Weishen Pan

Yingheng Wang, Yair Schiff, Aaron Gokaslan et al.

While diffusion models excel at generating high-quality samples, their latent variables typically lack semantic meaning and are not suitable for representation learning. Here, we propose InfoDiffusion, an algorithm that augments diffusion models with low-dimensional latent variables that capture high-level factors of variation in the data. InfoDiffusion relies on a learning objective regularized with the mutual information between observed and hidden variables, which improves latent space quality and prevents the latents from being ignored by expressive diffusion-based decoders. Empirically, we find that InfoDiffusion learns disentangled and human-interpretable latent representations that are competitive with state-of-the-art generative and contrastive methods, while retaining the high sample quality of diffusion models. Our method enables manipulating the attributes of generated images and has the potential to assist tasks that require exploring a learned latent space to generate quality samples, e.g., generative design.

Sen Cui, Weishen Pan, Changshui Zhang et al.

Algorithmic fairness has been a serious concern and received lots of interest in machine learning community. In this paper, we focus on the bipartite ranking scenario, where the instances come from either the positive or negative class and the goal is to learn a ranking function that ranks positive instances higher than negative ones. While there could be a trade-off between fairness and performance, we propose a model agnostic post-processing framework xOrder for achieving fairness in bipartite ranking and maintaining the algorithm classification performance. In particular, we optimize a weighted sum of the utility as identifying an optimal warping path across different protected groups and solve it through a dynamic programming process. xOrder is compatible with various classification models and ranking fairness metrics, including supervised and unsupervised fairness metrics. In addition to binary groups, xOrder can be applied to multiple protected groups. We evaluate our proposed algorithm on four benchmark data sets and two real-world patient electronic health record repositories. xOrder consistently achieves a better balance between the algorithm utility and ranking fairness on a variety of datasets with different metrics. From the visualization of the calibrated ranking scores, xOrder mitigates the score distribution shifts of different groups compared with baselines. Moreover, additional analytical results verify that xOrder achieves a robust performance when faced with fewer samples and a bigger difference between training and testing ranking score distributions.

Yuyu Liu, Jiannan Yang, Ziyang Yu et al.

Missing data in single-cell sequencing datasets poses significant challenges for extracting meaningful biological insights. However, existing imputation approaches, which often assume uniformity and data completeness, struggle to address cases with large patches of missing data. In this paper, we present CROT, an optimal transport-based imputation algorithm designed to handle patch-based missing data in tabular formats. Our approach effectively captures the underlying data structure in the presence of significant missingness. Notably, it achieves superior imputation accuracy while significantly reducing runtime, demonstrating its scalability and efficiency for large-scale datasets. This work introduces a robust solution for imputation in heterogeneous, high-dimensional datasets with structured data absence, addressing critical challenges in both biological and clinical data analysis. Our code is available at Anomalous Github.

Jacqueline Maasch, Weishen Pan, Shantanu Gupta et al.

Causal discovery is crucial for causal inference in observational studies, as it can enable the identification of valid adjustment sets (VAS) for unbiased effect estimation. However, global causal discovery is notoriously hard in the nonparametric setting, with exponential time and sample complexity in the worst case. To address this, we propose local discovery by partitioning (LDP): a local causal discovery method that is tailored for downstream inference tasks without requiring parametric and pretreatment assumptions. LDP is a constraint-based procedure that returns a VAS for an exposure-outcome pair under latent confounding, given sufficient conditions. The total number of independence tests performed is worst-case quadratic with respect to the cardinality of the variable set. Asymptotic theoretical guarantees are numerically validated on synthetic graphs. Adjustment sets from LDP yield less biased and more precise average treatment effect estimates than baseline discovery algorithms, with LDP outperforming on confounder recall, runtime, and test count for VAS discovery. Notably, LDP ran at least 1300x faster than baselines on a benchmark.

Wenxin Chen, Weishen Pan, Kyra Gan et al.

