Discovering Latent Causal Graphs from Spatiotemporal Data
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA（计算机科学与工程系，加州大学圣地亚哥分校，拉乔拉，美国）；Halıcıoglu Data Science Institute, University of California, San Diego, La Jolla, USA（Halıcıoglu数据科学研究所，加州大学圣地亚哥分校，拉乔拉，美国）；Scripps Institution of Oceanography, University of California, San Diego, La Jolla, USA（斯克里普斯海洋研究所，加州大学圣地亚哥分校，拉乔拉，美国）
Kun Wang, Sumanth Varambally, Duncan Watson-Parris, Yi-An Ma, Rose Yu
Many important phenomena in scientific fields like climate, neuroscience, and epidemiology are naturally represented as spatiotemporal gridded data with complex interactions. Inferring causal relationships from these data is a challenging problem compounded by the high dimensionality of such data and the correlations between spatially proximate points. We present SPACY (SPAtiotemporal Causal discoverY), a novel framework based on variational inference, designed to model latent time series and their causal relationships from spatiotemporal data. SPACY alleviates the high-dimensional challenge by discovering causal structures in the latent space. To aggregate spatially proximate, correlated grid points, we use spatial factors, parametrized by spatial kernel functions, to map observational time series to latent representations. Theoretically, we generalize the problem to a continuous spatial domain and establish identifiability when the observations arise from a nonlinear, invertible function of the product of latent series and spatial factors. Using this approach, we avoid assumptions that are often unverifiable, including those about instantaneous effects or sufficient variability. Empirically, SPACY outperforms state-of-the-art baselines on synthetic data, even in challenging settings where existing methods struggle, while remaining scalable for large grids. SPACY also identifies key known phenomena from real-world climate data. An implementation of SPACY is available at https://github.com/Rose-STL-Lab/SPACY/
The Institute of Scientific and Industrial Research, Osaka University（大阪大学产业科学研究所）；Graduate School of Science, Osaka University（大阪大学研究生院）；Graduate School of Informatics, Kyoto University（京都大学情报学研究科）
Discovering causal relations among observed variables in a given data set is a main topic in studies of statistics and artificial intelligence. Recently, some techniques to discover an identifiable causal structure have been explored based on non-Gaussianity of the observed data distribution. However, most of these are limited to continuous data. In this paper, we present a novel causal model for binary data and propose a new approach to derive an identifiable causal structure governing the data based on skew Bernoulli distributions of external noise. Experimental evaluation shows excellent pe…
Discovering Mixtures of Structural Causal Models from Time Series Data
Halıcıoğlu Data Science Institute, University of California, San Diego（加利福尼亚大学圣迭戈分校哈利西奥格鲁数据科学学院）；Department of Computer Science and Engineering, University of California, San Diego（加利福尼亚大学圣迭戈分校计算机科学与工程系）
DeepMind（深度思维）；University of Oxford（牛津大学）；Imperial College London（帝国理工学院）
Causal models of agents have been used to analyse the safety aspects of machine learning systems. But identifying agents is non-trivial -- often the causal model is just assumed by the modeler without much justification -- and modelling failures can lead to mistakes in the safety analysis. This paper proposes the first formal causal definition of agents -- roughly that agents are systems that would adapt their policy if their actions influenced the world in a different way. From this we derive the first causal discovery algorithm for discovering agents from empirical data, and give algorithms …
Faced with data-driven policies, individuals will manipulate their features to obtain favorable decisions. While earlier works cast these manipulations as undesirable gaming, recent works have adopted a more nuanced causal framing in which manipulations can improve outcomes of interest, and setting coherent mechanisms requires accounting for both predictive accuracy and improvement of the outcome. Typically, these works focus on known causal graphs, consisting only of an outcome and its parents. In this paper, we introduce a general framework in which an outcome and n observed features are rel…
German Aerospace Center（德国航空航天中心）；Institute of Data Science（数据科学研究所）；Technische Universität Berlin（柏林工业大学）
The paper introduces a novel conditional independence (CI) based method for linear and nonlinear, lagged and contemporaneous causal discovery from observational time series in the causally sufficient case. Existing CI-based methods such as the PC algorithm and also common methods from other frameworks suffer from low recall and partially inflated false positives for strong autocorrelation which is an ubiquitous challenge in time series. The novel method, PCMCI$^+$, extends PCMCI [Runge et al., 2019b] to include discovery of contemporaneous links. PCMCI$^+$ improves the reliability of CI tests …
