Tengwei Song

Xi Weng, Yunhao Ni, Tengwei Song et al.

Whitening loss offers a theoretical guarantee against feature collapse in self-supervised learning (SSL) with joint embedding architectures. Typically, it involves a hard whitening approach, transforming the embedding and applying loss to the whitened output. In this work, we introduce Spectral Transformation (ST), a framework to modulate the spectrum of embedding and to seek for functions beyond whitening that can avoid dimensional collapse. We show that whitening is a special instance of ST by definition, and our empirical investigations unveil other ST instances capable of preventing collapse. Additionally, we propose a novel ST instance named IterNorm with trace loss (INTL). Theoretical analysis confirms INTL's efficacy in preventing collapse and modulating the spectrum of embedding toward equal-eigenvalues during optimization. Our experiments on ImageNet classification and COCO object detection demonstrate INTL's potential in learning superior representations. The code is available at https://github.com/winci-ai/INTL.

Tengwei Song, Long Yin, Zhen Han et al.

Predicting enzyme-substrate interactions has long been a fundamental problem in biochemistry and metabolic engineering. While existing methods could leverage databases of expert-curated enzyme-substrate pairs for models to learn from known pair interactions, the databases are often sparse, i.e., there are only limited and incomplete examples of such pairs, and also labor-intensive to maintain. This lack of sufficient training data significantly hinders the ability of traditional enzyme prediction models to generalize to unseen interactions. In this work, we try to exploit chemical reaction equations from domain-specific databases, given their easier accessibility and denser, more abundant data. However, interactions of multiple compounds, e.g., educts and products, with the same enzymes create complex relational data patterns that traditional models cannot easily capture. To tackle that, we represent chemical reaction equations as triples of (educt, enzyme, product) within a knowledge graph, such that we can take advantage of knowledge graph embedding (KGE) to infer missing enzyme-substrate pairs for graph completion. Particularly, in order to capture intricate relationships among compounds, we propose our knowledge-enhanced hypergraph model for enzyme prediction, i.e., Hyper-Enz, which integrates a hypergraph transformer with a KGE model to learn representations of the hyper-edges that involve multiple educts and products. Also, a multi-expert paradigm is introduced to guide the learning of enzyme-substrate interactions with both the proposed model and chemical reaction equations. Experimental results show a significant improvement, with up to a 88% relative improvement in average enzyme retrieval accuracy and 30% improvement in pair-level prediction compared to traditional models, demonstrating the effectiveness of our approach.

Tengwei Song, Jie Luo, Lei Huang

Knowledge graph embedding models learn the representations of entities and relations in the knowledge graphs for predicting missing links (relations) between entities. Their effectiveness are deeply affected by the ability of modeling and inferring different relation patterns such as symmetry, asymmetry, inversion, composition and transitivity. Although existing models are already able to model many of these relations patterns, transitivity, a very common relation pattern, is still not been fully supported. In this paper, we first theoretically show that the transitive relations can be modeled with projections. We then propose the Rot-Pro model which combines the projection and relational rotation together. We prove that Rot-Pro can infer all the above relation patterns. Experimental results show that the proposed Rot-Pro model effectively learns the transitivity pattern and achieves the state-of-the-art results on the link prediction task in the datasets containing transitive relations.