OntoProtein: Protein Pretraining With Gene Ontology Embedding

Self-supervised protein language models have proved their effectiveness in learning the proteins representations. With the increasing computational power, current protein language models pre-trained with millions of diverse sequences can advance the parameter scale from million-level to billion-level and achieve remarkable improvement. However, those prevailing approaches rarely consider incorporating knowledge graphs (KGs), which can provide rich structured knowledge facts for better protein representations. We argue that informative biology knowledge in KGs can enhance protein representation with external knowledge. In this work, we propose OntoProtein, the first general framework that makes use of structure in GO (Gene Ontology) into protein pre-training models. We construct a novel large-scale knowledge graph that consists of GO and its related proteins, and gene annotation texts or protein sequences describe all nodes in the graph. We propose novel contrastive learning with knowledge-aware negative sampling to jointly optimize the knowledge graph and protein embedding during pre-training. Experimental results show that OntoProtein can surpass state-of-the-art methods with pre-trained protein language models in TAPE benchmark and yield better performance compared with baselines in protein-protein interaction and protein function prediction. Code and datasets are available in https://github.com/zjunlp/OntoProtein.

On Exploring Pose Estimation as an Auxiliary Learning Task for Visible-Infrared Person Re-identification

Visible-infrared person re-identification (VI-ReID) has been challenging due to the existence of large discrepancies between visible and infrared modalities. Most pioneering approaches reduce intra-class variations and inter-modality discrepancies by learning modality-shared and ID-related features. However, an explicit modality-shared cue, i.e., body keypoints, has not been fully exploited in VI-ReID. Additionally, existing feature learning paradigms imposed constraints on either global features or partitioned feature stripes, which neglect the prediction consistency of global and part features. To address the above problems, we exploit Pose Estimation as an auxiliary learning task to assist the VI-ReID task in an end-to-end framework. By jointly training these two tasks in a mutually beneficial manner, our model learns higher quality modality-shared and ID-related features. On top of it, the learnings of global features and local features are seamlessly synchronized by Hierarchical Feature Constraint (HFC), where the former supervises the latter using the knowledge distillation strategy. Experimental results on two benchmark VI-ReID datasets show that the proposed method consistently improves state-of-the-art methods by significant margins. Specifically, our method achieves nearly 20$\%$ mAP improvements against the state-of-the-art method on the RegDB dataset. Our intriguing findings highlight the usage of auxiliary task learning in VI-ReID.

Cross-Modality Deep Feature Learning for Brain Tumor Segmentation

Recent advances in machine learning and prevalence of digital medical images have opened up an opportunity to address the challenging brain tumor segmentation (BTS) task by using deep convolutional neural networks. However, different from the RGB image data that are very widespread, the medical image data used in brain tumor segmentation are relatively scarce in terms of the data scale but contain the richer information in terms of the modality property. To this end, this paper proposes a novel cross-modality deep feature learning framework to segment brain tumors from the multi-modality MRI data. The core idea is to mine rich patterns across the multi-modality data to make up for the insufficient data scale. The proposed cross-modality deep feature learning framework consists of two learning processes: the cross-modality feature transition (CMFT) process and the cross-modality feature fusion (CMFF) process, which aims at learning rich feature representations by transiting knowledge across different modality data and fusing knowledge from different modality data, respectively. Comprehensive experiments are conducted on the BraTS benchmarks, which show that the proposed cross-modality deep feature learning framework can effectively improve the brain tumor segmentation performance when compared with the baseline methods and state-of-the-art methods.

Molecular Contrastive Learning with Chemical Element Knowledge Graph

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available in supplementary materials.

Principled Representation Learning for Entity Alignment

Embedding-based entity alignment (EEA) has recently received great attention. Despite significant performance improvement, few efforts have been paid to facilitate understanding of EEA methods. Most existing studies rest on the assumption that a small number of pre-aligned entities can serve as anchors connecting the embedding spaces of two KGs. Nevertheless, no one investigates the rationality of such an assumption. To fill the research gap, we define a typical paradigm abstracted from existing EEA methods and analyze how the embedding discrepancy between two potentially aligned entities is implicitly bounded by a predefined margin in the scoring function. Further, we find that such a bound cannot guarantee to be tight enough for alignment learning. We mitigate this problem by proposing a new approach, named NeoEA, to explicitly learn KG-invariant and principled entity embeddings. In this sense, an EEA model not only pursues the closeness of aligned entities based on geometric distance, but also aligns the neural ontologies of two KGs by eliminating the discrepancy in embedding distribution and underlying ontology knowledge. Our experiments demonstrate consistent and significant improvement in performance against the best-performing EEA methods.

