Lingjing Kong

Lingjing Kong, Martin Q. Ma, Guangyi Chen et al.

Masked autoencoder (MAE), a simple and effective self-supervised learning framework based on the reconstruction of masked image regions, has recently achieved prominent success in a variety of vision tasks. Despite the emergence of intriguing empirical observations on MAE, a theoretically principled understanding is still lacking. In this work, we formally characterize and justify existing empirical insights and provide theoretical guarantees of MAE. We formulate the underlying data-generating process as a hierarchical latent variable model and show that under reasonable assumptions, MAE provably identifies a set of latent variables in the hierarchical model, explaining why MAE can extract high-level information from pixels. Further, we show how key hyperparameters in MAE (the masking ratio and the patch size) determine which true latent variables to be recovered, therefore influencing the level of semantic information in the representation. Specifically, extremely large or small masking ratios inevitably lead to low-level representations. Our theory offers coherent explanations of existing empirical observations and provides insights for potential empirical improvements and fundamental limitations of the masking-reconstruction paradigm. We conduct extensive experiments to validate our theoretical insights.

Lingjing Kong, Biwei Huang, Feng Xie et al.

Identifying latent variables and causal structures from observational data is essential to many real-world applications involving biological data, medical data, and unstructured data such as images and languages. However, this task can be highly challenging, especially when observed variables are generated by causally related latent variables and the relationships are nonlinear. In this work, we investigate the identification problem for nonlinear latent hierarchical causal models in which observed variables are generated by a set of causally related latent variables, and some latent variables may not have observed children. We show that the identifiability of causal structures and latent variables (up to invertible transformations) can be achieved under mild assumptions: on causal structures, we allow for multiple paths between any pair of variables in the graph, which relaxes latent tree assumptions in prior work; on structural functions, we permit general nonlinearity and multi-dimensional continuous variables, alleviating existing work's parametric assumptions. Specifically, we first develop an identification criterion in the form of novel identifiability guarantees for an elementary latent variable model. Leveraging this criterion, we show that both causal structures and latent variables of the hierarchical model can be identified asymptotically by explicitly constructing an estimation procedure. To the best of our knowledge, our work is the first to establish identifiability guarantees for both causal structures and latent variables in nonlinear latent hierarchical models.

Lingjing Kong, Shaoan Xie, Weiran Yao et al.

Unsupervised domain adaptation is critical to many real-world applications where label information is unavailable in the target domain. In general, without further assumptions, the joint distribution of the features and the label is not identifiable in the target domain. To address this issue, we rely on the property of minimal changes of causal mechanisms across domains to minimize unnecessary influences of distribution shifts. To encode this property, we first formulate the data-generating process using a latent variable model with two partitioned latent subspaces: invariant components whose distributions stay the same across domains and sparse changing components that vary across domains. We further constrain the domain shift to have a restrictive influence on the changing components. Under mild conditions, we show that the latent variables are partially identifiable, from which it follows that the joint distribution of data and labels in the target domain is also identifiable. Given the theoretical insights, we propose a practical domain adaptation framework called iMSDA. Extensive experimental results reveal that iMSDA outperforms state-of-the-art domain adaptation algorithms on benchmark datasets, demonstrating the effectiveness of our framework.

Lingjing Kong, Shaoan Xie, Guangyi Chen et al.

Deep generative models, while revolutionizing fields like image and text generation, largely operate as opaque black boxes, hindering human understanding, control, and alignment. While methods like sparse autoencoders (SAEs) show remarkable empirical success, they often lack theoretical guarantees, risking subjective insights. Our primary objective is to establish a principled foundation for interpretable generative models. We demonstrate that the principle of causal minimality -- favoring the simplest causal explanation -- can endow the latent representations of diffusion vision and autoregressive language models with clear causal interpretation and robust, component-wise identifiable control. We introduce a novel theoretical framework for hierarchical selection models, where higher-level concepts emerge from the constrained composition of lower-level variables, better capturing the complex dependencies in data generation. Under theoretically derived minimality conditions (manifesting as sparsity or compression constraints), we show that learned representations can be equivalent to the true latent variables of the data-generating process. Empirically, applying these constraints to leading generative models allows us to extract their innate hierarchical concept graphs, offering fresh insights into their internal knowledge organization. Furthermore, these causally grounded concepts serve as levers for fine-grained model steering, paving the way for transparent, reliable systems.

