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Farimah Poursafaei

farimah.poursafaei@mila.quebec
Postdoctorat - McGill University
Superviseur⋅e principal⋅e
Reihaneh Rabbany
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Publications

On the Scalability of GNNs for Molecular Graphs
Maciej Sypetkowski
Frederik Wenkel
Farimah Poursafaei
Nia Dickson
Karush Suri
Philip Fradkin
Dominique Beaini
Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have obse… (voir plus)rved a strong relationship between model size, dataset size, and performance. However, structure-based architectures such as Graph Neural Networks (GNNs) are yet to show the benefits of scale mainly due to the lower efficiency of sparse operations, large data requirements, and lack of clarity about the effectiveness of various architectures. We address this drawback of GNNs by studying their scaling behavior. Specifically, we analyze message-passing networks, graph Transformers, and hybrid architectures on the largest public collection of 2D molecular graphs. For the first time, we observe that GNNs benefit tremendously from the increasing scale of depth, width, number of molecules, number of labels, and the diversity in the pretraining datasets, resulting in a 30.25% improvement when scaling to 1 billion parameters and 28.98% improvement when increasing size of dataset to eightfold. We further demonstrate strong finetuning scaling behavior on 38 tasks, outclassing previous large models. We hope that our work paves the way for an era where foundational GNNs drive pharmaceutical drug discovery.
2024-03-04
ICLR.cc/2024/Workshop/DPFM (poster)
openreview.net
openreview.net
Temporal Graph Analysis with TGX
Razieh Shirzadkhani
Shenyang Huang
Elahe Kooshafar
Reihaneh Rabbany
Farimah Poursafaei
Real-world networks, with their evolving relations, are best captured as temporal graphs. However, existing software libraries are largely d… (voir plus)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.
2024-01-01
WSDM (publié)
doi.org
arxiv.org
Exhaustive Evaluation of Dynamic Link Prediction
Farimah Poursafaei
Reihaneh Rabbany
Dynamic link prediction is a crucial task in the study of evolving graphs, which serve as abstract models for various real-world application… (voir plus)s. Recent dynamic graph representation learning models have claimed near-perfect performance in this task. However, we argue that the standard evaluation strategy for dynamic link prediction overlooks the sparsity and recurrence patterns inherent in dynamic networks. Specifically, the current strategy suffers from issues such as evaluating models on a balanced set of positive and negative edges, neglecting the reassessment of frequently recurring positive edges, and lacking a comprehensive evaluation of both recurring and new edges.To address these limitations, we propose a novel evaluation strategy called EXHAUSTIVE, which takes into account all relevant negative edges and separately assesses the performance on recurring and new edges. Using our proposed evaluation strategy, we compare the performance of five state-of-the-art dynamic graph learning models on seven benchmark datasets. Compared to the previous common evaluation strategy, we observe an average drop of 62% in Average Precision for dynamic link prediction. Additionally, the ranking of the models also changes under the new evaluation setting. Furthermore, we demonstrate that while all models perform considerably worse when predicting new edges compared to recurring ones, the best performing models differ between the two scenarios. This highlights the importance of employing the proposed evaluation strategy for both the assessment and design of dynamic link prediction models. By adopting our novel evaluation strategy, researchers can obtain a more accurate understanding of model performance in dynamic link prediction, leading to improved evaluation and design of such models.
2023-12-04
2023 IEEE International Conference on Data Mining Workshops (ICDMW) (publié)
doi.org
Temporal Graph Benchmark for Machine Learning on Temporal Graphs
Shenyang Huang
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… (voir plus)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/.
openreview.net
Active Keyword Selection to Track Evolving Topics on Twitter
Sacha Lévy
Farimah Poursafaei
Kellin Pelrine
Reihaneh Rabbany
How can we study social interactions on evolving topics at a mass scale? Over the past decade, researchers from diverse fields such as econo… (voir plus)mics, political science, and public health have often done this by querying Twitter's public API endpoints with hand-picked topical keywords to search or stream discussions. However, despite the API's accessibility, it remains difficult to select and update keywords to collect high-quality data relevant to topics of interest. In this paper, we propose an active learning method for rapidly refining query keywords to increase both the yielded topic relevance and dataset size. We leverage a large open-source COVID-19 Twitter dataset to illustrate the applicability of our method in tracking Tweets around the key sub-topics of Vaccine, Mask, and Lockdown. Our experiments show that our method achieves an average topic-related keyword recall 2x higher than baselines. We open-source our code along with a web interface for keyword selection to make data collection from Twitter more systematic for researchers.
2022-12-01
2022 IEEE International Conference on Data Mining Workshops (ICDMW) (publié)
doi.org
arxiv.org
A Strong Node Classification Baseline for Temporal Graphs
Farimah Poursafaei
Željko Žilić
Reihaneh Rabbany
2022-04-20
Proceedings of the 2022 SIAM International Conference on Data Mining (SDM) (publié)
doi.org
Towards Better Evaluation for Dynamic Link Prediction
Farimah Poursafaei
Andy Huang
Shenyang Huang
Kellin Pelrine
Reihaneh Rabbany
Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In th… (voir plus)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.
openreview.net
SigTran: Signature Vectors for Detecting Illicit Activities in Blockchain Transaction Networks
Farimah Poursafaei
Reihaneh Rabbany
Željko Žilić
2021-05-09
Advances in Knowledge Discovery and Data Mining (publié)
doi.org