arXiv subjects

Kui Yu

Publications and source records attributed to Kui Yu.

At least 37 records · Page 2Linked to original sources

arXiv2022

Explanatory causal effects for model agnostic explanations

This paper studies the problem of estimating the contributions of features to the prediction of a specific instance by a machine learning model and the overall contribution of a feature to the model. The causal effect of a feature (variable) on the predicted outcome reflects the contribution of the feature to a prediction very well. A challenge is that most existing causal effects cannot be estimated from data without a known causal graph. In this paper, we define an explanatory causal effect based on a hypothetical ideal experiment. The definition brings several benefits to model agnostic explanations. First, explanations are transparent and have causal meanings. Second, the explanatory causal effect estimation can be data driven. Third, the causal effects provide both a local explanation for a specific prediction and a global explanation showing the overall importance of a feature in a predictive model. We further propose a method using individual and combined variables based on explanatory causal effects for explanations. We show the definition and the method work with experiments on some real-world data sets.

cs.LG↗

arXiv2022

Discovering Ancestral Instrumental Variables for Causal Inference from Observational Data

Instrumental variable (IV) is a powerful approach to inferring the causal effect of a treatment on an outcome of interest from observational data even when there exist latent confounders between the treatment and the outcome. However, existing IV methods require that an IV is selected and justified with domain knowledge. An invalid IV may lead to biased estimates. Hence, discovering a valid IV is critical to the applications of IV methods. In this paper, we study and design a data-driven algorithm to discover valid IVs from data under mild assumptions. We develop the theory based on partial ancestral graphs (PAGs) to support the search for a set of candidate Ancestral IVs (AIVs), and for each possible AIV, the identification of its conditioning set. Based on the theory, we propose a data-driven algorithm to discover a pair of IVs from data. The experiments on synthetic and real-world datasets show that the developed IV discovery algorithm estimates accurate estimates of causal effects in comparison with the state-of-the-art IV based causal effect estimators.

cs.AI↗

arXiv2021

Feature Selection for Efficient Local-to-Global Bayesian Network Structure Learning

Local-to-global learning approach plays an essential role in Bayesian network (BN) structure learning. Existing local-to-global learning algorithms first construct the skeleton of a DAG (directed acyclic graph) by learning the MB (Markov blanket) or PC (parents and children) of each variable in a data set, then orient edges in the skeleton. However, existing MB or PC learning methods are often computationally expensive especially with a large-sized BN, resulting in inefficient local-to-global learning algorithms. To tackle the problem, in this paper, we develop an efficient local-to-global learning approach using feature selection. Specifically, we first analyze the rationale of the well-known Minimum-Redundancy and Maximum-Relevance (MRMR) feature selection approach for learning a PC set of a variable. Based on the analysis, we propose an efficient F2SL (feature selection-based structure learning) approach to local-to-global BN structure learning. The F2SL approach first employs the MRMR approach to learn a DAG skeleton, then orients edges in the skeleton. Employing independence tests or score functions for orienting edges, we instantiate the F2SL approach into two new algorithms, F2SL-c (using independence tests) and F2SL-s (using score functions). Compared to the state-of-the-art local-to-global BN learning algorithms, the experiments validated that the proposed algorithms in this paper are more efficient and provide competitive structure learning quality than the compared algorithms.

cs.LG↗

arXiv2021

Any Part of Bayesian Network Structure Learning

We study an interesting and challenging problem, learning any part of a Bayesian network (BN) structure. In this challenge, it will be computationally inefficient using existing global BN structure learning algorithms to find an entire BN structure to achieve the part of a BN structure in which we are interested. And local BN structure learning algorithms encounter the false edge orientation problem when they are directly used to tackle this challenging problem. In this paper, we first present a new concept of Expand-Backtracking to explain why local BN structure learning methods have the false edge orientation problem, then propose APSL, an efficient and accurate Any Part of BN Structure Learning algorithm. Specifically, APSL divides the V-structures in a Markov blanket (MB) into two types: collider V-structure and non-collider V-structure, then it starts from a node of interest and recursively finds both collider V-structures and non-collider V-structures in the found MBs, until the part of a BN structure in which we are interested are oriented. To improve the efficiency of APSL, we further design the APSL-FS algorithm using Feature Selection, APSL-FS. Using six benchmark BNs, the extensive experiments have validated the efficiency and accuracy of our methods.

