The Landscape of Causal Discovery Data: Grounding Causal Discovery in Real-World Applications

Causal discovery aims to automatically uncover causal relationships from data, a capability with significant potential across many scientific disciplines. However, its real-world applications remain limited. Current methods often rely on unrealistic assumptions and are evaluated only on simple synthetic toy datasets, often with inadequate evaluation metrics. In this paper, we substantiate these claims by performing a systematic review of the recent causal discovery literature. We present applications in biology, neuroscience, and Earth sciences - fields where causal discovery holds promise for addressing key challenges. We highlight available simulated and real-world datasets from these domains and discuss common assumption violations that have spurred the development of new methods. Our goal is to encourage the community to adopt better evaluation practices by utilizing realistic datasets and more adequate metrics.

General Causal Imputation via Synthetic Interventions

Given two sets of elements (such as cell types and drug compounds), researchers typically only have access to a limited subset of their interactions. The task of causal imputation involves using this subset to predict unobserved interactions. Squires et al. (2022) have proposed two estimators for this task based on the synthetic interventions (SI) estimator: SI-A (for actions) and SI-C (for contexts). We extend their work and introduce a novel causal imputation estimator, generalized synthetic interventions (GSI). We prove the identifiability of this estimator for data generated from a more complex latent factor model. On synthetic and real data we show empirically that it recovers or outperforms their estimators.

In-context learning and Occam's razor

The goal of machine learning is generalization. While the No Free Lunch Theorem states that we cannot obtain theoretical guarantees for generalization without further assumptions, in practice we observe that simple models which explain the training data generalize best: a principle called Occam's razor. Despite the need for simple models, most current approaches in machine learning only minimize the training error, and at best indirectly promote simplicity through regularization or architecture design. Here, we draw a connection between Occam's razor and in-context learning: an emergent ability of certain sequence models like Transformers to learn at inference time from past observations in a sequence. In particular, we show that the next-token prediction loss used to train in-context learners is directly equivalent to a data compression technique called prequential coding, and that minimizing this loss amounts to jointly minimizing both the training error and the complexity of the model that was implicitly learned from context. Our theory and the empirical experiments we use to support it not only provide a normative account of in-context learning, but also elucidate the shortcomings of current in-context learning methods, suggesting ways in which they can be improved. We make our code available at https://github.com/3rdCore/PrequentialCode.

Causal Representation Learning in Temporal Data via Single-Parent Decoding

Scientific research often seeks to understand the causal structure underlying high-level variables in a system. For example, climate scientists study how phenomena, such as El Ni\~no, affect other climate processes at remote locations across the globe. However, scientists typically collect low-level measurements, such as geographically distributed temperature readings. From these, one needs to learn both a mapping to causally-relevant latent variables, such as a high-level representation of the El Ni\~no phenomenon and other processes, as well as the causal model over them. The challenge is that this task, called causal representation learning, is highly underdetermined from observational data alone, requiring other constraints during learning to resolve the indeterminacies. In this work, we consider a temporal model with a sparsity assumption, namely single-parent decoding: each observed low-level variable is only affected by a single latent variable. Such an assumption is reasonable in many scientific applications that require finding groups of low-level variables, such as extracting regions from geographically gridded measurement data in climate research or capturing brain regions from neural activity data. We demonstrate the identifiability of the resulting model and propose a differentiable method, Causal Discovery with Single-parent Decoding (CDSD), that simultaneously learns the underlying latents and a causal graph over them. We assess the validity of our theoretical results using simulated data and showcase the practical validity of our method in an application to real-world data from the climate science field.

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.

Does learning the right latent variables necessarily improve in-context learning?