Lingjing Kong, Shaoan Xie, Yang Jiao et al.

Compositional generalization -- the ability to understand and generate novel combinations of learned concepts -- enables models to extend their capabilities beyond limited experiences. While effective, the data structures and principles that enable this crucial capability remain poorly understood. We propose that compositional generalization fundamentally requires decomposing high-level concepts into basic, low-level concepts that can be recombined across similar contexts, similar to how humans draw analogies between concepts. For example, someone who has never seen a peacock eating rice can envision this scene by relating it to their previous observations of a chicken eating rice. In this work, we formalize these intuitive processes using principles of causal modularity and minimal changes. We introduce a hierarchical data-generating process that naturally encodes different levels of concepts and their interaction mechanisms. Theoretically, we demonstrate that this approach enables compositional generalization supporting complex relations between composed concepts, advancing beyond prior work that assumes simpler interactions like additive effects. Critically, we also prove that this latent hierarchical structure is provably recoverable (identifiable) from observable data like text-image pairs, a necessary step for learning such a generative process. To validate our theory, we apply insights from our theoretical framework and achieve significant improvements on benchmark datasets.

Hanqi Yan, Lingjing Kong, Lin Gui et al.

Counterfactual generation lies at the core of various machine learning tasks, including image translation and controllable text generation. This generation process usually requires the identification of the disentangled latent representations, such as content and style, that underlie the observed data. However, it becomes more challenging when faced with a scarcity of paired data and labeling information. Existing disentangled methods crucially rely on oversimplified assumptions, such as assuming independent content and style variables, to identify the latent variables, even though such assumptions may not hold for complex data distributions. For instance, food reviews tend to involve words like tasty, whereas movie reviews commonly contain words such as thrilling for the same positive sentiment. This problem is exacerbated when data are sampled from multiple domains since the dependence between content and style may vary significantly over domains. In this work, we tackle the domain-varying dependence between the content and the style variables inherent in the counterfactual generation task. We provide identification guarantees for such latent-variable models by leveraging the relative sparsity of the influences from different latent variables. Our theoretical insights enable the development of a doMain AdapTive counTerfactual gEneration model, called (MATTE). Our theoretically grounded framework achieves state-of-the-art performance in unsupervised style transfer tasks, where neither paired data nor style labels are utilized, across four large-scale datasets. Code is available at https://github.com/hanqi-qi/Matte.git

Haolin Chen, Deon Metelski, Leon Qi et al.

End-to-end automation of realistic healthcare operations stresses three capabilities underrepresented in current benchmarks: policy density, decisions must be grounded in a large library of medical, insurance, and operational rules; Multi-role composition: a single task requires the agent to play multiple roles with handoffs; and multilateral interaction: intermediate workflow steps are multi-turn dialogs, such as peer-to-peer review and patient outreach. We introduce $χ$-Bench, a benchmark of long-horizon healthcare workflows across three domains: provider prior authorization, payer utilization management, and care management. Each task hands the agent a clinical case in a high-fidelity simulator of 20 healthcare apps exposed via 87 MCP tools, which it must drive to a terminal status through tool calls and writing the role's artifacts, guided by a 1,290+ document managed-care operations handbook skill. Across 30 agent harness/models configurations, the best agent resolves only 28.0% of tasks, no agent clears 20% on strict pass^3, and executing all tasks in a single session slumps the performance to 3.8%. These results raise the hypothesis that similar gaps are likely to surface in other policy-dense, role-composed, irreversible enterprise domains.

Shaoan Xie, Lingjing Kong, Yujia Zheng et al. · stanford

Contrastive Language-Image Pre-training (CLIP)~\citep{radford2021learning} has emerged as a pivotal model in computer vision and multimodal learning, achieving state-of-the-art performance at aligning visual and textual representations through contrastive learning. However, CLIP struggles with potential information misalignment in many image-text datasets and suffers from entangled representation. On the one hand, short captions for a single image in datasets like MSCOCO may describe disjoint regions in the image, leaving the model uncertain about which visual features to retain or disregard. On the other hand, directly aligning long captions with images can lead to the retention of entangled details, preventing the model from learning disentangled, atomic concepts -- ultimately limiting its generalization on certain downstream tasks involving short prompts. In this paper, we establish theoretical conditions that enable flexible alignment between textual and visual representations across varying levels of granularity. Specifically, our framework ensures that a model can not only \emph{preserve} cross-modal semantic information in its entirety but also \emph{disentangle} visual representations to capture fine-grained textual concepts. Building on this foundation, we introduce \ours, a novel approach that identifies and aligns the most relevant visual and textual representations in a modular manner. Superior performance across various tasks demonstrates its capability to handle information misalignment and supports our identification theory. The code is available at https://github.com/Mid-Push/SmartCLIP.

