16 accepted papers
Protein-protein interactions (PPIs) are mediated at the residue level. Most sequence-based PPI models consider residue-residue interactions across two proteins, which can yield accurate interaction scores but are too slow to scale. At proteome scale, identifying candidate PPIs requires evaluating ne…
One fundamental challenge in graph machine learning is generalizing to new graphs. Many existing methods following the inductive setup can generalize to test graphs with new structures, but assuming the feature and label spaces remain the same as the training ones. This paper introduces a fully-ind…
Efficient long-context modeling remains a critical challenge for natural language processing (NLP), as the time complexity of the predominant Transformer architecture scales quadratically with the sequence length. While state-space models (SSMs) offer alternative sub-quadratic solutions, they strugg…
Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current…
Graph Foundation Models (GFMs) are emerging as a significant research topic in the graph domain, aiming to develop graph models trained on extensive and diverse data to enhance their applicability across various tasks and domains. Developing GFMs presents unique challenges over traditional Graph Neu…
We propose ProtLLM, a versatile cross-modal large language model (LLM) for both protein-centric and protein-language tasks. ProtLLM features a unique dynamic protein mounting mechanism, enabling it to handle complex inputs where the natural language text is interspersed with an arbitrary number of p…
Text-attributed graphs (TAGs) are prevalent in various real-world scenarios, where each node is associated with a text description. The cornerstone of representation learning on TAGs lies in the seamless integration of textual semantics within individual nodes and the topological connections across…
In person re-identification (ReID) task, it is still challenging to learn discriminative representation by deep learning, due to limited data. Generally speaking, the model will get better performance when increasing the amount of data. The addition of similar classes strengthens the ability of the…
This paper studies learning on text-attributed graphs (TAGs), where each node is associated with a text description. An ideal solution for such a problem would be integrating both the text and graph structure information with large language models and graph neural networks (GNNs). However, the probl…
Embedding models have shown great power in knowledge graph completion (KGC) task. By learning structural constraints for each training triple, these methods implicitly memorize intrinsic relation rules to infer missing links. However, this paper points out that the multi-hop relation rules are hard…
Graph neural networks (GNNs) have demonstrated great success in representation learning for graph-structured data. The layer-wise graph convolution in GNNs is shown to be powerful at capturing graph topology. During this process, GNNs are usually guided by pre-defined kernels such as Laplacian matri…
The effectiveness of knowledge graph embedding (KGE) largely depends on the ability to model intrinsic relation patterns and mapping properties. However, existing approaches can only capture some of them with insufficient modeling capacity. In this work, we propose a more powerful KGE framework name…
Prescription (aka Rx) drugs can be easily overprescribed and lead to drug abuse or opioid overdose. Accordingly, a state-run prescription drug monitoring program (PDMP) in the United States has been developed to reduce overprescribing. However, PDMP has limited capability in detecting patients' pote…
Heterogeneous Graph Neural Networks (HGNNs) have drawn increasing attention in recent years and achieved outstanding performance in many tasks. The success of the existing HGNNs relies on one fundamental assumption, i.e., the original heterogeneous graph structure is reliable. However, this assumpti…
Vehicle re-identification (re-ID) is of great significance to urban operation, management, security and has gained more attention in recent years. However, two critical challenges in vehicle re-ID have primarily been underestimated, i.e., 1): how to make full use of raw data, and 2): how to learn a…
As heterogeneous networks have become increasingly ubiquitous, Heterogeneous Information Network (HIN) embedding, aiming to project nodes into a low-dimensional space while preserving the heterogeneous structure, has drawn increasing attention in recent years. Many of the existing HIN embedding meth…