Tengwei Song

Tengwei Song, Min Wu, Yuan Fang

Molecular representation learning plays a crucial role in advancing applications such as drug discovery and material design. Existing work leverages 2D and 3D modalities of molecular information for pre-training, aiming to capture comprehensive structural and geometric insights. However, these methods require paired 2D and 3D molecular data to train the model effectively and prevent it from collapsing into a single modality, posing limitations in scenarios where a certain modality is unavailable or computationally expensive to generate. To overcome this limitation, we propose FlexMol, a flexible molecule pre-training framework that learns unified molecular representations while supporting single-modality input. Specifically, inspired by the unified structure in vision-language models, our approach employs separate models for 2D and 3D molecular data, leverages parameter sharing to improve computational efficiency, and utilizes a decoder to generate features for the missing modality. This enables a multistage continuous learning process where both modalities contribute collaboratively during training, while ensuring robustness when only one modality is available during inference. Extensive experiments demonstrate that FlexMol achieves superior performance across a wide range of molecular property prediction tasks, and we also empirically demonstrate its effectiveness with incomplete data. Our code and data are available at https://github.com/tewiSong/FlexMol.

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.

Jian Chen, Wenye Ma, Penghang Liu et al.

Multimodal Large Language Models (MLLMs) have achieved remarkable visual reasoning abilities in natural images, text-rich documents, and graphic designs. However, their ability to interpret music sheets remains underexplored. To bridge this gap, we introduce MusiXQA, the first comprehensive dataset for evaluating and advancing MLLMs in music sheet understanding. MusiXQA features high-quality synthetic music sheets generated via MusiXTeX, with structured annotations covering note pitch and duration, chords, clefs, key/time signatures, and text, enabling diverse visual QA tasks. Through extensive evaluations, we reveal significant limitations of current state-of-the-art MLLMs in this domain. Beyond benchmarking, we developed Phi-3-MusiX, an MLLM fine-tuned on our dataset, achieving significant performance gains over GPT-based methods. The proposed dataset and model establish a foundation for future advances in MLLMs for music sheet understanding. Code, data, and model will be released upon acceptance.

Tengwei Song, Xudong Ma, Yang Liu et al.

We focus on obtaining robust knowledge graph embedding under perturbation in the embedding space. To address these challenges, we introduce a novel framework, Robust Knowledge Graph Embedding via Denoising, which enhances the robustness of KGE models on noisy triples. By treating KGE methods as energy-based models, we leverage the established connection between denoising and score matching, enabling the training of a robust denoising KGE model. Furthermore, we propose certified robustness evaluation metrics for KGE methods based on the concept of randomized smoothing. Through comprehensive experiments on benchmark datasets, our framework consistently shows superior performance compared to existing state-of-the-art KGE methods when faced with perturbed entity embedding.

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.