Yunlong Deng, Guangyi Chen, Tianpei Gu et al. · stanford

Vision-Language Models (VLMs) integrate visual knowledge with the analytical capabilities of Large Language Models (LLMs) through supervised visual instruction tuning, using image-question-answer triplets. However, the potential of VLMs trained without supervised instruction remains largely unexplored. This study validates that VLMs possess inherent self-refinement capabilities, enabling them to generate high-quality supervised data without external inputs and thereby learn autonomously. Specifically, to stimulate the self-refinement ability of VLMs, we propose a self-refinement framework based on a Triangular Consistency principle: within the image-query-answer triangle, any masked elements should be consistently and accurately reconstructed. The framework involves three steps: (1) We enable the instruction generation ability of VLMs by adding multi-task instruction tuning like image$\rightarrow$question-answer or image-answer$\rightarrow$question. (2) We generate image-query-answer triplets from unlabeled images and use the Triangular Consistency principle for filtering. (3) The model is further updated using the filtered synthetic data. To investigate the underlying mechanisms behind this self-refinement capability, we conduct a theoretical analysis from a causal perspective. Using the widely recognized LLaVA-1.5 as our baseline, our experiments reveal that the model can autonomously achieve consistent, though deliberately modest, improvements across multiple benchmarks without any external supervision, such as human annotations or environmental feedback. We expect that the insights of this study on the self-refinement ability of VLMs can inspire future research on the learning mechanism of VLMs. Code is available at https://github.com/dengyl20/SRF-LLaVA-1.5.

Yuewen Sun, Lingjing Kong, Guangyi Chen et al.

Prevalent in biomedical applications (e.g., human phenotype research), multimodal datasets can provide valuable insights into the underlying physiological mechanisms. However, current machine learning (ML) models designed to analyze these datasets often lack interpretability and identifiability guarantees, which are essential for biomedical research. Recent advances in causal representation learning have shown promise in identifying interpretable latent causal variables with formal theoretical guarantees. Unfortunately, most current work on multimodal distributions either relies on restrictive parametric assumptions or yields only coarse identification results, limiting their applicability to biomedical research that favors a detailed understanding of the mechanisms. In this work, we aim to develop flexible identification conditions for multimodal data and principled methods to facilitate the understanding of biomedical datasets. Theoretically, we consider a nonparametric latent distribution (c.f., parametric assumptions in previous work) that allows for causal relationships across potentially different modalities. We establish identifiability guarantees for each latent component, extending the subspace identification results from previous work. Our key theoretical contribution is the structural sparsity of causal connections between modalities, which, as we will discuss, is natural for a large collection of biomedical systems. Empirically, we present a practical framework to instantiate our theoretical insights. We demonstrate the effectiveness of our approach through extensive experiments on both numerical and synthetic datasets. Results on a real-world human phenotype dataset are consistent with established biomedical research, validating our theoretical and methodological framework.

Lingjing Kong, Guangyi Chen, Petar Stojanov et al. · pku

Canonical work handling distribution shifts typically necessitates an entire target distribution that lands inside the training distribution. However, practical scenarios often involve only a handful of target samples, potentially lying outside the training support, which requires the capability of extrapolation. In this work, we aim to provide a theoretical understanding of when extrapolation is possible and offer principled methods to achieve it without requiring an on-support target distribution. To this end, we formulate the extrapolation problem with a latent-variable model that embodies the minimal change principle in causal mechanisms. Under this formulation, we cast the extrapolation problem into a latent-variable identification problem. We provide realistic conditions on shift properties and the estimation objectives that lead to identification even when only one off-support target sample is available, tackling the most challenging scenarios. Our theory reveals the intricate interplay between the underlying manifold's smoothness and the shift properties. We showcase how our theoretical results inform the design of practical adaptation algorithms. Through experiments on both synthetic and real-world data, we validate our theoretical findings and their practical implications.

Yuejiang Liu, Fan Feng, Lingjing Kong et al.

