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Prevalent in biological applications (e.g., human phenotype measurements), multimodal datasets can provide valuable insights into the underlying biological mechanisms. However, current machine learning models designed to analyze such datasets still lack interpretability and theoretical guarantees, which are essential to biological applications. Recent advances in causal representation learning have shown promise in uncovering the interpretable latent causal variables with formal theoretical certificates. Unfortunately, existing works for multimodal distributions either rely on restrictive parametric assumptions or provide rather coarse identification results, limiting their applicability to biological research which 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 biological datasets. Theoretically, we consider a flexible nonparametric latent distribution (c.f., parametric assumptions in prior work) permitting causal relationships across potentially different modalities. We establish identifiability guarantees for each latent component, extending the subspace identification results from prior work. Our key theoretical ingredient is the structural sparsity of the causal connections among distinct modalities, which, as we will discuss, is natural for a large collection of biological systems. Empirically, we propose 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 medical research, validating our theoretical and methodological framework.

Causal Temporal Representation Learning (Ctrl) methods aim to identify the temporal causal dynamics of complex nonstationary temporal sequences. Despite the success of existing Ctrl methods, they require either directly observing the domain variables or assuming a Markov prior on them. Such requirements limit the application of these methods in real-world scenarios when we do not have such prior knowledge of the domain variables. To address this problem, this work adopts a sparse transition assumption, aligned with intuitive human understanding, and presents identifiability results from a theoretical perspective. In particular, we explore under what conditions on the significance of the variability of the transitions we can build a model to identify the distribution shifts. Based on the theoretical result, we introduce a novel framework, Causal Temporal Representation Learning with Nonstationary Sparse Transition (CtrlNS), designed to leverage the constraints on transition sparsity and conditional independence to reliably identify both distribution shifts and latent factors. Our experimental evaluations on synthetic and real-world datasets demonstrate significant improvements over existing baselines, highlighting the effectiveness of our approach.

Identifying the causal relations between interested variables plays a pivotal role in representation learning as it provides deep insights into the dataset. Identifiability, as the central theme of this approach, normally hinges on leveraging data from multiple distributions (intervention, distribution shift, time series, etc.). Despite the exciting development in this field, a practical but often overlooked problem is: what if those distribution shifts happen sequentially? In contrast, any intelligence possesses the capacity to abstract and refine learned knowledge sequentially -- lifelong learning. In this paper, with a particular focus on the nonlinear independent component analysis (ICA) framework, we move one step forward toward the question of enabling models to learn meaningful (identifiable) representations in a sequential manner, termed continual causal representation learning. We theoretically demonstrate that model identifiability progresses from a subspace level to a component-wise level as the number of distributions increases. Empirically, we show that our method achieves performance comparable to nonlinear ICA methods trained jointly on multiple offline distributions and, surprisingly, the incoming new distribution does not necessarily benefit the identification of all latent variables., Comment: 9 pages, 5 Figures

Recent works have introduced GNN-to-MLP knowledge distillation (KD) frameworks to combine both GNN's superior performance and MLP's fast inference speed. However, existing KD frameworks are primarily designed for node classification within single graphs, leaving their applicability to graph classification largely unexplored. Two main challenges arise when extending KD for node classification to graph classification: (1) The inherent sparsity of learning signals due to soft labels being generated at the graph level; (2) The limited expressiveness of student MLPs, especially in datasets with limited input feature spaces. To overcome these challenges, we introduce MuGSI, a novel KD framework that employs Multi-granularity Structural Information for graph classification. Specifically, we propose multi-granularity distillation loss in MuGSI to tackle the first challenge. This loss function is composed of three distinct components: graph-level distillation, subgraph-level distillation, and node-level distillation. Each component targets a specific granularity of the graph structure, ensuring a comprehensive transfer of structural knowledge from the teacher model to the student model. To tackle the second challenge, MuGSI proposes to incorporate a node feature augmentation component, thereby enhancing the expressiveness of the student MLPs and making them more capable learners. We perform extensive experiments across a variety of datasets and different teacher/student model architectures. The experiment results demonstrate the effectiveness, efficiency, and robustness of MuGSI. Codes are publicly available at: \textbf{\url{https://github.com/tianyao-aka/MuGSI}.}, Comment: 12 pages, 4 figures. Accepted by TheWebConf2024

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.

