Rohan Gumaste

Gabrielle Cohn, Rohan Gumaste, Minh Hoang et al.

Protein homology search underlies function annotation, structure prediction, and evolutionary analysis, but remains challenging in the "twilight zone," where global sequence similarity is weak and classical alignment methods lose sensitivity. Protein language models provide context-aware representations that could improve alignment sensitivity in this regime. However, prior protein embedding-based retrieval pipelines often pool these representations into a single vector, potentially obscuring local motifs, domains, or conserved residues that reveal remote homology. We introduce ProtoCol, a model which represents proteins as sets of residue embeddings and uses ColBERT-style late interaction to test whether residue-level comparison improves homolog retrieval. ProtoCol encodes proteins independently, keeps candidate representations pre-computable, and scores candidates with MaxSim over residue embeddings. On SCOPe superfamily and Pfam clan benchmarks, ProtoCol outperforms sequence-composition, alignment-based, pooled PLM, and trained single-vector baselines, supporting late interaction as an effective retrieval layer for remote homology search.

Yinglun Xu, Rohan Gumaste, Gagandeep Singh

We study the problem of universal black-boxed reward poisoning attacks against general offline reinforcement learning with deep neural networks. We consider a black-box threat model where the attacker is entirely oblivious to the learning algorithm, and its budget is limited by constraining the amount of corruption at each data point and the total perturbation. We require the attack to be universally efficient against any efficient algorithms that might be used by the agent. We propose an attack strategy called the `policy contrast attack.' The idea is to find low- and high-performing policies covered by the dataset and make them appear to be high- and low-performing to the agent, respectively. To the best of our knowledge, we propose the first universal black-box reward poisoning attack in the general offline RL setting. We provide theoretical insights on the attack design and empirically show that our attack is efficient against current state-of-the-art offline RL algorithms in different learning datasets.

Yinglun Xu, David Zhu, Rohan Gumaste et al.

Offline reinforcement learning has become one of the most practical RL settings. However, most existing works on offline RL focus on the standard setting with scalar reward feedback. It remains unknown how to universally transfer the existing rich understanding of offline RL from the reward-based to the preference-based setting. In this work, we propose a general framework to bridge this gap. Our key insight is transforming preference feedback to scalar rewards via binary reward labeling (BRL), and then any reward-based offline RL algorithms can be applied to the dataset with the reward labels. The information loss during the feedback signal transition is minimized with binary reward labeling in the practical learning scenarios. We theoretically show the connection between several recent PBRL techniques and our framework combined with specific offline RL algorithms. By combining reward labeling with different algorithms, our framework can lead to new and potentially more efficient offline PBRL algorithms. We empirically test our framework on preference datasets based on the standard D4RL benchmark. When combined with a variety of efficient reward-based offline RL algorithms, the learning result achieved under our framework is comparable to training the same algorithm on the dataset with actual rewards in many cases and better than the recent PBRL baselines in most cases.

Yinglun Xu, Tarun Suresh, Rohan Gumaste et al.

Preference-based reinforcement learning (PBRL) in the offline setting has succeeded greatly in industrial applications such as chatbots. A two-step learning framework where one applies a reinforcement learning step after a reward modeling step has been widely adopted for the problem. However, such a method faces challenges from the risk of reward hacking and the complexity of reinforcement learning. To overcome the challenge, our insight is that both challenges come from the state-actions not supported in the dataset. Such state-actions are unreliable and increase the complexity of the reinforcement learning problem at the second step. Based on the insight, we develop a novel two-step learning method called PRC: preference-based reinforcement learning with constrained actions. The high-level idea is to limit the reinforcement learning agent to optimize over a constrained action space that excludes the out-of-distribution state-actions. We empirically verify that our method has high learning efficiency on various datasets in robotic control environments.