Erdun Gao

Zuopeng Yang, Tianshu Chu, Xin Lin et al.

The recent success of text-to-image generation diffusion models has also revolutionized semantic image editing, enabling the manipulation of images based on query/target texts. Despite these advancements, a significant challenge lies in the potential introduction of contextual prior bias in pre-trained models during image editing, e.g., making unexpected modifications to inappropriate regions. To address this issue, we present a novel approach called Dual-Cycle Diffusion, which generates an unbiased mask to guide image editing. The proposed model incorporates a Bias Elimination Cycle that consists of both a forward path and an inverted path, each featuring a Structural Consistency Cycle to ensure the preservation of image content during the editing process. The forward path utilizes the pre-trained model to produce the edited image, while the inverted path converts the result back to the source image. The unbiased mask is generated by comparing differences between the processed source image and the edited image to ensure that both conform to the same distribution. Our experiments demonstrate the effectiveness of the proposed method, as it significantly improves the D-CLIP score from 0.272 to 0.283. The code will be available at https://github.com/JohnDreamer/DualCycleDiffsion.

Erdun Gao, Ignavier Ng, Mingming Gong et al.

State-of-the-art causal discovery methods usually assume that the observational data is complete. However, the missing data problem is pervasive in many practical scenarios such as clinical trials, economics, and biology. One straightforward way to address the missing data problem is first to impute the data using off-the-shelf imputation methods and then apply existing causal discovery methods. However, such a two-step method may suffer from suboptimality, as the imputation algorithm may introduce bias for modeling the underlying data distribution. In this paper, we develop a general method, which we call MissDAG, to perform causal discovery from data with incomplete observations. Focusing mainly on the assumptions of ignorable missingness and the identifiable additive noise models (ANMs), MissDAG maximizes the expected likelihood of the visible part of observations under the expectation-maximization (EM) framework. In the E-step, in cases where computing the posterior distributions of parameters in closed-form is not feasible, Monte Carlo EM is leveraged to approximate the likelihood. In the M-step, MissDAG leverages the density transformation to model the noise distributions with simpler and specific formulations by virtue of the ANMs and uses a likelihood-based causal discovery algorithm with directed acyclic graph constraint. We demonstrate the flexibility of MissDAG for incorporating various causal discovery algorithms and its efficacy through extensive simulations and real data experiments.

Yuhang Liu, Erdun Gao, Dong Gong et al.

Developing human understandable interpretation of large language models (LLMs) becomes increasingly critical for their deployment in essential domains. Mechanistic interpretability seeks to mitigate the issues through extracts human-interpretable process and concepts from LLMs' activations. Sparse autoencoders (SAEs) have emerged as a popular approach for extracting interpretable and monosemantic concepts by decomposing the LLM internal representations into a dictionary. Despite their empirical progress, SAEs suffer from a fundamental theoretical ambiguity: the well-defined correspondence between LLM representations and human-interpretable concepts remains unclear. This lack of theoretical grounding gives rise to several methodological challenges, including difficulties in principled method design and evaluation criteria. In this work, we show that, under mild assumptions, LLM representations can be approximated as a {linear mixture} of the log-posteriors over concepts given the input context, through the lens of a latent variable model where concepts are treated as latent variables. This motivates a principled framework for concept extraction, namely Concept Component Analysis (ConCA), which aims to recover the log-posterior of each concept from LLM representations through a {unsupervised} linear unmixing process. We explore a specific variant, termed sparse ConCA, which leverages a sparsity prior to address the inherent ill-posedness of the unmixing problem. We implement 12 sparse ConCA variants and demonstrate their ability to extract meaningful concepts across multiple LLMs, offering theory-backed advantages over SAEs.

Danru Xu, Erdun Gao, Wei Huang et al.

