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 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.

Muesli: Combining Improvements in Policy Optimization

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.

Synthetic Returns for Long-Term Credit Assignment

Since the earliest days of reinforcement learning, the workhorse method for assigning credit to actions over time has been temporal-difference (TD) learning, which propagates credit backward timestep-by-timestep. This approach suffers when delays between actions and rewards are long and when intervening unrelated events contribute variance to long-term returns. We propose state-associative (SA) learning, where the agent learns associations between states and arbitrarily distant future rewards, then propagates credit directly between the two. In this work, we use SA-learning to model the contribution of past states to the current reward. With this model we can predict each state's contribution to the far future, a quantity we call "synthetic returns". TD-learning can then be applied to select actions that maximize these synthetic returns (SRs). We demonstrate the effectiveness of augmenting agents with SRs across a range of tasks on which TD-learning alone fails. We show that the learned SRs are interpretable: they spike for states that occur after critical actions are taken. Finally, we show that our IMPALA-based SR agent solves Atari Skiing -- a game with a lengthy reward delay that posed a major hurdle to deep-RL agents -- 25 times faster than the published state-of-the-art.

A case for new neural network smoothness constraints

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.

Beyond Tabula-Rasa: a Modular Reinforcement Learning Approach for Physically Embedded 3D Sokoban

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/

Divide-and-Conquer Monte Carlo Tree Search For Goal-Directed Planning

Standard planners for sequential decision making (including Monte Carlo planning, tree search, dynamic programming, etc.) are constrained by an implicit sequential planning assumption: The order in which a plan is constructed is the same in which it is executed. We consider alternatives to this assumption for the class of goal-directed Reinforcement Learning (RL) problems. Instead of an environment transition model, we assume an imperfect, goal-directed policy. This low-level policy can be improved by a plan, consisting of an appropriate sequence of sub-goals that guide it from the start to the goal state. We propose a planning algorithm, Divide-and-Conquer Monte Carlo Tree Search (DC-MCTS), for approximating the optimal plan by means of proposing intermediate sub-goals which hierarchically partition the initial tasks into simpler ones that are then solved independently and recursively. The algorithm critically makes use of a learned sub-goal proposal for finding appropriate partitions trees of new tasks based on prior experience. Different strategies for learning sub-goal proposals give rise to different planning strategies that strictly generalize sequential planning. We show that this algorithmic flexibility over planning order leads to improved results in navigation tasks in grid-worlds as well as in challenging continuous control environments.

Causally Correct Partial Models for Reinforcement Learning

In reinforcement learning, we can learn a model of future observations and rewards, and use it to plan the agent's next actions. However, jointly modeling future observations can be computationally expensive or even intractable if the observations are high-dimensional (e.g. images). For this reason, previous works have considered partial models, which model only part of the observation. In this paper, we show that partial models can be causally incorrect: they are confounded by the observations they don't model, and can therefore lead to incorrect planning. To address this, we introduce a general family of partial models that are provably causally correct, yet remain fast because they do not need to fully model future observations.

Combining Q-Learning and Search with Amortized Value Estimates

We introduce "Search with Amortized Value Estimates" (SAVE), an approach for combining model-free Q-learning with model-based Monte-Carlo Tree Search (MCTS). In SAVE, a learned prior over state-action values is used to guide MCTS, which estimates an improved set of state-action values. The new Q-estimates are then used in combination with real experience to update the prior. This effectively amortizes the value computation performed by MCTS, resulting in a cooperative relationship between model-free learning and model-based search. SAVE can be implemented on top of any Q-learning agent with access to a model, which we demonstrate by incorporating it into agents that perform challenging physical reasoning tasks and Atari. SAVE consistently achieves higher rewards with fewer training steps, and---in contrast to typical model-based search approaches---yields strong performance with very small search budgets. By combining real experience with information computed during search, SAVE demonstrates that it is possible to improve on both the performance of model-free learning and the computational cost of planning.