arXiv subjects

Thuc Duy Le

Publications and source records attributed to Thuc Duy Le.

36 records · Page 2Linked to original sources

arXiv2023

Conditional Instrumental Variable Regression with Representation Learning for Causal Inference

This paper studies the challenging problem of estimating causal effects from observational data, in the presence of unobserved confounders. The two-stage least square (TSLS) method and its variants with a standard instrumental variable (IV) are commonly used to eliminate confounding bias, including the bias caused by unobserved confounders, but they rely on the linearity assumption. Besides, the strict condition of unconfounded instruments posed on a standard IV is too strong to be practical. To address these challenging and practical problems of the standard IV method (linearity assumption and the strict condition), in this paper, we use a conditional IV (CIV) to relax the unconfounded instrument condition of standard IV and propose a non-linear CIV regression with Confounding Balancing Representation Learning, CBRL.CIV, for jointly eliminating the confounding bias from unobserved confounders and balancing the observed confounders, without the linearity assumption. We theoretically demonstrate the soundness of CBRL.CIV. Extensive experiments on synthetic and two real-world datasets show the competitive performance of CBRL.CIV against state-of-the-art IV-based estimators and superiority in dealing with the non-linear situation.

cs.LG↗

arXiv2023

Learning Conditional Instrumental Variable Representation for Causal Effect Estimation

One of the fundamental challenges in causal inference is to estimate the causal effect of a treatment on its outcome of interest from observational data. However, causal effect estimation often suffers from the impacts of confounding bias caused by unmeasured confounders that affect both the treatment and the outcome. The instrumental variable (IV) approach is a powerful way to eliminate the confounding bias from latent confounders. However, the existing IV-based estimators require a nominated IV, and for a conditional IV (CIV) the corresponding conditioning set too, for causal effect estimation. This limits the application of IV-based estimators. In this paper, by leveraging the advantage of disentangled representation learning, we propose a novel method, named DVAE.CIV, for learning and disentangling the representations of CIV and the representations of its conditioning set for causal effect estimations from data with latent confounders. Extensive experimental results on both synthetic and real-world datasets demonstrate the superiority of the proposed DVAE.CIV method against the existing causal effect estimators.

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arXiv2023

Linking a predictive model to causal effect estimation

A predictive model makes outcome predictions based on some given features, i.e., it estimates the conditional probability of the outcome given a feature vector. In general, a predictive model cannot estimate the causal effect of a feature on the outcome, i.e., how the outcome will change if the feature is changed while keeping the values of other features unchanged. This is because causal effect estimation requires interventional probabilities. However, many real world problems such as personalised decision making, recommendation, and fairness computing, need to know the causal effect of any feature on the outcome for a given instance. This is different from the traditional causal effect estimation problem with a fixed treatment variable. This paper first tackles the challenge of estimating the causal effect of any feature (as the treatment) on the outcome w.r.t. a given instance. The theoretical results naturally link a predictive model to causal effect estimations and imply that a predictive model is causally interpretable when the conditions identified in the paper are satisfied. The paper also reveals the robust property of a causally interpretable model. We use experiments to demonstrate that various types of predictive models, when satisfying the conditions identified in this paper, can estimate the causal effects of features as accurately as state-of-the-art causal effect estimation methods. We also show the potential of such causally interpretable predictive models for robust predictions and personalised decision making.

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arXiv2022

Causal Inference with Conditional Instruments using Deep Generative Models

The instrumental variable (IV) approach is a widely used way to estimate the causal effects of a treatment on an outcome of interest from observational data with latent confounders. A standard IV is expected to be related to the treatment variable and independent of all other variables in the system. However, it is challenging to search for a standard IV from data directly due to the strict conditions. The conditional IV (CIV) method has been proposed to allow a variable to be an instrument conditioning on a set of variables, allowing a wider choice of possible IVs and enabling broader practical applications of the IV approach. Nevertheless, there is not a data-driven method to discover a CIV and its conditioning set directly from data. To fill this gap, in this paper, we propose to learn the representations of the information of a CIV and its conditioning set from data with latent confounders for average causal effect estimation. By taking advantage of deep generative models, we develop a novel data-driven approach for simultaneously learning the representation of a CIV from measured variables and generating the representation of its conditioning set given measured variables. Extensive experiments on synthetic and real-world datasets show that our method outperforms the existing IV methods.

