Alert button
Picture for Siqi Liu

Siqi Liu

Alert button

Virchow: A Million-Slide Digital Pathology Foundation Model

Sep 15, 2023
Eugene Vorontsov, Alican Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Siqi Liu, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, Eric Robert, Yi Kan Wang, Jeremy D. Kunz, Matthew C. H. Lee, Jan Bernhard, Ran A. Godrich, Gerard Oakley, Ewan Millar, Matthew Hanna, Juan Retamero, William A. Moye, Razik Yousfi, Christopher Kanan, David Klimstra, Brandon Rothrock, Thomas J. Fuchs

Computational pathology uses artificial intelligence to enable precision medicine and decision support systems through the analysis of whole slide images. It has the potential to revolutionize the diagnosis and treatment of cancer. However, a major challenge to this objective is that for many specific computational pathology tasks the amount of data is inadequate for development. To address this challenge, we created Virchow, a 632 million parameter deep neural network foundation model for computational pathology. Using self-supervised learning, Virchow is trained on 1.5 million hematoxylin and eosin stained whole slide images from diverse tissue groups, which is orders of magnitude more data than previous works. When evaluated on downstream tasks including tile-level pan-cancer detection and subtyping and slide-level biomarker prediction, Virchow outperforms state-of-the-art systems both on internal datasets drawn from the same population as the pretraining data as well as external public datasets. Virchow achieves 93% balanced accuracy for pancancer tile classification, and AUCs of 0.983 for colon microsatellite instability status prediction and 0.967 for breast CDH1 status prediction. The gains in performance highlight the importance of pretraining on massive pathology image datasets, suggesting pretraining on even larger datasets could continue improving performance for many high-impact applications where limited amounts of training data are available, such as drug outcome prediction.

Viaarxiv icon

EDIS: Entity-Driven Image Search over Multimodal Web Content

May 23, 2023
Siqi Liu, Weixi Feng, Wenhu Chen, William Yang Wang

Figure 1 for EDIS: Entity-Driven Image Search over Multimodal Web Content
Figure 2 for EDIS: Entity-Driven Image Search over Multimodal Web Content
Figure 3 for EDIS: Entity-Driven Image Search over Multimodal Web Content
Figure 4 for EDIS: Entity-Driven Image Search over Multimodal Web Content

Making image retrieval methods practical for real-world search applications requires significant progress in dataset scales, entity comprehension, and multimodal information fusion. In this work, we introduce \textbf{E}ntity-\textbf{D}riven \textbf{I}mage \textbf{S}earch (EDIS), a challenging dataset for cross-modal image search in the news domain. EDIS consists of 1 million web images from actual search engine results and curated datasets, with each image paired with a textual description. Unlike datasets that assume a small set of single-modality candidates, EDIS reflects real-world web image search scenarios by including a million multimodal image-text pairs as candidates. EDIS encourages the development of retrieval models that simultaneously address cross-modal information fusion and matching. To achieve accurate ranking results, a model must: 1) understand named entities and events from text queries, 2) ground entities onto images or text descriptions, and 3) effectively fuse textual and visual representations. Our experimental results show that EDIS challenges state-of-the-art methods with dense entities and a large-scale candidate set. The ablation study also proves that fusing textual features with visual features is critical in improving retrieval results.

Viaarxiv icon

Beyond Object Recognition: A New Benchmark towards Object Concept Learning

Dec 06, 2022
Yong-Lu Li, Yue Xu, Xinyu Xu, Xiaohan Mao, Yuan Yao, Siqi Liu, Cewu Lu

Figure 1 for Beyond Object Recognition: A New Benchmark towards Object Concept Learning
Figure 2 for Beyond Object Recognition: A New Benchmark towards Object Concept Learning
Figure 3 for Beyond Object Recognition: A New Benchmark towards Object Concept Learning
Figure 4 for Beyond Object Recognition: A New Benchmark towards Object Concept Learning

Understanding objects is a central building block of artificial intelligence, especially for embodied AI. Even though object recognition excels with deep learning, current machines still struggle to learn higher-level knowledge, e.g., what attributes an object has, and what can we do with an object. In this work, we propose a challenging Object Concept Learning (OCL) task to push the envelope of object understanding. It requires machines to reason out object affordances and simultaneously give the reason: what attributes make an object possesses these affordances. To support OCL, we build a densely annotated knowledge base including extensive labels for three levels of object concept (category, attribute, affordance), and the causal relations of three levels. By analyzing the causal structure of OCL, we present a baseline, Object Concept Reasoning Network (OCRN). It leverages causal intervention and concept instantiation to infer the three levels following their causal relations. In experiments, OCRN effectively infers the object knowledge while following the causalities well. Our data and code are available at https://mvig-rhos.com/ocl.

