# HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning

arXiv: https://arxiv.org/abs/2404.01693 · HTML: https://mlsanity.com/paper/2404.01693/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 22 of its 41 references that are in the map.
- First posted on arXiv 2 Apr 2024.

## Builds on (most cited first, 22 of 22)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [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)
- [Geometric and Physical Quantities Improve E(3) Equivariant Message Passing](https://mlsanity.com/paper/2110.02905/) (2021)
- [GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural Networks](https://mlsanity.com/paper/2302.08043/) (2023)
- [Protein Representation Learning by Geometric Structure Pretraining](https://mlsanity.com/paper/2203.06125/) (2022)
- [Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking](https://mlsanity.com/paper/2111.07786/) (2021)
- [PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding](https://mlsanity.com/paper/2206.02096/) (2022)
- [ATOM3D: Tasks On Molecules in Three Dimensions](https://mlsanity.com/paper/2012.04035/) (2020)
- [Equivariant Graph Mechanics Networks with Constraints](https://mlsanity.com/paper/2203.06442/) (2022)
- [Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity](https://mlsanity.com/paper/2107.10670/) (2021)
- [End-to-End Full-Atom Antibody Design](https://mlsanity.com/paper/2302.00203/) (2023)
- [Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning](https://mlsanity.com/paper/2306.01474/) (2023)
- [ECRECer: Enzyme Commission Number Recommendation and Benchmarking based on Multiagent Dual-core Learning](https://mlsanity.com/paper/2202.03632/) (2022)

## Built on by (most cited first, 2 of 2)

- [dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen](https://mlsanity.com/paper/2503.01910/) (2025)
- [CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction](https://mlsanity.com/paper/2409.03773/) (2024)

## Abstract (arXiv)

Understanding and leveraging the 3D structures of proteins is central to a variety of biological and drug discovery tasks. While deep learning has been applied successfully for structure-based protein function prediction tasks, current methods usually employ distinct training for each task. However, each of the tasks is of small size, and such a single-task strategy hinders the models' performance and generalization ability. As some labeled 3D protein datasets are biologically related, combining multi-source datasets for larger-scale multi-task learning is one way to overcome this problem. In this paper, we propose a neural network model to address multiple tasks jointly upon the input of 3D protein structures. In particular, we first construct a standard structure-based multi-task benchmark called Protein-MT, consisting of 6 biologically relevant tasks, including affinity prediction and property prediction, integrated from 4 public datasets. Then, we develop a novel graph neural network for multi-task learning, dubbed Heterogeneous Multichannel Equivariant Network (HeMeNet), which is E(3) equivariant and able to capture heterogeneous relationships between different atoms. Besides, HeMeNet can achieve task-specific learning via the task-aware readout mechanism. Extensive evaluations on our benchmark verify the effectiveness of multi-task learning, and our model generally surpasses state-of-the-art models.