Comparative evaluation of multiple dynamic treatment policies is essential for healthcare and policy decisions, yet conventional longitudinal causal inference methods estimate each in isolation, preventing information sharing across counterfactuals. We demonstrate that this separate estimation paradigm induces a structurally uncontrolled second-order bias, inflating finite-sample variance even after standard debiasing with longitudinal targeted maximum likelihood estimation(LTMLE). To address this, we propose a policy-aware reparameterization of Iterative Conditional Expectation (ICE) Q-functions that enables joint estimation through shared representations. We implement this approach in the Policy-Encoded Q Network (PEQ-Net), an architecture centered on a shared policy encoder. The encoder is trained using kernel mean embeddings, ensuring that the learned representation space reflects population-level policy dissimilarities. After applying an LTMLE correction step, we prove this design imposes a structural constraint on the second-order remainder, thereby stabilizing finite-sample variance. Experiments on semi-synthetic datasets demonstrate that PEQ-Net consistently outperforms existing ICE-based methods, achieving substantial reductions in root-mean-square error, particularly when evaluating closely related policies.

Ziang Yan, Jian Liang, Weishen Pan et al.

Object detection when provided image-level labels instead of instance-level labels (i.e., bounding boxes) during training is an important problem in computer vision, since large scale image datasets with instance-level labels are extremely costly to obtain. In this paper, we address this challenging problem by developing an Expectation-Maximization (EM) based object detection method using deep convolutional neural networks (CNNs). Our method is applicable to both the weakly-supervised and semi-supervised settings. Extensive experiments on PASCAL VOC 2007 benchmark show that (1) in the weakly supervised setting, our method provides significant detection performance improvement over current state-of-the-art methods, (2) having access to a small number of strongly (instance-level) annotated images, our method can almost match the performace of the fully supervised Fast RCNN. We share our source code at https://github.com/ZiangYan/EM-WSD.

Wenxin Chen, Weishen Pan, Kyra Gan et al.

Estimating longitudinal treatment effects is essential for sequential decision-making but is challenging due to treatment-confounder feedback. While Iterative Conditional Expectation (ICE) G-computation offers a principled approach, its recursive structure suffers from error propagation, corrupting the learned outcome regression models. We propose D3-Net, a framework that mitigates error propagation in ICE training and then applies a robust final correction. First, to interrupt error propagation during learning, we train the ICE sequence using Sequential Doubly Robust (SDR) pseudo-outcomes, which provide bias-corrected targets for each regression. Second, we employ a multi-task Transformer with a covariate simulator head for auxiliary supervision, regularizing representations against corruption by noisy pseudo-outcomes, and a target network to stabilize training dynamics. For the final estimate, we discard the SDR correction and instead use the uncorrected nuisance models to perform Longitudinal Targeted Minimum Loss-Based Estimation (LTMLE) on the original outcomes. This second-stage, targeted debiasing ensures robustness and optimal finite-sample properties. Comprehensive experiments demonstrate that our model, D3-Net, robustly reduces bias and variance across different horizons, counterfactuals, and time-varying confoundings, compared to existing state-of-the-art ICE-based estimators.

Wenxin Chen, Weishen Pan, Kyra Gan et al.

Current subgroup identification methods typically follow a two-step approach: first estimate conditional average treatment effects and then apply thresholding or rule-based procedures to define subgroups. While intuitive, this decoupled approach fails to incorporate key constraints essential for real-world clinical decision-making, such as subgroup size and propensity overlap. These constraints operate on fundamentally different axes than CATE estimation and are not naturally accommodated within existing frameworks, thereby limiting the practical applicability of these methods. We propose a unified optimization framework that directly solves the primal constrained optimization problem to identify optimal subgroups. Our key innovation is a reformulation of the constrained primal problem as an unconstrained differentiable min-max objective, solved via a gradient descent-ascent algorithm. We theoretically establish that our solution converges to a feasible and locally optimal solution. Unlike threshold-based CATE methods that apply constraints as post-hoc filters, our approach enforces them directly during optimization. The framework is model-agnostic, compatible with a wide range of CATE estimators, and extensible to additional constraints like cost limits or fairness criteria. Extensive experiments on synthetic and real-world datasets demonstrate its effectiveness in identifying high-benefit subgroups while maintaining better satisfaction of constraints.

