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Proteins, often represented as multi-modal data of 1D sequences and 2D/3D structures, provide a motivating example for the communities of machine learning and computational biology to advance multi-modal representation learning. Protein language models over sequences and geometric deep learning over structures learn excellent single-modality representations for downstream tasks. It is thus desirable to fuse the single-modality models for better representation learning, but it remains an open question on how to fuse them effectively into multi-modal representation learning with a modest computational cost yet significant downstream performance gain. To answer the question, we propose to make use of separately pretrained single-modality models, integrate them in parallel connections, and continuously pretrain them end-to-end under the framework of multimodal contrastive learning. The technical challenge is to construct views for both intra- and inter-modality contrasts while addressing the heterogeneity of various modalities, particularly various levels of semantic robustness. We address the challenge by using domain knowledge of protein homology to inform the design of positive views, specifically protein classifications of families (based on similarities in sequences) and superfamilies (based on similarities in structures). We also assess the use of such views compared to, together with, and composed to other positive views such as identity and cropping. Extensive experiments on enzyme classification and protein function prediction benchmarks demonstrate the potential of domain-informed view construction and combination in multi-modal contrastive learning 

Previous approaches on 3D shape segmentation mostly rely on heuristic processing and hand-tuned geometric descriptors. In this paper, we propose a novel 3D shape representation learning approach, Directionally Convolutional Network (DCN), to solve the shape segmentation problem. DCN extends convolution operations from images to the surface mesh of 3D shapes. With DCN, we learn effective shape representations from raw geometric features, i.e., face normals and distances, to achieve robust segmentation. More specifically, a two-stream segmentation framework is proposed: one stream is made up by the proposed DCN with the face normals as the input, and the other stream is implemented by a neural network with the face distance histogram as the input. The learned shape representations from the two streams are fused by an element-wise product. Finally, Conditional Random Field (CRF) is applied to optimize the segmentation. Through extensive experiments conducted on benchmark datasets, we demonstrate that our approach outperforms the current state-of-the-arts (both classic and deep learning-based) on a large variety of 3D shapes.