DiscoGen: Learning to Discover Gene Regulatory Networks

Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs, perturbational data is required. However, most GRN discovery methods only operate on observational data. Recent advances in neural network-based causal discovery methods have significantly improved causal discovery, including handling interventional data, improvements in performance and scalability. However, applying state-of-the-art (SOTA) causal discovery methods in biology poses challenges, such as noisy data and a large number of samples. Thus, adapting the causal discovery methods is necessary to handle these challenges. In this paper, we introduce DiscoGen, a neural network-based GRN discovery method that can denoise gene expression measurements and handle interventional data. We demonstrate that our model outperforms SOTA neural network-based causal discovery methods.

Learning How to Infer Partial MDPs for In-Context Adaptation and Exploration

To generalize across tasks, an agent should acquire knowledge from past tasks that facilitate adaptation and exploration in future tasks. We focus on the problem of in-context adaptation and exploration, where an agent only relies on context, i.e., history of states, actions and/or rewards, rather than gradient-based updates. Posterior sampling (extension of Thompson sampling) is a promising approach, but it requires Bayesian inference and dynamic programming, which often involve unknowns (e.g., a prior) and costly computations. To address these difficulties, we use a transformer to learn an inference process from training tasks and consider a hypothesis space of partial models, represented as small Markov decision processes that are cheap for dynamic programming. In our version of the Symbolic Alchemy benchmark, our method's adaptation speed and exploration-exploitation balance approach those of an exact posterior sampling oracle. We also show that even though partial models exclude relevant information from the environment, they can nevertheless lead to good policies.

Learning Latent Structural Causal Models

Causal learning has long concerned itself with the accurate recovery of underlying causal mechanisms. Such causal modelling enables better explanations of out-of-distribution data. Prior works on causal learning assume that the high-level causal variables are given. However, in machine learning tasks, one often operates on low-level data like image pixels or high-dimensional vectors. In such settings, the entire Structural Causal Model (SCM) -- structure, parameters, \textit{and} high-level causal variables -- is unobserved and needs to be learnt from low-level data. We treat this problem as Bayesian inference of the latent SCM, given low-level data. For linear Gaussian additive noise SCMs, we present a tractable approximate inference method which performs joint inference over the causal variables, structure and parameters of the latent SCM from random, known interventions. Experiments are performed on synthetic datasets and a causally generated image dataset to demonstrate the efficacy of our approach. We also perform image generation from unseen interventions, thereby verifying out of distribution generalization for the proposed causal model.

Towards Understanding How Machines Can Learn Causal Overhypotheses

Recent work in machine learning and cognitive science has suggested that understanding causal information is essential to the development of intelligence. The extensive literature in cognitive science using the ``blicket detector'' environment shows that children are adept at many kinds of causal inference and learning. We propose to adapt that environment for machine learning agents. One of the key challenges for current machine learning algorithms is modeling and understanding causal overhypotheses: transferable abstract hypotheses about sets of causal relationships. In contrast, even young children spontaneously learn and use causal overhypotheses. In this work, we present a new benchmark -- a flexible environment which allows for the evaluation of existing techniques under variable causal overhypotheses -- and demonstrate that many existing state-of-the-art methods have trouble generalizing in this environment. The code and resources for this benchmark are available at https://github.com/CannyLab/casual_overhypotheses.

On the Generalization and Adaption Performance of Causal Models

Learning models that offer robust out-of-distribution generalization and fast adaptation is a key challenge in modern machine learning. Modelling causal structure into neural networks holds the promise to accomplish robust zero and few-shot adaptation. Recent advances in differentiable causal discovery have proposed to factorize the data generating process into a set of modules, i.e. one module for the conditional distribution of every variable where only causal parents are used as predictors. Such a modular decomposition of knowledge enables adaptation to distributions shifts by only updating a subset of parameters. In this work, we systematically study the generalization and adaption performance of such modular neural causal models by comparing it to monolithic models and structured models where the set of predictors is not constrained to causal parents. Our analysis shows that the modular neural causal models outperform other models on both zero and few-shot adaptation in low data regimes and offer robust generalization. We also found that the effects are more significant for sparser graphs as compared to denser graphs.

Temporal Latent Bottleneck: Synthesis of Fast and Slow Processing Mechanisms in Sequence Learning

Recurrent neural networks have a strong inductive bias towards learning temporally compressed representations, as the entire history of a sequence is represented by a single vector. By contrast, Transformers have little inductive bias towards learning temporally compressed representations, as they allow for attention over all previously computed elements in a sequence. Having a more compressed representation of a sequence may be beneficial for generalization, as a high-level representation may be more easily re-used and re-purposed and will contain fewer irrelevant details. At the same time, excessive compression of representations comes at the cost of expressiveness. We propose a solution which divides computation into two streams. A slow stream that is recurrent in nature aims to learn a specialized and compressed representation, by forcing chunks of $K$ time steps into a single representation which is divided into multiple vectors. At the same time, a fast stream is parameterized as a Transformer to process chunks consisting of $K$ time-steps conditioned on the information in the slow-stream. In the proposed approach we hope to gain the expressiveness of the Transformer, while encouraging better compression and structuring of representations in the slow stream. We show the benefits of the proposed method in terms of improved sample efficiency and generalization performance as compared to various competitive baselines for visual perception and sequential decision making tasks.

Learning to Induce Causal Structure

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 then evaluating them using either score-based methods (including continuous optimization) or independence tests. In this work, instead of proposing scoring function or independence tests, we 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. We show that the proposed model generalizes not only to new synthetic graphs but also to naturalistic graphs.

Retrieval-Augmented Reinforcement Learning

Most deep reinforcement learning (RL) algorithms distill experience into parametric behavior policies or value functions via gradient updates. While effective, this approach has several disadvantages: (1) it is computationally expensive, (2) it can take many updates to integrate experiences into the parametric model, (3) experiences that are not fully integrated do not appropriately influence the agent's behavior, and (4) behavior is limited by the capacity of the model. In this paper we explore an alternative paradigm in which we train a network to map a dataset of past experiences to optimal behavior. Specifically, we augment an RL agent with a retrieval process (parameterized as a neural network) that has direct access to a dataset of experiences. This dataset can come from the agent's past experiences, expert demonstrations, or any other relevant source. The retrieval process is trained to retrieve information from the dataset that may be useful in the current context, to help the agent achieve its goal faster and more efficiently. We integrate our method into two different RL agents: an offline DQN agent and an online R2D2 agent. In offline multi-task problems, we show that the retrieval-augmented DQN agent avoids task interference and learns faster than the baseline DQN agent. On Atari, we show that retrieval-augmented R2D2 learns significantly faster than the baseline R2D2 agent and achieves higher scores. We run extensive ablations to measure the contributions of the components of our proposed method.

Learning Causal Overhypotheses through Exploration in Children and Computational Models

Despite recent progress in reinforcement learning (RL), RL algorithms for exploration still remain an active area of research. Existing methods often focus on state-based metrics, which do not consider the underlying causal structures of the environment, and while recent research has begun to explore RL environments for causal learning, these environments primarily leverage causal information through causal inference or induction rather than exploration. In contrast, human children - some of the most proficient explorers - have been shown to use causal information to great benefit. In this work, we introduce a novel RL environment designed with a controllable causal structure, which allows us to evaluate exploration strategies used by both agents and children in a unified environment. In addition, through experimentation on both computation models and children, we demonstrate that there are significant differences between information-gain optimal RL exploration in causal environments and the exploration of children in the same environments. We conclude with a discussion of how these findings may inspire new directions of research into efficient exploration and disambiguation of causal structures for RL algorithms.