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Among the many variants of graph neural network (GNN) architectures capable of modeling data with cross-instance relations, an important subclass involves layers designed such that the forward pass iteratively reduces a graph-regularized…

Graph Neural Networks (GNNs) are a framework for graph representation learning, where a model learns to generate low dimensional node embeddings that encapsulate structural and feature-related information. GNNs are usually trained in an…

The ability to compute similarity scores between graphs based on metrics such as Graph Edit Distance (GED) is important in many real-world applications. Computing exact GED values is typically an NP-hard problem and traditional algorithms…

We leverage physics-embedded differentiable graph network simulators (GNS) to accelerate particulate and fluid simulations to solve forward and inverse problems. GNS represents the domain as a graph with particles as nodes and learned…

The advent of Graph Neural Networks (GNNs) has revolutionized the field of machine learning, offering a novel paradigm for learning on graph-structured data. Unlike traditional neural networks, GNNs are capable of capturing complex…

Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our…

In this thesis we look into programming by example (PBE), which is about finding a program mapping given inputs to given outputs. PBE has traditionally seen a split between formal versus neural approaches, where formal approaches typically…

Graph Convolutional Networks (GCNs) have achieved impressive empirical advancement across a wide variety of semi-supervised node classification tasks. Despite their great success, training GCNs on large graphs suffers from computational and…

Learning the physical simulation on large-scale meshes with flat Graph Neural Networks (GNNs) and stacking Message Passings (MPs) is challenging due to the scaling complexity w.r.t. the number of nodes and over-smoothing. There has been…

Graph Neural Networks (GNN) have been shown to work effectively for modeling graph structured data to solve tasks such as node classification, link prediction and graph classification. There has been some recent progress in defining the…

Graph Prompt Feature (GPF) learning has been widely used in adapting pre-trained GNN model on the downstream task. GPFs first introduce some prompt atoms and then learns the optimal prompt vector for each graph node using the linear…

Mini-batch training of Graph Neural Networks (GNNs) is fundamentally different from training on i.i.d. data: sampling a subgraph alters the topology and introduces boundary effects, leading prior work to develop structure-aware samplers…

Image segmentation plays an essential role in nuclei image analysis. Recently, the segment anything model has made a significant breakthrough in such tasks. However, the current model exists two major issues for cell segmentation: (1) the…

Representing a signal as a continuous function parameterized by neural network (a.k.a. Implicit Neural Representations, INRs) has attracted increasing attention in recent years. Neural Processes (NPs), which model the distributions over…

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with…

Graph Neural Networks (GNNs) are emerging as a powerful tool for learning from graph-structured data and performing sophisticated inference tasks in various application domains. Although GNNs have been shown to be effective on modest-sized…

Graph neural networks (GNNs) have emerged as a powerful tool for learning software engineering tasks including code completion, bug finding, and program repair. They benefit from leveraging program structure like control flow graphs, but…

Score-based algorithms that learn the structure of Bayesian networks can be used for both exact and approximate solutions. While approximate learning scales better with the number of variables, it can be computationally expensive in the…

Machine learning techniques have recently been adopted in various applications in medicine, biology, chemistry, and material engineering. An important task is to predict the properties of molecules, which serves as the main subroutine in…

The Graph Convolutional Network (GCN) model and its variants are powerful graph embedding tools for facilitating classification and clustering on graphs. However, a major challenge is to reduce the complexity of layered GCNs and make them…