Publications

Bayes-MIL: A New Probabilistic Perspective on Attention-based Multiple Instance Learning for Whole Slide Images
Yufei Cui
Ziquan Liu
Xiangyu Liu
Xue (Steve) Liu
Cong Wang
Tei-Wei Kuo
Chun Jason Xue
Antoni Bert Chan
Multiple instance learning (MIL) is a popular weakly-supervised learning model on the whole slide image (WSI) for AI-assisted pathology diag… (see more)nosis. The recent advance in attention-based MIL allows the model to find its region-of-interest (ROI) for interpretation by learning the attention weights for image patches of WSI slides. However, we empirically find that the interpretability of some related methods is either untrustworthy as the principle of MIL is violated or unsatisfactory as the high-attention regions are not consistent with experts’ annotations. In this paper, we propose Bayes-MIL to address the problem from a probabilistic perspective. The induced patch-level uncertainty is proposed as a new measure of MIL interpretability, which outperforms previous methods in matching doctors annotations. We design a slide-dependent patch regularizer (SDPR) for the attention, imposing constraints derived from the MIL assumption, on the attention distribution. SDPR explicitly constrains the model to generate correct attention values. The spatial information is further encoded by an approximate convolutional conditional random field (CRF), for better interpretability. Experimental results show Bayes-MIL outperforms the related methods in patch-level and slide-level metrics and provides much better interpretable ROI on several large-scale WSI datasets.
2023-01-01
International Conference on Learning Representations (published)
dblp.uni-trier.de
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Yoshua Bengio
Xavier Bresson
Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes… (see more) critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.
2023-01-01
ArXiv (preprint)
arxiv.org
arxiv.org
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Yoshua Bengio
Xavier Bresson
Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes… (see more) critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.
2023-01-01
ArXiv (preprint)
arxiv.org
arxiv.org
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Yoshua Bengio
Xavier Bresson
Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes… (see more) critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.
2023-01-01
ArXiv (preprint)
arxiv.org
arxiv.org
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Anh Tuan Luu
Yoshua Bengio
Xavier Bresson
arxiv.org
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Yoshua Bengio
Xavier Bresson
Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes… (see more) critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.
2023-01-01
ArXiv (preprint)
arxiv.org
arxiv.org
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Yoshua Bengio
Xavier Bresson
Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes… (see more) critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.
2023-01-01
ArXiv (preprint)
arxiv.org
arxiv.org
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Yoshua Bengio
Xavier Bresson
Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes… (see more) critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.
2023-01-01
ArXiv (preprint)
arxiv.org
arxiv.org
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi
Chaitanya K. Joshi
Thomas Laurent
Yoshua Bengio
Xavier Bresson
Graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. As the field grows, it becomes… (see more) critical to identify key architectures and validate new ideas that generalize to larger, more complex datasets. Unfortunately, it has been increasingly difficult to gauge the effectiveness of new models in the absence of a standardized benchmark with consistent experimental settings. In this paper, we introduce a reproducible GNN benchmarking framework, with the facility for researchers to add new models conveniently for arbitrary datasets. We demonstrate the usefulness of our framework by presenting a principled investigation into the recent Weisfeiler-Lehman GNNs (WL-GNNs) compared to message passing-based graph convolutional networks (GCNs) for a variety of graph tasks, i.e. graph regression/classification and node/link prediction, with medium-scale datasets.
2023-01-01
ArXiv (preprint)
arxiv.org
arxiv.org
Benchmarking State-Merging Algorithms for Learning Regular Languages.
Adil Soubki
Jeffrey Heinz
François Coste
Faissal Ouardi
Guillaume Rabusseau
2023-01-01
International Conference on Graphics and Interaction (published)
dblp.uni-trier.de
Best-Case Retrieval Evaluation: Improving the Sensitivity of Reciprocal Rank with Lexicographic Precision
Fernando Diaz
Across a variety of ranking tasks, researchers use reciprocal rank to measure the effectiveness for users interested in exactly one relevant… (see more) item. Despite its widespread use, evidence suggests that reciprocal rank is brittle when discriminating between systems. This brittleness, in turn, is compounded in modern evaluation settings where current, high-precision systems may be difficult to distinguish. We address the lack of sensitivity of reciprocal rank by introducing and connecting it to the concept of best-case retrieval, an evaluation method focusing on assessing the quality of a ranking for the most satisfied possible user across possible recall requirements. This perspective allows us to generalize reciprocal rank and define a new preference-based evaluation we call lexicographic precision or lexiprecision. By mathematical construction, we ensure that lexiprecision preserves differences detected by reciprocal rank, while empirically improving sensitivity and robustness across a broad set of retrieval and recommendation tasks.
2023-01-01
EVIA (published)
doi.org
arxiv.org
Bigger, Better, Faster: Human-level Atari with human-level efficiency
Max Schwarzer
Johan Samir Obando Ceron
Aaron Courville
Marc Gendron-Bellemare
Rishabh Agarwal
Pablo Samuel Castro
We introduce a value-based RL agent, which we call BBF, that achieves super-human performance in the Atari 100K benchmark. BBF relies on sca… (see more)ling the neural networks used for value estimation, as well as a number of other design choices that enable this scaling in a sample-efficient manner. We conduct extensive analyses of these design choices and provide insights for future work. We end with a discussion about updating the goalposts for sample-efficient RL research on the ALE. We make our code and data publicly available at https://github.com/google-research/google-research/tree/master/bigger_better_faster.
2023-01-01
ICML (published)
doi.org
openreview.net