1,131 research outputs found
Tensor Analysis and Fusion of Multimodal Brain Images
Current high-throughput data acquisition technologies probe dynamical systems
with different imaging modalities, generating massive data sets at different
spatial and temporal resolutions posing challenging problems in multimodal data
fusion. A case in point is the attempt to parse out the brain structures and
networks that underpin human cognitive processes by analysis of different
neuroimaging modalities (functional MRI, EEG, NIRS etc.). We emphasize that the
multimodal, multi-scale nature of neuroimaging data is well reflected by a
multi-way (tensor) structure where the underlying processes can be summarized
by a relatively small number of components or "atoms". We introduce
Markov-Penrose diagrams - an integration of Bayesian DAG and tensor network
notation in order to analyze these models. These diagrams not only clarify
matrix and tensor EEG and fMRI time/frequency analysis and inverse problems,
but also help understand multimodal fusion via Multiway Partial Least Squares
and Coupled Matrix-Tensor Factorization. We show here, for the first time, that
Granger causal analysis of brain networks is a tensor regression problem, thus
allowing the atomic decomposition of brain networks. Analysis of EEG and fMRI
recordings shows the potential of the methods and suggests their use in other
scientific domains.Comment: 23 pages, 15 figures, submitted to Proceedings of the IEE
MCNS: Mining Causal Natural Structures Inside Time Series via A Novel Internal Causality Scheme
Causal inference permits us to discover covert relationships of various
variables in time series. However, in most existing works, the variables
mentioned above are the dimensions. The causality between dimensions could be
cursory, which hinders the comprehension of the internal relationship and the
benefit of the causal graph to the neural networks (NNs). In this paper, we
find that causality exists not only outside but also inside the time series
because it reflects a succession of events in the real world. It inspires us to
seek the relationship between internal subsequences. However, the challenges
are the hardship of discovering causality from subsequences and utilizing the
causal natural structures to improve NNs. To address these challenges, we
propose a novel framework called Mining Causal Natural Structure (MCNS), which
is automatic and domain-agnostic and helps to find the causal natural
structures inside time series via the internal causality scheme. We evaluate
the MCNS framework and impregnation NN with MCNS on time series classification
tasks. Experimental results illustrate that our impregnation, by refining
attention, shape selection classification, and pruning datasets, drives NN,
even the data itself preferable accuracy and interpretability. Besides, MCNS
provides an in-depth, solid summary of the time series and datasets.Comment: 9 pages, 6 figure
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
Interpretability and Explainability: A Machine Learning Zoo Mini-tour
In this review, we examine the problem of designing interpretable and
explainable machine learning models. Interpretability and explainability lie at
the core of many machine learning and statistical applications in medicine,
economics, law, and natural sciences. Although interpretability and
explainability have escaped a clear universal definition, many techniques
motivated by these properties have been developed over the recent 30 years with
the focus currently shifting towards deep learning methods. In this review, we
emphasise the divide between interpretability and explainability and illustrate
these two different research directions with concrete examples of the
state-of-the-art. The review is intended for a general machine learning
audience with interest in exploring the problems of interpretation and
explanation beyond logistic regression or random forest variable importance.
This work is not an exhaustive literature survey, but rather a primer focusing
selectively on certain lines of research which the authors found interesting or
informative
Bayesian Dynamic DAG Learning: Application in Discovering Dynamic Effective Connectome of Brain
Understanding the complex mechanisms of the brain can be unraveled by
extracting the Dynamic Effective Connectome (DEC). Recently, score-based
Directed Acyclic Graph (DAG) discovery methods have shown significant
improvements in extracting the causal structure and inferring effective
connectivity. However, learning DEC through these methods still faces two main
challenges: one with the fundamental impotence of high-dimensional dynamic DAG
discovery methods and the other with the low quality of fMRI data. In this
paper, we introduce Bayesian Dynamic DAG learning with M-matrices Acyclicity
characterization \textbf{(BDyMA)} method to address the challenges in
discovering DEC. The presented dynamic causal model enables us to discover
bidirected edges as well. Leveraging an unconstrained framework in the BDyMA
method leads to more accurate results in detecting high-dimensional networks,
achieving sparser outcomes, making it particularly suitable for extracting DEC.
