DiscoBAX: Discovery of Optimal Intervention Sets in Genomic Experiment Design

The discovery of therapeutics to treat genetically-driven pathologies relies on identifying genes involved in the underlying disease mechanisms. Existing approaches search over the billions of potential interventions to maximize the expected influence on the target phenotype. However, to reduce the risk of failure in future stages of trials, practical experiment design aims to find a set of interventions that maximally change a target phenotype via diverse mechanisms. We propose DiscoBAX, a sample-efficient method for maximizing the rate of significant discoveries per experiment while simultaneously probing for a wide range of diverse mechanisms during a genomic experiment campaign. We provide theoretical guarantees of approximate optimality under standard assumptions, and conduct a comprehensive experimental evaluation covering both synthetic as well as real-world experimental design tasks. DiscoBAX outperforms existing state-of-the-art methods for experimental design, selecting effective and diverse perturbations in biological systems.

Doubly Robust Structure Identification from Temporal Data

Learning the causes of time-series data is a fundamental task in many applications, spanning from finance to earth sciences or bio-medical applications. Common approaches for this task are based on vector auto-regression, and they do not take into account unknown confounding between potential causes. However, in settings with many potential causes and noisy data, these approaches may be substantially biased. Furthermore, potential causes may be correlated in practical applications. Moreover, existing algorithms often do not work with cyclic data. To address these challenges, we propose a new doubly robust method for Structure Identification from Temporal Data ( SITD ). We provide theoretical guarantees, showing that our method asymptotically recovers the true underlying causal structure. Our analysis extends to cases where the potential causes have cycles and they may be confounded. We further perform extensive experiments to showcase the superior performance of our method.

Diffusion Based Causal Representation Learning

Causal reasoning can be considered a cornerstone of intelligent systems. Having access to an underlying causal graph comes with the promise of cause-effect estimation and the identification of efficient and safe interventions. However, learning causal representations remains a major challenge, due to the complexity of many real-world systems. Previous works on causal representation learning have mostly focused on Variational Auto-Encoders (VAE). These methods only provide representations from a point estimate, and they are unsuitable to handle high dimensions. To overcome these problems, we proposed a new Diffusion-based Causal Representation Learning (DCRL) algorithm. This algorithm uses diffusion-based representations for causal discovery. DCRL offers access to infinite dimensional latent codes, which encode different levels of information in the latent code. In a first proof of principle, we investigate the use of DCRL for causal representation learning. We further demonstrate experimentally that this approach performs comparably well in identifying the causal structure and causal variables.

Causal machine learning for single-cell genomics

Advances in single-cell omics allow for unprecedented insights into the transcription profiles of individual cells. When combined with large-scale perturbation screens, through which specific biological mechanisms can be targeted, these technologies allow for measuring the effect of targeted perturbations on the whole transcriptome. These advances provide an opportunity to better understand the causative role of genes in complex biological processes such as gene regulation, disease progression or cellular development. However, the high-dimensional nature of the data, coupled with the intricate complexity of biological systems renders this task nontrivial. Within the machine learning community, there has been a recent increase of interest in causality, with a focus on adapting established causal techniques and algorithms to handle high-dimensional data. In this perspective, we delineate the application of these methodologies within the realm of single-cell genomics and their challenges. We first present the model that underlies most of current causal approaches to single-cell biology and discuss and challenge the assumptions it entails from the biological point of view. We then identify open problems in the application of causal approaches to single-cell data: generalising to unseen environments, learning interpretable models, and learning causal models of dynamics. For each problem, we discuss how various research directions - including the development of computational approaches and the adaptation of experimental protocols - may offer ways forward, or on the contrary pose some difficulties. With the advent of single cell atlases and increasing perturbation data, we expect causal models to become a crucial tool for informed experimental design.

Real Robot Challenge 2022: Learning Dexterous Manipulation from Offline Data in the Real World

Experimentation on real robots is demanding in terms of time and costs. For this reason, a large part of the reinforcement learning (RL) community uses simulators to develop and benchmark algorithms. However, insights gained in simulation do not necessarily translate to real robots, in particular for tasks involving complex interactions with the environment. The Real Robot Challenge 2022 therefore served as a bridge between the RL and robotics communities by allowing participants to experiment remotely with a real robot - as easily as in simulation. In the last years, offline reinforcement learning has matured into a promising paradigm for learning from pre-collected datasets, alleviating the reliance on expensive online interactions. We therefore asked the participants to learn two dexterous manipulation tasks involving pushing, grasping, and in-hand orientation from provided real-robot datasets. An extensive software documentation and an initial stage based on a simulation of the real set-up made the competition particularly accessible. By giving each team plenty of access budget to evaluate their offline-learned policies on a cluster of seven identical real TriFinger platforms, we organized an exciting competition for machine learners and roboticists alike. In this work we state the rules of the competition, present the methods used by the winning teams and compare their results with a benchmark of state-of-the-art offline RL algorithms on the challenge datasets.

