Derivative-free tree optimization for complex systems

A tremendous range of design tasks in materials, physics, and biology can be formulated as finding the optimum of an objective function depending on many parameters without knowing its closed-form expression or the derivative. Traditional derivative-free optimization techniques often rely on strong assumptions about objective functions, thereby failing at optimizing non-convex systems beyond 100 dimensions. Here, we present a tree search method for derivative-free optimization that enables accelerated optimal design of high-dimensional complex systems. Specifically, we introduce stochastic tree expansion, dynamic upper confidence bound, and short-range backpropagation mechanism to evade local optimum, iteratively approximating the global optimum using machine learning models. This development effectively confronts the dimensionally challenging problems, achieving convergence to global optima across various benchmark functions up to 2,000 dimensions, surpassing the existing methods by 10- to 20-fold. Our method demonstrates wide applicability to a wide range of real-world complex systems spanning materials, physics, and biology, considerably outperforming state-of-the-art algorithms. This enables efficient autonomous knowledge discovery and facilitates self-driving virtual laboratories. Although we focus on problems within the realm of natural science, the advancements in optimization techniques achieved herein are applicable to a broader spectrum of challenges across all quantitative disciplines.

The Essential Role of Causality in Foundation World Models for Embodied AI

Recent advances in foundation models, especially in large multi-modal models and conversational agents, have ignited interest in the potential of generally capable embodied agents. Such agents would require the ability to perform new tasks in many different real-world environments. However, current foundation models fail to accurately model physical interactions with the real world thus not sufficient for Embodied AI. The study of causality lends itself to the construction of veridical world models, which are crucial for accurately predicting the outcomes of possible interactions. This paper focuses on the prospects of building foundation world models for the upcoming generation of embodied agents and presents a novel viewpoint on the significance of causality within these. We posit that integrating causal considerations is vital to facilitate meaningful physical interactions with the world. Finally, we demystify misconceptions about causality in this context and present our outlook for future research.

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.