arXiv subjects

Fan Li

Publications and source records attributed to Fan Li.

At least 235 records · Page 13Linked to original sources

arXiv2023

PStrata: An R Package for Principal Stratification

Post-treatment confounding is a common problem in causal inference, including special cases of noncompliance, truncation by death, surrogate endpoint, etc. Principal stratification (Frangakis and Rubin 2002) is a general framework for defining and estimating causal effects in the presence of post-treatment confounding. A prominent special case is the instrumental variable approach to noncompliance in randomized experiments (Angrist, Imbens, and Rubin 1996). Despite its versatility, principal stratification is not accessible to the vast majority of applied researchers because its inherent latent mixture structure requires complex inference tools and highly customized programming. We develop the R package PStrata to automatize statistical analysis of principal stratification for several common scenarios. PStrata supports both Bayesian and frequentist paradigms. For the Bayesian paradigm, the computing architecture combines R, C++, Stan, where R provides user-interface, Stan automatizes posterior sampling, and C++ bridges the two by automatically generating Stan code. For the Frequentist paradigm, PStrata implements a triply-robust weighting estimator. PStrata accommodates regular outcomes and time-to-event outcomes with both unstructured and clustered data.

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arXiv2023

Theoretical Evaluation of the Capacity-Achieving Distribution for IM-DD Fiber-Optic Channels

The capacity and capacity-achieving distribution for intensity-modulation and direct-detection (IM-DD) fiber-optic channels is theoretically investigated. Different from coherent fiber-optic channels, we indicate that the capacity-achieving distribution of IM-DD systems should be discussed separately in two cases: 1) IM-DD systems without optical amplifier, which are constrained in peak power; 2) IM-DD systems with optical amplifier, which are the average power constraint (APC) system. For the two models, the maximum mutual information achieving distribution, instead of the maximum input entropy achieving distribution, is numerically computed by the iterative Blahut-Arimoto (BA) algorithm. For the IM-DD system under peak power constraint (PPC), a dynamic-assignment BA algorithm is applied to find the capacity-achieving distribution with minimum cardinality. It is observed that the maximum difference between the minimum input cardinality and capacity is around 0.8 bits. For a fixed support input cardinality, although the observed shaping gain is small and only appears in low peak-signal-to-noise ratio (PSNR) regions in the PPC IM-DD system, the probabilistic shaping technique can also be used to introduce rate adaptation to the system by adjusting the shaping and FEC overheads since the capacity-achieving distribution is symmetric. In the IM-DD system under APC, a modified BA algorithm is investigated to solve for the capacity and capacity-achieving distribution, and a significant shaping gain is observed. For PAM8 and PAM16 modulation formats, 0.294 bits/symbol and 0.531 bits/symbol shaping gain can be obtained at the SNR of 20dB. Furthermore, since the capacity-achieving distribution is asymmetric in this case, a practical discussion of the PS technique is also presented.

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arXiv2023

A Probabilistic Generative Model for Tracking Multi-Knowledge Concept Mastery Probability

Knowledge tracing aims to track students' knowledge status over time to predict students' future performance accurately. Markov chain-based knowledge tracking (MCKT) models can track knowledge concept mastery probability over time. However, as the number of tracked knowledge concepts increases, the time complexity of MCKT predicting student performance increases exponentially (also called explaining away problem. In addition, the existing MCKT models only consider the relationship between students' knowledge status and problems when modeling students' responses but ignore the relationship between knowledge concepts in the same problem. To address these challenges, we propose an inTerpretable pRobAbilistiC gEnerative moDel (TRACED), which can track students' numerous knowledge concepts mastery probabilities over time. To solve \emph{explain away problem}, we design Long and Short-Term Memory (LSTM)-based networks to approximate the posterior distribution, predict students' future performance, and propose a heuristic algorithm to train LSTMs and probabilistic graphical model jointly. To better model students' exercise responses, we proposed a logarithmic linear model with three interactive strategies, which models students' exercise responses by considering the relationship among students' knowledge status, knowledge concept, and problems. We conduct experiments with four real-world datasets in three knowledge-driven tasks. The experimental results show that TRACED outperforms existing knowledge tracing methods in predicting students' future performance and can learn the relationship among students, knowledge concepts, and problems from students' exercise sequences. We also conduct several case studies. The case studies show that TRACED exhibits excellent interpretability and thus has the potential for personalized automatic feedback in the real-world educational environment.