A tutorial on discovering and quantifying the effect of latent causal sources of multimodal EHR data
Department of Biomedical Informatics Vanderbilt University Medical Center（生物医学信息学系范德堡大学医学中心）；Department of Biomedical Informatics University of Pittsburgh（生物医学信息学系匹兹堡大学）；Departments of Medicine & Biomedical Informatics Vanderbilt University Medical Center（医学与生物医学信息学系范德堡大学医学中心）；Departments of Biomedical Informatics & Computer Science Vanderbilt University Medical Center & Vanderbilt University（生物医学信息学与计算机科学系范德堡大学医学中心及范德堡大学）
Applied AI Lab（应用人工智能实验室）；University of Oxford（牛津大学）；MPI for Intelligent Systems（马克斯·普朗克智能系统研究所）
Latent world models allow agents to reason about complex environments with high-dimensional observations. However, adapting to new environments and effectively leveraging previous knowledge remain significant challenges. We present variational causal dynamics (VCD), a structured world model that exploits the invariance of causal mechanisms across environments to achieve fast and modular adaptation. By causally factorising a transition model, VCD is able to identify reusable components across different environments. This is achieved by combining causal discovery and variational inference to lea…
Causality for Earth Science -- A Review on Time-series and Spatiotemporal Causality Methods
University of Maryland Baltimore County（马里兰大学巴尔的摩分校）；NSF HDR Institute for Harnessing Data and Model Revolution in the Polar Regions (iHARP)（NSF HDR极地地区数据与模型变革研究所）；University of North Texas（北得克萨斯大学）
Modern disease mapping draws upon a wealth of high resolution spatial data products reflecting environmental and/or socioeconomic factors as covariates, or `features', within a geostatistical framework to improve predictions of disease risk. Feature selection is an important step in building these models, helping to reduce overfitting and computational complexity, and to improve model interpretability. Selecting only features that have a causal relationship with the response variable could potentially improve predictions and generalisability, but identifying these causal features from non-inte…
Beyond Stationarity in Time Series: Discovering Causal Structures and Latent Regimes via Markov Blankets
Univ. Grenoble Alpes（格勒诺布尔大学）；CNRS（法国国家科学研究中心）；Grenoble INP（格勒诺布尔国立高等工程学院）；LIG（信息与信号处理实验室）；Sorbonne Université（索邦大学）；INSERM（法国国家健康与医学研究院）；Institut Pierre Louis d’Epidémiologie et de Santé Publique（皮埃尔·路易流行病学与公共卫生研究所）
We present PredRNN++, an improved recurrent network for video predictive learning. In pursuit of a greater spatiotemporal modeling capability, our approach increases the transition depth between adjacent states by leveraging a novel recurrent unit, which is named Causal LSTM for re-organizing the spatial and temporal memories in a cascaded mechanism. However, there is still a dilemma in video predictive learning: increasingly deep-in-time models have been designed for capturing complex variations, while introducing more difficulties in the gradient back-propagation. To alleviate this undesirab…
Unifying Physics- and Data-Driven Modeling via Novel Causal Spatiotemporal Graph Neural Network for Interpretable Epidemic Forecasting
Frankfurt Institute for Advanced Studies（法兰克福高等研究院）；Goethe Universität Frankfurt（法兰克福大学）；Xidian-FIAS International Joint Research Center（西电-法兰克福高等研究院国际联合研究中心）；School of Science and Engineering, The Chinese University of Hong Kong（香港中文大学（深圳）理工学院）；GSI Helmholtzzentrum für Schwerionenforschung GmbH（GSI亥姆霍兹重离子研究中心）
This paper presents a novel data-driven technique based on the spatiotemporal pattern network (STPN) for energy/power prediction for complex dynamical systems. Built on symbolic dynamic filtering, the STPN framework is used to capture not only the individual system characteristics but also the pair-wise causal dependencies among different sub-systems. For quantifying the causal dependency, a mutual information based metric is presented. An energy prediction approach is subsequently proposed based on the STPN framework. For validating the proposed scheme, two case studies are presented, one inv…
Reconstructing the causal relationships behind the phenomena we observe is a fundamental challenge in all areas of science. Discovering causal relationships through experiments is often infeasible, unethical, or expensive in complex systems. However, increases in computational power allow us to process the ever-growing amount of data that modern science generates, leading to an emerging interest in the causal discovery problem from observational data. This work evaluates the LPCMCI algorithm, which aims to find generators compatible with a multi-dimensional, highly autocorrelated time series w…