Additionally, the score function of the BDyMA method allows the incorporation
of prior knowledge into the process of dynamic causal discovery which further
enhances the accuracy of results. Comprehensive simulations on synthetic data
and experiments on Human Connectome Project (HCP) data demonstrate that our
method can handle both of the two main challenges, yielding more accurate and
reliable DEC compared to state-of-the-art and baseline methods. Additionally,
we investigate the trustworthiness of DTI data as prior knowledge for DEC
discovery and show the improvements in DEC discovery when the DTI data is
incorporated into the process
Deep Causal Learning: Representation, Discovery and Inference
Causal learning has attracted much attention in recent years because
causality reveals the essential relationship between things and indicates how
the world progresses. However, there are many problems and bottlenecks in
traditional causal learning methods, such as high-dimensional unstructured
variables, combinatorial optimization problems, unknown intervention,
unobserved confounders, selection bias and estimation bias. Deep causal
learning, that is, causal learning based on deep neural networks, brings new
insights for addressing these problems. While many deep learning-based causal
discovery and causal inference methods have been proposed, there is a lack of
reviews exploring the internal mechanism of deep learning to improve causal
learning. In this article, we comprehensively review how deep learning can
contribute to causal learning by addressing conventional challenges from three
aspects: representation, discovery, and inference. We point out that deep
causal learning is important for the theoretical extension and application
expansion of causal science and is also an indispensable part of general
artificial intelligence. We conclude the article with a summary of open issues
and potential directions for future work
Anomaly Detection and Exploratory Causal Analysis for SAP HANA
Nowadays, the good functioning of the equipment, networks and systems will be the key for the business of a company to continue operating because it is never avoidable for the companies to use information technology to support their business in the era of big data. However, the technology is never infallible, faults that give rise to sometimes critical situations may appear at any time. To detect and prevent failures, it is very essential to have a good monitoring system which is responsible for controlling the technology used by a company (hardware, networks and communications, operating systems or applications, among others) in order to analyze their operation and performance, and to detect and alert about possible errors. The aim of this thesis is thus to further advance the field of anomaly detection and exploratory causal inference which are two major research areas in a monitoring system, to provide efficient algorithms with regards to the usability, maintainability and scalability. The analyzed results can be viewed as a starting point for the root cause analysis of the system performance issues and to avoid falls in the system or minimize the time of resolution of the issues in the future. The algorithms were performed on the historical data of SAP HANA database at last and the results gained in this thesis indicate that the tools have succeeded in providing some useful information for diagnosing the performance issues of the system
CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis
There is a recent trend to leverage the power of graph neural networks (GNNs)
for brain-network based psychiatric diagnosis, which,in turn, also motivates an
urgent need for psychiatrists to fully understand the decision behavior of the
used GNNs. However, most of the existing GNN explainers are either post-hoc in
which another interpretive model needs to be created to explain a well-trained
GNN, or do not consider the causal relationship between the extracted
explanation and the decision, such that the explanation itself contains
spurious correlations and suffers from weak faithfulness. In this work, we
propose a granger causality-inspired graph neural network (CI-GNN), a built-in
interpretable model that is able to identify the most influential subgraph
(i.e., functional connectivity within brain regions) that is causally related
to the decision (e.g., major depressive disorder patients or healthy controls),
without the training of an auxillary interpretive network. CI-GNN learns
disentangled subgraph-level representations {\alpha} and \b{eta} that encode,
respectively, the causal and noncausal aspects of original graph under a graph
variational autoencoder framework, regularized by a conditional mutual
information (CMI) constraint. We theoretically justify the validity of the CMI
regulation in capturing the causal relationship. We also empirically evaluate
the performance of CI-GNN against three baseline GNNs and four state-of-the-art
GNN explainers on synthetic data and three large-scale brain disease datasets.
We observe that CI-GNN achieves the best performance in a wide range of metrics
and provides more reliable and concise explanations which have clinical
evidence.Comment: 45 pages, 13 figure
Data based identification and prediction of nonlinear and complex dynamical systems
We thank Dr. R. Yang (formerly at ASU), Dr. R.-Q. Su (formerly at ASU), and Mr. Zhesi Shen for their contributions to a number of original papers on which this Review is partly based. This work was supported by ARO under Grant No. W911NF-14-1-0504. W.-X. Wang was also supported by NSFC under Grants No. 61573064 and No. 61074116, as well as by the Fundamental Research Funds for the Central Universities, Beijing Nova Programme.Peer reviewedPostprin
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