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arXiv2023

CADG: A Model Based on Cross Attention for Domain Generalization

In Domain Generalization (DG) tasks, models are trained by using only training data from the source domains to achieve generalization on an unseen target domain, this will suffer from the distribution shift problem. So it's important to learn a classifier to focus on the common representation which can be used to classify on multi-domains, so that this classifier can achieve a high performance on an unseen target domain as well. With the success of cross attention in various cross-modal tasks, we find that cross attention is a powerful mechanism to align the features come from different distributions. So we design a model named CADG (cross attention for domain generalization), wherein cross attention plays a important role, to address distribution shift problem. Such design makes the classifier can be adopted on multi-domains, so the classifier will generalize well on an unseen domain. Experiments show that our proposed method achieves state-of-the-art performance on a variety of domain generalization benchmarks compared with other single model and can even achieve a better performance than some ensemble-based methods.

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arXiv2023

Principal Stratification with Time-to-Event Outcomes

Post-randomization events, also known as intercurrent events, such as treatment noncompliance and censoring due to a terminal event, are common in clinical trials. Principal stratification is a framework for causal inference in the presence of intercurrent events. Despite the extensive existing literature, there lacks generally applicable and accessible methods for principal stratification analysis with time-to-event outcomes. In this paper, we specify two causal estimands for time-to-event outcomes in principal stratification. For estimation, we adopt the general strategy of latent mixture modeling and derive the corresponding likelihood function. For computational convenience, we illustrate the general strategy with a mixture of Bayesian parametric Weibull-Cox proportional model for the outcome. We utilize the Stan programming language to obtain automatic posterior sampling of the model parameters via the Hamiltonian Monte Carlo. We provide the analytical forms of the causal estimands as functions of the model parameters and an alternative numerical method when analytical forms are not available. We apply the proposed method to the ADAPTABLE trial to evaluate the causal effect of taking 81 mg versus 325 mg aspirin on the risk of major adverse cardiovascular events.

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arXiv2022

Bayesian semi-parametric inference for clustered recurrent events with zero-inflation and a terminal event/4163305

Recurrent event data are common in clinical studies when participants are followed longitudinally, and are often subject to a terminal event. With the increasing popularity of large pragmatic trials with a heterogeneous source population, participants are often nested in clinics and can be either susceptible or structurally unsusceptible to the recurrent process. These complications require new modeling strategies to accommodate potential zero-event inflation as well as hierarchical data structures in both the terminal and non-terminal event processes. In this paper, we develop a Bayesian semi-parametric model to jointly characterize the zero-inflated recurrent event process and the terminal event process. We use a point mass mixture of non-homogeneous Poisson processes to describe the recurrent intensity and introduce shared random effects from different sources to bridge the non-terminal and terminal event processes. To achieve robustness, we consider nonparametric Dirichlet processes to model the residual of the accelerated failure time model for the survival process as well as the cluster-specific frailty distribution, and develop a Markov Chain Monte Carlo algorithm for posterior inference. We demonstrate the superiority of our proposed model compared with competing models via simulations and apply our method to a pragmatic cluster randomized trial for fall injury prevention among the elderly.