* Preprint. Webpage: https://mvig-rhos.com/ocl 
Viaarxiv icon

Turbocharging Solution Concepts: Solving NEs, CEs and CCEs with Neural Equilibrium Solvers

Oct 17, 2022
Luke Marris, Ian Gemp, Thomas Anthony, Andrea Tacchetti, Siqi Liu, Karl Tuyls

Figure 1 for Turbocharging Solution Concepts: Solving NEs, CEs and CCEs with Neural Equilibrium Solvers
Figure 2 for Turbocharging Solution Concepts: Solving NEs, CEs and CCEs with Neural Equilibrium Solvers
Figure 3 for Turbocharging Solution Concepts: Solving NEs, CEs and CCEs with Neural Equilibrium Solvers
Figure 4 for Turbocharging Solution Concepts: Solving NEs, CEs and CCEs with Neural Equilibrium Solvers

Solution concepts such as Nash Equilibria, Correlated Equilibria, and Coarse Correlated Equilibria are useful components for many multiagent machine learning algorithms. Unfortunately, solving a normal-form game could take prohibitive or non-deterministic time to converge, and could fail. We introduce the Neural Equilibrium Solver which utilizes a special equivariant neural network architecture to approximately solve the space of all games of fixed shape, buying speed and determinism. We define a flexible equilibrium selection framework, that is capable of uniquely selecting an equilibrium that minimizes relative entropy, or maximizes welfare. The network is trained without needing to generate any supervised training data. We show remarkable zero-shot generalization to larger games. We argue that such a network is a powerful component for many possible multiagent algorithms.

* NeurIPS 2022 
Viaarxiv icon

Developing, Evaluating and Scaling Learning Agents in Multi-Agent Environments

Sep 22, 2022
Ian Gemp, Thomas Anthony, Yoram Bachrach, Avishkar Bhoopchand, Kalesha Bullard, Jerome Connor, Vibhavari Dasagi, Bart De Vylder, Edgar Duenez-Guzman, Romuald Elie, Richard Everett, Daniel Hennes, Edward Hughes, Mina Khan, Marc Lanctot, Kate Larson, Guy Lever, Siqi Liu, Luke Marris, Kevin R. McKee, Paul Muller, Julien Perolat, Florian Strub, Andrea Tacchetti, Eugene Tarassov, Zhe Wang, Karl Tuyls

The Game Theory & Multi-Agent team at DeepMind studies several aspects of multi-agent learning ranging from computing approximations to fundamental concepts in game theory to simulating social dilemmas in rich spatial environments and training 3-d humanoids in difficult team coordination tasks. A signature aim of our group is to use the resources and expertise made available to us at DeepMind in deep reinforcement learning to explore multi-agent systems in complex environments and use these benchmarks to advance our understanding. Here, we summarise the recent work of our team and present a taxonomy that we feel highlights many important open challenges in multi-agent research.

* Published in AI Communications 2022 
Viaarxiv icon

DynaConF: Dynamic Forecasting of Non-Stationary Time-Series

Sep 17, 2022
Siqi Liu, Andreas Lehrmann

Figure 1 for DynaConF: Dynamic Forecasting of Non-Stationary Time-Series
Figure 2 for DynaConF: Dynamic Forecasting of Non-Stationary Time-Series
Figure 3 for DynaConF: Dynamic Forecasting of Non-Stationary Time-Series
Figure 4 for DynaConF: Dynamic Forecasting of Non-Stationary Time-Series

Deep learning models have shown impressive results in a variety of time series forecasting tasks, where modeling the conditional distribution of the future given the past is the essence. However, when this conditional distribution is non-stationary, it poses challenges for these models to learn consistently and to predict accurately. In this work, we propose a new method to model non-stationary conditional distributions over time by clearly decoupling stationary conditional distribution modeling from non-stationary dynamics modeling. Our method is based on a Bayesian dynamic model that can adapt to conditional distribution changes and a deep conditional distribution model that can handle large multivariate time series using a factorized output space. Our experimental results on synthetic and popular public datasets show that our model can adapt to non-stationary time series better than state-of-the-art deep learning solutions.