Learning the underlying Bayesian Networks (BNs), represented by directed acyclic graphs (DAGs), of the concerned events from purely-observational data is a crucial part of evidential reasoning. This task remains challenging due to the large and discrete search space. A recent flurry of developments followed NOTEARS[1] recast this combinatorial problem into a continuous optimization problem by leveraging an algebraic equality characterization of acyclicity. However, the continuous optimization methods suffer from obtaining non-spare graphs after the numerical optimization, which leads to the inflexibility to rule out the potentially cycle-inducing edges or false discovery edges with small values. To address this issue, in this paper, we develop a completely data-driven DAG structure learning method without a predefined value to post-threshold small values. We name our method NOTEARS with adaptive Lasso (NOTEARS-AL), which is achieved by applying the adaptive penalty method to ensure the sparsity of the estimated DAG. Moreover, we show that NOTEARS-AL also inherits the oracle properties under some specific conditions. Extensive experiments on both synthetic and a real-world dataset demonstrate that our method consistently outperforms NOTEARS.

Wenkang Jiang, Yuhang Liu, Erdun Gao et al.

Single-cell perturbation prediction aims to infer how cells respond to unseen interventions and to achieve out-of-distribution (OOD) generalization, providing a computational route to understanding how perturbations reshape cellular programs over time. Existing machine learning methods have made important progress, but typically capture only one side of the response. Latent causal approaches seek mechanisms that support generalization and interpretation, yet often treat perturbation effects as static outcomes. Temporal models describe how gene expression changes across time, but usually do not explicitly recover the latent causal generative mechanisms driving these changes. In practice, perturbation effects are both latent and dynamical: interventions act through unobserved cellular programs, whose states evolve over time and give rise to observed expression profiles. Motivated by this view, we propose a latent dynamical causal generative model for single-cell perturbation data that jointly captures latent cellular programs, perturbation-conditioned mechanisms, and temporal evolution. We further provide an identifiability analysis showing that, under suitable conditions, the latent causal variables are recoverable up to standard equivalence classes. Guided by this analysis, we develop CITE-VAE, a learning framework for recovering latent cellular programs and their perturbation-driven dynamics from single-cell sequencing data. Experiments on Causal-3DIdent validate the theoretical results and the effectiveness of the proposed method in controlled settings. Additional experiments on real-world CRISPR-based single-cell perturbation data show improved generalization to unseen perturbations compared with state-of-the-art baselines, highlighting the practical robustness of our approach.

Wenkang Jiang, Yuhang Liu, Yichao Cai et al.

Single-cell perturbation modeling is fundamental for understanding and predicting cellular responses to genetic perturbations. However, existing approaches, from causal representation learning to foundation models, often struggle with an overlooked challenge: gene expression is dominated by perturbation-invariant information, while perturbation-specific signals are intrinsically sparse. As a result, learned representations either entangle invariant and perturbation-specific information, leading to spurious and non-generalizable predictors, or suppress perturbation-specific signals altogether, rendering them ineffective for prediction. To address this, we propose PerturbedVAE, a general framework designed to resolve this signal imbalance. The framework explicitly separates perturbation-specific information from dominant invariant structure and recovers causal representations to effectively utilize such information for prediction. We further provide an identifiability analysis that characterizes the conditions under which sparse perturbation effects can be reliably recovered, thereby clarifying how the framework can be concretely specified under such conditions. Empirically, PerturbedVAE achieves state-of-the-art performance on a widely used benchmark across multiple evaluation settings, yielding significant gains on out-of-distribution combinatorial predictions and uncovering interpretable perturbation-response programs.

Erdun Gao, Liang Zhang, Jake Fawkes et al.

Randomized Controlled Trials (RCTs) represent the gold standard for causal inference yet remain a scarce resource. While large-scale observational data is often available, it is utilized only for retrospective fusion, and remains discarded in prospective trial design due to bias concerns. We argue this "tabula rasa" data acquisition strategy is fundamentally inefficient. In this work, we propose Active Residual Learning, a new paradigm that leverages the observational model as a foundational prior. This approach shifts the experimental focus from learning target causal quantities from scratch to efficiently estimating the residuals required to correct observational bias. To operationalize this, we introduce the R-Design framework. Theoretically, we establish two key advantages: (1) a structural efficiency gap, proving that estimating smooth residual contrasts admits strictly faster convergence rates than reconstructing full outcomes; and (2) information efficiency, where we quantify the redundancy in standard parameter-based acquisition (e.g., BALD), demonstrating that such baselines waste budget on task-irrelevant nuisance uncertainty. We propose R-EPIG (Residual Expected Predictive Information Gain), a unified criterion that directly targets the causal estimand, minimizing residual uncertainty for estimation or clarifying decision boundaries for policy. Experiments on synthetic and semi-synthetic benchmarks demonstrate that R-Design significantly outperforms baselines, confirming that repairing a biased model is far more efficient than learning one from scratch.

