Multi-level protein pre-training with Vabs-Net

In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing structure-based pre-trained models primarily focus on the residue level, i.e., alpha carbon atoms, while ignoring other atoms like side chain atoms. We argue that modeling proteins at both residue and atom levels is important since the side chain atoms can also be crucial for numerous downstream tasks, for example, molecular docking. Nevertheless, we find that naively combining residue and atom information during pre-training typically fails. We identify a key reason is the information leakage caused by the inclusion of atom structure in the input, which renders residue-level pre-training tasks trivial and results in insufficiently expressive residue representations. To address this issue, we introduce a span mask pre-training strategy on 3D protein chains to learn meaningful representations of both residues and atoms. This leads to a simple yet effective approach to learning protein representation suitable for diverse downstream tasks. Extensive experimental results on binding site prediction and function prediction tasks demonstrate our proposed pre-training approach significantly outperforms other methods. Our code will be made public.

Multidimensional Information Assisted Deep Learning Realizing Flexible Recognition of Vortex Beam Modes

Because of the unlimited range of state space, orbital angular momentum (OAM) as a new degree of freedom of light has attracted great attention in optical communication field. Recently there are a number of researches applying deep learning on recognition of OAM modes through atmospheric turbulence. However, there are several limitations in previous deep learning recognition methods. They all require a constant distance between the laser and receiver, which makes them clumsy and not practical. As far as we know, previous deep learning methods cannot sort vortex beams with positive and negative topological charges, which can reduce information capacity. A Multidimensional Information Assisted Deep Learning Flexible Recognition (MIADLFR) method is proposed in this letter. In MIADLR we utilize not only the intensity profile, also spectrum information to recognize OAM modes unlimited by distance and sign of topological charge (TC). As far as we know, we first make use of multidimensional information to recognize OAM modes and we first utilize spectrum information to recognize OAM modes. Recognition of OAM modes unlimited by distance and sign of TC achieved by MIADLFR method can make optical communication and detection by OAM light much more attractive.