Existing methods for multi-modal time series representation learning aim to disentangle the modality-shared and modality-specific latent variables. Although achieving notable performances on downstream tasks, they usually assume an orthogonal latent space. However, the modality-specific and modality-shared latent variables might be dependent on real-world scenarios. Therefore, we propose a general generation process, where the modality-shared and modality-specific latent variables are dependent, and further develop a \textbf{M}ulti-mod\textbf{A}l \textbf{TE}mporal Disentanglement (\textbf{MATE}) model. Specifically, our \textbf{MATE} model is built on a temporally variational inference architecture with the modality-shared and modality-specific prior networks for the disentanglement of latent variables. Furthermore, we establish identifiability results to show that the extracted representation is disentangled. More specifically, we first achieve the subspace identifiability for modality-shared and modality-specific latent variables by leveraging the pairing of multi-modal data. Then we establish the component-wise identifiability of modality-specific latent variables by employing sufficient changes of historical latent variables. Extensive experimental studies on multi-modal sensors, human activity recognition, and healthcare datasets show a general improvement in different downstream tasks, highlighting the effectiveness of our method in real-world scenarios.

Temporally causal representation learning aims to identify the latent causal process from time series observations, but most methods require the assumption that the latent causal processes do not have instantaneous relations. Although some recent methods achieve identifiability in the instantaneous causality case, they require either interventions on the latent variables or grouping of the observations, which are in general difficult to obtain in real-world scenarios. To fill this gap, we propose an \textbf{ID}entification framework for instantane\textbf{O}us \textbf{L}atent dynamics (\textbf{IDOL}) by imposing a sparse influence constraint that the latent causal processes have sparse time-delayed and instantaneous relations. Specifically, we establish identifiability results of the latent causal process based on sufficient variability and the sparse influence constraint by employing contextual information of time series data. Based on these theories, we incorporate a temporally variational inference architecture to estimate the latent variables and a gradient-based sparsity regularization to identify the latent causal process. Experimental results on simulation datasets illustrate that our method can identify the latent causal process. Furthermore, evaluations on multiple human motion forecasting benchmarks with instantaneous dependencies indicate the effectiveness of our method in real-world settings.

Temporal distribution shifts are ubiquitous in time series data. One of the most popular methods assumes that the temporal distribution shift occurs uniformly to disentangle the stationary and nonstationary dependencies. But this assumption is difficult to meet, as we do not know when the distribution shifts occur. To solve this problem, we propose to learn IDentifiable latEnt stAtes (IDEA) to detect when the distribution shifts occur. Beyond that, we further disentangle the stationary and nonstationary latent states via sufficient observation assumption to learn how the latent states change. Specifically, we formalize the causal process with environment-irrelated stationary and environment-related nonstationary variables. Under mild conditions, we show that latent environments and stationary/nonstationary variables are identifiable. Based on these theories, we devise the IDEA model, which incorporates an autoregressive hidden Markov model to estimate latent environments and modular prior networks to identify latent states. The IDEA model outperforms several latest nonstationary forecasting methods on various benchmark datasets, highlighting its advantages in real-world scenarios.

Conventional causal discovery methods rely on centralized data, which is inconsistent with the decentralized nature of data in many real-world situations. This discrepancy has motivated the development of federated causal discovery (FCD) approaches. However, existing FCD methods may be limited by their potentially restrictive assumptions of identifiable functional causal models or homogeneous data distributions, narrowing their applicability in diverse scenarios. In this paper, we propose a novel FCD method attempting to accommodate arbitrary causal models and heterogeneous data. We first utilize a surrogate variable corresponding to the client index to account for the data heterogeneity across different clients. We then develop a federated conditional independence test (FCIT) for causal skeleton discovery and establish a federated independent change principle (FICP) to determine causal directions. These approaches involve constructing summary statistics as a proxy of the raw data to protect data privacy. Owing to the nonparametric properties, FCIT and FICP make no assumption about particular functional forms, thereby facilitating the handling of arbitrary causal models. We conduct extensive experiments on synthetic and real datasets to show the efficacy of our method. The code is available at https://github.com/lokali/FedCDH.git., Comment: ICLR 2024

Identifying the underlying time-delayed latent causal processes in sequential data is vital for grasping temporal dynamics and making downstream reasoning. While some recent methods can robustly identify these latent causal variables, they rely on strict assumptions about the invertible generation process from latent variables to observed data. However, these assumptions are often hard to satisfy in real-world applications containing information loss. For instance, the visual perception process translates a 3D space into 2D images, or the phenomenon of persistence of vision incorporates historical data into current perceptions. To address this challenge, we establish an identifiability theory that allows for the recovery of independent latent components even when they come from a nonlinear and non-invertible mix. Using this theory as a foundation, we propose a principled approach, CaRiNG, to learn the CAusal RepresentatIon of Non-invertible Generative temporal data with identifiability guarantees. Specifically, we utilize temporal context to recover lost latent information and apply the conditions in our theory to guide the training process. Through experiments conducted on synthetic datasets, we validate that our CaRiNG method reliably identifies the causal process, even when the generation process is non-invertible. Moreover, we demonstrate that our approach considerably improves temporal understanding and reasoning in practical applications., Comment: To appear at ICML 2024, 24 pages

