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Protein language models (pLMs) have recently gained significant attention for their ability to uncover relationships between sequence, struc… (see more)ture, and function from evolutionary statistics, thereby accelerating therapeutic drug discovery. These models learn from large protein databases that are continuously updated by the biology community and whose dynamic nature motivates the application of continual learning, not only to keep up with the ever-growing data, but also as an opportunity to take advantage of the temporal meta-information that is created during this process. As a result, we introduce the Continual Pretraining of Protein Language Models (CoPeP) benchmark, a novel benchmark for evaluating continual learning approaches on pLMs. Specifically, we curate a sequence of protein datasets derived from the UniProt Knowledgebase spanning a decade and define metrics to assess pLM performance across 31 protein understanding tasks. We evaluate several methods from the continual learning literature, including replay, unlearning, and plasticity-based methods, some of which have never been applied to models and data of this scale. Our findings reveal that incorporating temporal meta-information improves perplexity by up to 7% even when compared to training on data from all tasks jointly. Moreover, even at scale, several continual learning methods outperform naive continual pretraining. The CoPeP benchmark offers an exciting opportunity to study these methods at scale in an impactful real-world application.
In streaming Reinforcement Learning (RL), transitions are observed and discarded immediately after a single update. While this minimizes res… (see more)ource usage for on-device applications, it makes agents notoriously sample-inefficient, since value-based losses alone struggle to extract meaningful representations from transient data. We propose extending Self-Predictive Representations (SPR) to the streaming pipeline to maximize the utility of every observed frame. However, due to the highly correlated samples induced by the streaming regime, naively applying this auxiliary loss results in training instabilities. Thus, we introduce orthogonal gradient updates relative to the momentum target and resolve gradient conflicts arising from streaming-specific optimizers. Validated across the Atari, MinAtar, and Octax suites, our approach systematically outperforms existing streaming baselines. Latent-space analysis, including t-SNE visualizations and effective-rank measurements, confirms that our method learns significantly richer representations, bridging the performance gap caused by the absence of a replay buffer, while remaining efficient enough to train on just a few CPU cores.
2025-12-31
International Conference on Machine Learning (Accept (regular))
Large language models (LLMs) are increasingly deployed for tasks requiring complex reasoning, prompting significant interest in improving th… (see more)eir reasoning abilities through post-training. Especially RL based methods using verifiable reward, like the state-of-the-art GRPO, have shown to tremendously improve reasoning behaviors when applied as post-training methods. However, the lack of an explicit reward or critic model limits GRPO's ability to assign fine-grained credit across token sequences. In this work, we present GRPO-
Proto-value functions (PVFs) introduced Laplacian embeddings as an effective feature basis for value-function approximation; however, their … (see more)utility remained limited to small, fully known state spaces. Recent work has scaled Laplacian embeddings to high-dimensional inputs, using them for reward shaping and option discovery in goal-directed tasks, yet only as auxiliary signals, rather than directly using them as features for value functions. In this paper, we learn Laplacian eigenvectors online and employ them as features for Q-learning in 23 Atari games. We empirically demonstrate that these online–learned embeddings substantially improve model-free RL in large, high-dimensional domains. We demonstrate that enriching state representations with action embeddings yields additional gains under both behavior-policy and uniform-random policies. Additionally, we introduce the Fusion architecture, which augments the representation with useful inductive bias at the embedding level. To assess the usefulness of each embedding used in the Fusion architecture, we use Shapley values analysis.
*In silico* design and optimization of new materials primarily relies on high-accuracy atomic simulators that perform density functional the… (see more)ory (DFT) calculations. While recent works showcase the strong potential of machine learning to accelerate the material design process, they mostly consist of generative approaches that do not use direct DFT signals as feedback to improve training and generation mainly due to DFT's high computational cost. To aid the adoption of direct DFT signals in the materials design loop through online reinforcement learning (RL), we propose **CrystalGym**, an open-source RL environment for crystalline material discovery. Using CrystalGym, we benchmark value- and policy-based reinforcement learning algorithms for designing various crystals conditioned on target properties. Concretely, we optimize for challenging properties like the band gap, bulk modulus, and density, which are directly calculated from DFT in the environment. While none of the algorithms we benchmark solve all CrystalGym tasks, our extensive experiments and ablations show different sample efficiencies and ease of convergence to optimality for different algorithms and environment settings. Our goal is for CrystalGym to serve as a test bed for reinforcement learning researchers and material scientists to address these real-world design problems with practical applications. Furthermore, we introduce a novel class of challenges for reinforcement learning methods dealing with time-consuming reward signals, paving the way for future interdisciplinary research for machine learning motivated by real-world applications.
2025-03-02
AI4MAT @ International Conference on Learning Representations (spotlight)
Traditional multi-agent reinforcement learning (MARL) systems can develop cooperative strategies through repeated interactions. However, the… (see more)se systems are unable to perform well on any other setting than the one they have been trained on, and struggle to successfully cooperate with unfamiliar collaborators. This is particularly visible in the Hanabi benchmark, a popular 2-to-5 player cooperative card-game which requires complex reasoning and precise assistance to other agents. Current MARL agents for Hanabi can only learn one specific game-setting (e.g., 2-player games), and play with the same algorithmic agents. This is in stark contrast to humans, who can quickly adjust their strategies to work with unfamiliar partners or situations. In this paper, we introduce Recurrent Replay Relevance Distributed DQN (R3D2), a generalist agent for Hanabi, designed to overcome these limitations. We reformulate the task using text, as language has been shown to improve transfer. We then propose a distributed MARL algorithm that copes with the resulting dynamic observation- and action-space. In doing so, our agent is the first that can play all game settings concurrently, and extend strategies learned from one setting to other ones. As a consequence, our agent also demonstrates the ability to collaborate with different algorithmic agents -- agents that are themselves unable to do so. The implementation code is available at:
Property-driven AI-automated material discovery presents unique challenges owing to the complex nature of the chemical structural space and … (see more)computationally expensive simulations. For crystalline solids, the band gap is an important property for designing semiconductors and batteries. However, optimizing crystals for a target band gap is difficult and not well-explored. Reinforcement learning (RL) shows promise towards optimizing crystals, as it can freely explore the chemical space. However, it relies on regular band gap evaluations, which can only be accurately computed through expensive Density Functional Theory (DFT) simulations. In this study, we propose an active learning-inspired pipeline that combines RL and DFT simulations for optimizing crystal compositions given a target band gap. The pipeline includes an RL policy for predicting atom types and a band gap network that is fine-tuned with DFT data. Preliminary results indicate the need for furthering the state-of-the-art to address the inherent challenges of the problem.
2024-07-07
AI4Mat @ University of Natural Resources and Life Sciences, Vienna (poster)