Marianne Arriola, Weishen Pan, Manqi Zhou et al.

Joint analysis of multi-omic single-cell data across cohorts has significantly enhanced the comprehensive analysis of cellular processes. However, most of the existing approaches for this purpose require access to samples with complete modality availability, which is impractical in many real-world scenarios. In this paper, we propose (Single-Cell Cross-Cohort Cross-Category) integration, a novel framework that learns unified cell representations under domain shift without requiring full-modality reference samples. Our generative approach learns rich cross-modal and cross-domain relationships that enable imputation of these missing modalities. Through experiments on real-world multi-omic datasets, we demonstrate that offers a robust solution to single-cell tasks such as cell type clustering, cell type classification, and feature imputation.

Suraj Rajendran, Weishen Pan, Mert R. Sabuncu et al.

Machine learning (ML) in healthcare presents numerous opportunities for enhancing patient care, population health, and healthcare providers' workflows. However, the real-world clinical and cost benefits remain limited due to challenges in data privacy, heterogeneous data sources, and the inability to fully leverage multiple data modalities. In this perspective paper, we introduce "patchwork learning" (PL), a novel paradigm that addresses these limitations by integrating information from disparate datasets composed of different data modalities (e.g., clinical free-text, medical images, omics) and distributed across separate and secure sites. PL allows the simultaneous utilization of complementary data sources while preserving data privacy, enabling the development of more holistic and generalizable ML models. We present the concept of patchwork learning and its current implementations in healthcare, exploring the potential opportunities and applicable data sources for addressing various healthcare challenges. PL leverages bridging modalities or overlapping feature spaces across sites to facilitate information sharing and impute missing data, thereby addressing related prediction tasks. We discuss the challenges associated with PL, many of which are shared by federated and multimodal learning, and provide recommendations for future research in this field. By offering a more comprehensive approach to healthcare data integration, patchwork learning has the potential to revolutionize the clinical applicability of ML models. This paradigm promises to strike a balance between personalization and generalizability, ultimately enhancing patient experiences, improving population health, and optimizing healthcare providers' workflows.

Weishen Pan, Sen Cui, Hongyi Wen et al.

Selection bias is prevalent in the data for training and evaluating recommendation systems with explicit feedback. For example, users tend to rate items they like. However, when rating an item concerning a specific user, most of the recommendation algorithms tend to rely too much on his/her rating (feedback) history. This introduces implicit bias on the recommendation system, which is referred to as user feedback-loop bias in this paper. We propose a systematic and dynamic way to correct such bias and to obtain more diverse and objective recommendations by utilizing temporal rating information. Specifically, our method includes a deep-learning component to learn each user's dynamic rating history embedding for the estimation of the probability distribution of the items that the user rates sequentially. These estimated dynamic exposure probabilities are then used as propensity scores to train an inverse-propensity-scoring (IPS) rating predictor. We empirically validated the existence of such user feedback-loop bias in real world recommendation systems and compared the performance of our method with the baseline models that are either without de-biasing or with propensity scores estimated by other methods. The results show the superiority of our approach.

Sen Cui, Weishen Pan, Jian Liang et al.

Federated learning (FL) has gain growing interests for its capability of learning from distributed data sources collectively without the need of accessing the raw data samples across different sources. So far FL research has mostly focused on improving the performance, how the algorithmic disparity will be impacted for the model learned from FL and the impact of algorithmic disparity on the utility inconsistency are largely unexplored. In this paper, we propose an FL framework to jointly consider performance consistency and algorithmic fairness across different local clients (data sources). We derive our framework from a constrained multi-objective optimization perspective, in which we learn a model satisfying fairness constraints on all clients with consistent performance. Specifically, we treat the algorithm prediction loss at each local client as an objective and maximize the worst-performing client with fairness constraints through optimizing a surrogate maximum function with all objectives involved. A gradient-based procedure is employed to achieve the Pareto optimality of this optimization problem. Theoretical analysis is provided to prove that our method can converge to a Pareto solution that achieves the min-max performance with fairness constraints on all clients. Comprehensive experiments on synthetic and real-world datasets demonstrate the superiority that our approach over baselines and its effectiveness in achieving both fairness and consistency across all local clients.