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arXiv2022

Power analyses for stepped wedge designs with multivariate continuous outcomes

Multivariate outcomes are common in pragmatic cluster randomized trials. While sample size calculation procedures for multivariate outcomes exist under parallel assignment, none have been developed for a stepped wedge design. In this article, we present computationally efficient power and sample size procedures for stepped wedge cluster randomized trials (SW-CRTs) with multivariate outcomes that differentiate the within-period and between-period intracluster correlation coefficients (ICCs). Under a multivariate linear mixed model, we derive the joint distribution of the intervention test statistics which can be used for determining power under different hypotheses and provide an example using the commonly utilized intersection-union test for co-primary outcomes. Simplifications under a common treatment effect and common ICCs across endpoints and an extension to closed cohort designs are also provided. Finally, under the common ICC across endpoints assumption, we formally prove that the multivariate linear mixed model leads to a more efficient treatment effect estimator compared to the univariate linear mixed model, providing a rigorous justification on the use of the former with multivariate outcomes. We illustrate application of the proposed methods using data from an existing SW-CRT and present extensive simulations to validate the methods.

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arXiv2022

Overlapping oriented imbalanced ensemble learning method based on projective clustering and stagewise hybrid sampling

The challenge of imbalanced learning lies not only in class imbalance problem, but also in the class overlapping problem which is complex. However, most of the existing algorithms mainly focus on the former. The limitation prevents the existing methods from breaking through. To address this limitation, this paper proposes an ensemble learning algorithm based on dual clustering and stage-wise hybrid sampling (DCSHS). The DCSHS has three parts. Firstly, we design a projection clustering combination framework (PCC) guided by Davies-Bouldin clustering effectiveness index (DBI), which is used to obtain high-quality clusters and combine them to obtain a set of cross-complete subsets (CCS) with balanced class and low overlapping. Secondly, according to the characteristics of subset classes, a stage-wise hybrid sampling algorithm is designed to realize the de-overlapping and balancing of subsets. Finally, a projective clustering transfer mapping mechanism (CTM) is constructed for all processed subsets by means of transfer learning, thereby reducing class overlapping and explore structure information of samples. The major advantage of our algorithm is that it can exploit the intersectionality of the CCS to realize the soft elimination of overlapping majority samples, and learn as much information of overlapping samples as possible, thereby enhancing the class overlapping while class balancing. In the experimental section, more than 30 public datasets and over ten representative algorithms are chosen for verification. The experimental results show that the DCSHS is significantly best in terms of various evaluation criteria.

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arXiv2022

Leveraging baseline covariates to analyze small cluster-randomized trials with a rare binary outcome

Cluster-randomized trials (CRTs) involve randomizing entire groups of participants -- called clusters -- to treatment arms but are often comprised of a limited or fixed number of available clusters. While covariate adjustment can account for chance imbalances between treatment arms and increase statistical efficiency in individually-randomized trials, analytical methods for individual-level covariate adjustment in small CRTs have received little attention to date. In this paper, we systematically investigate, through extensive simulations, the operating characteristics of propensity score weighting and multivariable regression as two individual-level covariate adjustment strategies for estimating the participant-average causal effect in small CRTs with a rare binary outcome and identify scenarios where each adjustment strategy has a relative efficiency advantage over the other to make practical recommendations. We also examine the finite-sample performance of the bias-corrected sandwich variance estimators associated with propensity score weighting and multivariable regression for quantifying the uncertainty in estimating the participant-average treatment effect. To illustrate the methods for individual-level covariate adjustment, we reanalyze a recent CRT testing a sedation protocol in 31 pediatric intensive care units.

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arXiv2022

The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

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arXiv2022

Person Text-Image Matching via Text-Feature Interpretability Embedding and External Attack Node Implantation

Person text-image matching, also known as text based person search, aims to retrieve images of specific pedestrians using text descriptions. Although person text-image matching has made great research progress, existing methods still face two challenges. First, the lack of interpretability of text features makes it challenging to effectively align them with their corresponding image features. Second, the same pedestrian image often corresponds to multiple different text descriptions, and a single text description can correspond to multiple different images of the same identity. The diversity of text descriptions and images makes it difficult for a network to extract robust features that match the two modalities. To address these problems, we propose a person text-image matching method by embedding text-feature interpretability and an external attack node. Specifically, we improve the interpretability of text features by providing them with consistent semantic information with image features to achieve the alignment of text and describe image region features.To address the challenges posed by the diversity of text and the corresponding person images, we treat the variation caused by diversity to features as caused by perturbation information and propose a novel adversarial attack and defense method to solve it. In the model design, graph convolution is used as the basic framework for feature representation and the adversarial attacks caused by text and image diversity on feature extraction is simulated by implanting an additional attack node in the graph convolution layer to improve the robustness of the model against text and image diversity. Extensive experiments demonstrate the effectiveness and superiority of text-pedestrian image matching over existing methods. The source code of the method is published at

