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.

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 evaluating them using either score-based methods (including continuous optimization) or independence tests. In our work, we instead 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. The learned model generalizes to new synthetic graphs, is robust to train-test distribution shifts, and achieves state-of-the-art performance on naturalistic graphs for low sample complexity.

We propose a novel policy update that combines regularized policy optimization with model learning as an auxiliary loss. The update (henceforth Muesli) matches MuZero's state-of-the-art performance on Atari. Notably, Muesli does so without using deep search: it acts directly with a policy network and has computation speed comparable to model-free baselines. The Atari results are complemented by extensive ablations, and by additional results on continuous control and 9x9 Go.

How sensitive should machine learning models be to input changes? We tackle the question of model smoothness and show that it is a useful inductive bias which aids generalization, adversarial robustness, generative modeling and reinforcement learning. We explore current methods of imposing smoothness constraints and observe they lack the flexibility to adapt to new tasks, they don't account for data modalities, they interact with losses, architectures and optimization in ways not yet fully understood. We conclude that new advances in the field are hinging on finding ways to incorporate data, tasks and learning into our definitions of smoothness.

Intelligent robots need to achieve abstract objectives using concrete, spatiotemporally complex sensory information and motor control. Tabula rasa deep reinforcement learning (RL) has tackled demanding tasks in terms of either visual, abstract, or physical reasoning, but solving these jointly remains a formidable challenge. One recent, unsolved benchmark task that integrates these challenges is Mujoban, where a robot needs to arrange 3D warehouses generated from 2D Sokoban puzzles. We explore whether integrated tasks like Mujoban can be solved by composing RL modules together in a sense-plan-act hierarchy, where modules have well-defined roles similarly to classic robot architectures. Unlike classic architectures that are typically model-based, we use only model-free modules trained with RL or supervised learning. We find that our modular RL approach dramatically outperforms the state-of-the-art monolithic RL agent on Mujoban. Further, learned modules can be reused when, e.g., using a different robot platform to solve the same task. Together our results give strong evidence for the importance of research into modular RL designs. Project website: https://sites.google.com/view/modular-rl/

A plethora of problems in AI, engineering and the sciences are naturally formalized as inference in discrete probabilistic models. Exact inference is often prohibitively expensive, as it may require evaluating the (unnormalized) target density on its entire domain. Here we consider the setting where only a limited budget of calls to the unnormalized density oracle is available, raising the challenge of where in the domain to allocate these function calls in order to construct a good approximate solution. We formulate this problem as an instance of sequential decision-making under uncertainty and leverage methods from reinforcement learning for probabilistic inference with budget constraints. In particular, we propose the TreeSample algorithm, an adaptation of Monte Carlo Tree Search to approximate inference. This algorithm caches all previous queries to the density oracle in an explicit search tree, and dynamically allocates new queries based on a "best-first" heuristic for exploration, using existing upper confidence bound methods. Our non-parametric inference method can be effectively combined with neural networks that compile approximate conditionals of the target, which are then used to guide the inference search and enable generalization across multiple target distributions. We show empirically that TreeSample outperforms standard approximate inference methods on synthetic factor graphs.

We investigate using reinforcement learning agents as generative models of images (extending arXiv:1804.01118). A generative agent controls a simulated painting environment, and is trained with rewards provided by a discriminator network simultaneously trained to assess the realism of the agent's samples, either unconditional or reconstructions. Compared to prior work, we make a number of improvements to the architectures of the agents and discriminators that lead to intriguing and at times surprising results. We find that when sufficiently constrained, generative agents can learn to produce images with a degree of visual abstraction, despite having only ever seen real photographs (no human brush strokes). And given enough time with the painting environment, they can produce images with considerable realism. These results show that, under the right circumstances, some aspects of human drawing can emerge from simulated embodiment, without the need for external supervision, imitation or social cues. Finally, we note the framework's potential for use in creative applications.

We introduce two novel tree search algorithms that use a policy to guide search. The first algorithm is a best-first enumeration that uses a cost function that allows us to provide an upper bound on the number of nodes to be expanded before reaching a goal state. We show that this best-first algorithm is particularly well suited for ``needle-in-a-haystack'' problems. The second algorithm, which is based on sampling, provides an upper bound on the expected number of nodes to be expanded before reaching a set of goal states. We show that this algorithm is better suited for problems where many paths lead to a goal. We validate these tree search algorithms on 1,000 computer-generated levels of Sokoban, where the policy used to guide search comes from a neural network trained using A3C. Our results show that the policy tree search algorithms we introduce are competitive with a state-of-the-art domain-independent planner that uses heuristic search.

Memory-based neural networks model temporal data by leveraging an ability to remember information for long periods. It is unclear, however, whether they also have an ability to perform complex relational reasoning with the information they remember. Here, we first confirm our intuitions that standard memory architectures may struggle at tasks that heavily involve an understanding of the ways in which entities are connected -- i.e., tasks involving relational reasoning. We then improve upon these deficits by using a new memory module -- a Relational Memory Core (RMC) -- which employs multi-head dot product attention to allow memories to interact. Finally, we test the RMC on a suite of tasks that may profit from more capable relational reasoning across sequential information, and show large gains in RL domains (BoxWorld & Mini PacMan), program evaluation, and language modeling, achieving state-of-the-art results on the WikiText-103, Project Gutenberg, and GigaWord datasets.

Memory-based neural networks model temporal data by leveraging an ability to remember information for long periods. It is unclear, however, whether they also have an ability to perform complex relational reasoning with the information they remember. Here, we first confirm our intuitions that standard memory architectures may struggle at tasks that heavily involve an understanding of the ways in which entities are connected -- i.e., tasks involving relational reasoning. We then improve upon these deficits by using a new memory module -- a Relational Memory Core (RMC) -- which employs multi-head dot product attention to allow memories to interact. Finally, we test the RMC on a suite of tasks that may profit from more capable relational reasoning across sequential information, and show large gains in RL domains (BoxWorld & Mini PacMan), program evaluation, and language modeling, achieving state-of-the-art results on the WikiText-103, Project Gutenberg, and GigaWord datasets.