Shenyang Huang

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets

Dominique Beaini

Joao Alex Cunha

Zhiyi Li

Gabriela Moisescu-Pareja

Oleksandr Dymov

Samuel Maddrell-Mander

Callum McLean

Jama Hussein Mohamud

Michael Craig

Cristian Gabellini

Kerstin Klaser

Josef Dean

Cas Wognum … (see 14 more)

Maciej Sypetkowski

Hadrien Mary

Therence Bois

Andrew Fitzgibbon

Błażej Banaszewski

Chad Martin

Dominic Masters

Recently, pre-trained foundation models have shown significant advancements in multiple fields. However, the lack of datasets with labeled f… (see more)eatures and codebases has hindered the development of a supervised foundation model for molecular tasks. Here, we have carefully curated seven datasets specifically tailored for node- and graph-level prediction tasks to facilitate supervised learning on molecules. Moreover, to support the development of multi-task learning on our proposed datasets, we created the Graphium graph machine learning library. Our dataset collection encompasses two distinct categories. Firstly, the TOYMIX category modifies three small existing datasets with additional data for multi-task learning. Secondly, the LARGEMIX category includes four large-scale datasets with 344M graph-level data points and 409M node-level data points from ∼5M unique molecules. Finally, the ultra-large dataset contains 2,210M graph-level data points and 2,031M node-level data points coming from 86M molecules. Hence our datasets represent an order of magnitude increase in data volume compared to other 2D-GNN datasets. In addition, recognizing that molecule-related tasks often span multiple levels, we have designed our library to explicitly support multi-tasking, offering a diverse range of multi-level representations, i.e., representations at the graph, node, edge, and node-pair level. We equipped the library with an extensive collection of models and features to cover different levels of molecule analysis. By combining our curated datasets with this versatile library, we aim to accelerate the development of molecule foundation models. Datasets and code are available at https://github.com/datamol-io/graphium.

2024-05-06

International Conference on Learning Representations (Accept (poster))

Temporal Graph Analysis with TGX

Real-world networks, with their evolving relations, are best captured as temporal graphs. However, existing software libraries are largely d… (see more)esigned for static graphs where the dynamic nature of temporal graphs is ignored. Bridging this gap, we introduce TGX, a Python package specially designed for analysis of temporal networks that encompasses an automated pipeline for data loading, data processing, and analysis of evolving graphs. TGX provides access to eleven built-in datasets and eight external Temporal Graph Benchmark (TGB) datasets as well as any novel datasets in the .csv format. Beyond data loading, TGX facilitates data processing functionalities such as discretization of temporal graphs and node subsampling to accelerate working with larger datasets. For comprehensive investigation, TGX offers network analysis by providing a diverse set of measures, including average node degree and the evolving number of nodes and edges per timestamp. Additionally, the package consolidates meaningful visualization plots indicating the evolution of temporal patterns, such as Temporal Edge Appearance (TEA) and Temporal Edge Trafficc (TET) plots. The TGX package is a robust tool for examining the features of temporal graphs and can be used in various areas like studying social networks, citation networks, and tracking user interactions. We plan to continuously support and update TGX based on community feedback. TGX is publicly available on: https://github.com/ComplexData-MILA/TGX.

2024-03-03

Proceedings of the 17th ACM International Conference on Web Search and Data Mining (published)