Although graph neural networks have achieved great success in the task of molecular property prediction in recent years, their generalization ability under out-of-distribution (OOD) settings is still under-explored. Different from existing methods that learn discriminative representations for prediction, we propose a generative model with semantic-components identifiability, named SCI. We demonstrate that the latent variables in this generative model can be explicitly identified into semantic-relevant (SR) and semantic-irrelevant (SI) components, which contributes to better OOD generalization by involving minimal change properties of causal mechanisms. Specifically, we first formulate the data generation process from the atom level to the molecular level, where the latent space is split into SI substructures, SR substructures, and SR atom variables. Sequentially, to reduce misidentification, we restrict the minimal changes of the SR atom variables and add a semantic latent substructure regularization to mitigate the variance of the SR substructure under augmented domain changes. Under mild assumptions, we prove the block-wise identifiability of the SR substructure and the comment-wise identifiability of SR atom variables. Experimental studies achieve state-of-the-art performance and show general improvement on 21 datasets in 3 mainstream benchmarks. Moreover, the visualization results of the proposed SCI method provide insightful case studies and explanations for the prediction results. The code is available at: https://github.com/DMIRLAB-Group/SCI.

In unsupervised causal representation learning for sequential data with time-delayed latent causal influences, strong identifiability results for the disentanglement of causally-related latent variables have been established in stationary settings by leveraging temporal structure. However, in nonstationary setting, existing work only partially addressed the problem by either utilizing observed auxiliary variables (e.g., class labels and/or domain indexes) as side information or assuming simplified latent causal dynamics. Both constrain the method to a limited range of scenarios. In this study, we further explored the Markov Assumption under time-delayed causally related process in nonstationary setting and showed that under mild conditions, the independent latent components can be recovered from their nonlinear mixture up to a permutation and a component-wise transformation, without the observation of auxiliary variables. We then introduce NCTRL, a principled estimation framework, to reconstruct time-delayed latent causal variables and identify their relations from measured sequential data only. Empirical evaluations demonstrated the reliable identification of time-delayed latent causal influences, with our methodology substantially outperforming existing baselines that fail to exploit the nonstationarity adequately and then, consequently, cannot distinguish distribution shifts., Comment: NeurIPS 2023. arXiv admin note: text overlap with arXiv:2210.13647

Multi-source domain adaptation (MSDA) methods aim to transfer knowledge from multiple labeled source domains to an unlabeled target domain. Although current methods achieve target joint distribution identifiability by enforcing minimal changes across domains, they often necessitate stringent conditions, such as an adequate number of domains, monotonic transformation of latent variables, and invariant label distributions. These requirements are challenging to satisfy in real-world applications. To mitigate the need for these strict assumptions, we propose a subspace identification theory that guarantees the disentanglement of domain-invariant and domain-specific variables under less restrictive constraints regarding domain numbers and transformation properties, thereby facilitating domain adaptation by minimizing the impact of domain shifts on invariant variables. Based on this theory, we develop a Subspace Identification Guarantee (SIG) model that leverages variational inference. Furthermore, the SIG model incorporates class-aware conditional alignment to accommodate target shifts where label distributions change with the domains. Experimental results demonstrate that our SIG model outperforms existing MSDA techniques on various benchmark datasets, highlighting its effectiveness in real-world applications., Comment: NeurIPS2023 Spotlight

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., Comment: ICML 2022

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., Comment: CVPR 2023 Highlight

Graph neural networks aim to learn representations for graph-structured data and show impressive performance, particularly in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we theoretically find that the feature space tends to be linearly correlated due to repeated aggregations. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability., Comment: Accepted by ICML'23

Recently in the field of unsupervised representation learning, strong identifiability results for disentanglement of causally-related latent variables have been established by exploiting certain side information, such as class labels, in addition to independence. However, most existing work is constrained by functional form assumptions such as independent sources or further with linear transitions, and distribution assumptions such as stationary, exponential family distribution. It is unknown whether the underlying latent variables and their causal relations are identifiable if they have arbitrary, nonparametric causal influences in between. In this work, we establish the identifiability theories of nonparametric latent causal processes from their nonlinear mixtures under fixed temporal causal influences and analyze how distribution changes can further benefit the disentanglement. We propose \textbf{\texttt{TDRL}}, a principled framework to recover time-delayed latent causal variables and identify their relations from measured sequential data under stationary environments and under different distribution shifts. Specifically, the framework can factorize unknown distribution shifts into transition distribution changes under fixed and time-varying latent causal relations, and under observation changes in observation. Through experiments, we show that time-delayed latent causal influences are reliably identified and that our approach considerably outperforms existing baselines that do not correctly exploit this modular representation of changes. Our code is available at: \url{https://github.com/weirayao/tdrl}., Comment: NeurIPS 2022. arXiv admin note: text overlap with arXiv:2202.04828