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arXiv2022

A new Stack Autoencoder: Neighbouring Sample Envelope Embedded Stack Autoencoder Ensemble Model

Stack autoencoder (SAE), as a representative deep network, has unique and excellent performance in feature learning, and has received extensive attention from researchers. However, existing deep SAEs focus on original samples without considering the hierarchical structural information between samples. To address this limitation, this paper proposes a new SAE model-neighbouring envelope embedded stack autoencoder ensemble (NE_ESAE). Firstly, the neighbouring sample envelope learning mechanism (NSELM) is proposed for preprocessing of input of SAE. NSELM constructs sample pairs by combining neighbouring samples. Besides, the NSELM constructs a multilayer sample spaces by multilayer iterative mean clustering, which considers the similar samples and generates layers of envelope samples with hierarchical structural information. Second, an embedded stack autoencoder (ESAE) is proposed and trained in each layer of sample space to consider the original samples during training and in the network structure, thereby better finding the relationship between original feature samples and deep feature samples. Third, feature reduction and base classifiers are conducted on the layers of envelope samples respectively, and output classification results of every layer of samples. Finally, the classification results of the layers of envelope sample space are fused through the ensemble mechanism. In the experimental section, the proposed algorithm is validated with over ten representative public datasets. The results show that our method significantly has better performance than existing traditional feature learning methods and the representative deep autoencoders.

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arXiv2022

Tight Mutual Information Estimation With Contrastive Fenchel-Legendre Optimization

Successful applications of InfoNCE and its variants have popularized the use of contrastive variational mutual information (MI) estimators in machine learning. While featuring superior stability, these estimators crucially depend on costly large-batch training, and they sacrifice bound tightness for variance reduction. To overcome these limitations, we revisit the mathematics of popular variational MI bounds from the lens of unnormalized statistical modeling and convex optimization. Our investigation not only yields a new unified theoretical framework encompassing popular variational MI bounds but also leads to a novel, simple, and powerful contrastive MI estimator named as FLO. Theoretically, we show that the FLO estimator is tight, and it provably converges under stochastic gradient descent. Empirically, our FLO estimator overcomes the limitations of its predecessors and learns more efficiently. The utility of FLO is verified using an extensive set of benchmarks, which also reveals the trade-offs in practical MI estimation.

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arXiv2022

Bayesian Causal Inference: A Critical Review

This paper provides a critical review of the Bayesian perspective of causal inference based on the potential outcomes framework. We review the causal estimands, identification assumptions, the general structure of Bayesian inference of causal effects, and sensitivity analysis. We highlight issues that are unique to Bayesian causal inference, including the role of the propensity score, definition of identifiability, the choice of priors in both low and high dimensional regimes. We point out the central role of covariate overlap and more generally the design stage in Bayesian causal inference. We extend the discussion to two complex assignment mechanisms: instrumental variable and time-varying treatments. Throughout, we illustrate the key concepts via examples.

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arXiv2022

Using propensity scores for racial disparities analysis

Propensity score plays a central role in causal inference, but its use is not limited to causal comparisons. As a covariate balancing tool, propensity score can be used for controlled descriptive comparisons between groups whose memberships are not manipulable. A prominent example is racial disparities in health care. However, conceptual confusion and hesitation persists for using propensity score in racial disparities studies. In this commentary, we argue that propensity score, possibly combined with other methods, is an effective tool for racial disparities analysis. We describe relevant estimands, target population, and assumptions. In particular, we clarify that a controlled descriptive comparisons require weaker assumptions than a causal comparison. We discuss three common propensity score weighting strategies: overlap weighting, inverse probability weighting and average treatment effect for treated weighting. We further describe how to combine weighting with the rank-and-replace adjustment method to produce racial disparity estimates concordant to the Institute of Medicine's definition. The method is illustrated by a re-analysis of the Medical Expenditure Panel Survey data.

