation method, grounded in our theoretical finding, that enables learning
consistent latent causal representations. Our experimental results, obtained
from both synthetic and real-world data, validate our theoretical contributions
concerning identifiability and consistency
Learning Temporal Dependence from Time-Series Data with Latent Variables
We consider the setting where a collection of time series, modeled as random
processes, evolve in a causal manner, and one is interested in learning the
graph governing the relationships of these processes. A special case of wide
interest and applicability is the setting where the noise is Gaussian and
relationships are Markov and linear. We study this setting with two additional
features: firstly, each random process has a hidden (latent) state, which we
use to model the internal memory possessed by the variables (similar to hidden
Markov models). Secondly, each variable can depend on its latent memory state
through a random lag (rather than a fixed lag), thus modeling memory recall
with differing lags at distinct times. Under this setting, we develop an
estimator and prove that under a genericity assumption, the parameters of the
model can be learned consistently. We also propose a practical adaption of this
estimator, which demonstrates significant performance gains in both synthetic
and real-world datasets
Discovering Causal Relations and Equations from Data
Physics is a field of science that has traditionally used the scientific
method to answer questions about why natural phenomena occur and to make
testable models that explain the phenomena. Discovering equations, laws and
principles that are invariant, robust and causal explanations of the world has
been fundamental in physical sciences throughout the centuries. Discoveries
emerge from observing the world and, when possible, performing interventional
studies in the system under study. With the advent of big data and the use of
data-driven methods, causal and equation discovery fields have grown and made
progress in computer science, physics, statistics, philosophy, and many applied
fields. All these domains are intertwined and can be used to discover causal
relations, physical laws, and equations from observational data. This paper
reviews the concepts, methods, and relevant works on causal and equation
discovery in the broad field of Physics and outlines the most important
challenges and promising future lines of research. We also provide a taxonomy
for observational causal and equation discovery, point out connections, and
showcase a complete set of case studies in Earth and climate sciences, fluid
dynamics and mechanics, and the neurosciences. This review demonstrates that
discovering fundamental laws and causal relations by observing natural
phenomena is being revolutionised with the efficient exploitation of
observational data, modern machine learning algorithms and the interaction with
domain knowledge. Exciting times are ahead with many challenges and
opportunities to improve our understanding of complex systems.Comment: 137 page
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