PROTOCOL: Late Interaction Retrieval for Protein Homolog Search

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.

IterGen: Iterative Structured LLM Generation

Large Language Models (LLMs) are widely used for tasks such as natural language and code generation. Still, their outputs often suffer from issues like privacy violations, and semantically inaccurate code generation. Current libraries for LLM generation rely on left-to-right decoding without systematic support for backtracking, limiting the ability to correct or refine outputs mid-generation. To address this issue, we introduce IterGen, an intuitive framework for iterative, grammar-guided LLM generation that enables users to move both forward and backward within the generated output based on grammar symbols. By leveraging a symbol-to-position mapping, IterGen ensures efficient and structured generation while allowing for corrections during the process. We demonstrate IterGen's effectiveness in two important applications: reducing privacy leakage in LLM outputs and improving the accuracy of LLM-generated SQL queries. Our code is available at https://github.com/uiuc-arc/itergen

Reward Poisoning Attack Against Offline Reinforcement Learning

We study the problem of reward poisoning attacks against general offline reinforcement learning with deep neural networks for function approximation. We consider a black-box threat model where the attacker is completely oblivious to the learning algorithm and its budget is limited by constraining both the amount of corruption at each data point, and the total perturbation. We propose an attack strategy called `policy contrast attack'. The high-level idea is to make some low-performing policies appear as high-performing while making high-performing policies appear as low-performing. To the best of our knowledge, we propose the first 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 kinds of learning datasets.