3D-Transformer: Molecular Representation with Transformer in 3D Space

Spatial structures in the 3D space are important to determine molecular properties. Recent papers use geometric deep learning to represent molecules and predict properties. These papers, however, are computationally expensive in capturing long-range dependencies of input atoms; and have not considered the non-uniformity of interatomic distances, thus failing to learn context-dependent representations at different scales. To deal with such issues, we introduce 3D-Transformer, a variant of the Transformer for molecular representations that incorporates 3D spatial information. 3D-Transformer operates on a fully-connected graph with direct connections between atoms. To cope with the non-uniformity of interatomic distances, we develop a multi-scale self-attention module that exploits local fine-grained patterns with increasing contextual scales. As molecules of different sizes rely on different kinds of spatial features, we design an adaptive position encoding module that adopts different position encoding methods for small and large molecules. Finally, to attain the molecular representation from atom embeddings, we propose an attentive farthest point sampling algorithm that selects a portion of atoms with the assistance of attention scores, overcoming handicaps of the virtual node and previous distance-dominant downsampling methods. We validate 3D-Transformer across three important scientific domains: quantum chemistry, material science, and proteomics. Our experiments show significant improvements over state-of-the-art models on the crystal property prediction task and the protein-ligand binding affinity prediction task, and show better or competitive performance in quantum chemistry molecular datasets. This work provides clear evidence that biochemical tasks can gain consistent benefits from 3D molecular representations and different tasks require different position encoding methods.

Dynamic Modeling of Hand-Object Interactions via Tactile Sensing

Tactile sensing is critical for humans to perform everyday tasks. While significant progress has been made in analyzing object grasping from vision, it remains unclear how we can utilize tactile sensing to reason about and model the dynamics of hand-object interactions. In this work, we employ a high-resolution tactile glove to perform four different interactive activities on a diversified set of objects. We build our model on a cross-modal learning framework and generate the labels using a visual processing pipeline to supervise the tactile model, which can then be used on its own during the test time. The tactile model aims to predict the 3d locations of both the hand and the object purely from the touch data by combining a predictive model and a contrastive learning module. This framework can reason about the interaction patterns from the tactile data, hallucinate the changes in the environment, estimate the uncertainty of the prediction, and generalize to unseen objects. We also provide detailed ablation studies regarding different system designs as well as visualizations of the predicted trajectories. This work takes a step on dynamics modeling in hand-object interactions from dense tactile sensing, which opens the door for future applications in activity learning, human-computer interactions, and imitation learning for robotics.

Middle-level Fusion for Lightweight RGB-D Salient Object Detection

Most existing RGB-D salient object detection (SOD) models require large computational costs and memory consumption to accurately detect the salient objects. This limits the real-life applications of these RGB-D SOD models. To address this issue, a novel lightweight RGB-D SOD model is presented in this paper. Different from most existing models which usually employ the two-stream or single-stream structure, we propose to employ the middle-level fusion structure for designing lightweight RGB-D SOD model, due to the fact that the middle-level fusion structure can simultaneously exploit the modality-shared and modality-specific information as the two-stream structure and can significantly reduce the network's parameters as the single-stream structure. Based on this structure, a novel information-aware multi-modal feature fusion (IMFF) module is first designed to effectively capture the cross-modal complementary information. Then, a novel lightweight feature-level and decision-level feature fusion (LFDF) module is designed to aggregate the feature-level and the decision-level saliency information in different stages with less parameters. With IMFF and LFDF modules incorporated in the middle-level fusion structure, our proposed model has only 3.9M parameters and runs at 33 FPS. Furthermore, the experimental results on several benchmark datasets verify the effectiveness and superiority of the proposed method over some state-of-the-art methods.

Exploring Modality-shared Appearance Features and Modality-invariant Relation Features for Cross-modality Person Re-Identification

Most existing cross-modality person re-identification works rely on discriminative modality-shared features for reducing cross-modality variations and intra-modality variations. Despite some initial success, such modality-shared appearance features cannot capture enough modality-invariant discriminative information due to a massive discrepancy between RGB and infrared images. To address this issue, on the top of appearance features, we further capture the modality-invariant relations among different person parts (referred to as modality-invariant relation features), which are the complement to those modality-shared appearance features and help to identify persons with similar appearances but different body shapes. To this end, a Multi-level Two-streamed Modality-shared Feature Extraction (MTMFE) sub-network is designed, where the modality-shared appearance features and modality-invariant relation features are first extracted in a shared 2D feature space and a shared 3D feature space, respectively. The two features are then fused into the final modality-shared features such that both cross-modality variations and intra-modality variations can be reduced. Besides, a novel cross-modality quadruplet loss is proposed to further reduce the cross-modality variations. Experimental results on several benchmark datasets demonstrate that our proposed method exceeds state-of-the-art algorithms by a noticeable margin.