University of Oxford（牛津大学）；The Alan Turing Institute（艾伦图灵研究所）；University College London（伦敦大学学院）
Discovering the causal effect of a decision is critical to nearly all forms of decision-making. In particular, it is a key quantity in drug development, in crafting government policy, and when implementing a real-world machine learning system. Given only observational data, confounders often obscure the true causal effect. Luckily, in some cases, it is possible to recover the causal effect by using certain observed variables to adjust for the effects of confounders. However, without access to the true causal model, finding this adjustment requires brute-force search. In this work, we present a…
Institute of Scientific and Industrial Research, Osaka University（大阪大学产业科学研究所）；Graduate School of Science, Osaka University（大阪大学理学研究科）；Graduate School of Informatics, Kyoto University（京都大学信息学研究科）
Discovering causal relations among observed variables in a given data set is a major objective in studies of statistics and artificial intelligence. Recently, some techniques to discover a unique causal model have been explored based on non-Gaussianity of the observed data distribution. However, most of these are limited to continuous data. In this paper, we present a novel causal model for binary data and propose an efficient new approach to deriving the unique causal model governing a given binary data set under skew distributions of external binary noises. Experimental evaluation shows exce…
University of Tübingen（蒂宾根大学）；University of Hohenheim（霍恩海姆大学）
Knowledge about the hidden factors that determine particular system dynamics is crucial for both explaining them and pursuing goal-directed interventions. Inferring these factors from time series data without supervision remains an open challenge. Here, we focus on spatiotemporal processes, including wave propagation and weather dynamics, for which we assume that universal causes (e.g. physics) apply throughout space and time. A recently introduced DIstributed SpatioTemporal graph Artificial Neural network Architecture (DISTANA) is used and enhanced to learn such processes, requiring fewer par…
Discovering and Reasoning of Causality in the Hidden World with Large Language Models
TMLR Group, Hong Kong Baptist University（香港 Baptist 大学 TMLR 组）；Mohamed bin Zayed University of Artificial Intelligence（Mohamed bin Zayed 人工智能大学）；Department of Philosophy, Carnegie Mellon University（哲学系，卡内基梅隆大学）；School of Computer Science, The University of Sydney（悉尼大学计算机科学学院）；School of Mathematics and Statistics, The University of Melbourne（墨尔本大学数学与统计学学院）；The Chinese University of Hong Kong（香港中文大学）
Spotify（声田）；University College London（伦敦大学学院）；Babylon Health（巴比伦健康）
The discovery of causal relationships is a fundamental problem in science and medicine. In recent years, many elegant approaches to discovering causal relationships between two variables from observational data have been proposed. However, most of these deal only with purely directed causal relationships and cannot detect latent common causes. Here, we devise a general heuristic which takes a causal discovery algorithm that can only distinguish purely directed causal relations and modifies it to also detect latent common causes. We apply our method to two directed causal discovery algorithms, …
Babylon Health（巴比伦健康）；University College London（伦敦大学学院）
Causal knowledge is vital for effective reasoning in science, as causal relations, unlike correlations, allow one to reason about the outcomes of interventions. Algorithms that can discover causal relations from observational data are based on the assumption that all variables have been jointly measured in a single dataset. In many cases this assumption fails. Previous approaches to overcoming this shortcoming devised algorithms that returned all joint causal structures consistent with the conditional independence information contained in each individual dataset. But, as conditional independen…
We propose a new method of discovering causal relationships in temporal data based on the notion of causal compression. To this end, we adopt the Pearlian graph setting and the directed information as an information theoretic tool for quantifying causality. We introduce chain rule for directed information and use it to motivate causal sparsity. We show two applications of the proposed method: causal time series segmentation which selects time points capturing the incoming and outgoing causal flow between time points belonging to different signals, and causal bipartite graph recovery. We prove …
University of Oxford（牛津大学）；Department of Statistics（统计系）；DeepMind（DeepMind（深度思维））
