Sparsity regularization via tree-structured environments for disentangled representations

Many causal systems such as biological processes in cells can only be observed indirectly via measurements, such as gene expression. Causal representation learning -- the task of correctly mapping low-level observations to latent causal variables -- could advance scientific understanding by enabling inference of latent variables such as pathway activation. In this paper, we develop methods for inferring latent variables from multiple related datasets (environments) and tasks. As a running example, we consider the task of predicting a phenotype from gene expression, where we often collect data from multiple cell types or organisms that are related in known ways. The key insight is that the mapping from latent variables driven by gene expression to the phenotype of interest changes sparsely across closely related environments. To model sparse changes, we introduce Tree-Based Regularization (TBR), an objective that minimizes both prediction error and regularizes closely related environments to learn similar predictors. We prove that under assumptions about the degree of sparse changes, TBR identifies the true latent variables up to some simple transformations. We evaluate the theory empirically with both simulations and ground-truth gene expression data. We find that TBR recovers the latent causal variables better than related methods across these settings, even under settings that violate some assumptions of the theory.

Leveraging Structure Between Environments: Phylogenetic Regularization Incentivizes Disentangled Representations

Many causal systems such as biological processes in cells can only be observed indirectly via measurements, such as gene expression. Causal representation learning -- the task of correctly mapping low-level observations to latent causal variables -- could advance scientific understanding by enabling inference of latent variables such as pathway activation. In this paper, we develop methods for inferring latent variables from multiple related datasets (environments) and tasks. As a running example, we consider the task of predicting a phenotype from gene expression, where we often collect data from multiple cell types or organisms that are related in known ways. The key insight is that the mapping from latent variables driven by gene expression to the phenotype of interest changes sparsely across closely related environments. To model sparse changes, we introduce Tree-Based Regularization (TBR), an objective that minimizes both prediction error and regularizes closely related environments to learn similar predictors. We prove that under assumptions about the degree of sparse changes, TBR identifies the true latent variables up to some simple transformations. We evaluate the theory empirically with both simulations and ground-truth gene expression data. We find that TBR recovers the latent causal variables better than related methods across these settings, even under settings that violate some assumptions of the theory.

A Sparsity Principle for Partially Observable Causal Representation Learning

Causal representation learning aims at identifying high-level causal variables from perceptual data. Most methods assume that all latent causal variables are captured in the high-dimensional observations. We instead consider a partially observed setting, in which each measurement only provides information about a subset of the underlying causal state. Prior work has studied this setting with multiple domains or views, each depending on a fixed subset of latents. Here, we focus on learning from unpaired observations from a dataset with an instance-dependent partial observability pattern. Our main contribution is to establish two identifiability results for this setting: one for linear mixing functions without parametric assumptions on the underlying causal model, and one for piecewise linear mixing functions with Gaussian latent causal variables. Based on these insights, we propose two methods for estimating the underlying causal variables by enforcing sparsity in the inferred representation. Experiments on different simulated datasets and established benchmarks highlight the effectiveness of our approach in recovering the ground-truth latents.

Nonparametric Partial Disentanglement via Mechanism Sparsity: Sparse Actions, Interventions and Sparse Temporal Dependencies

This work introduces a novel principle for disentanglement we call mechanism sparsity regularization, which applies when the latent factors of interest depend sparsely on observed auxiliary variables and/or past latent factors. We propose a representation learning method that induces disentanglement by simultaneously learning the latent factors and the sparse causal graphical model that explains them. We develop a nonparametric identifiability theory that formalizes this principle and shows that the latent factors can be recovered by regularizing the learned causal graph to be sparse. More precisely, we show identifiablity up to a novel equivalence relation we call "consistency", which allows some latent factors to remain entangled (hence the term partial disentanglement). To describe the structure of this entanglement, we introduce the notions of entanglement graphs and graph preserving functions. We further provide a graphical criterion which guarantees complete disentanglement, that is identifiability up to permutations and element-wise transformations. We demonstrate the scope of the mechanism sparsity principle as well as the assumptions it relies on with several worked out examples. For instance, the framework shows how one can leverage multi-node interventions with unknown targets on the latent factors to disentangle them. We further draw connections between our nonparametric results and the now popular exponential family assumption. Lastly, we propose an estimation procedure based on variational autoencoders and a sparsity constraint and demonstrate it on various synthetic datasets. This work is meant to be a significantly extended version of Lachapelle et al. (2022).

