NeurIPS 2023 Papers

A common assumption in causal inference from observational data is that there is no hidden confounding. Yet it is, in general, impossible to verify the presence of hidden confounding factors from a single dataset. Under the assumption of independent causal mechanisms underlying the data-generating process, we demonstrate a way to detect unobserved confounders when having multiple observational datasets coming from different environments. We present a theory for testable conditional independencies that are only absent when there is hidden confounding and examine cases where we violate its assumptions: degenerate & dependent mechanisms, and faithfulness violations. Additionally, we propose a procedure to test these independencies and study its empirical finite-sample behavior using simulation studies and semi-synthetic data based on a real-world dataset. In most cases, the proposed procedure correctly predicts the presence of hidden confounding, particularly when the confounding bias is large.

Recent research indicates that the performance of machine learning models can be improved by aligning the geometry of the latent space with the underlying data structure. Rather than relying solely on Euclidean space, researchers have proposed using hyperbolic and spherical spaces with constant curvature, or combinations thereof, to better model the latent space and enhance model performance. However, little attention has been given to the problem of automatically identifying the optimal latent geometry for the downstream task. We mathematically define this novel formulation and coin it as neural latent geometry search (NLGS). More specifically, we introduce an initial attempt to search for a latent geometry composed of a product of constant curvature model spaces with a small number of query evaluations, under some simplifying assumptions. To accomplish this, we propose a novel notion of distance between candidate latent geometries based on the Gromov-Hausdorff distance from metric geometry. In order to compute the Gromov-Hausdorff distance, we introduce a mapping function that enables the comparison of different manifolds by embedding them in a common high-dimensional ambient space. We then design a graph search space based on the notion of smoothness between latent geometries and employ the calculated distances as an additional inductive bias. Finally, we use Bayesian optimization to search for the optimal latent geometry in a query-efficient manner. This is a general method which can be applied to search for the optimal latent geometry for a variety of models and downstream tasks. We perform experiments on synthetic and real-world datasets to identify the optimal latent geometry for multiple machine learning problems.

There is substantial experimental evidence that learning and memory-related behaviours rely on local synaptic changes, but the search for distinct plasticity rules has been driven by human intuition, with limited success for multiple, co-active plasticity rules in biological networks. More recently, automated meta-learning approaches have been used in simplified settings, such as rate networks and small feed-forward spiking networks. Here, we develop a simulation-based inference (SBI) method for sequentially filtering plasticity rules through an increasingly fine mesh of constraints that can be modified on-the-fly. This method, _filter SBI_, allows us to infer entire families of complex and co-active plasticity rules in spiking networks. We first consider flexibly parameterized doublet (Hebbian) rules, and find that the set of inferred rules contains solutions that extend and refine -and also reject- predictions from mean-field theory. Next, we expand the search space of plasticity rules by modelling them as multi-layer perceptrons that combine several plasticity-relevant factors, such as weight, voltage, triplets and co-dependency. Out of the millions of possible rules, we identify thousands of unique rule combinations that satisfy biological constraints like plausible activity and weight dynamics. The resulting rules can be used as a starting point for further investigations into specific network computations, and already suggest refinements and predictions for classical experimental approaches on plasticity. This flexible approach for principled exploration of complex plasticity rules in large recurrent spiking networks presents the most advanced search tool to date for enabling robust predictions and deep insights into the plasticity mechanisms underlying brain function.

Representation learning assumes that real-world data is generated by a few semantically meaningful generative factors (i.e., sources of variation) and aims to discover them in the latent space. These factors are expected to be causally disentangled, meaning that distinct factors are encoded into separate latent variables, and changes in one factor will not affect the values of the others. Compared to statistical independence, causal disentanglement allows more controllable data generation, improved robustness, and better generalization. However, most existing work assumes unconfoundedness in the discovery process, that there are no common causes to the generative factors and thus obtain only statistical independence. In this paper, we recognize the importance of modeling confounders in discovering causal generative factors. Unfortunately, such factors are not identifiable without proper inductive bias. We fill the gap by introducing a framework entitled Confounded-Disentanglement (C-Disentanglement), the first framework that explicitly introduces the inductive bias of confounder via labels from domain expertise. In addition, we accordingly propose an approach to sufficiently identify the causally-disentangled factors under any inductive bias of the confounder. We conduct extensive experiments on both synthetic and real-world datasets. Our method demonstrates competitive results compared to various SOTA baselines in obtaining causally disentangled features and downstream tasks under domain shifts.