Zuopeng Yang, Jiluan Fan, Anli Yan et al.

Multimodal Large Language Models (MLLMs) bridge the gap between visual and textual data, enabling a range of advanced applications. However, complex internal interactions among visual elements and their alignment with text can introduce vulnerabilities, which may be exploited to bypass safety mechanisms. To address this, we analyze the relationship between image content and task and find that the complexity of subimages, rather than their content, is key. Building on this insight, we propose the Distraction Hypothesis, followed by a novel framework called Contrasting Subimage Distraction Jailbreaking (CS-DJ), to achieve jailbreaking by disrupting MLLMs alignment through multi-level distraction strategies. CS-DJ consists of two components: structured distraction, achieved through query decomposition that induces a distributional shift by fragmenting harmful prompts into sub-queries, and visual-enhanced distraction, realized by constructing contrasting subimages to disrupt the interactions among visual elements within the model. This dual strategy disperses the model's attention, reducing its ability to detect and mitigate harmful content. Extensive experiments across five representative scenarios and four popular closed-source MLLMs, including GPT-4o-mini, GPT-4o, GPT-4V, and Gemini-1.5-Flash, demonstrate that CS-DJ achieves average success rates of 52.40% for the attack success rate and 74.10% for the ensemble attack success rate. These results reveal the potential of distraction-based approaches to exploit and bypass MLLMs' defenses, offering new insights for attack strategies.

Boming Xia, Liming Zhu, Erdun Gao et al.

Uncertainty in large language model (LLM)-based systems is often studied at the level of a single model output, yet deployed LLM applications are compound systems in which uncertainty is transformed and reused across model internals, workflow stages, component boundaries, persistent state, and human or organisational processes. Without principled treatment of how uncertainty is carried and reused across these boundaries, early errors can propagate and compound in ways that are difficult to detect and govern. This paper develops a systems-level account of uncertainty propagation. It introduces a conceptual framing for characterising propagated uncertainty signals, presents a structured taxonomy spanning intra-model (P1), system-level (P2), and socio-technical (P3) propagation mechanisms, synthesises cross-cutting engineering insights, and identifies five open research challenges.

Yuhang Liu, Dong Gong, Yichao Cai et al.

The remarkable achievements of large language models (LLMs) have led many to conclude that they exhibit a form of intelligence. This is as opposed to explanations of their capabilities based on their ability to perform relatively simple manipulations of vast volumes of data. To illuminate the distinction between these explanations, we introduce a novel generative model that generates tokens on the basis of human-interpretable concepts represented as latent discrete variables. Under mild conditions, even when the mapping from the latent space to the observed space is non-invertible, we establish an identifiability result, i.e., the representations learned by LLMs through next-token prediction can be approximately modeled as the logarithm of the posterior probabilities of these latent discrete concepts given input context, up to an invertible linear transformation. This theoretical finding not only provides evidence that LLMs capture underlying generative factors, but also provide a unified prospective for understanding of the linear representation hypothesis. Taking this a step further, our finding motivates a reliable evaluation of sparse autoencoders by treating the performance of supervised concept extractors as an upper bound. Pushing this idea even further, it inspires a structural variant that enforces dependence among latent concepts in addition to promoting sparsity. Empirically, we validate our theoretical results through evaluations on both simulation data and the Pythia, Llama, and DeepSeek model families, and demonstrate the effectiveness of our structured sparse autoencoder.

Yuhang Liu, Zhen Zhang, Dong Gong et al.

