Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

Evolutionary science provides evidence that diversity confers resilience. Yet, traditional multi-agent reinforcement learning techniques commonly enforce homogeneity to increase training sample efficiency. When a system of learning agents is not constrained to homogeneous policies, individual agents may develop diverse behaviors, resulting in emergent complementarity that benefits the system. Despite this feat, there is a surprising lack of tools that measure behavioral diversity in systems of learning agents. Such techniques would pave the way towards understanding the impact of diversity in collective resilience and performance. In this paper, we introduce System Neural Diversity (SND): a measure of behavioral heterogeneity for multi-agent systems where agents have stochastic policies. %over a continuous state space. We discuss and prove its theoretical properties, and compare it with alternate, state-of-the-art behavioral diversity metrics used in cross-disciplinary domains. Through simulations of a variety of multi-agent tasks, we show how our metric constitutes an important diagnostic tool to analyze latent properties of behavioral heterogeneity. By comparing SND with task reward in static tasks, where the problem does not change during training, we show that it is key to understanding the effectiveness of heterogeneous vs homogeneous agents. In dynamic tasks, where the problem is affected by repeated disturbances during training, we show that heterogeneous agents are first able to learn specialized roles that allow them to cope with the disturbance, and then retain these roles when the disturbance is removed. SND allows a direct measurement of this latent resilience, while other proxies such as task performance (reward) fail to.

Real-world problems often require reasoning about hybrid beliefs, over both discrete and continuous random variables. Yet, such a setting has hardly been investigated in the context of planning. Moreover, existing online Partially Observable Markov Decision Processes (POMDPs) solvers do not support hybrid beliefs directly. In particular, these solvers do not address the added computational burden due to an increasing number of hypotheses with the planning horizon, which can grow exponentially. As part of this work, we present a novel algorithm, Hybrid Belief Monte Carlo Planning (HB-MCP) that utilizes the Monte Carlo Tree Search (MCTS) algorithm to solve a POMDP while maintaining a hybrid belief. We illustrate how the upper confidence bound (UCB) exploration bonus can be leveraged to guide the growth of hypotheses trees alongside the belief trees. We then evaluate our approach in highly aliased simulated environments where unresolved data association leads to multi-modal belief hypotheses.

Representation learning and exploration are among the key challenges for any deep reinforcement learning agent. In this work, we provide a singular value decomposition based method that can be used to obtain representations that preserve the underlying transition structure in the domain. Perhaps interestingly, we show that these representations also capture the relative frequency of state visitations, thereby providing an estimate for pseudo-counts for free. To scale this decomposition method to large-scale domains, we provide an algorithm that never requires building the transition matrix, can make use of deep networks, and also permits mini-batch training. Further, we draw inspiration from predictive state representations and extend our decomposition method to partially observable environments. With experiments on multi-task settings with partially observable domains, we show that the proposed method can not only learn useful representation on DM-Lab-30 environments (that have inputs involving language instructions, pixel images, and rewards, among others) but it can also be effective at hard exploration tasks in DM-Hard-8 environments.

We introduce Robust Exploration via Clusteringbased Online Density Estimation (RECODE), a nonparametric method for novelty-based exploration that estimates visitation counts for clusters of states based on their similarity in a chosen embedding space. By adapting classical clustering to the nonstationary setting of Deep RL, RECODE can efficiently track state visitation counts over thousands of episodes. We further propose a novel generalization of the inverse dynamics loss, which leverages masked transformer architectures for multi-step prediction; which in conjunction with RECODE achieves a new state-of-the-art in Figure 1: A key result of RECODE is that it allows us to a suite of challenging 3D-exploration tasks in leverage more powerful state representations for long-term DM-HARD-8. RECODE also sets new state-of-theart novelty estimation; enabling to achieve a new state-of-theart in hard exploration Atari games, and is the first in the challenging 3D task suite DM-HARD-8.