Discovering the causal structure among a set of variables is a fundamental problem in many areas of science. In this paper, we propose Kernel Conditional Deviance for Causal Inference (KCDC) a fully nonparametric causal discovery method based on purely observational data. From a novel interpretation of the notion of asymmetry between cause and effect, we derive a corresponding asymmetry measure using the framework of reproducing kernel Hilbert spaces. Based on this, we propose three decision rules for causal discovery. We demonstrate the wide applicability of our method across a range of diver…
Huazhong University of Science and Technology（华中科技大学）；KTH Royal Institute of Technology（瑞典皇家理工学院）；Georgia Institute of Technology（佐治亚理工学院）；Wuhan University（武汉大学）；University of Cambridge（剑桥大学）；University of Luxembourg（卢森堡大学）；Weill Cornell Medical College（威尔康奈尔医学院）
The study presents a general framework for discovering underlying Partial Differential Equations (PDEs) using measured spatiotemporal data. The method, called Sparse Spatiotemporal System Discovery ($\text{S}^3\text{d}$), decides which physical terms are necessary and which can be removed (because they are physically negligible in the sense that they do not affect the dynamics too much) from a pool of candidate functions. The method is built on the recent development of Sparse Bayesian Learning; which enforces the sparsity in the to-be-identified PDEs, and therefore can balance the model compl…
ETH Zürich（苏黎世联邦理工学院）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；IBM Research Zürich（苏黎世IBM研究院）
Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experi…
University of Amsterdam（阿姆斯特丹大学）；Microsoft Research Cambridge（微软剑桥研究院）
We consider the problem of discovering causal relations from independence constraints selection bias in addition to confounding is present. While the seminal FCI algorithm is sound and complete in this setup, no criterion for the causal interpretation of its output under selection bias is presently known. We focus instead on local patterns of independence relations, where we find no sound method for only three variable that can include background knowledge. Y-Structure patterns are shown to be sound in predicting causal relations from data under selection bias, where cycles may be present. We …
Bureau of Economic Geology, Jackson School of Geosciences, The University of Texas at Austin（德克萨斯大学奥斯汀分校杰克逊地球科学学院经济地质局）
A fundamental problem in geophysical modeling is related to the identification and approximation of causal structures among physical processes. However, resolving the bidirectional mappings between physical parameters and model state variables (i.e., solving the forward and inverse problems) is challenging, especially when parameter dimensionality is high. Deep learning has opened a new door toward knowledge representation and complex pattern identification. In particular, the recently introduced generative adversarial networks (GANs) hold strong promises in learning cross-domain mappings for …
Experimental data is often affected by uncontrolled variables that make analysis and interpretation difficult. For spatiotemporal systems, this problem is further exacerbated by their intricate dynamics. Modern machine learning methods are particularly well-suited for analyzing and modeling complex datasets, but to be effective in science, the result needs to be interpretable. We demonstrate an unsupervised learning technique for extracting interpretable physical parameters from noisy spatiotemporal data and for building a transferable model of the system. In particular, we implement a physics…
Discovering the Precursors of Traffic Breakdowns Using Spatiotemporal Graph Attribution Networks
Department of Civil Engineering and Engineering Mechanics, Columbia University School of Economics, Minzu University of China（土木工程与工程力学系，哥伦比亚大学经济学院，中国民族大学）；Vehicle and Mobility Systems Department, Argonne National Laboratory（车辆与移动系统部，阿贡国家实验室）；School of Sustainable Engineering and the Built Environment, Arizona State University（可持续工程与环境学院，亚利桑那州立大学）
Imperial College London（帝国理工学院）；IBM Research Europe（IBM欧洲研究院）；Trinity College Dublin（都柏林圣三一学院）；University of Rostock（罗斯托克大学）
Many large-scale applications can be elegantly represented using graph structures. Their scalability, however, is often limited by the domain knowledge required to apply them. To address this problem, we propose a novel Causal Temporal Graph Convolutional Neural Network (CTGCN). Our CTGCN architecture is based on a causal discovery mechanism, and is capable of discovering the underlying causal processes. The major advantages of our approach stem from its ability to overcome computational scalability problems with a divide and conquer technique, and from the greater explainability of prediction…
Differentiable Causal Discovery For Latent Hierarchical Causal Models