With the increasing attention to large vision-language models such as CLIP, there has been a significant amount of effort dedicated to building efficient prompts. Unlike conventional methods of only learning one single prompt, we propose to learn multiple comprehensive prompts to describe diverse characteristics of categories such as intrinsic attributes or extrinsic contexts. However, directly matching each prompt to the same visual feature is problematic, as it pushes the prompts to converge to one point. To solve this problem, we propose to apply optimal transport to match the vision and text modalities. Specifically, we first model images and the categories with visual and textual feature sets. Then, we apply a two-stage optimization strategy to learn the prompts. In the inner loop, we optimize the optimal transport distance to align visual features and prompts by the Sinkhorn algorithm, while in the outer loop, we learn the prompts by this distance from the supervised data. Extensive experiments are conducted on the few-shot recognition task and the improvement demonstrates the superiority of our method. The code is available at https://github.com/CHENGY12/PLOT., Comment: ICLR 2023, Spotlight

Human behavior has the nature of indeterminacy, which requires the pedestrian trajectory prediction system to model the multi-modality of future motion states. Unlike existing stochastic trajectory prediction methods which usually use a latent variable to represent multi-modality, we explicitly simulate the process of human motion variation from indeterminate to determinate. In this paper, we present a new framework to formulate the trajectory prediction task as a reverse process of motion indeterminacy diffusion (MID), in which we progressively discard indeterminacy from all the walkable areas until reaching the desired trajectory. This process is learned with a parameterized Markov chain conditioned by the observed trajectories. We can adjust the length of the chain to control the degree of indeterminacy and balance the diversity and determinacy of the predictions. Specifically, we encode the history behavior information and the social interactions as a state embedding and devise a Transformer-based diffusion model to capture the temporal dependencies of trajectories. Extensive experiments on the human trajectory prediction benchmarks including the Stanford Drone and ETH/UCY datasets demonstrate the superiority of our method. Code is available at https://github.com/gutianpei/MID., Comment: Accepted to CVPR2022

One critical challenge of time-series modeling is how to learn and quickly correct the model under unknown distribution shifts. In this work, we propose a principled framework, called LiLY, to first recover time-delayed latent causal variables and identify their relations from measured temporal data under different distribution shifts. The correction step is then formulated as learning the low-dimensional change factors with a few samples from the new environment, leveraging the identified causal structure. Specifically, the framework factorizes unknown distribution shifts into transition distribution changes caused by fixed dynamics and time-varying latent causal relations, and by global changes in observation. We establish the identifiability theories of nonparametric latent causal dynamics from their nonlinear mixtures under fixed dynamics and under changes. Through experiments, we show that time-delayed latent causal influences are reliably identified from observed variables under different distribution changes. By exploiting this modular representation of changes, we can efficiently learn to correct the model under unknown distribution shifts with only a few samples.

Recent progress has shown that large-scale pre-training using contrastive image-text pairs can be a promising alternative for high-quality visual representation learning from natural language supervision. Benefiting from a broader source of supervision, this new paradigm exhibits impressive transferability to downstream classification tasks and datasets. However, the problem of transferring the knowledge learned from image-text pairs to more complex dense prediction tasks has barely been visited. In this work, we present a new framework for dense prediction by implicitly and explicitly leveraging the pre-trained knowledge from CLIP. Specifically, we convert the original image-text matching problem in CLIP to a pixel-text matching problem and use the pixel-text score maps to guide the learning of dense prediction models. By further using the contextual information from the image to prompt the language model, we are able to facilitate our model to better exploit the pre-trained knowledge. Our method is model-agnostic, which can be applied to arbitrary dense prediction systems and various pre-trained visual backbones including both CLIP models and ImageNet pre-trained models. Extensive experiments demonstrate the superior performance of our methods on semantic segmentation, object detection, and instance segmentation tasks. Code is available at https://github.com/raoyongming/DenseCLIP, Comment: Accepted to CVPR2022. Project page: https://denseclip.ivg-research.xyz

Attention mechanism has demonstrated great potential in fine-grained visual recognition tasks. In this paper, we present a counterfactual attention learning method to learn more effective attention based on causal inference. Unlike most existing methods that learn visual attention based on conventional likelihood, we propose to learn the attention with counterfactual causality, which provides a tool to measure the attention quality and a powerful supervisory signal to guide the learning process. Specifically, we analyze the effect of the learned visual attention on network prediction through counterfactual intervention and maximize the effect to encourage the network to learn more useful attention for fine-grained image recognition. Empirically, we evaluate our method on a wide range of fine-grained recognition tasks where attention plays a crucial role, including fine-grained image categorization, person re-identification, and vehicle re-identification. The consistent improvement on all benchmarks demonstrates the effectiveness of our method. Code is available at https://github.com/raoyongming/CAL, Comment: Accepted to ICCV 2021