Directed acyclic graphs (DAGs) are fundamental graph structures in causal modeling, but identifying the desired DAG from observational data often requires strong assumptions that may not hold in real-world scenarios, especially for latent causal models and complex multimodal data. This raises the question of whether we can relax or bypass the DAG assumption while maintaining practical utility. In this work, we propose a novel latent partial causal model for multimodal data, featuring two latent coupled variables, connected by an undirected edge, to represent the transfer of knowledge across modalities. Under specific statistical assumptions, we establish an identifiability result, demonstrating that representations learned by multimodal contrastive learning correspond to the latent coupled variables up to a trivial transformation. This result deepens our understanding of the why multimodal contrastive learning works, highlights its potential for disentanglement, and expands the utility of pre-trained models like CLIP. Synthetic experiments confirm the robustness of our findings, even when the assumptions are partially violated. Most importantly, experiments on a pre-trained CLIP model embodies disentangled representations, enabling few-shot learning and improving domain generalization across diverse real-world datasets. Together, these contributions push the boundaries of multimodal contrastive learning, both theoretically and, crucially, in practical applications.

Yichao Cai, Yuhang Liu, Erdun Gao et al.

Multimodal representation learning, exemplified by multimodal contrastive learning (MMCL) using image-text pairs, aims to learn powerful representations by aligning cues across modalities. This approach relies on the core assumption that the exemplar image-text pairs constitute two representations of an identical concept. However, recent research has revealed that real-world datasets often exhibit cross-modal misalignment. There are two distinct viewpoints on how to address this issue: one suggests mitigating the misalignment, and the other leveraging it. We seek here to reconcile these seemingly opposing perspectives, and to provide a practical guide for practitioners. Using latent variable models we thus formalize cross-modal misalignment by introducing two specific mechanisms: Selection bias, where some semantic variables are absent in the text, and perturbation bias, where semantic variables are altered -- both leading to misalignment in data pairs. Our theoretical analysis demonstrates that, under mild assumptions, the representations learned by MMCL capture exactly the information related to the subset of the semantic variables invariant to selection and perturbation biases. This provides a unified perspective for understanding misalignment. Based on this, we further offer actionable insights into how misalignment should inform the design of real-world ML systems. We validate our theoretical findings via extensive empirical studies on both synthetic data and real image-text datasets, shedding light on the nuanced impact of cross-modal misalignment on multimodal representation learning.

Erdun Gao, Jake Fawkes, Dino Sejdinovic

Estimating the Conditional Average Treatment Effect (CATE) is often constrained by the high cost of obtaining outcome measurements, making active learning essential. However, conventional active learning strategies suffer from a fundamental objective mismatch. They are designed to reduce uncertainty in model parameters or in observable factual outcomes, failing to directly target the unobservable causal quantities that are the true objects of interest. To address this misalignment, we introduce the principle of causal objective alignment, which posits that acquisition functions should target unobservable causal quantities, such as the potential outcomes and the CATE, rather than indirect proxies. We operationalize this principle through the Causal-EPIG framework, which adapts the information-theoretic criterion of Expected Predictive Information Gain (EPIG) to explicitly quantify the value of a query in terms of reducing uncertainty about unobservable causal quantities. From this unified framework, we derive two distinct strategies that embody a fundamental trade-off: a comprehensive approach that robustly models the full causal mechanisms via the joint potential outcomes, and a focused approach that directly targets the CATE estimand for maximum sample efficiency. Extensive experiments demonstrate that our strategies consistently outperform standard baselines, and crucially, reveal that the optimal strategy is context-dependent, contingent on the base estimator and data complexity. Our framework thus provides a principled guide for sample-efficient CATE estimation in practice.

