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Vincent Mallet

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ICLR Conference 2025 Conference Paper

AtomSurf: Surface Representation for Learning on Protein Structures

Vincent Mallet
Yangyang Miao
Souhaib Attaiki
Bruno Correia
Maks Ovsjanikov

While there has been significant progress in evaluating and comparing different representations for learning on protein data, the role of surface-based learning approaches remains not well-understood. In particular, there is a lack of direct and fair benchmark comparison between the best available surface-based learning methods against alternative representations such as graphs. Moreover, the few existing surface-based approaches either use surface information in isolation or, at best, perform global pooling between surface and graph-based architectures. In this work, we fill this gap by first adapting a state-of-the-art surface encoder for protein learning tasks. We then perform a direct and fair comparison of the resulting method against alternative approaches within the Atom3D benchmark, highlighting the limitations of pure surface-based learning. Finally, we propose an integrated approach, which allows learned feature sharing between graphs and surface representations on the level of nodes and vertices \textit{across all layers}. We demonstrate that the resulting architecture achieves state-of-the-art results on all tasks in the Atom3D benchmark, while adhering to the strict benchmark protocol, as well as more broadly on binding site identification and binding pocket classification. Furthermore, we use coarsened surfaces and optimize our approach for efficiency, making our tool competitive in training and inference time with existing techniques. Code can be found online: https://github.com/Vincentx15/atomsurf

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NeurIPS Conference 2021 Conference Paper

Reverse-Complement Equivariant Networks for DNA Sequences

Vincent Mallet
Jean-Philippe Vert

As DNA sequencing technologies keep improving in scale and cost, there is a growing need to develop machine learning models to analyze DNA sequences, e. g. , to decipher regulatory signals from DNA fragments bound by a particular protein of interest. As a double helix made of two complementary strands, a DNA fragment can be sequenced as two equivalent, so-called reverse complement (RC) sequences of nucleotides. To take into account this inherent symmetry of the data in machine learning models can facilitate learning. In this sense, several authors have recently proposed particular RC-equivariant convolutional neural networks (CNNs). However, it remains unknown whether other RC-equivariant architecture exist, which could potentially increase the set of basic models adapted to DNA sequences for practitioners. Here, we close this gap by characterizing the set of all linear RC-equivariant layers, and show in particular that new architectures exist beyond the ones already explored. We further discuss RC-equivariant pointwise nonlinearities adapted to different architectures, as well as RC-equivariant embeddings of $k$-mers as an alternative to one-hot encoding of nucleotides. We show experimentally that the new architectures can outperform existing ones.

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