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arXiv2022

Improving sandwich variance estimation for marginal Cox analysis of cluster randomized trials

Cluster randomized trials (CRTs) frequently recruit a small number of clusters, therefore necessitating the application of small-sample corrections for valid inference. A recent systematic review indicated that CRTs reporting right-censored, time-to-event outcomes are not uncommon, and that the marginal Cox proportional hazards model is one of the common approaches used for primary analysis. While small-sample corrections have been studied under marginal models with continuous, binary and count outcomes, no prior research has been devoted to the development and evaluation of bias-corrected sandwich variance estimators when clustered time-to-event outcomes are analyzed by the marginal Cox model. To improve current practice, we propose 9 bias-corrected sandwich variance estimators for the analysis of CRTs using the marginal Cox model, and report on a simulation study to evaluate their small-sample properties. Our results indicate that the optimal choice of bias-corrected sandwich variance estimator for CRTs with survival outcomes can depend on the variability of cluster sizes, and can also slightly differ whether it is evaluated according to relative bias or type I error rate. Finally, we illustrate the new variance estimators in a real-world CRT where the conclusion about intervention effectiveness differs depending on the use of small-sample bias corrections. The proposed sandwich variance estimators are implemented in an R package CoxBcv.

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arXiv2022

Envelope imbalanced ensemble model with deep sample learning and local-global structure consistency

The class imbalance problem is important and challenging. Ensemble approaches are widely used to tackle this problem because of their effectiveness. However, existing ensemble methods are always applied into original samples, while not considering the structure information among original samples. The limitation will prevent the imbalanced learning from being better. Besides, research shows that the structure information among samples includes local and global structure information. Based on the analysis above, an imbalanced ensemble algorithm with the deep sample pre-envelope network (DSEN) and local-global structure consistency mechanism (LGSCM) is proposed here to solve the problem.This algorithm can guarantee high-quality deep envelope samples for considering the local manifold and global structures information, which is helpful for imbalance learning. First, the deep sample envelope pre-network (DSEN) is designed to mine structure information among samples.Then, the local manifold structure metric (LMSM) and global structure distribution metric (GSDM) are designed to construct LGSCM to enhance distribution consistency of interlayer samples. Next, the DSEN and LGSCM are put together to form the final deep sample envelope network (DSEN-LG). After that, base classifiers are applied on the layers of deep samples respectively.Finally, the predictive results from base classifiers are fused through bagging ensemble learning mechanism. To demonstrate the effectiveness of the proposed method, forty-four public datasets and more than ten representative relevant algorithms are chosen for verification. The experimental results show that the algorithm is significantly better than other imbalanced ensemble algorithms.

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arXiv2022

Addressing Extreme Propensity Scores in Estimating Counterfactual Survival Functions via the Overlap Weights

The inverse probability weighting approach is popular for evaluating treatment effects in observational studies, but extreme propensity scores could bias the estimator and induce excessive variance. Recently, the overlap weighting approach has been proposed to alleviate this problem, which smoothly down-weighs the subjects with extreme propensity scores. Although advantages of overlap weighting have been extensively demonstrated in literature with continuous and binary outcomes, research on its performance with time-to-event or survival outcomes is limited. In this article, we propose two weighting estimators that combine propensity score weighting and inverse probability of censoring weighting to estimate the counterfactual survival functions. These estimators are applicable to the general class of balancing weights, which includes inverse probability weighting, trimming, and overlap weighting as special cases. We conduct simulations to examine the empirical performance of these estimators with different weighting schemes in terms of bias, variance, and 95% confidence interval coverage, under various degree of covariate overlap between treatment groups and censoring rate. We demonstrate that overlap weighting consistently outperforms inverse probability weighting and associated trimming methods in bias, variance, and coverage for time-to-event outcomes, and the advantages increase as the degree of covariate overlap between the treatment groups decreases.

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