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Massive Multiple-Input Multiple-Out (MIMO) detection is an important problem in modern wireless communication systems. While traditional Belief Propagation (BP) detectors perform poorly on loopy graphs, the recent Graph Neural Networks…
Graph similarity search is among the most important graph-based applications, e.g. finding the chemical compounds that are most similar to a query compound. Graph similarity computation, such as Graph Edit Distance (GED) and Maximum Common…
We present a geometry-aware method for heterogeneous single-particle cryogenic electron microscopy (cryo-EM) reconstruction that predicts atomic backbone conformations. To incorporate protein-structure priors, we represent the backbone as a…
The person re-identification task requires to robustly estimate visual similarities between person images. However, existing person re-identification models mostly estimate the similarities of different image pairs of probe and gallery…
Identifying novel functional protein structures is at the heart of molecular engineering and molecular biology, requiring an often computationally exhaustive search. We introduce the use of a Deep Convolutional Generative Adversarial…
This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does…
Graphs are one of the most important data structures for representing pairwise relations between objects. Specifically, a graph embedded in a Euclidean space is essential to solving real problems, such as physical simulations. A crucial…
Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks…
Spherical equivariant graph neural networks (EGNNs) provide a principled framework for learning on three-dimensional molecular and biomolecular systems, where predictions must respect the rotational symmetries inherent in physics. These…
Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing. While deep graph models have demonstrated success in modeling complex biological systems, existing…
We focus on an important yet challenging problem: using a 2D deep network to deal with 3D segmentation for medical image analysis. Existing approaches either applied multi-view planar (2D) networks or directly used volumetric (3D) networks…
Graph Edit Distance (GED) is a fundamental, albeit NP-hard, metric for structural graph similarity. Recent neural graph matching architectures approximate GED by first encoding graphs with a Graph Neural Network (GNN) and then applying…
Graph neural networks (GNNs) for link prediction can loosely be divided into two broad categories. First, \emph{node-wise} architectures pre-compute individual embeddings for each node that are later combined by a simple decoder to make…
The distance-geometric graph representation adopts a unified scheme (distance) for representing the geometry of three-dimensional(3D) graphs. It is invariant to rotation and translation of the graph and it reflects pair-wise node…
Proteins interact to form complexes to carry out essential biological functions. Computational methods have been developed to predict the structures of protein complexes. However, an important challenge in protein complex structure…
Shape-based virtual screening is widely employed in ligand-based drug design to search chemical libraries for molecules with similar 3D shapes yet novel 2D chemical structures compared to known ligands. 3D deep generative models have the…
Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph…
Inferring missing links or detecting spurious ones based on observed graphs, known as link prediction, is a long-standing challenge in graph data analysis. With the recent advances in deep learning, graph neural networks have been used for…
We introduce Hyperdimensional Graph Learner (HDGL), a novel method for node classification and link prediction in graphs. HDGL maps node features into a very high-dimensional space (\textit{hyperdimensional} or HD space for short) using the…
The arc of drug discovery entails a multiparameter optimization problem spanning vast length scales. They key parameters range from solubility (angstroms) to protein-ligand binding (nanometers) to in vivo toxicity (meters). Through feature…