cs.LG↗

arXiv2021

A general framework for causal classification

In many applications, there is a need to predict the effect of an intervention on different individuals from data. For example, which customers are persuadable by a product promotion? which patients should be treated with a certain type of treatment? These are typical causal questions involving the effect or the change in outcomes made by an intervention. The questions cannot be answered with traditional classification methods as they only use associations to predict outcomes. For personalised marketing, these questions are often answered with uplift modelling. The objective of uplift modelling is to estimate causal effect, but its literature does not discuss when the uplift represents causal effect. Causal heterogeneity modelling can solve the problem, but its assumption of unconfoundedness is untestable in data. So practitioners need guidelines in their applications when using the methods. In this paper, we use causal classification for a set of personalised decision making problems, and differentiate it from classification. We discuss the conditions when causal classification can be resolved by uplift (and causal heterogeneity) modelling methods. We also propose a general framework for causal classification, by using off-the-shelf supervised methods for flexible implementations. Experiments have shown two instantiations of the framework work for causal classification and for uplift (causal heterogeneity) modelling, and are competitive with the other uplift (causal heterogeneity) modelling methods.

cs.LG↗

arXiv2021

Causal Learner: A Toolbox for Causal Structure and Markov Blanket Learning

Causal Learner is a toolbox for learning causal structure and Markov blanket (MB) from data. It integrates functions for generating simulated Bayesian network data, a set of state-of-the-art global causal structure learning algorithms, a set of state-of-the-art local causal structure learning algorithms, a set of state-of-the-art MB learning algorithms, and functions for evaluating algorithms. The data generation part of Causal Learner is written in R, and the rest of Causal Learner is written in MATLAB. Causal Learner aims to provide researchers and practitioners with an open-source platform for causal learning from data and for the development and evaluation of new causal learning algorithms. The Causal Learner project is available at http://bigdata.ahu.edu.cn/causal-learner.

cs.LG↗

arXiv2021

A Local Similarity-Preserving Framework for Nonlinear Dimensionality Reduction with Neural Networks

Real-world data usually have high dimensionality and it is important to mitigate the curse of dimensionality. High-dimensional data are usually in a coherent structure and make the data in relatively small true degrees of freedom. There are global and local dimensionality reduction methods to alleviate the problem. Most of existing methods for local dimensionality reduction obtain an embedding with the eigenvalue or singular value decomposition, where the computational complexities are very high for a large amount of data. Here we propose a novel local nonlinear approach named Vec2vec for general purpose dimensionality reduction, which generalizes recent advancements in embedding representation learning of words to dimensionality reduction of matrices. It obtains the nonlinear embedding using a neural network with only one hidden layer to reduce the computational complexity. To train the neural network, we build the neighborhood similarity graph of a matrix and define the context of data points by exploiting the random walk properties. Experiments demenstrate that Vec2vec is more efficient than several state-of-the-art local dimensionality reduction methods in a large number of high-dimensional data. Extensive experiments of data classification and clustering on eight real datasets show that Vec2vec is better than several classical dimensionality reduction methods in the statistical hypothesis test, and it is competitive with recently developed state-of-the-art UMAP.

cs.LG↗

arXiv2021

Towards Efficient Local Causal Structure Learning

Local causal structure learning aims to discover and distinguish direct causes (parents) and direct effects (children) of a variable of interest from data. While emerging successes have been made, existing methods need to search a large space to distinguish direct causes from direct effects of a target variable T. To tackle this issue, we propose a novel Efficient Local Causal Structure learning algorithm, named ELCS. Specifically, we first propose the concept of N-structures, then design an efficient Markov Blanket (MB) discovery subroutine to integrate MB learning with N-structures to learn the MB of T and simultaneously distinguish direct causes from direct effects of T. With the proposed MB subroutine, ELCS starts from the target variable, sequentially finds MBs of variables connected to the target variable and simultaneously constructs local causal structures over MBs until the direct causes and direct effects of the target variable have been distinguished. Using eight Bayesian networks the extensive experiments have validated that ELCS achieves better accuracy and efficiency than the state-of-the-art algorithms.

cs.LG↗

arXiv2021

Towards Efficient Local Causal Structure Learning

Local causal structure learning aims to discover and distinguish direct causes (parents) and direct effects (children) of a variable of interest from data. While emerging successes have been made, existing methods need to search a large space to distinguish direct causes from direct effects of a target variable \emph{T}. To tackle this issue, we propose a novel Efficient Local Causal Structure learning algorithm, named ELCS. Specifically, we first propose the concept of N-structures, then design an efficient Markov Blanket (MB) discovery subroutine to integrate MB learning with N-structures to learn the MB of \emph{T} and simultaneously distinguish direct causes from direct effects of \emph{T}. With the proposed MB subroutine, ELCS starts from the target variable, sequentially finds MBs of variables connected to the target variable and simultaneously constructs local causal structures over MBs until the direct causes and direct effects of the target variable have been distinguished. Using eight Bayesian networks the extensive experiments have validated that ELCS achieves better accuracy and efficiency than the state-of-the-art algorithms.

cs.AI↗

arXiv2020

Causal query in observational data with hidden variables

This paper discusses the problem of causal query in observational data with hidden variables, with the aim of seeking the change of an outcome when "manipulating" a variable while given a set of plausible confounding variables which affect the manipulated variable and the outcome. Such an "experiment on data" to estimate the causal effect of the manipulated variable is useful for validating an experiment design using historical data or for exploring confounders when studying a new relationship. However, existing data-driven methods for causal effect estimation face some major challenges, including poor scalability with high dimensional data, low estimation accuracy due to heuristics used by the global causal structure learning algorithms, and the assumption of causal sufficiency when hidden variables are inevitable in data. In this paper, we develop a theorem for using local search to find a superset of the adjustment (or confounding) variables for causal effect estimation from observational data under a realistic pretreatment assumption. The theorem ensures that the unbiased estimate of causal effect is included in the set of causal effects estimated by the superset of adjustment variables. Based on the developed theorem, we propose a data-driven algorithm for causal query. Experiments show that the proposed algorithm is faster and produces better causal effect estimation than an existing data-driven causal effect estimation method with hidden variables. The causal effects estimated by the proposed algorithm are as accurate as those by the state-of-the-art methods using domain knowledge.

cs.AI↗

arXiv2020

Learning causal representations for robust domain adaptation

Domain adaptation solves the learning problem in a target domain by leveraging the knowledge in a relevant source domain. While remarkable advances have been made, almost all existing domain adaptation methods heavily require large amounts of unlabeled target domain data for learning domain invariant representations to achieve good generalizability on the target domain. In fact, in many real-world applications, target domain data may not always be available. In this paper, we study the cases where at the training phase the target domain data is unavailable and only well-labeled source domain data is available, called robust domain adaptation. To tackle this problem, under the assumption that causal relationships between features and the class variable are robust across domains, we propose a novel Causal AutoEncoder (CAE), which integrates deep autoencoder and causal structure learning into a unified model to learn causal representations only using data from a single source domain. Specifically, a deep autoencoder model is adopted to learn low-dimensional representations, and a causal structure learning model is designed to separate the low-dimensional representations into two groups: causal representations and task-irrelevant representations. Using three real-world datasets the extensive experiments have validated the effectiveness of CAE compared to eleven state-of-the-art methods.

cs.LG↗

arXiv2020

Towards unique and unbiased causal effect estimation from data with hidden variables

Causal effect estimation from observational data is a crucial but challenging task. Currently, only a limited number of data-driven causal effect estimation methods are available. These methods either provide only a bound estimation of the causal effect of a treatment on the outcome, or generate a unique estimation of the causal effect, but making strong assumptions on data and having low efficiency. In this paper, we identify a practical problem setting and propose an approach to achieving unique and unbiased estimation of causal effects from data with hidden variables. For the approach, we have developed the theorems to support the discovery of the proper covariate sets for confounding adjustment (adjustment sets). Based on the theorems, two algorithms are proposed for finding the proper adjustment sets from data with hidden variables to obtain unbiased and unique causal effect estimation. Experiments with synthetic datasets generated using five benchmark Bayesian networks and four real-world datasets have demonstrated the efficiency and effectiveness of the proposed algorithms, indicating the practicability of the identified problem setting and the potential of the proposed approach in real-world applications.

stat.ME↗

arXiv2020

Atomic structure of CdS magic-size clusters by X-ray absorption spectroscopy

Magic-size clusters are ultra-small colloidal semiconductor systems that are intensively studied due to their monodisperse nature and sharp UV-vis absorption peak compared with regular quantum dots. However, the small size of such clusters (<2 nm), and the large surface-to-bulk ratio significantly limit characterisation techniques that can be utilised. Here we demonstrate how a combination of EXAFS and XANES can be used to obtain information about sample stoichiometry and cluster symmetry. Investigating two types of clusters that show sharp UV-vis absorption peaks at 311 nm and 322 nm, we found that both samples possess approximately 2:1 Cd:S ratio and have similar nearest-neighbour structural arrangements. However, both samples demonstrate a significant departure from the tetrahedral structural arrangement, with an average bond angle determined to be around 106.1 degree showing a bi-fold bond angle distribution. Our results suggest that both samples are quazi-isomers. Their core structure has identical chemical composition but a different atomic arrangement with distinct bond angle distributions.

