Leonardo Cotta

Nikita Dhawan, Leonardo Cotta, Karen Ullrich et al. · deepmind, utoronto

Knowing the effect of an intervention is critical for human decision-making, but current approaches for causal effect estimation rely on manual data collection and structuring, regardless of the causal assumptions. This increases both the cost and time-to-completion for studies. We show how large, diverse observational text data can be mined with large language models (LLMs) to produce inexpensive causal effect estimates under appropriate causal assumptions. We introduce NATURAL, a novel family of causal effect estimators built with LLMs that operate over datasets of unstructured text. Our estimators use LLM conditional distributions (over variables of interest, given the text data) to assist in the computation of classical estimators of causal effect. We overcome a number of technical challenges to realize this idea, such as automating data curation and using LLMs to impute missing information. We prepare six (two synthetic and four real) observational datasets, paired with corresponding ground truth in the form of randomized trials, which we used to systematically evaluate each step of our pipeline. NATURAL estimators demonstrate remarkable performance, yielding causal effect estimates that fall within 3 percentage points of their ground truth counterparts, including on real-world Phase 3/4 clinical trials. Our results suggest that unstructured text data is a rich source of causal effect information, and NATURAL is a first step towards an automated pipeline to tap this resource.

Leonardo Cotta, Gal Yehuda, Assaf Schuster et al. · deepmind, utoronto

Designing models that are both expressive and preserve known invariances of tasks is an increasingly hard problem. Existing solutions tradeoff invariance for computational or memory resources. In this work, we show how to leverage randomness and design models that are both expressive and invariant but use less resources. Inspired by randomized algorithms, our key insight is that accepting probabilistic notions of universal approximation and invariance can reduce our resource requirements. More specifically, we propose a class of binary classification models called Randomized Linear Classifiers (RLCs). We give parameter and sample size conditions in which RLCs can, with high probability, approximate any (smooth) function while preserving invariance to compact group transformations. Leveraging this result, we design three RLCs that are provably probabilistic invariant for classification tasks over sets, graphs, and spherical data. We show how these models can achieve probabilistic invariance and universality using less resources than (deterministic) neural networks and their invariant counterparts. Finally, we empirically demonstrate the benefits of this new class of models on invariant tasks where deterministic invariant neural networks are known to struggle.

Leonardo Cotta, Beatrice Bevilacqua, Nesreen Ahmed et al.

Existing causal models for link prediction assume an underlying set of inherent node factors -- an innate characteristic defined at the node's birth -- that governs the causal evolution of links in the graph. In some causal tasks, however, link formation is path-dependent: The outcome of link interventions depends on existing links. Unfortunately, these existing causal methods are not designed for path-dependent link formation, as the cascading functional dependencies between links (arising from path dependence) are either unidentifiable or require an impractical number of control variables. To overcome this, we develop the first causal model capable of dealing with path dependencies in link prediction. In this work we introduce the concept of causal lifting, an invariance in causal models of independent interest that, on graphs, allows the identification of causal link prediction queries using limited interventional data. Further, we show how structural pairwise embeddings exhibit lower bias and correctly represent the task's causal structure, as opposed to existing node embeddings, e.g., graph neural network node embeddings and matrix factorization. Finally, we validate our theoretical findings on three scenarios for causal link prediction tasks: knowledge base completion, covariance matrix estimation and consumer-product recommendations.

Nikita Dhawan, Daniel Shen, Leonardo Cotta et al.

Causal inference, especially in observational studies, relies on untestable assumptions about the true data-generating process. Sensitivity analysis helps us determine how robust our conclusions are when we alter these underlying assumptions. Existing frameworks for sensitivity analysis are concerned with worst-case changes in assumptions. In this work, we argue that using such pessimistic criteria can often become uninformative or lead to conclusions contradicting our prior knowledge about the world. To demonstrate this claim, we generalize the recent s-value framework (Gupta & Rothenhäusler, 2023) to estimate the sensitivity of three different common assumptions in causal inference. Empirically, we find that, indeed, worst-case conclusions about sensitivity can rely on unrealistic changes in the data-generating process. To overcome this, we extend the s-value framework with a new sensitivity analysis criterion: Bayesian Sensitivity Value (BSV), which computes the expected sensitivity of an estimate to assumption violations under priors constructed from real-world evidence. We use Monte Carlo approximations to estimate this quantity and illustrate its applicability in an observational study on the effect of diabetes treatments on weight loss.

