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.

Probabilistic Federated Prompt-Tuning with Non-IID and Imbalanced Data

Fine-tuning pre-trained models is a popular approach in machine learning for solving complex tasks with moderate data. However, fine-tuning the entire pre-trained model is ineffective in federated data scenarios where local data distributions are diversely skewed. To address this, we explore integrating federated learning with a more effective prompt-tuning method, optimizing for a small set of input prefixes to reprogram the pre-trained model's behavior. Our approach transforms federated learning into a distributed set modeling task, aggregating diverse sets of prompts to globally fine-tune the pre-trained model. We benchmark various baselines based on direct adaptations of existing federated model aggregation techniques and introduce a new probabilistic prompt aggregation method that substantially outperforms these baselines. Our reported results on a variety of computer vision datasets confirm that the proposed method is most effective to combat extreme data heterogeneity in federated learning.