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arXiv2022

Local search for efficient causal effect estimation

Causal effect estimation from observational data is a challenging problem, especially with high dimensional data and in the presence of unobserved variables. The available data-driven methods for tackling the problem either provide an estimation of the bounds of a causal effect (i.e. nonunique estimation) or have low efficiency. The major hurdle for achieving high efficiency while trying to obtain unique and unbiased causal effect estimation is how to find a proper adjustment set for confounding control in a fast way, given the huge covariate space and considering unobserved variables. In this paper, we approach the problem as a local search task for finding valid adjustment sets in data. We establish the theorems to support the local search for adjustment sets, and we show that unique and unbiased estimation can be achieved from observational data even when there exist unobserved variables. We then propose a data-driven algorithm that is fast and consistent under mild assumptions. We also make use of a frequent pattern mining method to further speed up the search of minimal adjustment sets for causal effect estimation. Experiments conducted on extensive synthetic and real-world datasets demonstrate that the proposed algorithm outperforms the state-of-the-art criteria/estimators in both accuracy and time-efficiency.

stat.ME↗

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.

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arXiv2022

Identify treatment effect patterns for personalised decisions

In personalised decision making, evidence is required to determine whether an action (treatment) is suitable for an individual. Such evidence can be obtained by modelling treatment effect heterogeneity in subgroups. The existing interpretable modelling methods take a top-down approach to search for subgroups with heterogeneous treatment effects and they may miss the most specific and relevant context for an individual. In this paper, we design a \emph{Treatment effect pattern (TEP)} to represent treatment effect heterogeneity in data. To achieve an interpretable presentation of TEPs, we use a local causal structure around the outcome to explicitly show how those important variables are used in modelling. We also derive a formula for unbiasedly estimating the \emph{Conditional Average Causal Effect (CATE)} using the local structure in our problem setting. In the discovery process, we aim at minimising heterogeneity within each subgroup represented by a pattern. We propose a bottom-up search algorithm to discover the most specific patterns fitting individual circumstances the best for personalised decision making. Experiments show that the proposed method models treatment effect heterogeneity better than three other existing tree based methods in synthetic and real world data sets.

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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.

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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.

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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↗

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.

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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.

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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↗

arXiv2015

Causal Decision Trees

Uncovering causal relationships in data is a major objective of data analytics. Causal relationships are normally discovered with designed experiments, e.g. randomised controlled trials, which, however are expensive or infeasible to be conducted in many cases. Causal relationships can also be found using some well designed observational studies, but they require domain experts' knowledge and the process is normally time consuming. Hence there is a need for scalable and automated methods for causal relationship exploration in data. Classification methods are fast and they could be practical substitutes for finding causal signals in data. However, classification methods are not designed for causal discovery and a classification method may find false causal signals and miss the true ones. In this paper, we develop a causal decision tree where nodes have causal interpretations. Our method follows a well established causal inference framework and makes use of a classic statistical test. The method is practical for finding causal signals in large data sets.

cs.AI↗

arXiv2015

From Observational Studies to Causal Rule Mining

Randomised controlled trials (RCTs) are the most effective approach to causal discovery, but in many circumstances it is impossible to conduct RCTs. Therefore observational studies based on passively observed data are widely accepted as an alternative to RCTs. However, in observational studies, prior knowledge is required to generate the hypotheses about the cause-effect relationships to be tested, hence they can only be applied to problems with available domain knowledge and a handful of variables. In practice, many data sets are of high dimensionality, which leaves observational studies out of the opportunities for causal discovery from such a wealth of data sources. In another direction, many efficient data mining methods have been developed to identify associations among variables in large data sets. The problem is, causal relationships imply associations, but the reverse is not always true. However we can see the synergy between the two paradigms here. Specifically, association rule mining can be used to deal with the high-dimensionality problem while observational studies can be utilised to eliminate non-causal associations. In this paper we propose the concept of causal rules (CRs) and develop an algorithm for mining CRs in large data sets. We use the idea of retrospective cohort studies to detect CRs based on the results of association rule mining. Experiments with both synthetic and real world data sets have demonstrated the effectiveness and efficiency of CR mining. In comparison with the commonly used causal discovery methods, the proposed approach in general is faster and has better or competitive performance in finding correct or sensible causes. It is also capable of finding a cause consisting of multiple variables, a feature that other causal discovery methods do not possess.

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