Laplacian Change Point Detection for Single and Multi-view Dynamic Graphs

Samy Coulombe

Dynamic graphs are rich data structures that are used to model complex relationships between entities over time. In particular, anomaly dete… (see more)ction in temporal graphs is crucial for many real world applications such as intrusion identification in network systems, detection of ecosystem disturbances and detection of epidemic outbreaks. In this paper, we focus on change point detection in dynamic graphs and address three main challenges associated with this problem: i). how to compare graph snapshots across time, ii). how to capture temporal dependencies, and iii). how to combine different views of a temporal graph. To solve the above challenges, we first propose Laplacian Anomaly Detection (LAD) which uses the spectrum of graph Laplacian as the low dimensional embedding of the graph structure at each snapshot. LAD explicitly models short term and long term dependencies by applying two sliding windows. Next, we propose MultiLAD, a simple and effective generalization of LAD to multi-view graphs. MultiLAD provides the first change point detection method for multi-view dynamic graphs. It aggregates the singular values of the normalized graph Laplacian from different views through the scalar power mean operation. Through extensive synthetic experiments, we show that i). LAD and MultiLAD are accurate and outperforms state-of-the-art baselines and their multi-view extensions by a large margin, ii). MultiLAD's advantage over contenders significantly increases when additional views are available, and iii). MultiLAD is highly robust to noise from individual views. In five real world dynamic graphs, we demonstrate that LAD and MultiLAD identify significant events as top anomalies such as the implementation of government COVID-19 interventions which impacted the population mobility in multi-view traffic networks.

2023-11-05

ACM Transactions on Knowledge Discovery from Data (published)

Temporal Graph Benchmark for Machine Learning on Temporal Graphs

Farimah Poursafaei

Jacob Danovitch

Matthias Fey

Weihua Hu

Emanuele Rossi

Jure Leskovec

Michael M. Bronstein

Guillaume Rabusseau

Reihaneh Rabbany

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and r… (see more)obust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

2023-09-24

NeurIPS.cc/2023/Track/Datasets_and_Benchmarks (poster)

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets (Ultra Large Dataset)

Dominique Beaini

Joao Alex Cunha

Zhiyi Li

Gabriela Moisescu-Pareja

Oleksandr Dymov

Samuel Maddrell-Mander

Callum McLean

Ali Parviz

Luis T. Díaz Müller

Jama Hussein Mohamud

Michael Craig

Cristian Gabellini

Jian Tang … (see 8 more)

Christopher G. Morris

Mirco Ravanelli

Guy Wolf

Prudencio Tossou

Hadrien Mary

Błażej Banaszewski

Chad Martin

Dominic Masters

2023-09-21

Zenodo (unknown)

GPS++: Reviving the Art of Message Passing for Molecular Property Prediction

Dominic Masters

Josef Dean

Kerstin Klaser

Zhiyi Li

Samuel Maddrell-Mander

Adam Sanders

Hatem Helal

Deniz Beker

Andrew William Fitzgibbon

Ladislav Rampasek

Dominique Beaini

2023-07-29

TMLR (accepted)

Fast and Attributed Change Detection on Dynamic Graphs with Density of States

2023-05-14

arXiv (preprint)

Towards Better Evaluation for Dynamic Link Prediction

Andy Huang

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In th… (see more)is work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization-based baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings which highlights that the negative edges used in the current evaluation are easy. To sample more challenging negative edges, we introduce two novel negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.

2022-09-15

NeurIPS.cc/2022/Track/Datasets_and_Benchmarks (accepted)

Understanding Capacity Saturation in Incremental Learning

Vincent François-Lavet

Guillaume Rabusseau

2021-06-07

Canadian Conference on AI (published)

Incorporating dynamic flight network in SEIR to model mobility between populations

Xiaoye Ding

Abby Leung

Reihaneh Rabbany

Current efforts of modelling COVID-19 are often based on the standard compartmental models such as SEIR and their variations. As pre-symptom… (see more)atic and asymptomatic cases can spread the disease between populations through travel, it is important to incorporate mobility between populations into the epidemiological modelling. In this work, we propose to modify the commonly-used SEIR model to account for the dynamic flight network, by estimating the imported cases based on the air traffic volume as well as the test positive rate at the source. This modification, called Flight-SEIR, can potentially enable 1). early detection of outbreaks due to imported pre-symptomatic and asymptomatic cases, 2). more accurate estimation of the reproduction number and 3). evaluation of the impact of travel restrictions and the implications of lifting these measures. The proposed Flight-SEIR is essential in navigating through this pandemic and the next ones, given how interconnected our world has become.

2020-12-31

Applied Network Science (published)

Scalable Change Point Detection for Dynamic Graphs