Viaarxiv icon

Simplex Neural Population Learning: Any-Mixture Bayes-Optimality in Symmetric Zero-sum Games

May 31, 2022
Siqi Liu, Marc Lanctot, Luke Marris, Nicolas Heess

Figure 1 for Simplex Neural Population Learning: Any-Mixture Bayes-Optimality in Symmetric Zero-sum Games
Figure 2 for Simplex Neural Population Learning: Any-Mixture Bayes-Optimality in Symmetric Zero-sum Games
Figure 3 for Simplex Neural Population Learning: Any-Mixture Bayes-Optimality in Symmetric Zero-sum Games
Figure 4 for Simplex Neural Population Learning: Any-Mixture Bayes-Optimality in Symmetric Zero-sum Games

Learning to play optimally against any mixture over a diverse set of strategies is of important practical interests in competitive games. In this paper, we propose simplex-NeuPL that satisfies two desiderata simultaneously: i) learning a population of strategically diverse basis policies, represented by a single conditional network; ii) using the same network, learn best-responses to any mixture over the simplex of basis policies. We show that the resulting conditional policies incorporate prior information about their opponents effectively, enabling near optimal returns against arbitrary mixture policies in a game with tractable best-responses. We verify that such policies behave Bayes-optimally under uncertainty and offer insights in using this flexibility at test time. Finally, we offer evidence that learning best-responses to any mixture policies is an effective auxiliary task for strategic exploration, which, by itself, can lead to more performant populations.

Viaarxiv icon

Revisiting Gaussian mixture critics in off-policy reinforcement learning: a sample-based approach

Apr 22, 2022
Bobak Shahriari, Abbas Abdolmaleki, Arunkumar Byravan, Abe Friesen, Siqi Liu, Jost Tobias Springenberg, Nicolas Heess, Matt Hoffman, Martin Riedmiller

Figure 1 for Revisiting Gaussian mixture critics in off-policy reinforcement learning: a sample-based approach
Figure 2 for Revisiting Gaussian mixture critics in off-policy reinforcement learning: a sample-based approach
Figure 3 for Revisiting Gaussian mixture critics in off-policy reinforcement learning: a sample-based approach
Figure 4 for Revisiting Gaussian mixture critics in off-policy reinforcement learning: a sample-based approach

Actor-critic algorithms that make use of distributional policy evaluation have frequently been shown to outperform their non-distributional counterparts on many challenging control tasks. Examples of this behavior include the D4PG and DMPO algorithms as compared to DDPG and MPO, respectively [Barth-Maron et al., 2018; Hoffman et al., 2020]. However, both agents rely on the C51 critic for value estimation.One major drawback of the C51 approach is its requirement of prior knowledge about the minimum andmaximum values a policy can attain as well as the number of bins used, which fixes the resolution ofthe distributional estimate. While the DeepMind control suite of tasks utilizes standardized rewards and episode lengths, thus enabling the entire suite to be solved with a single setting of these hyperparameters, this is often not the case. This paper revisits a natural alternative that removes this requirement, namelya mixture of Gaussians, and a simple sample-based loss function to train it in an off-policy regime. We empirically evaluate its performance on a broad range of continuous control tasks and demonstrate that it eliminates the need for these distributional hyperparameters and achieves state-of-the-art performance on a variety of challenging tasks (e.g. the humanoid, dog, quadruped, and manipulator domains). Finallywe provide an implementation in the Acme agent repository.

Viaarxiv icon

Revisiting Gaussian mixture critic in off-policy reinforcement learning: a sample-based approach

Apr 21, 2022
Bobak Shahriari, Abbas Abdolmaleki, Arunkumar Byravan, Abe Friesen, Siqi Liu, Jost Tobias Springenberg, Nicolas Heess, Matt Hoffman, Martin Riedmiller

Figure 1 for Revisiting Gaussian mixture critic in off-policy reinforcement learning: a sample-based approach
Figure 2 for Revisiting Gaussian mixture critic in off-policy reinforcement learning: a sample-based approach
Figure 3 for Revisiting Gaussian mixture critic in off-policy reinforcement learning: a sample-based approach
Figure 4 for Revisiting Gaussian mixture critic in off-policy reinforcement learning: a sample-based approach

Actor-critic algorithms that make use of distributional policy evaluation have frequently been shown to outperform their non-distributional counterparts on many challenging control tasks. Examples of this behavior include the D4PG and DMPO algorithms as compared to DDPG and MPO, respectively [Barth-Maron et al., 2018; Hoffman et al., 2020]. However, both agents rely on the C51 critic for value estimation.One major drawback of the C51 approach is its requirement of prior knowledge about the minimum andmaximum values a policy can attain as well as the number of bins used, which fixes the resolution ofthe distributional estimate. While the DeepMind control suite of tasks utilizes standardized rewards and episode lengths, thus enabling the entire suite to be solved with a single setting of these hyperparameters, this is often not the case. This paper revisits a natural alternative that removes this requirement, namelya mixture of Gaussians, and a simple sample-based loss function to train it in an off-policy regime. We empirically evaluate its performance on a broad range of continuous control tasks and demonstrate that it eliminates the need for these distributional hyperparameters and achieves state-of-the-art performance on a variety of challenging tasks (e.g. the humanoid, dog, quadruped, and manipulator domains). Finallywe provide an implementation in the Acme agent repository.

Viaarxiv icon