A central problem in the theory of multi-agent reinforcement learning (MARL) is to understand what structural conditions and algorithmic principles lead to sample-efficient learning guarantees, and how these considerations change as we move from few to many agents. We study this question in a general framework for interactive decision making with multiple agents, encompassing Markov games with function approximation and normal-form games with bandit feedback. We focus on equilibrium computation, in which a centralized learning algorithm aims to compute an equilibrium by controlling multiple agents that interact with an unknown environment. Our main contributions are: - We provide upper and lower bounds on the optimal sample complexity for multi-agent decision making based on a multi-agent generalization of the Decision-Estimation Coefficient, a complexity measure introduced by Foster et al. (2021) in the single-agent counterpart to our setting. Compared to the best results for the single-agent setting, our bounds have additional gaps. We show that no "reasonable" complexity measure can close these gaps, highlighting a striking separation between single and multiple agents. - We show that characterizing the statistical complexity for multi-agent decision making is equivalent to characterizing the statistical complexity of single-agent decision making, but with hidden (unobserved) rewards, a framework that subsumes variants of the partial monitoring problem. As a consequence, we characterize the statistical complexity for hidden-reward interactive decision making to the best extent possible. Building on this development, we provide several new structural results, including 1) conditions under which the statistical complexity of multi-agent decision making can be reduced to that of single-agent, and 2) conditions under which the so-called curse of multiple agents can be avoided.

We present a study using new computational methods, based on a novel combination of machine learning for inferring admixture hidden Markov models and probabilistic model checking, to uncover interaction styles in a mobile app. These styles are then used to inform a redesign, which is implemented, deployed, and then analysed using the same methods. The data sets are logged user traces, collected over two six-month deployments of each version, involving thousands of users and segmented into different time intervals. The methods do not assume tasks or absolute metrics such as measures of engagement, but uncover the styles through unsupervised inference of clusters and analysis with probabilistic temporal logic. For both versions there was a clear distinction between the styles adopted by users during the first day/week/month of usage, and during the second and third months, a result we had not anticipated.

As space becomes more congested, on orbit inspection is an increasingly relevant activity whether to observe a defunct satellite for planning repairs or to de-orbit it. However, the task of on orbit inspection itself is challenging, typically requiring the careful coordination of multiple observer satellites. This is complicated by a highly nonlinear environment where the target may be unknown or moving unpredictably without time for continuous command and control from the ground. There is a need for autonomous, robust, decentralized solutions to the inspection task. To achieve this, we consider a hierarchical, learned approach for the decentralized planning of multi-agent inspection of a tumbling target. Our solution consists of two components: a viewpoint or high-level planner trained using deep reinforcement learning and a navigation planner handling point-to-point navigation between pre-specified viewpoints. We present a novel problem formulation and methodology that is suitable not only to reinforcement learning-derived robust policies, but extendable to unknown target geometries and higher fidelity information theoretic objectives received directly from sensor inputs. Operating under limited information, our trained multi-agent high-level policies successfully contextualize information within the global hierarchical environment and are correspondingly able to inspect over 90% of non-convex tumbling targets, even in the absence of additional agent attitude control.

We provide a novel method for sensitivity analysis of parametric robust Markov chains. These models incorporate parameters and sets of probability distributions to alleviate the often unrealistic assumption that precise probabilities are available. We measure sensitivity in terms of partial derivatives with respect to the uncertain transition probabilities regarding measures such as the expected reward. As our main contribution, we present an efficient method to compute these partial derivatives. To scale our approach to models with thousands of parameters, we present an extension of this method that selects the subset of $k$ parameters with the highest partial derivative. Our methods are based on linear programming and differentiating these programs around a given value for the parameters. The experiments show the applicability of our approach on models with over a million states and thousands of parameters. Moreover, we embed the results within an iterative learning scheme that profits from having access to a dedicated sensitivity analysis.

Left: an abstract depiction of an MDP where single-step RL fails to discover the optimal policy. Right: A notional illustrative example where we might expect full "multi-step" RL methods (such as ILQL) to perform significantly better than "single-step" methods. In this example, good utterances tend to start with "The movie was...", while bad utterances start with "The movie wasn't..." However, the very best examples also start with "The movie wasn't...", requiring multi-step planning or multiple steps of policy improvement to derive effective strategies. Methods that implement just a single step of policy improvement will fail to produce maximally positive sentiment outputs. While this example may appear somewhat contrived, we see in our experiments that multi-step RL methods do lead to improvements in a number of more real settings. Since ILQL performs multiple steps of policy improvement, it can significantly improve over Monte Carlo estimators or single-step RL when the underlying data is sub-optimal. One example corresponds to the notional task in Figure 4, in which the optimal sequence of actions requires traversing a state that's also frequented by sub-optimal examples. In this case, single-step RL will learn to take actions that appear safer according to the dataset -- such as the transition "The movie" "was" in Figure 4 -- whereas full ("multi-step") RL methods would recover the optimal policy. We demonstrate this empirically on the Wordle game below.