Discovering causal relationship using multivariate functional data has received a significant amount of attention very recently. In this article, we introduce a functional linear structural equation model for causal structure learning when the underlying graph involving the multivariate functions may have cycles. To enhance interpretability, our model involves a low-dimensional causal embedded space such that all the relevant causal information in the multivariate functional data is preserved in this lower-dimensional subspace. We prove that the proposed model is causally identifiable under standard assumptions that are often made in the causal discovery literature. To carry out inference of our model, we develop a fully Bayesian framework with suitable prior specifications and uncertainty quantification through posterior summaries. We illustrate the superior performance of our method over existing methods in terms of causal graph estimation through extensive simulation studies. We also demonstrate the proposed method using a brain EEG dataset.

Anomaly detection (AD) is the machine learning task of identifying highly discrepant abnormal samples by solely relying on the consistency of the normal training samples. Under the constraints of a distribution shift, the assumption that training samples and test samples are drawn from the same distribution breaks down. In this work, by leveraging tools from causal inference we attempt to increase the resilience of anomaly detection models to different kinds of distribution shifts. We begin by elucidating a simple yet necessary statistical property that ensures invariant representations, which is critical for robust AD under both domain and covariate shifts. From this property, we derive a regularization term which, when minimized, leads to partial distribution invariance across environments. Through extensive experimental evaluation on both synthetic and real-world tasks, covering a range of six different AD methods, we demonstrated significant improvements in out-of-distribution performance. Under both covariate and domain shift, models regularized with our proposed term showed marked increased robustness. Code is available at: https://github.com/JoaoCarv/invariant-anomaly-detection

Variable importance assessment has become a crucial step in machine-learning applications when using complex learners, such as deep neural networks, on large-scale data. Removal-based importance assessment is currently the reference approach, particularly when statistical guarantees are sought to justify variable inclusion. It is often implemented with variable permutation schemes. On the flip side, these approaches risk misidentifying unimportant variables as important in the presence of correlations among covariates. Here we develop a systematic approach for studying Conditional Permutation Importance (CPI) that is model agnostic and computationally lean, as well as reusable benchmarks of state-of-the-art variable importance estimators. We show theoretically and empirically that \textit{CPI} overcomes the limitations of standard permutation importance by providing accurate type-I error control. When used with a deep neural network, \textit{CPI} consistently showed top accuracy across benchmarks. An experiment on real-world data analysis in a large-scale medical dataset showed that \textit{CPI} provides a more parsimonious selection of statistically significant variables. Our results suggest that \textit{CPI} can be readily used as drop-in replacement for permutation-based methods.

In natural vision, feedback connections support versatile visual inference capabilities such as making sense of the occluded or noisy bottom-up sensory information or mediating pure top-down processes such as imagination. However, the mechanisms by which the feedback pathway learns to give rise to these capabilities flexibly are not clear. We propose that top-down effects emerge through alignment between feedforward and feedback pathways, each optimizing its own objectives. To achieve this co-optimization, we introduce Feedback-Feedforward Alignment (FFA), a learning algorithm that leverages feedback and feedforward pathways as mutual credit assignment computational graphs, enabling alignment. In our study, we demonstrate the effectiveness of FFA in co-optimizing classification and reconstruction tasks on widely used MNIST and CIFAR10 datasets. Notably, the alignment mechanism in FFA endows feedback connections with emergent visual inference functions, including denoising, resolving occlusions, hallucination, and imagination. Moreover, FFA offers bio-plausibility compared to traditional backpropagation (BP) methods in implementation. By repurposing the computational graph of credit assignment into a goal-driven feedback pathway, FFA alleviates weight transport problems encountered in BP, enhancing the bio-plausibility of the learning algorithm. Our study presents FFA as a promising proof-of-concept for the mechanisms underlying how feedback connections in the visual cortex support flexible visual functions. This work also contributes to the broader field of visual inference underlying perceptual phenomena and has implications for developing more biologically inspired learning algorithms.

