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Transcriptional profiling on microarrays to obtain gene expressions has been used to facilitate cancer diagnosis. We propose a deep generative machine learning architecture (called DeepCancer) that learn features from unlabeled microarray…

Graphical models can represent a multivariate distribution in a convenient and accessible form as a graph. Causal models can be viewed as a special class of graphical models that not only represent the distribution of the observed system…

Lung cancer is one of the most deadly diseases in the world. Detecting such tumors at an early stage can be a tedious task. Existing deep learning architecture for lung nodule identification used complex architecture with large number of…

Diffusion-based graph generative models have recently obtained promising results for graph generation. However, existing diffusion-based graph generative models are mostly one-shot generative models that apply Gaussian diffusion in the…

Large-scale graphs with node attributes are increasingly common in various real-world applications. Creating synthetic, attribute-rich graphs that mirror real-world examples is crucial, especially for sharing graph data for analysis and…

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) using one formulation. We first formulate prediction…

A graphical model is a statistical model that is associated to a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models admit…

Generative models aim to learn the distribution of observed data by generating new instances. With the advent of neural networks, deep generative models, including variational autoencoders (VAEs), generative adversarial networks (GANs), and…

We study the problem of generating graph signals from unknown distributions defined over given graphs, relevant to domains such as recommender systems or sensor networks. Our approach builds on generative diffusion models, which are well…

Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…

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…

Graph-based semi-supervised learning (SSL) algorithms predict labels for all nodes based on provided labels of a small set of seed nodes. Classic methods capture the graph structure through some underlying diffusion process that propagates…

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…

Inferring temporal interaction graphs and higher-order structure from neural signals is a key problem in building generative models for systems neuroscience. Foundation models for large-scale neural data represent shared latent structures…

With the increase in the use of deep learning for computer-aided diagnosis in medical images, the criticism of the black-box nature of the deep learning models is also on the rise. The medical community needs interpretable models for both…

Deep generative models produce data according to a learned representation, e.g. diffusion models, through a process of approximation computing possible samples. Approximation can be understood as reconstruction and the large datasets used…

Understanding propagation structures in graph diffusion processes, such as epidemic spread or misinformation diffusion, is a fundamental yet challenging problem. While existing methods primarily focus on source localization, they cannot…

Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in…

We present a new unified graph-based representation of medical data, combining genetic information and medical records of patients with medical knowledge via a unique knowledge graph. This approach allows us to infer meaningful information…

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent…