arXiv subjects

Jiuyong Li

Publications and source records attributed to Jiuyong Li.

At least 73 records · Page 4Linked to original sources

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↗

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

Sufficient Dimension Reduction for Average Causal Effect Estimation

Having a large number of covariates can have a negative impact on the quality of causal effect estimation since confounding adjustment becomes unreliable when the number of covariates is large relative to the samples available. Propensity score is a common way to deal with a large covariate set, but the accuracy of propensity score estimation (normally done by logistic regression) is also challenged by large number of covariates. In this paper, we prove that a large covariate set can be reduced to a lower dimensional representation which captures the complete information for adjustment in causal effect estimation. The theoretical result enables effective data-driven algorithms for causal effect estimation. We develop an algorithm which employs a supervised kernel dimension reduction method to search for a lower dimensional representation for the original covariates, and then utilizes nearest neighbor matching in the reduced covariate space to impute the counterfactual outcomes to avoid large-sized covariate set problem. The proposed algorithm is evaluated on two semi-synthetic and three real-world datasets and the results have demonstrated the effectiveness of the algorithm.

stat.ME↗

arXiv2020

Computational methods for cancer driver discovery: A survey

Motivation: Uncovering the genomic causes of cancer, known as cancer driver genes, is a fundamental task in biomedical research. Cancer driver genes drive the development and progression of cancer, thus identifying cancer driver genes and their regulatory mechanism is crucial to the design of cancer treatment and intervention. Many computational methods, which take the advantages of computer science and data science, have been developed to utilise multiple types of genomic data to reveal cancer drivers and their regulatory mechanism behind cancer development and progression. Due to the complexity of the mechanistic insight of cancer genes in driving cancer and the fast development of the field, it is necessary to have a comprehensive review about the current computational methods for discovering different types of cancer drivers. Results: We survey computational methods for identifying cancer drivers from genomic data. We categorise the methods into three groups, methods for single driver identification, methods for driver module identification, and methods for identifying personalised cancer drivers. We also conduct a case study to compare the performance of the current methods. We further analyse the advantages and limitations of the current methods, and discuss the challenges and future directions of the topic. In addition, we investigate the resources for discovering and validating cancer drivers in order to provide a one-stop reference of the tools to facilitate cancer driver discovery. The ultimate goal of the paper is to help those interested in the topic to establish a solid background to carry out further research in the field.

q-bio.GN↗

arXiv2019

Linking Graph Entities with Multiplicity and Provenance

Entity linking and resolution is a fundamental database problem with applications in data integration, data cleansing, information retrieval, knowledge fusion, and knowledge-base population. It is the task of accurately identifying multiple, differing, and possibly contradicting representations of the same real-world entity in data. In this work, we propose an entity linking and resolution system capable of linking entities across different databases and mentioned-entities extracted from text data. Our entity linking/resolution solution, called Certus, uses a graph model to represent the profiles of entities. The graph model is versatile, thus, it is capable of handling multiple values for an attribute or a relationship, as well as the provenance descriptions of the values. Provenance descriptions of a value provide the settings of the value, such as validity periods, sources, security requirements, etc. This paper presents the architecture for the entity linking system, the logical, physical, and indexing models used in the system, and the general linking process. Furthermore, we demonstrate the performance of update operations of the physical storage models when the system is implemented in two state-of-the-art database management systems, HBase and Postgres.

cs.DB↗

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

An exploration of algorithmic discrimination in data and classification

Algorithmic discrimination is an important aspect when data is used for predictive purposes. This paper analyzes the relationships between discrimination and classification, data set partitioning, and decision models, as well as correlation. The paper uses real world data sets to demonstrate the existence of discrimination and the independence between the discrimination of data sets and the discrimination of classification models.

cs.CY↗

arXiv2018

FairMod - Making Predictive Models Discrimination Aware

Predictive models such as decision trees and neural networks may produce discrimination in their predictions. This paper proposes a method to post-process the predictions of a predictive model to make the processed predictions non-discriminatory. The method considers multiple protected variables together. Multiple protected variables make the problem more challenging than a simple protected variable. The method uses a well-cited discrimination metric and adapts it to allow the specification of explanatory variables, such as position, profession, education, that describe the contexts of the applications. It models the post-processing of predictions problem as a nonlinear optimization problem to find best adjustments to the predictions so that the discrimination constraints of all protected variables are all met at the same time. The proposed method is independent of classification methods. It can handle the cases that existing methods cannot handle: satisfying multiple protected attributes at the same time, allowing multiple explanatory attributes, and being independent of classification model types. An evaluation using four real world data sets shows that the proposed method is as effectively as existing methods, in addition to its extra power.

cs.AI↗

arXiv2018

Discovering Context Specific Causal Relationships

With the increasing need of personalised decision making, such as personalised medicine and online recommendations, a growing attention has been paid to the discovery of the context and heterogeneity of causal relationships. Most existing methods, however, assume a known cause (e.g. a new drug) and focus on identifying from data the contexts of heterogeneous effects of the cause (e.g. patient groups with different responses to the new drug). There is no approach to efficiently detecting directly from observational data context specific causal relationships, i.e. discovering the causes and their contexts simultaneously. In this paper, by taking the advantages of highly efficient decision tree induction and the well established causal inference framework, we propose the Tree based Context Causal rule discovery (TCC) method, for efficient exploration of context specific causal relationships from data. Experiments with both synthetic and real world data sets show that TCC can effectively discover context specific causal rules from the data.

cs.AI↗

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↗

arXiv2017

Building Diversified Multiple Trees for Classification in High Dimensional Noisy Biomedical Data

It is common that a trained classification model is applied to the operating data that is deviated from the training data because of noise. This paper demonstrates that an ensemble classifier, Diversified Multiple Tree (DMT), is more robust in classifying noisy data than other widely used ensemble methods. DMT is tested on three real world biomedical data sets from different laboratories in comparison with four benchmark ensemble classifiers. Experimental results show that DMT is significantly more accurate than other benchmark ensemble classifiers on noisy test data. We also discuss a limitation of DMT and its possible variations.

cs.LG↗

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↗

arXiv2016

A fast PC algorithm for high dimensional causal discovery with multi-core PCs

Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC algorithm, in the worst-case, is exponential to the number of nodes (variables), and thus it is inefficient when being applied to high dimensional data, e.g. gene expression datasets. On another note, the advancement of computer hardware in the last decade has resulted in the widespread availability of multi-core personal computers. There is a significant motivation for designing a parallelised PC algorithm that is suitable for personal computers and does not require end users' parallel computing knowledge beyond their competency in using the PC algorithm. In this paper, we develop parallel-PC, a fast and memory efficient PC algorithm using the parallel computing technique. We apply our method to a range of synthetic and real-world high dimensional datasets. Experimental results on a dataset from the DREAM 5 challenge show that the original PC algorithm could not produce any results after running more than 24 hours; meanwhile, our parallel-PC algorithm managed to finish within around 12 hours with a 4-core CPU computer, and less than 6 hours with a 8-core CPU computer. Furthermore, we integrate parallel-PC into a causal inference method for inferring miRNA-mRNA regulatory relationships. The experimental results show that parallel-PC helps improve both the efficiency and accuracy of the causal inference algorithm.

cs.AI↗

arXiv2015

Mining Combined Causes in Large Data Sets

In recent years, many methods have been developed for detecting causal relationships in observational data. Some of them have the potential to tackle large data sets. However, these methods fail to discover a combined cause, i.e. a multi-factor cause consisting of two or more component variables which individually are not causes. A straightforward approach to uncovering a combined cause is to include both individual and combined variables in the causal discovery using existing methods, but this scheme is computationally infeasible due to the huge number of combined variables. In this paper, we propose a novel approach to address this practical causal discovery problem, i.e. mining combined causes in large data sets. The experiments with both synthetic and real world data sets show that the proposed method can obtain high-quality causal discoveries with a high computational efficiency.

cs.AI↗

arXiv2015

ParallelPC: an R package for efficient constraint based causal exploration

Discovering causal relationships from data is the ultimate goal of many research areas. Constraint based causal exploration algorithms, such as PC, FCI, RFCI, PC-simple, IDA and Joint-IDA have achieved significant progress and have many applications. A common problem with these methods is the high computational complexity, which hinders their applications in real world high dimensional datasets, e.g gene expression datasets. In this paper, we present an R package, ParallelPC, that includes the parallelised versions of these causal exploration algorithms. The parallelised algorithms help speed up the procedure of experimenting big datasets and reduce the memory used when running the algorithms. The package is not only suitable for super-computers or clusters, but also convenient for researchers using personal computers with multi core CPUs. Our experiment results on real world datasets show that using the parallelised algorithms it is now practical to explore causal relationships in high dimensional datasets with thousands of variables in a single multicore computer. ParallelPC is available in CRAN repository at https://cran.rproject.org/web/packages/ParallelPC/index.html.

cs.AI↗