Multi-View Causal Representation Learning with Partial Observability

We present a unified framework for studying the identifiability of representations learned from simultaneously observed views, such as different data modalities. We allow a partially observed setting in which each view constitutes a nonlinear mixture of a subset of underlying latent variables, which can be causally related. We prove that the information shared across all subsets of any number of views can be learned up to a smooth bijection using contrastive learning and a single encoder per view. We also provide graphical criteria indicating which latent variables can be identified through a simple set of rules, which we refer to as identifiability algebra. Our general framework and theoretical results unify and extend several previous works on multi-view nonlinear ICA, disentanglement, and causal representation learning. We experimentally validate our claims on numerical, image, and multi-modal data sets. Further, we demonstrate that the performance of prior methods is recovered in different special cases of our setup. Overall, we find that access to multiple partial views enables us to identify a more fine-grained representation, under the generally milder assumption of partial observability.

Additive Decoders for Latent Variables Identification and Cartesian-Product Extrapolation

We tackle the problems of latent variables identification and "out-of-support" image generation in representation learning. We show that both are possible for a class of decoders that we call additive, which are reminiscent of decoders used for object-centric representation learning (OCRL) and well suited for images that can be decomposed as a sum of object-specific images. We provide conditions under which exactly solving the reconstruction problem using an additive decoder is guaranteed to identify the blocks of latent variables up to permutation and block-wise invertible transformations. This guarantee relies only on very weak assumptions about the distribution of the latent factors, which might present statistical dependencies and have an almost arbitrarily shaped support. Our result provides a new setting where nonlinear independent component analysis (ICA) is possible and adds to our theoretical understanding of OCRL methods. We also show theoretically that additive decoders can generate novel images by recombining observed factors of variations in novel ways, an ability we refer to as Cartesian-product extrapolation. We show empirically that additivity is crucial for both identifiability and extrapolation on simulated data.

Synergies Between Disentanglement and Sparsity: a Multi-Task Learning Perspective

Although disentangled representations are often said to be beneficial for downstream tasks, current empirical and theoretical understanding is limited. In this work, we provide evidence that disentangled representations coupled with sparse base-predictors improve generalization. In the context of multi-task learning, we prove a new identifiability result that provides conditions under which maximally sparse base-predictors yield disentangled representations. Motivated by this theoretical result, we propose a practical approach to learn disentangled representations based on a sparsity-promoting bi-level optimization problem. Finally, we explore a meta-learning version of this algorithm based on group Lasso multiclass SVM base-predictors, for which we derive a tractable dual formulation. It obtains competitive results on standard few-shot classification benchmarks, while each task is using only a fraction of the learned representations.

Partial Disentanglement via Mechanism Sparsity

Disentanglement via mechanism sparsity was introduced recently as a principled approach to extract latent factors without supervision when the causal graph relating them in time is sparse, and/or when actions are observed and affect them sparsely. However, this theory applies only to ground-truth graphs satisfying a specific criterion. In this work, we introduce a generalization of this theory which applies to any ground-truth graph and specifies qualitatively how disentangled the learned representation is expected to be, via a new equivalence relation over models we call consistency. This equivalence captures which factors are expected to remain entangled and which are not based on the specific form of the ground-truth graph. We call this weaker form of identifiability partial disentanglement. The graphical criterion that allows complete disentanglement, proposed in an earlier work, can be derived as a special case of our theory. Finally, we enforce graph sparsity with constrained optimization and illustrate our theory and algorithm in simulations.

Discovering Latent Causal Variables via Mechanism Sparsity: A New Principle for Nonlinear ICA

It can be argued that finding an interpretable low-dimensional representation of a potentially high-dimensional phenomenon is central to the scientific enterprise. Independent component analysis (ICA) refers to an ensemble of methods which formalize this goal and provide estimation procedure for practical application. This work proposes mechanism sparsity regularization as a new principle to achieve nonlinear ICA when latent factors depend sparsely on observed auxiliary variables and/or past latent factors. We show that the latent variables can be recovered up to a permutation if one regularizes the latent mechanisms to be sparse and if some graphical criterion is satisfied by the data generating process. As a special case, our framework shows how one can leverage unknown-target interventions on the latent factors to disentangle them, thus drawing further connections between ICA and causality. We validate our theoretical results with toy experiments.

On the Convergence of Continuous Constrained Optimization for Structure Learning

Structure learning of directed acyclic graphs (DAGs) is a fundamental problem in many scientific endeavors. A new line of work, based on NOTEARS (Zheng et al., 2018), reformulates the structure learning problem as a continuous optimization one by leveraging an algebraic characterization of DAG constraint. The constrained problem is typically solved using the augmented Lagrangian method (ALM) which is often preferred to the quadratic penalty method (QPM) by virtue of its convergence result that does not require the penalty coefficient to go to infinity, hence avoiding ill-conditioning. In this work, we review the standard convergence result of the ALM and show that the required conditions are not satisfied in the recent continuous constrained formulation for learning DAGs. We demonstrate empirically that its behavior is akin to that of the QPM which is prone to ill-conditioning, thus motivating the use of second-order method in this setting. We also establish the convergence guarantee of QPM to a DAG solution, under mild conditions, based on a property of the DAG constraint term.