Reinforcement Learning for Sequence Design Leveraging Protein Language Models

Protein sequence design, determined by amino acid sequences, are essential to protein engineering problems in drug discovery. Prior approaches have resorted to evolutionary strategies or Monte-Carlo methods for protein design, but often fail to exploit the structure of the combinatorial search space, to generalize to unseen sequences. In the context of discrete black box optimization over large search spaces, learning a mutation policy to generate novel sequences with reinforcement learning is appealing. Recent advances in protein language models (PLMs) trained on large corpora of protein sequences offer a potential solution to this problem by scoring proteins according to their biological plausibility (such as the TM-score). In this work, we propose to use PLMs as a reward function to generate new sequences. Yet the PLM can be computationally expensive to query due to its large size. To this end, we propose an alternative paradigm where optimization can be performed on scores from a smaller proxy model that is periodically finetuned, jointly while learning the mutation policy. We perform extensive experiments on various sequence lengths to benchmark RL-based approaches, and provide comprehensive evaluations along biological plausibility and diversity of the protein. Our experimental results include favorable evaluations of the proposed sequences, along with high diversity scores, demonstrating that RL is a strong candidate for biological sequence design. Finally, we provide a modular open source implementation can be easily integrated in most RL training loops, with support for replacing the reward model with other PLMs, to spur further research in this domain. The code for all experiments is provided in the supplementary material.

Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation

Proteins are essential for almost all biological processes and derive their diverse functions from complex 3D structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive bias of amino acid sequences and introduce FoldFlow-2, a novel sequence-conditioned SE(3)-equivariant flow matching model for protein structure generation. FoldFlow-2 presents substantial new architectural features over the previous FoldFlow family of models including a protein large language model to encode sequence, a new multi-modal fusion trunk that combines structure and sequence representations, and a geometric transformer based decoder. To increase diversity and novelty of generated samples -- crucial for de-novo drug design -- we train FoldFlow-2 at scale on a new dataset that is an order of magnitude larger than PDB datasets of prior works, containing both known proteins in PDB and high-quality synthetic structures achieved through filtering. We further demonstrate the ability to align FoldFlow-2 to arbitrary rewards, e.g. increasing secondary structures diversity, by introducing a Reinforced Finetuning (ReFT) objective. We empirically observe that FoldFlow-2 outperforms previous state-of-the-art protein structure-based generative models, improving over RFDiffusion in terms of unconditional generation across all metrics including designability, diversity, and novelty across all protein lengths, as well as exhibiting generalization on the task of equilibrium conformation sampling. Finally, we demonstrate that a fine-tuned FoldFlow-2 makes progress on challenging conditional design tasks such as designing scaffolds for the VHH nanobody.

Learning Latent Dynamic Robust Representations for World Models

Visual Model-Based Reinforcement Learning (MBRL) promises to encapsulate agent's knowledge about the underlying dynamics of the environment, enabling learning a world model as a useful planner. However, top MBRL agents such as Dreamer often struggle with visual pixel-based inputs in the presence of exogenous or irrelevant noise in the observation space, due to failure to capture task-specific features while filtering out irrelevant spatio-temporal details. To tackle this problem, we apply a spatio-temporal masking strategy, a bisimulation principle, combined with latent reconstruction, to capture endogenous task-specific aspects of the environment for world models, effectively eliminating non-essential information. Joint training of representations, dynamics, and policy often leads to instabilities. To further address this issue, we develop a Hybrid Recurrent State-Space Model (HRSSM) structure, enhancing state representation robustness for effective policy learning. Our empirical evaluation demonstrates significant performance improvements over existing methods in a range of visually complex control tasks such as Maniskill \cite{gu2023maniskill2} with exogenous distractors from the Matterport environment. Our code is avaliable at https://github.com/bit1029public/HRSSM.

Generalizing Multi-Step Inverse Models for Representation Learning to Finite-Memory POMDPs

Discovering an informative, or agent-centric, state representation that encodes only the relevant information while discarding the irrelevant is a key challenge towards scaling reinforcement learning algorithms and efficiently applying them to downstream tasks. Prior works studied this problem in high-dimensional Markovian environments, when the current observation may be a complex object but is sufficient to decode the informative state. In this work, we consider the problem of discovering the agent-centric state in the more challenging high-dimensional non-Markovian setting, when the state can be decoded from a sequence of past observations. We establish that generalized inverse models can be adapted for learning agent-centric state representation for this task. Our results include asymptotic theory in the deterministic dynamics setting as well as counter-examples for alternative intuitive algorithms. We complement these findings with a thorough empirical study on the agent-centric state discovery abilities of the different alternatives we put forward. Particularly notable is our analysis of past actions, where we show that these can be a double-edged sword: making the algorithms more successful when used correctly and causing dramatic failure when used incorrectly.