General-purpose world models promise scalable policy evaluation, optimization, and planning, yet achieving the required level of robustness remains challenging. Unlike policy learning, which primarily focuses on optimal actions, a world model must be reliable over a much broader range of suboptimal actions, which are often insufficiently covered by action-labeled interaction data. To address this challenge, we propose World Action Verifier (WAV), a framework that enables world models to identify their own prediction errors and self-improve. The key idea is to decompose action-conditioned state prediction into two factors -- state plausibility and action reachability -- and verify each separately. We show that these verification problems can be substantially easier than predicting future states due to two underlying asymmetries: the broader availability of action-free data and the lower dimensionality of action-relevant features. Leveraging these asymmetries, we augment a world model with (i) a diverse subgoal generator obtained from video corpora and (ii) a sparse inverse model that infers actions from a subset of state features. By enforcing cycle consistency among generated subgoals, inferred actions, and forward rollouts, WAV provides an effective verification mechanism in under-explored regimes, where existing methods typically fail. Across nine tasks spanning MiniGrid, RoboMimic, and ManiSkill, our method achieves 2x higher sample efficiency while improving downstream policy performance by 18%.

Shaoan Xie, Lingjing Kong, Xiangchen Song et al.

Diffusion language models (dLLMs) offer a promising, non-autoregressive paradigm for text generation, yet training them for complex reasoning remains a key challenge. Current reinforcement learning approaches often rely on sparse, outcome-based rewards, which can reinforce flawed reasoning paths that lead to coincidentally correct answers. We argue that this stems from a fundamental mismatch with the natural structure of reasoning. We first propose a theoretical framework that formalizes complex problem solving as a hierarchical selection process, where an intractable global constraint is decomposed into a series of simpler, localized logical steps. This framework provides a principled foundation for algorithm design, including theoretical insights into the identifiability of this latent reasoning structure. Motivated by this theory, we identify unstructured refinement -- a failure mode where a model's iterative steps do not contribute meaningfully to the solution -- as a core deficiency in existing methods. We then introduce Step-Aware Policy Optimization (SAPO), a novel RL algorithm that aligns the dLLM's denoising process with the latent reasoning hierarchy. By using a process-based reward function that encourages incremental progress, SAPO guides the model to learn structured, coherent reasoning paths. Our empirical results show that this principled approach significantly improves performance on challenging reasoning benchmarks and enhances the interpretability of the generation process.

Yunlong Deng, Boyang Sun, Yan Li et al. · stanford

Due to their inherent complexity, reasoning tasks have long been regarded as rigorous benchmarks for assessing the capabilities of machine learning models, especially large language models (LLMs). Although humans can solve these tasks with ease, existing models, even after extensive pre-training and post-training at scale, still fail to perform reasoning reliably. In this paper, we revisit reasoning tasks from a causal perspective, seeking to understand their behavior in latent space and to offer insights for addressing their challenges. Specifically, we cast reasoning tasks as a selection mechanism, in which high-level logical concepts function as selection operators on the given observations, such as, identifying the correct answer in a math problem or filling the appropriate entry in Sudoku. We emphasize two key properties of this formulation that shed light on the difficulty of reasoning tasks. First, the latent space exceeds the observation space in complexity, even when the correct answer is fully determined by the observed input. Second, the latent variables, corresponding to logical thought, are densely structured and exhibit strong dependencies. Building on this formulation, we introduce a framework, called SR$^2$, that incorporates the estimated latent variables as feedback into the selection mechanism, thereby facilitating the learning of dense dependencies among latent representations. The framework consists of three key modules: reflective representation learning, dependency self-refinement, and periodic intermediate alignment. Experimentally, we show that our approach yields significant gains in reasoning accuracy, for example, attaining over 10$\%$ improvement in performance with 8$\times$ fewer parameters on the Sudoku and Maze tasks over the recent advances.

Lingjing Kong, Guangyi Chen, Biwei Huang et al.

Learning concepts from natural high-dimensional data (e.g., images) holds potential in building human-aligned and interpretable machine learning models. Despite its encouraging prospect, formalization and theoretical insights into this crucial task are still lacking. In this work, we formalize concepts as discrete latent causal variables that are related via a hierarchical causal model that encodes different abstraction levels of concepts embedded in high-dimensional data (e.g., a dog breed and its eye shapes in natural images). We formulate conditions to facilitate the identification of the proposed causal model, which reveals when learning such concepts from unsupervised data is possible. Our conditions permit complex causal hierarchical structures beyond latent trees and multi-level directed acyclic graphs in prior work and can handle high-dimensional, continuous observed variables, which is well-suited for unstructured data modalities such as images. We substantiate our theoretical claims with synthetic data experiments. Further, we discuss our theory's implications for understanding the underlying mechanisms of latent diffusion models and provide corresponding empirical evidence for our theoretical insights.

