14 accepted papers
Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternativ…
Self-reflection for Large LanguageModels (LLMs) has gained significant attention. Existing approaches involve models iterating and improving their previous responses based on LLMs’ internal reflection ability or external feedback. However, recent research has raised doubts about whether intrinsic se…
The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast majority of spectral measurements remain in the "dark chemical s…
Finding Minimal Unsatisfiable Subsets (MUSes) of boolean constraints is a common problem in infeasibility analysis of over-constrained systems. However, because of the exponential search space of the problem, enumerating MUSes is extremely time-consuming in real applications. In this work, we propos…
The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure…
Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative grap…
Self-supervised training methods for transformers have demonstrated remarkable performance across various domains. Previous transformer-based models, such as masked autoencoders (MAE), typically utilize a single normalization layer for both the [CLS] symbol and the tokens. We propose in this paper a…
Accurate prediction of dynamical systems in unstructured meshes has recently shown successes in scientific simulations. Many dynamical systems have a nonnegligible level of stochasticity introduced by various factors (e.g. chaoticity), so there is a need for a unified framework that captures both de…
Auto-regressive sequence models for physics prediction are often restricted to low-dimensional systems, as memory cost increases with both spatial extents and sequence length. On the other hand, graph-based next-step prediction models have recently been very successful in modeling complex high-dimen…
A graph generative model defines a distribution over graphs. Typically, the model consists of a sequential process that creates and adds nodes and edges. Such sequential process defines an ordering of the nodes in the graph. The computation of the model’s likelihood requires to marginalize the node…
Recent works apply Graph Neural Networks (GNNs) to graph matching tasks and show promising results. Considering that model outputs are complex matchings, we devise several techniques to improve the learning of GNNs and obtain a new model, Stochastic Iterative Graph MAtching (SIGMA). Our model predic…
GP Inference on large datasets is computationally expensive, especially when the observation likelihood is non-Gaussian. To reduce the computation, many recent variational inference methods define the variational distribution based on a small number of inducing points. These methods have a hard trad…
Transfer learning through fine-tuning a pre-trained neural network with an extremely large dataset, such as ImageNet, can significantly accelerate training while the accuracy is frequently bottlenecked by the limited dataset size of the new target task. To solve the problem, some regularization meth…
Word embeddings are an effective tool to analyze language. They have been recently extended to model other types of data beyond text, such as items in recommendation systems. Embedding models consider the probability of a target observation (a word or an item) conditioned on the elements in the cont…