PcLast: Discovering Plannable Continuous Latent States

Goal-conditioned planning benefits from learned low-dimensional representations of rich, high-dimensional observations. While compact latent representations, typically learned from variational autoencoders or inverse dynamics, enable goal-conditioned planning they ignore state affordances, thus hampering their sample-efficient planning capabilities. In this paper, we learn a representation that associates reachable states together for effective onward planning. We first learn a latent representation with multi-step inverse dynamics (to remove distracting information); and then transform this representation to associate reachable states together in $\ell_2$ space. Our proposals are rigorously tested in various simulation testbeds. Numerical results in reward-based and reward-free settings show significant improvements in sampling efficiency, and yields layered state abstractions that enable computationally efficient hierarchical planning.

Understanding and Addressing the Pitfalls of Bisimulation-based Representations in Offline Reinforcement Learning

While bisimulation-based approaches hold promise for learning robust state representations for Reinforcement Learning (RL) tasks, their efficacy in offline RL tasks has not been up to par. In some instances, their performance has even significantly underperformed alternative methods. We aim to understand why bisimulation methods succeed in online settings, but falter in offline tasks. Our analysis reveals that missing transitions in the dataset are particularly harmful to the bisimulation principle, leading to ineffective estimation. We also shed light on the critical role of reward scaling in bounding the scale of bisimulation measurements and of the value error they induce. Based on these findings, we propose to apply the expectile operator for representation learning to our offline RL setting, which helps to prevent overfitting to incomplete data. Meanwhile, by introducing an appropriate reward scaling strategy, we avoid the risk of feature collapse in representation space. We implement these recommendations on two state-of-the-art bisimulation-based algorithms, MICo and SimSR, and demonstrate performance gains on two benchmark suites: D4RL and Visual D4RL. Codes are provided at \url{https://github.com/zanghyu/Offline_Bisimulation}.

Ignorance is Bliss: Robust Control via Information Gating

Informational parsimony -- i.e., using the minimal information required for a task, -- provides a useful inductive bias for learning representations that achieve better generalization by being robust to noise and spurious correlations. We propose information gating in the pixel space as a way to learn more parsimonious representations. Information gating works by learning masks that capture only the minimal information required to solve a given task. Intuitively, our models learn to identify which visual cues actually matter for a given task. We gate information using a differentiable parameterization of the signal-to-noise ratio, which can be applied to arbitrary values in a network, e.g.~masking out pixels at the input layer. We apply our approach, which we call InfoGating, to various objectives such as: multi-step forward and inverse dynamics, Q-learning, behavior cloning, and standard self-supervised tasks. Our experiments show that learning to identify and use minimal information can improve generalization in downstream tasks -- e.g., policies based on info-gated images are considerably more robust to distracting/irrelevant visual features.

Offline Policy Optimization in RL with Variance Regularizaton

Learning policies from fixed offline datasets is a key challenge to scale up reinforcement learning (RL) algorithms towards practical applications. This is often because off-policy RL algorithms suffer from distributional shift, due to mismatch between dataset and the target policy, leading to high variance and over-estimation of value functions. In this work, we propose variance regularization for offline RL algorithms, using stationary distribution corrections. We show that by using Fenchel duality, we can avoid double sampling issues for computing the gradient of the variance regularizer. The proposed algorithm for offline variance regularization (OVAR) can be used to augment any existing offline policy optimization algorithms. We show that the regularizer leads to a lower bound to the offline policy optimization objective, which can help avoid over-estimation errors, and explains the benefits of our approach across a range of continuous control domains when compared to existing state-of-the-art algorithms.

Representation Learning in Deep RL via Discrete Information Bottleneck

Several self-supervised representation learning methods have been proposed for reinforcement learning (RL) with rich observations. For real-world applications of RL, recovering underlying latent states is crucial, particularly when sensory inputs contain irrelevant and exogenous information. In this work, we study how information bottlenecks can be used to construct latent states efficiently in the presence of task-irrelevant information. We propose architectures that utilize variational and discrete information bottlenecks, coined as RepDIB, to learn structured factorized representations. Exploiting the expressiveness bought by factorized representations, we introduce a simple, yet effective, bottleneck that can be integrated with any existing self-supervised objective for RL. We demonstrate this across several online and offline RL benchmarks, along with a real robot arm task, where we find that compressed representations with RepDIB can lead to strong performance improvements, as the learned bottlenecks help predict only the relevant state while ignoring irrelevant information.

Behavior Prior Representation learning for Offline Reinforcement Learning

Offline reinforcement learning (RL) struggles in environments with rich and noisy inputs, where the agent only has access to a fixed dataset without environment interactions. Past works have proposed common workarounds based on the pre-training of state representations, followed by policy training. In this work, we introduce a simple, yet effective approach for learning state representations. Our method, Behavior Prior Representation (BPR), learns state representations with an easy-to-integrate objective based on behavior cloning of the dataset: we first learn a state representation by mimicking actions from the dataset, and then train a policy on top of the fixed representation, using any off-the-shelf Offline RL algorithm. Theoretically, we prove that BPR carries out performance guarantees when integrated into algorithms that have either policy improvement guarantees (conservative algorithms) or produce lower bounds of the policy values (pessimistic algorithms). Empirically, we show that BPR combined with existing state-of-the-art Offline RL algorithms leads to significant improvements across several offline control benchmarks.