Fei Mi, Wanhao Zhou, Fengyu Cai et al.

As the labeling cost for different modules in task-oriented dialog (ToD) systems is expensive, a major challenge is to train different modules with the least amount of labeled data. Recently, large-scale pre-trained language models, have shown promising results for few-shot learning in ToD. In this paper, we devise a self-training approach to utilize the abundant unlabeled dialog data to further improve state-of-the-art pre-trained models in few-shot learning scenarios for ToD systems. Specifically, we propose a self-training approach that iteratively labels the most confident unlabeled data to train a stronger Student model. Moreover, a new text augmentation technique (GradAug) is proposed to better train the Student by replacing non-crucial tokens using a masked language model. We conduct extensive experiments and present analyses on four downstream tasks in ToD, including intent classification, dialog state tracking, dialog act prediction, and response selection. Empirical results demonstrate that the proposed self-training approach consistently improves state-of-the-art pre-trained models (BERT, ToD-BERT) when only a small number of labeled data are available.

Lingjing Kong, Tao Lin, Anastasia Koloskova et al.

Decentralized training of deep learning models enables on-device learning over networks, as well as efficient scaling to large compute clusters. Experiments in earlier works reveal that, even in a data-center setup, decentralized training often suffers from the degradation in the quality of the model: the training and test performance of models trained in a decentralized fashion is in general worse than that of models trained in a centralized fashion, and this performance drop is impacted by parameters such as network size, communication topology and data partitioning. We identify the changing consensus distance between devices as a key parameter to explain the gap between centralized and decentralized training. We show in theory that when the training consensus distance is lower than a critical quantity, decentralized training converges as fast as the centralized counterpart. We empirically validate that the relation between generalization performance and consensus distance is consistent with this theoretical observation. Our empirical insights allow the principled design of better decentralized training schemes that mitigate the performance drop. To this end, we provide practical training guidelines and exemplify its effectiveness on the data-center setup as the important first step.

Tao Lin, Lingjing Kong, Sebastian U. Stich et al.

Federated Learning (FL) is a machine learning setting where many devices collaboratively train a machine learning model while keeping the training data decentralized. In most of the current training schemes the central model is refined by averaging the parameters of the server model and the updated parameters from the client side. However, directly averaging model parameters is only possible if all models have the same structure and size, which could be a restrictive constraint in many scenarios. In this work we investigate more powerful and more flexible aggregation schemes for FL. Specifically, we propose ensemble distillation for model fusion, i.e. training the central classifier through unlabeled data on the outputs of the models from the clients. This knowledge distillation technique mitigates privacy risk and cost to the same extent as the baseline FL algorithms, but allows flexible aggregation over heterogeneous client models that can differ e.g. in size, numerical precision or structure. We show in extensive empirical experiments on various CV/NLP datasets (CIFAR-10/100, ImageNet, AG News, SST2) and settings (heterogeneous models/data) that the server model can be trained much faster, requiring fewer communication rounds than any existing FL technique so far.

Tao Lin, Lingjing Kong, Sebastian U. Stich et al.

Deep learning networks are typically trained by Stochastic Gradient Descent (SGD) methods that iteratively improve the model parameters by estimating a gradient on a very small fraction of the training data. A major roadblock faced when increasing the batch size to a substantial fraction of the training data for improving training time is the persistent degradation in performance (generalization gap). To address this issue, recent work propose to add small perturbations to the model parameters when computing the stochastic gradients and report improved generalization performance due to smoothing effects. However, this approach is poorly understood; it requires often model-specific noise and fine-tuning. To alleviate these drawbacks, we propose to use instead computationally efficient extrapolation (extragradient) to stabilize the optimization trajectory while still benefiting from smoothing to avoid sharp minima. This principled approach is well grounded from an optimization perspective and we show that a host of variations can be covered in a unified framework that we propose. We prove the convergence of this novel scheme and rigorously evaluate its empirical performance on ResNet, LSTM, and Transformer. We demonstrate that in a variety of experiments the scheme allows scaling to much larger batch sizes than before whilst reaching or surpassing SOTA accuracy.