Estimating individual treatment effects from observational data is challenging due to treatment selection bias. Prevalent methods mainly mitigate this issue by aligning different treatment groups in the latent space, the core of which is the calculation of distribution discrepancy. However, two issues that are often overlooked can render these methods invalid: (1) mini-batch sampling effects (MSE), where the calculated discrepancy is erroneous in non-ideal mini-batches with outcome imbalance and outliers; (2) unobserved confounder effects (UCE), where the unobserved confounders are not considered in the discrepancy calculation. Both of these issues invalidate the calculated discrepancy, mislead the training of estimators, and thus impede the handling of treatment selection bias. To tackle these issues, we propose Entire Space CounterFactual Regression (ESCFR), which is a new take on optimal transport technology in the context of causality. Specifically, based on the canonical optimal transport framework, we propose a relaxed mass-preserving regularizer to address the MSE issue and design a proximal factual outcome regularizer to handle the UCE issue. Extensive experiments demonstrate that ESCFR estimates distribution discrepancy accurately, handles the treatment selection bias effectively, and outperforms prevalent competitors significantly.

Neural posterior estimation methods based on discrete normalizing flows have become established tools for simulation-based inference (SBI), but scaling them to high-dimensional problems can be challenging. Building on recent advances in generative modeling, we here present flow matching posterior estimation (FMPE), a technique for SBI using continuous normalizing flows. Like diffusion models, and in contrast to discrete flows, flow matching allows for unconstrained architectures, providing enhanced flexibility for complex data modalities. Flow matching, therefore, enables exact density evaluation, fast training, and seamless scalability to large architectures---making it ideal for SBI. We show that FMPE achieves competitive performance on an established SBI benchmark, and then demonstrate its improved scalability on a challenging scientific problem: for gravitational-wave inference, FMPE outperforms methods based on comparable discrete flows, reducing training time by 30\% with substantially improved accuracy. Our work underscores the potential of FMPE to enhance performance in challenging inference scenarios, thereby paving the way for more advanced applications to scientific problems.

A fundamental problem in many sciences is the learning of causal structure underlying a system, typically through observation and experimentation. Commonly, one even collects data across multiple domains, such as gene sequencing from different labs, or neural recordings from different species. Although there exist methods for learning the equivalence class of causal diagrams from observational and experimental data, they are meant to operate in a single domain. In this paper, we develop a fundamental approach to structure learning in non-Markovian systems (i.e. when there exist latent confounders) leveraging observational and interventional data collected from multiple domains. Specifically, we start by showing that learning from observational data in multiple domains is equivalent to learning from interventional data with unknown targets in a single domain. But there are also subtleties when considering observational and experimental data. Using causal invariances derived from do-calculus, we define a property called S-Markov that connects interventional distributions from multiple-domains to graphical criteria on a selection diagram. Leveraging the S-Markov property, we introduce a new constraint-based causal discovery algorithm, S-FCI, that can learn from observational and interventional data from different domains. We prove that the algorithm is sound and subsumes existing constraint-based causal discovery algorithms.

Predicting how different interventions will causally affect a specific individual is important in a variety of domains such as personalized medicine, public policy, and online marketing. There are a large number of methods to predict the effect of an existing intervention based on historical data from individuals who received it. However, in many settings it is important to predict the effects of novel interventions (e.g., a newly invented drug), which these methods do not address. Here, we consider zero-shot causal learning: predicting the personalized effects of a novel intervention. We propose CaML, a causal meta-learning framework which formulates the personalized prediction of each intervention's effect as a task. CaML trains a single meta-model across thousands of tasks, each constructed by sampling an intervention, its recipients, and its nonrecipients. By leveraging both intervention information (e.g., a drug's attributes) and individual features (e.g., a patient's history), CaML is able to predict the personalized effects of novel interventions that do not exist at the time of training. Experimental results on real world datasets in large-scale medical claims and cell-line perturbations demonstrate the effectiveness of our approach. Most strikingly, CaML's zero-shot predictions outperform even strong baselines trained directly on data from the test interventions.

Abstaining classifiers have the option to abstain from making predictions on inputs that they are unsure about. These classifiers are becoming increasingly popular in high-stakes decision-making problems, as they can withhold uncertain predictions to improve their reliability and safety. When evaluating black-box abstaining classifier(s), however, we lack a principled approach that accounts for what the classifier would have predicted on its abstentions. These missing predictions matter when they can eventually be utilized, either directly or as a backup option in a failure mode. In this paper, we introduce a novel approach and perspective to the problem of evaluating and comparing abstaining classifiers by treating abstentions as missing data. Our evaluation approach is centered around defining the counterfactual score of an abstaining classifier, defined as the expected performance of the classifier had it not been allowed to abstain. We specify the conditions under which the counterfactual score is identifiable: if the abstentions are stochastic, and if the evaluation data is independent of the training data (ensuring that the predictions are missing at random), then the score is identifiable. Note that, if abstentions are deterministic, then the score is unidentifiable because the classifier can perform arbitrarily poorly on its abstentions. Leveraging tools from observational causal inference, we then develop nonparametric and doubly robust methods to efficiently estimate this quantity under identification. Our approach is examined in both simulated and real data experiments.

