# CAPSUL: A Comprehensive Human Protein Benchmark for Subcellular Localization

arXiv: https://arxiv.org/abs/2603.18571 · HTML: https://mlsanity.com/paper/2603.18571/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 56 references that are in the map.
- First posted on arXiv 19 Mar 2026.

## Builds on (most cited first, 12 of 12)

- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Class-Balanced Loss Based on Effective Number of Samples](https://mlsanity.com/paper/1901.05555/) (2019)
- [Learning Imbalanced Datasets with Label-Distribution-Aware Margin Loss](https://mlsanity.com/paper/1906.07413/) (2019)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Learning from Protein Structure with Geometric Vector Perceptrons](https://mlsanity.com/paper/2009.01411/) (2020)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [Protein Representation Learning by Geometric Structure Pretraining](https://mlsanity.com/paper/2203.06125/) (2022)
- [PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding](https://mlsanity.com/paper/2206.02096/) (2022)
- [Is Transfer Learning Necessary for Protein Landscape Prediction?](https://mlsanity.com/paper/2011.03443/) (2020)
- [Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model](https://mlsanity.com/paper/2110.15527/) (2021)
- [Directional diffusion models for graph representation learning](https://mlsanity.com/paper/2306.13210/) (2023)
- [Towards Understanding the Effect of Pretraining Label Granularity](https://mlsanity.com/paper/2303.16887/) (2023)

## Built on by (most cited first, 1 of 1)

- [Generative Modeling in Protein Design: Neural Representations, Conditional Generation, and Evaluation Standards](https://mlsanity.com/paper/2603.26378/) (2026)

## Abstract (arXiv)

Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called CAPSUL, a Comprehensive humAn Protein benchmark for SUbcellular Localization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern α-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.