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.