Counterfactual inference aims to answer retrospective "what if" questions and thus belongs to the most fine-grained type of inference in Pearl's causality ladder. Existing methods for counterfactual inference with continuous outcomes aim at point identification and thus make strong and unnatural assumptions about the underlying structural causal model. In this paper, we relax these assumptions and aim at partial counterfactual identification of continuous outcomes, i.e., when the counterfactual query resides in an ignorance interval with informative bounds. We prove that, in general, the ignorance interval of the counterfactual queries has non-informative bounds, already when functions of structural causal models are continuously differentiable. As a remedy, we propose a novel sensitivity model called Curvature Sensitivity Model. This allows us to obtain informative bounds by bounding the curvature of level sets of the functions. We further show that existing point counterfactual identification methods are special cases of our Curvature Sensitivity Model when the bound of the curvature is set to zero. We then propose an implementation of our Curvature Sensitivity Model in the form of a novel deep generative model, which we call Augmented Pseudo-Invertible Decoder. Our implementation employs (i) residual normalizing flows with (ii) variational augmentations. We empirically demonstrate the effectiveness of our Augmented Pseudo-Invertible Decoder. To the best of our knowledge, ours is the first partial identification model for Markovian structural causal models with continuous outcomes.

A popular perspective in Reinforcement learning (RL) casts the problem as probabilistic inference on a graphical model of the Markov decision process (MDP). The core object of study is the probability of each state-action pair being visited under the optimal policy. Previous approaches to approximate this quantity can be arbitrarily poor, leading to algorithms that do not implement genuine statistical inference and consequently do not perform well in challenging problems. In this work, we undertake a rigorous Bayesian treatment of the posterior probability of state-action optimality and clarify how it flows through the MDP. We first reveal that this quantity can indeed be used to generate a policy that explores efficiently, as measured by regret. Unfortunately, computing it is intractable, so we derive a new variational Bayesian approximation yielding a tractable convex optimization problem and establish that the resulting policy also explores efficiently. We call our approach VAPOR and show that it has strong connections to Thompson sampling, K-learning, and maximum entropy exploration. We conclude with some experiments demonstrating the performance advantage of a deep RL version of VAPOR.

In this paper, we investigate the problem of unsupervised domain adaptive hashing, which leverage knowledge from a label-rich source domain to expedite learning to hash on a label-scarce target domain. Although numerous existing approaches attempt to incorporate transfer learning techniques into deep hashing frameworks, they often neglect the essential invariance for adequate alignment between these two domains. Worse yet, these methods fail to distinguish between causal and non-causal effects embedded in images, rendering cross-domain retrieval ineffective. To address these challenges, we propose an Invariance-acquired Domain AdaptivE HAshing (IDEA) model. Our IDEA first decomposes each image into a causal feature representing label information, and a non-causal feature indicating domain information. Subsequently, we generate discriminative hash codes using causal features with consistency learning on both source and target domains. More importantly, we employ a generative model for synthetic samples to simulate the intervention of various non-causal effects, ultimately minimizing their impact on hash codes for domain invariance. Comprehensive experiments conducted on benchmark datasets validate the superior performance of our IDEA compared to a variety of competitive baselines.

Positive-Unlabeled (PU) learning aims to achieve high-accuracy binary classification with limited labeled positive examples and numerous unlabeled ones. Existing cost-sensitive-based methods often rely on strong assumptions that examples with an observed positive label were selected entirely at random. In fact, the uneven distribution of labels is prevalent in real-world PU problems, indicating that most actual positive and unlabeled data are subject to selection bias. In this paper, we propose a PU learning enhancement (PUe) algorithm based on causal inference theory, which employs normalized propensity scores and normalized inverse probability weighting (NIPW) techniques to reconstruct the loss function, thus obtaining a consistent, unbiased estimate of the classifier and enhancing the model's performance. Moreover, we investigate and propose a method for estimating propensity scores in deep learning using regularization techniques when the labeling mechanism is unknown. Our experiments on three benchmark datasets demonstrate the proposed PUe algorithm significantly improves the accuracy of classifiers on non-uniform label distribution datasets compared to advanced cost-sensitive PU methods. Codes are available at https://github.com/huawei-noah/Noah-research/tree/master/PUe and https://gitee.com/mindspore/models/tree/master/research/cv/PUe.