11 accepted papers
The multi-commodity flow (MCF) problem is a fundamental topic in network flow and combinatorial optimization, with broad applications in transportation, communication, and logistics, etc. Nowadays, the rapid expansion of allocation systems has posed challenges for existing optimization engines in ba…
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…
Building _Virtual Cells_ that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, pe…
Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures…
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…
Denoising diffusion probabilistic models (DDPMs) are becoming the leading paradigm for generative models. It has recently shown breakthroughs in audio synthesis, time series imputation and forecasting. In this paper, we propose Diffusion-TS, a novel diffusion-based framework that generates multivari…
Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. Th…
Unsupervised anomaly detection for multivariate time series (MTS) is a challenging task due to the difficulties of precisely learning the complex data patterns of MTS. The recent progress in sample generation achieved by diffusion models (DMs) motivates us to leverage the powerful learning ability o…
Reasoning on large-scale knowledge graphs has been long dominated by embedding methods. While path-based methods possess the inductive capacity that embeddings lack, their scalability is limited by the exponential number of paths. Here we present A\*Net, a scalable path-based method for knowledge gr…
Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many prote…
Prediction of brain functional activity is of great significance for neuroscience research. The brain functional activities at different regions are highly related, and their relationships can be captured with functional connectivity and structural connectivity. The existing works are challenging to…