Sen Cui, Jian Liang, Weishen Pan et al.

Federated learning (FL) refers to the paradigm of learning models over a collaborative research network involving multiple clients without sacrificing privacy. Recently, there have been rising concerns on the distributional discrepancies across different clients, which could even cause counterproductive consequences when collaborating with others. While it is not necessarily that collaborating with all clients will achieve the best performance, in this paper, we study a rational collaboration called ``collaboration equilibrium'' (CE), where smaller collaboration coalitions are formed. Each client collaborates with certain members who maximally improve the model learning and isolates the others who make little contribution. We propose the concept of benefit graph which describes how each client can benefit from collaborating with other clients and advance a Pareto optimization approach to identify the optimal collaborators. Then we theoretically prove that we can reach a CE from the benefit graph through an iterative graph operation. Our framework provides a new way of setting up collaborations in a research network. Experiments on both synthetic and real world data sets are provided to demonstrate the effectiveness of our method.

Weishen Pan, Sen Cui, Jiang Bian et al.

Algorithmic fairness has aroused considerable interests in data mining and machine learning communities recently. So far the existing research has been mostly focusing on the development of quantitative metrics to measure algorithm disparities across different protected groups, and approaches for adjusting the algorithm output to reduce such disparities. In this paper, we propose to study the problem of identification of the source of model disparities. Unlike existing interpretation methods which typically learn feature importance, we consider the causal relationships among feature variables and propose a novel framework to decompose the disparity into the sum of contributions from fairness-aware causal paths, which are paths linking the sensitive attribute and the final predictions, on the graph. We also consider the scenario when the directions on certain edges within those paths cannot be determined. Our framework is also model agnostic and applicable to a variety of quantitative disparity measures. Empirical evaluations on both synthetic and real-world data sets are provided to show that our method can provide precise and comprehensive explanations to the model disparities.

Weishen Pan, Changshui Zhang

As machine learning algorithms getting adopted in an ever-increasing number of applications, interpretation has emerged as a crucial desideratum. In this paper, we propose a mathematical definition for the human-interpretable model. In particular, we define interpretability between two information process systems. If a prediction model is interpretable by a human recognition system based on the above interpretability definition, the prediction model is defined as a completely human-interpretable model. We further design a practical framework to train a completely human-interpretable model by user interactions. Experiments on image datasets show the advantages of our proposed model in two aspects: 1) The completely human-interpretable model can provide an entire decision-making process that is human-understandable; 2) The completely human-interpretable model is more robust against adversarial attacks.

Sen Cui, Weishen Pan, Changshui Zhang et al.

Bipartite ranking, which aims to learn a scoring function that ranks positive individuals higher than negative ones from labeled data, is widely adopted in various applications where sample prioritization is needed. Recently, there have been rising concerns on whether the learned scoring function can cause systematic disparity across different protected groups defined by sensitive attributes. While there could be trade-off between fairness and performance, in this paper we propose a model agnostic post-processing framework for balancing them in the bipartite ranking scenario. Specifically, we maximize a weighted sum of the utility and fairness by directly adjusting the relative ordering of samples across groups. By formulating this problem as the identification of an optimal warping path across different protected groups, we propose a non-parametric method to search for such an optimal path through a dynamic programming process. Our method is compatible with various classification models and applicable to a variety of ranking fairness metrics. Comprehensive experiments on a suite of benchmark data sets and two real-world patient electronic health record repositories show that our method can achieve a great balance between the algorithm utility and ranking fairness. Furthermore, we experimentally verify the robustness of our method when faced with the fewer training samples and the difference between training and testing ranking score distributions.