cond-mat.mtrl-sci↗

arXiv2019

Causality-based Feature Selection: Methods and Evaluations

Feature selection is a crucial preprocessing step in data analytics and machine learning. Classical feature selection algorithms select features based on the correlations between predictive features and the class variable and do not attempt to capture causal relationships between them. It has been shown that the knowledge about the causal relationships between features and the class variable has potential benefits for building interpretable and robust prediction models, since causal relationships imply the underlying mechanism of a system. Consequently, causality-based feature selection has gradually attracted greater attentions and many algorithms have been proposed. In this paper, we present a comprehensive review of recent advances in causality-based feature selection. To facilitate the development of new algorithms in the research area and make it easy for the comparisons between new methods and existing ones, we develop the first open-source package, called CausalFS, which consists of most of the representative causality-based feature selection algorithms (available at https://github.com/kuiy/CausalFS). Using CausalFS, we conduct extensive experiments to compare the representative algorithms with both synthetic and real-world data sets. Finally, we discuss some challenging problems to be tackled in future causality-based feature selection research.

cs.LG↗

arXiv2018

A Unified View of Causal and Non-causal Feature Selection

In this paper, we aim to develop a unified view of causal and non-causal feature selection methods. The unified view will fill in the gap in the research of the relation between the two types of methods. Based on the Bayesian network framework and information theory, we first show that causal and non-causal feature selection methods share the same objective. That is to find the Markov blanket of a class attribute, the theoretically optimal feature set for classification. We then examine the assumptions made by causal and non-causal feature selection methods when searching for the optimal feature set, and unify the assumptions by mapping them to the restrictions on the structure of the Bayesian network model of the studied problem. We further analyze in detail how the structural assumptions lead to the different levels of approximations employed by the methods in their search, which then result in the approximations in the feature sets found by the methods with respect to the optimal feature set. With the unified view, we are able to interpret the output of non-causal methods from a causal perspective and derive the error bounds of both types of methods. Finally, we present practical understanding of the relation between causal and non-causal methods using extensive experiments with synthetic data and various types of real-word data.

cs.AI↗

arXiv2018

X-ray total scattering study of regular and magic-size nanoclusters of cadmium sulphide

Four kinds of magic-size CdS clusters and two different regular CdS quantum dots have been studied by x-ray total scattering technique and pair distribution function method. Results for the regular CdS quantum dots could be modelled as a mixed phase of atomic structures based on the two bulk crystalline phases, which is interpreted as representing the effects of stacking disorder. However, the results for the magic-size clusters were significantly different. On one hand, the short-range features in the pair distribution function reflect the bulk, indicating that these structures are based on the same tetrahedral coordination found in the bulk phases (and therefore excluding new types of structures such as cage-like arrangements of atoms). But on the other hand, the longer- range atomic structure clearly does not reflect the layer structures found in the bulk and the regular quantum dots. We compare the effects of two ligands, phenylacetic acid and oleic acid, showing that in two cases the ligand has little effect on the atomic structure of the magic-size nanocluster and in another it has a significant effect.

cond-mat.mes-hall↗

arXiv2018

Discovering Markov Blanket from Multiple interventional Datasets

In this paper, we study the problem of discovering the Markov blanket (MB) of a target variable from multiple interventional datasets. Datasets attained from interventional experiments contain richer causal information than passively observed data (observational data) for MB discovery. However, almost all existing MB discovery methods are designed for finding MBs from a single observational dataset. To identify MBs from multiple interventional datasets, we face two challenges: (1) unknown intervention variables; (2) nonidentical data distributions. To tackle the challenges, we theoretically analyze (a) under what conditions we can find the correct MB of a target variable, and (b) under what conditions we can identify the causes of the target variable via discovering its MB. Based on the theoretical analysis, we propose a new algorithm for discovering MBs from multiple interventional datasets, and present the conditions/assumptions which assure the correctness of the algorithm. To our knowledge, this work is the first to present the theoretical analyses about the conditions for MB discovery in multiple interventional datasets and the algorithm to find the MBs in relation to the conditions. Using benchmark Bayesian networks and real-world datasets, the experiments have validated the effectiveness and efficiency of the proposed algorithm in the paper.

cs.AI↗

arXiv2016

A Review on Algorithms for Constraint-based Causal Discovery

Causal discovery studies the problem of mining causal relationships between variables from data, which is of primary interest in science. During the past decades, significant amount of progresses have been made toward this fundamental data mining paradigm. Recent years, as the availability of abundant large-sized and complex observational data, the constrain-based approaches have gradually attracted a lot of interest and have been widely applied to many diverse real-world problems due to the fast running speed and easy generalizing to the problem of causal insufficiency. In this paper, we aim to review the constraint-based causal discovery algorithms. Firstly, we discuss the learning paradigm of the constraint-based approaches. Secondly and primarily, the state-of-the-art constraint-based casual inference algorithms are surveyed with the detailed analysis. Thirdly, several related open-source software packages and benchmark data repositories are briefly summarized. As a conclusion, some open problems in constraint-based causal discovery are outlined for future research.

cs.AI↗