Benchmarking Bayesian Causal Discovery Methods for Downstream Treatment Effect Estimation

The practical utility of causality in decision-making is widespread and brought about by the intertwining of causal discovery and causal inference. Nevertheless, a notable gap exists in the evaluation of causal discovery methods, where insufficient emphasis is placed on downstream inference. To address this gap, we evaluate seven established baseline causal discovery methods including a newly proposed method based on GFlowNets, on the downstream task of treatment effect estimation. Through the implementation of a distribution-level evaluation, we offer valuable and unique insights into the efficacy of these causal discovery methods for treatment effect estimation, considering both synthetic and real-world scenarios, as well as low-data scenarios. The results of our study demonstrate that some of the algorithms studied are able to effectively capture a wide range of useful and diverse ATE modes, while some tend to learn many low-probability modes which impacts the (unrelaxed) recall and precision.

Benchmarking Offline Reinforcement Learning on Real-Robot Hardware

Learning policies from previously recorded data is a promising direction for real-world robotics tasks, as online learning is often infeasible. Dexterous manipulation in particular remains an open problem in its general form. The combination of offline reinforcement learning with large diverse datasets, however, has the potential to lead to a breakthrough in this challenging domain analogously to the rapid progress made in supervised learning in recent years. To coordinate the efforts of the research community toward tackling this problem, we propose a benchmark including: i) a large collection of data for offline learning from a dexterous manipulation platform on two tasks, obtained with capable RL agents trained in simulation; ii) the option to execute learned policies on a real-world robotic system and a simulation for efficient debugging. We evaluate prominent open-sourced offline reinforcement learning algorithms on the datasets and provide a reproducible experimental setup for offline reinforcement learning on real systems.

BayesDAG: Gradient-Based Posterior Sampling for Causal Discovery

Bayesian causal discovery aims to infer the posterior distribution over causal models from observed data, quantifying epistemic uncertainty and benefiting downstream tasks. However, computational challenges arise due to joint inference over combinatorial space of Directed Acyclic Graphs (DAGs) and nonlinear functions. Despite recent progress towards efficient posterior inference over DAGs, existing methods are either limited to variational inference on node permutation matrices for linear causal models, leading to compromised inference accuracy, or continuous relaxation of adjacency matrices constrained by a DAG regularizer, which cannot ensure resulting graphs are DAGs. In this work, we introduce a scalable Bayesian causal discovery framework based on stochastic gradient Markov Chain Monte Carlo (SG-MCMC) that overcomes these limitations. Our approach directly samples DAGs from the posterior without requiring any DAG regularization, simultaneously draws function parameter samples and is applicable to both linear and nonlinear causal models. To enable our approach, we derive a novel equivalence to the permutation-based DAG learning, which opens up possibilities of using any relaxed gradient estimator defined over permutations. To our knowledge, this is the first framework applying gradient-based MCMC sampling for causal discovery. Empirical evaluations on synthetic and real-world datasets demonstrate our approach's effectiveness compared to state-of-the-art baselines.

DRCFS: Doubly Robust Causal Feature Selection

Knowing the features of a complex system that are highly relevant to a particular target variable is of fundamental interest in many areas of science. Existing approaches are often limited to linear settings, sometimes lack guarantees, and in most cases, do not scale to the problem at hand, in particular to images. We propose DRCFS, a doubly robust feature selection method for identifying the causal features even in nonlinear and high dimensional settings. We provide theoretical guarantees, illustrate necessary conditions for our assumptions, and perform extensive experiments across a wide range of simulated and semi-synthetic datasets. DRCFS significantly outperforms existing state-of-the-art methods, selecting robust features even in challenging highly non-linear and high-dimensional problems.

Understanding Causality with Large Language Models: Feasibility and Opportunities

We assess the ability of large language models (LLMs) to answer causal questions by analyzing their strengths and weaknesses against three types of causal question. We believe that current LLMs can answer causal questions with existing causal knowledge as combined domain experts. However, they are not yet able to provide satisfactory answers for discovering new knowledge or for high-stakes decision-making tasks with high precision. We discuss possible future directions and opportunities, such as enabling explicit and implicit causal modules as well as deep causal-aware LLMs. These will not only enable LLMs to answer many different types of causal questions for greater impact but also enable LLMs to be more trustworthy and efficient in general.