ICLR 2023 Papers

The fundamental challenge in causal induction is to infer the underlying graph structure given observational and/or interventional data. Most existing causal induction algorithms operate by generating candidate graphs and evaluating them using either score-based methods (including continuous optimization) or independence tests. In our work, we instead treat the inference process as a black box and design a neural network architecture that learns the mapping from both observational and interventional data to graph structures via supervised training on synthetic graphs. The learned model generalizes to new synthetic graphs, is robust to train-test distribution shifts, and achieves state-of-the-art performance on naturalistic graphs for low sample complexity.

Identifying nonlinear causal relationships in high-dimensional biological data is an important task. However, current neural network based causality detection approaches for such data suffer from poor interpretability and cannot scale well to the high dimensional regime. Here we present GEASS (Granger fEAture Selection of Spatiotemporal data), which identifies sparse Granger causality mechanisms of high dimensional spatiotemporal data by a single neural network. GEASS maximizes sparsity-regularized modified transfer entropy with a theoretical guarantee of recovering features with spatial/temporal Granger causal relationships. The sparsity regularization is achieved by a novel combinatorial stochastic gate layer to select sparse non-overlapping feature subsets. We demonstrate the efficacy of GEASS in several synthetic datasets and real biological data from single-cell RNA sequencing and spatial transcriptomics.

Estimating conditional average treatment effects (CATEs) from observational data is relevant in many fields such as personalized medicine. However, in practice, the treatment assignment is usually confounded by unobserved variables and thus introduces bias. A remedy to remove the bias is the use of instrumental variables (IVs). Such settings are widespread in medicine (e.g., trials where the treatment assignment is used as binary IV). In this paper, we propose a novel, multiply robust machine learning framework, called MRIV, for estimating CATEs using binary IVs and thus yield an unbiased CATE estimator. Different from previous work for binary IVs, our framework estimates the CATE directly via a pseudo-outcome regression. (1)~We provide a theoretical analysis where we show that our framework yields multiple robust convergence rates: our CATE estimator achieves fast convergence even if several nuisance estimators converge slowly. (2)~We further show that our framework asymptotically outperforms state-of-the-art plug-in IV methods for CATE estimation, in the sense that it achieves a faster rate of convergence if the CATE is smoother than the individual outcome surfaces. (3)~We build upon our theoretical results and propose a tailored deep neural network architecture called MRIV-Net for CATE estimation using binary IVs. Across various computational experiments, we demonstrate empirically that our MRIV-Net achieves state-of-the-art performance. To the best of our knowledge, our MRIV is the first multiply robust machine learning framework tailored to estimating CATEs in the binary IV setting.

While machine learning models rapidly advance the state-of-the-art on various real-world tasks, out-of-domain (OOD) generalization remains a challenging problem given the vulnerability of these models to spurious correlations. We propose a balanced mini-batch sampling strategy to transform a biased data distribution into a spurious-free balanced distribution, based on the invariance of the underlying causal mechanisms for the data generation process. We argue that the Bayes optimal classifiers trained on such balanced distribution are minimax optimal across a diverse enough environment space. We also provide an identifiability guarantee of the latent variable model of the proposed data generation process, when utilizing enough train environments. Experiments are conducted on DomainBed, demonstrating empirically that our method obtains the best performance across 20 baselines reported on the benchmark.

Graphical structures estimated by causal learning algorithms from time series data can provide highly misleading causal information if the causal timescale of the generating process fails to match the measurement timescale of the data. Existing algorithms provide limited resources to respond to this challenge, and so researchers must either use models that they know are likely misleading, or else forego causal learning entirely. Existing methods face up-to-four distinct shortfalls, as they might a) require that the difference between causal and measurement timescales is known; b) only handle very small number of random variables when the timescale difference is unknown; c) only apply to pairs of variables (albeit with fewer assumptions about prior knowledge); or d) be unable to find a solution given statistical noise in the data. This paper aims to address these challenges. We present an approach that combines constraint programming with both theoretical insights into the problem structure and prior information about admissible causal interactions to achieve speed up of multiple orders of magnitude. The resulting system scales to significantly larger sets of random variables ($>100$) without knowledge of the timescale difference while maintaining theoretical guarantees. This method is also robust to edge misidentification and can use parametric connection strengths, while optionally finding the optimal among many possible solutions.