Large autoregressive models like Transformers can solve tasks through in-context learning (ICL) without learning new weights, suggesting avenues for efficiently solving new tasks. For many tasks, e.g., linear regression, the data factorizes: examples are independent given a task latent that generates the data, e.g., linear coefficients. While an optimal predictor leverages this factorization by inferring task latents, it is unclear if Transformers implicitly do so or if they instead exploit heuristics and statistical shortcuts enabled by attention layers. Both scenarios have inspired active ongoing work. In this paper, we systematically investigate the effect of explicitly inferring task latents. We minimally modify the Transformer architecture with a bottleneck designed to prevent shortcuts in favor of more structured solutions, and then compare performance against standard Transformers across various ICL tasks. Contrary to intuition and some recent works, we find little discernible difference between the two; biasing towards task-relevant latent variables does not lead to better out-of-distribution performance, in general. Curiously, we find that while the bottleneck effectively learns to extract latent task variables from context, downstream processing struggles to utilize them for robust prediction. Our study highlights the intrinsic limitations of Transformers in achieving structured ICL solutions that generalize, and shows that while inferring the right latents aids interpretability, it is not sufficient to alleviate this problem.

Demystifying amortized causal discovery with transformers

Supervised learning approaches for causal discovery from observational data often achieve competitive performance despite seemingly avoiding explicit assumptions that traditional methods make for identifiability. In this work, we investigate CSIvA (Ke et al., 2023), a transformer-based model promising to train on synthetic data and transfer to real data. First, we bridge the gap with existing identifiability theory and show that constraints on the training data distribution implicitly define a prior on the test observations. Consistent with classical approaches, good performance is achieved when we have a good prior on the test data, and the underlying model is identifiable. At the same time, we find new trade-offs. Training on datasets generated from different classes of causal models, unambiguously identifiable in isolation, improves the test generalization. Performance is still guaranteed, as the ambiguous cases resulting from the mixture of identifiable causal models are unlikely to occur (which we formally prove). Overall, our study finds that amortized causal discovery still needs to obey identifiability theory, but it also differs from classical methods in how the assumptions are formulated, trading more reliance on assumptions on the noise type for fewer hypotheses on the mechanisms.

Evaluating Interventional Reasoning Capabilities of Large Language Models

Numerous decision-making tasks require estimating causal effects under interventions on different parts of a system. As practitioners consider using large language models (LLMs) to automate decisions, studying their causal reasoning capabilities becomes crucial. A recent line of work evaluates LLMs ability to retrieve commonsense causal facts, but these evaluations do not sufficiently assess how LLMs reason about interventions. Motivated by the role that interventions play in causal inference, in this paper, we conduct empirical analyses to evaluate whether LLMs can accurately update their knowledge of a data-generating process in response to an intervention. We create benchmarks that span diverse causal graphs (e.g., confounding, mediation) and variable types, and enable a study of intervention-based reasoning. These benchmarks allow us to isolate the ability of LLMs to accurately predict changes resulting from their ability to memorize facts or find other shortcuts. Our analysis on four LLMs highlights that while GPT- 4 models show promising accuracy at predicting the intervention effects, they remain sensitive to distracting factors in the prompts.

In-Context Learning Can Re-learn Forbidden Tasks

Despite significant investment into safety training, large language models (LLMs) deployed in the real world still suffer from numerous vulnerabilities. One perspective on LLM safety training is that it algorithmically forbids the model from answering toxic or harmful queries. To assess the effectiveness of safety training, in this work, we study forbidden tasks, i.e., tasks the model is designed to refuse to answer. Specifically, we investigate whether in-context learning (ICL) can be used to re-learn forbidden tasks despite the explicit fine-tuning of the model to refuse them. We first examine a toy example of refusing sentiment classification to demonstrate the problem. Then, we use ICL on a model fine-tuned to refuse to summarise made-up news articles. Finally, we investigate whether ICL can undo safety training, which could represent a major security risk. For the safety task, we look at Vicuna-7B, Starling-7B, and Llama2-7B. We show that the attack works out-of-the-box on Starling-7B and Vicuna-7B but fails on Llama2-7B. Finally, we propose an ICL attack that uses the chat template tokens like a prompt injection attack to achieve a better attack success rate on Vicuna-7B and Starling-7B. Trigger Warning: the appendix contains LLM-generated text with violence, suicide, and misinformation.