PEPE: Scalable extraction of multi-modal protein language model representations

MotivationProtein language models (PLMs) capture intricate amino-acid dependencies, producing embeddings that encode rich structural, functional, and evolutionary information. Despite their potential, current extraction workflows rely on arbitrary choices, with respect to embedding layer, pooling, and padding, that frequently yield suboptimal representations for feature extraction and downstream analyses. Large-scale embedding generation is further limited by inefficiencies in computation and memory: (i) accumulating all model outputs in memory before writing to disk causes severe bottlenecks, and (ii) repeatedly embedding identical sequences to extract different modes introduces redundant computation and drastically reduces throughput and scalability. ResultsWe introduce PEPE (Parallel Extraction for Protein Embeddings), a command-line tool and Python library that enables efficient, high-throughput, and multimodal extraction from protein language models. PEPEs parallelized and streaming-based architecture achieves runtimes several orders of magnitude faster than sequential approaches. Unlike conventional methods--whose peak memory usage scales linearly with output size and fails when memory capacity is exceeded--PEPE maintains stable, low memory consumption, enabling multimodal embedding extraction even beyond available RAM. PEPE supports a wide range of state-of-the-art and custom PLMs through a simple, flexible interface. By combining scalability, robustness, and ease of use, PEPE allows researchers to generate massive, information-rich embedding datasets efficiently, and facilitate the discovery of optimal representations for structural, functional, and evolutionary downstream tasks. By streamlining the generation of diverse embedding configurations, PEPE provides researchers with the necessary data to identify high-performing latent states for specific biological contexts without requiring additional computational resources. Availability and ImplementationPEPE is a command-line tool written in Python and published under MIT license. The source code and documentation are available at https://github.com/csi-greifflab/pepe-cli. PEPE is also available for installation from PyPI under https://pypi.org/project/pepe-cli and deposited on Zenodo at https://zenodo.org/records/15912054.