Gal Kesten-Pomeranz

Gal Kesten-Pomeranz, Yaniv Nikankin, Anja Reusch et al.

Protein sequences are abundant in repeating segments, both as exact copies and as approximate segments with mutations. These repeats are important for protein structure and function, motivating decades of algorithmic work on repeat identification. Recent work has shown that protein language models (PLMs) identify repeats, by examining their behavior in masked-token prediction. To elucidate their internal mechanisms, we investigate how PLMs detect both exact and approximate repeats. We find that the mechanism for approximate repeats functionally subsumes that of exact repeats. We then characterize this mechanism, revealing two main stages: PLMs first build feature representations using both general positional attention heads and biologically specialized components, such as neurons that encode amino-acid similarity. Then, induction heads attend to aligned tokens across repeated segments, promoting the correct answer. Our results reveal how PLMs solve this biological task by combining language-based pattern matching with specialized biological knowledge, thereby establishing a basis for studying more complex evolutionary processes in PLMs.

Yaniv Nikankin, Dana Arad, Itay Itzhak et al.

One of the main challenges in mechanistic interpretability is circuit discovery, determining which parts of a model perform a given task. We build on the Mechanistic Interpretability Benchmark (MIB) and propose three key improvements to circuit discovery. First, we use bootstrapping to identify edges with consistent attribution scores. Second, we introduce a simple ratio-based selection strategy to prioritize strong positive-scoring edges, balancing performance and faithfulness. Third, we replace the standard greedy selection with an integer linear programming formulation. Our methods yield more faithful circuits and outperform prior approaches across multiple MIB tasks and models. Our code is available at: https://github.com/technion-cs-nlp/MIB-Shared-Task.