University of California San Diego（加利福尼亚大学圣迭戈分校）；Carnegie Mellon University（卡内基梅隆大学）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Discovering causal models from observational and interventional data is an important first step preceding what-if analysis or counterfactual reasoning. As has been shown before, the direction of pairwise causal relations can, under certain conditions, be inferred from observational data via standard gradient-boosted classifiers (GBC) using carefully engineered statistical features. In this paper we apply deep convolutional neural networks (CNNs) to this problem by plotting attribute pairs as 2-D scatter plots that are fed to the CNN as images. We evaluate our approach on the 'Cause- Effect Pai…
Since December 2019, the world has been witnessing the gigantic effect of an unprecedented global pandemic called Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) - COVID-19. So far, 38,619,674 confirmed cases and 1,093,522 confirmed deaths due to COVID-19 have been reported. In the United States (US), the cases and deaths are recorded as 7,833,851 and 215,199. Several timely researches have discussed the local and global effects of the confounding factors on COVID-19 casualties in the US. However, most of these studies considered little about the time varying associations between an…
The problem of broad practical interest in spatiotemporal data analysis, i.e., discovering interpretable dynamic patterns from spatiotemporal data, is studied in this paper. Towards this end, we develop a time-varying reduced-rank vector autoregression (VAR) model whose coefficient matrices are parameterized by low-rank tensor factorization. Benefiting from the tensor factorization structure, the proposed model can simultaneously achieve model compression and pattern discovery. In particular, the proposed model allows one to characterize nonstationarity and time-varying system behaviors underl…
University of Melbourne（墨尔本大学）；University of Tartu（塔尔图大学）
This paper proposes an approach to analyze an event log of a business process in order to generate case-level recommendations of treatments that maximize the probability of a given outcome. Users classify the attributes in the event log into controllable and non-controllable, where the former correspond to attributes that can be altered during an execution of the process (the possible treatments). We use an action rule mining technique to identify treatments that co-occur with the outcome under some conditions. Since action rules are generated based on correlation rather than causation, we the…
Epileptic seizure activity shows complicated dynamics in both space and time. To understand the evolution and propagation of seizures spatially extended sets of data need to be analysed. We have previously described an efficient filtering scheme using variational Laplace that can be used in the Dynamic Causal Modelling (DCM) framework [Friston, 2003] to estimate the temporal dynamics of seizures recorded using either invasive or non-invasive electrical recordings (EEG/ECoG). Spatiotemporal dynamics are modelled using a partial differential equation -- in contrast to the ordinary differential e…
Discovering causal effects is at the core of scientific investigation but remains challenging when only observational data is available. In practice, causal networks are difficult to learn and interpret, and limited to relatively small datasets. We report a more reliable and scalable causal discovery method (iMIIC), based on a general mutual information supremum principle, which greatly improves the precision of inferred causal relations while distinguishing genuine causes from putative and latent causal effects. We showcase iMIIC on synthetic and real-life healthcare data from 396,179 breast …
Anti-discrimination is an increasingly important task in data science. In this paper, we investigate the problem of discovering both direct and indirect discrimination from the historical data, and removing the discriminatory effects before the data is used for predictive analysis (e.g., building classifiers). We make use of the causal network to capture the causal structure of the data. Then we model direct and indirect discrimination as the path-specific effects, which explicitly distinguish the two types of discrimination as the causal effects transmitted along different paths in the networ…
Amazon Research Tübingen（亚马逊图宾根研究院）；Monash University（莫纳什大学）；CISPA Helmholtz Center for Information Security（CISPA亥姆霍兹信息安全中心）
We study the problem of deriving policies, or rules, that when enacted on a complex system, cause a desired outcome. Absent the ability to perform controlled experiments, such rules have to be inferred from past observations of the system's behaviour. This is a challenging problem for two reasons: First, observational effects are often unrepresentative of the underlying causal effect because they are skewed by the presence of confounding factors. Second, naive empirical estimations of a rule's effect have a high variance, and, hence, their maximisation can lead to random results. To address th…