Erdun Gao, Dino Sejdinovic

Estimating causal quantities (CQs) typically requires large datasets, which can be expensive to obtain, especially when measuring individual outcomes is costly. This challenge highlights the importance of sample-efficient active learning strategies. To address the narrow focus of prior work on the conditional average treatment effect, we formalize the broader task of Actively estimating Causal Quantities (ActiveCQ) and propose a unified framework for this general problem. Built upon the insight that many CQs are integrals of regression functions, our framework models the regression function with a Gaussian Process. For the distribution component, we explore both a baseline using explicit density estimators and a more integrated method using conditional mean embeddings in a reproducing kernel Hilbert space. This latter approach offers key advantages: it bypasses explicit density estimation, operates within the same function space as the GP, and adaptively refines the distributional model after each update. Our framework enables the principled derivation of acquisition strategies from the CQ's posterior uncertainty; we instantiate this principle with two utility functions based on information gain and total variance reduction. A range of simulated and semi-synthetic experiments demonstrate that our principled framework significantly outperforms relevant baselines, achieving substantial gains in sample efficiency across a variety of CQs.

Xinshu Li, Ruoyu Wang, Erdun Gao et al.

Prompt learning has garnered attention for its efficiency over traditional model training and fine-tuning. However, existing methods, constrained by inadequate theoretical foundations, encounter difficulties in achieving causally invariant prompts, ultimately falling short of capturing robust features that generalize effectively across categories. To address these challenges, we introduce the $\textit{\textbf{DiCap}}$ model, a theoretically grounded $\textbf{Di}$ffusion-based $\textbf{C}$ounterf$\textbf{a}$ctual $\textbf{p}$rompt learning framework, which leverages a diffusion process to iteratively sample gradients from the marginal and conditional distributions of the causal model, guiding the generation of counterfactuals that satisfy the minimal sufficiency criterion. Grounded in rigorous theoretical derivations, this approach guarantees the identifiability of counterfactual outcomes while imposing strict bounds on estimation errors. We further employ a contrastive learning framework that leverages the generated counterfactuals, thereby enabling the refined extraction of prompts that are precisely aligned with the causal features of the data. Extensive experimental results demonstrate that our method performs excellently across tasks such as image classification, image-text retrieval, and visual question answering, with particularly strong advantages in unseen categories.

Erdun Gao, Junjia Chen, Li Shen et al.

To date, most directed acyclic graphs (DAGs) structure learning approaches require data to be stored in a central server. However, due to the consideration of privacy protection, data owners gradually refuse to share their personalized raw data to avoid private information leakage, making this task more troublesome by cutting off the first step. Thus, a puzzle arises: \textit{how do we discover the underlying DAG structure from decentralized data?} In this paper, focusing on the additive noise models (ANMs) assumption of data generation, we take the first step in developing a gradient-based learning framework named FedDAG, which can learn the DAG structure without directly touching the local data and also can naturally handle the data heterogeneity. Our method benefits from a two-level structure of each local model. The first level structure learns the edges and directions of the graph and communicates with the server to get the model information from other clients during the learning procedure, while the second level structure approximates the mechanisms among variables and personally updates on its own data to accommodate the data heterogeneity. Moreover, FedDAG formulates the overall learning task as a continuous optimization problem by taking advantage of an equality acyclicity constraint, which can be solved by gradient descent methods to boost the searching efficiency. Extensive experiments on both synthetic and real-world datasets verify the efficacy of the proposed method.

Erdun Gao, Zhibin Pan, Xinyi Gao

In traditional reversible data hiding (RDH) methods, researchers pay attention to enlarge the embedding capacity (EC) and to reduce the embedding distortion (ED). Recently, a completely novel RDH algorithm was developed to embed secret data into color image without changing the corresponding grayscale [1], which largely expands the applications of RDH. In [1], for color image, channel R and channel B are exploited to carry secret information, channel G is adjusted for balancing the modifications of channel R and channel B to keep the invariance of grayscale. However, we found that the embedding performance (EP) of that method is still unsatisfied and could be further enhanced. To improve the EP, an adaptive embedding pattern is introduced to enhance the competence of algorithm for selectively embedding different bits of secret data into pixels according to context information. Moreover, a novel two-level predictor is designed by uniting two normal predictors for reducing the ED for embedding more bits. Experimental results demonstrate that, compared to the previous method, our scheme could significantly enhance the image fidelity while keeping the grayscale invariant.