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ISCBacademy is an online webinar series including the ISCB COSI, COVID webinars, Indigenous Voices and practical tutorials. We aim to inspire, connect, and communicate the science while providing a hands-on experience accessing and using newly developed bioinformatics tools while ensuring best practices for rigour and reproducibility.
May 27, 2025 at 11:00 AM EDT
Understanding the language of proteins has been a major focus in computational biology, with recent advances in protein language models (pLMs) leading to increasingly powerful sequence representations. These developments hold great promise for critical tasks such as protein-protein interaction (PPI) prediction, which plays a fundamental role in biological processes. However, despite progress in sequence representations, significant challenges remain.
In our previous work, we demonstrated that reported performances of sequence-based PPI prediction models were largely inflated due to data leakage. When evaluated on a strongly leakage-reduced dataset, models performed randomly, highlighting the field's open challenges. This motivated further method development, which leveraged the now widely used ESM-2 protein sequence embeddings. In our recent publication, we evaluated the contribution of ESM-2 embeddings compared to model architecture. While the embeddings led to a substantial performance boost, accuracy plateaued at 0.65—regardless of model architecture. This suggests that the improvements stem from better sequence representations rather than increased model complexity.
We argue that sequence-based embeddings alone are insufficient to drive PPI prediction forward. Since protein interactions occur in three-dimensional space, incorporating structural information is crucial for generalizing to unseen proteins.
In this talk, I will introduce the field, discuss the pitfalls we encountered, and present our findings on the current limitations of sequence-based approaches.
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