Haonan Duan, Stephen Zhewen Lu, Caitlin Fiona Harrigan et al. · deepmind, utoronto

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems. We evaluated six frontier LLMs on 137 small systems, and released a total of 350 systems. Our evaluation shows that while more capable models demonstrated superior performance, all models' performance declined significantly as system complexity increased, suggesting substantial room for improvement in the scientific capabilities of LLM agents.

Leonardo Cotta, Chris J. Maddison

Frontier Large Language Models (LLMs) can be socially discriminatory or sensitive to spurious features of their inputs. Because only well-resourced corporations can train frontier LLMs, we need robust test-time strategies to control such biases. Existing solutions, which instruct the LLM to be fair or robust, rely on the model's implicit understanding of bias. Causality provides a rich formalism through which we can be explicit about our debiasing requirements. Yet, as we show, a naive application of the standard causal debiasing strategy, counterfactual data augmentation, fails under standard assumptions to debias predictions at an individual level at test time. To address this, we develop a stratified notion of debiasing called stratified invariance, which can capture a range of debiasing requirements from population level to individual level through an additional measurement that stratifies the predictions. We present a complete observational test for stratified invariance. Finally, we introduce a data augmentation strategy that guarantees stratified invariance at test time under suitable assumptions, together with a prompting strategy that encourages stratified invariance in LLMs. We show that our prompting strategy, unlike implicit instructions, consistently reduces the bias of frontier LLMs across a suite of synthetic and real-world benchmarks without requiring additional data, finetuning or pre-training.

Leonardo Cotta, Christopher Morris, Bruno Ribeiro

Graph neural networks (GNNs) have limited expressive power, failing to represent many graph classes correctly. While more expressive graph representation learning (GRL) alternatives can distinguish some of these classes, they are significantly harder to implement, may not scale well, and have not been shown to outperform well-tuned GNNs in real-world tasks. Thus, devising simple, scalable, and expressive GRL architectures that also achieve real-world improvements remains an open challenge. In this work, we show the extent to which graph reconstruction -- reconstructing a graph from its subgraphs -- can mitigate the theoretical and practical problems currently faced by GRL architectures. First, we leverage graph reconstruction to build two new classes of expressive graph representations. Secondly, we show how graph reconstruction boosts the expressive power of any GNN architecture while being a (provably) powerful inductive bias for invariances to vertex removals. Empirically, we show how reconstruction can boost GNN's expressive power -- while maintaining its invariance to permutations of the vertices -- by solving seven graph property tasks not solvable by the original GNN. Further, we demonstrate how it boosts state-of-the-art GNN's performance across nine real-world benchmark datasets.

Leonardo Cotta, Carlos H. C. Teixeira, Ananthram Swami et al.

Existing Graph Neural Network (GNN) methods that learn inductive unsupervised graph representations focus on learning node and edge representations by predicting observed edges in the graph. Although such approaches have shown advances in downstream node classification tasks, they are ineffective in jointly representing larger $k$-node sets, $k{>}2$. We propose MHM-GNN, an inductive unsupervised graph representation approach that combines joint $k$-node representations with energy-based models (hypergraph Markov networks) and GNNs. To address the intractability of the loss that arises from this combination, we endow our optimization with a loss upper bound using a finite-sample unbiased Markov Chain Monte Carlo estimator. Our experiments show that the unsupervised MHM-GNN representations of MHM-GNN produce better unsupervised representations than existing approaches from the literature.

Carlos H. C. Teixeira, Leonardo Cotta, Bruno Ribeiro et al.

In this work we propose R-GPM, a parallel computing framework for graph pattern mining (GPM) through a user-defined subgraph relation. More specifically, we enable the computation of statistics of patterns through their subgraph classes, generalizing traditional GPM methods. R-GPM provides efficient estimators for these statistics by employing a MCMC sampling algorithm combined with several optimizations. We provide both theoretical guarantees and empirical evaluations of our estimators in application scenarios such as stochastic optimization of deep high-order graph neural network models and pattern (motif) counting. We also propose and evaluate optimizations that enable improvements of our estimators accuracy, while reducing their computational costs in up to 3-orders-of-magnitude. Finally,we show that R-GPM is scalable, providing near-linear speedups on 44 cores in all of our tests.