2023-06-09 更新
Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning
Authors:Ronald Xie, Kuan Pang, Gary D. Bader, Bo Wang
Histology imaging is an important tool in medical diagnosis and research, enabling the examination of tissue structure and composition at the microscopic level. Understanding the underlying molecular mechanisms of tissue architecture is critical in uncovering disease mechanisms and developing effective treatments. Gene expression profiling provides insight into the molecular processes underlying tissue architecture, but the process can be time-consuming and expensive. In this study, we present BLEEP (Bi-modaL Embedding for Expression Prediction), a bi-modal embedding framework capable of generating spatially resolved gene expression profiles of whole-slide Hematoxylin and eosin (H&E) stained histology images. BLEEP uses a contrastive learning framework to construct a low-dimensional joint embedding space from a reference dataset using paired image and expression profiles at micrometer resolution. With this framework, the gene expression of any query image patch can be imputed using the expression profiles from the reference dataset. We demonstrate BLEEP’s effectiveness in gene expression prediction by benchmarking its performance on a human liver tissue dataset captured via the 10x Visium platform, where it achieves significant improvements over existing methods. Our results demonstrate the potential of BLEEP to provide insights into the molecular mechanisms underlying tissue architecture, with important implications in diagnosis and research of various diseases. The proposed framework can significantly reduce the time and cost associated with gene expression profiling, opening up new avenues for high-throughput analysis of histology images for both research and clinical applications.
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Multi-CLIP: Contrastive Vision-Language Pre-training for Question Answering tasks in 3D Scenes
Authors:Alexandros Delitzas, Maria Parelli, Nikolas Hars, Georgios Vlassis, Sotirios Anagnostidis, Gregor Bachmann, Thomas Hofmann
Training models to apply common-sense linguistic knowledge and visual concepts from 2D images to 3D scene understanding is a promising direction that researchers have only recently started to explore. However, it still remains understudied whether 2D distilled knowledge can provide useful representations for downstream 3D vision-language tasks such as 3D question answering. In this paper, we propose a novel 3D pre-training Vision-Language method, namely Multi-CLIP, that enables a model to learn language-grounded and transferable 3D scene point cloud representations. We leverage the representational power of the CLIP model by maximizing the agreement between the encoded 3D scene features and the corresponding 2D multi-view image and text embeddings in the CLIP space via a contrastive objective. To validate our approach, we consider the challenging downstream tasks of 3D Visual Question Answering (3D-VQA) and 3D Situated Question Answering (3D-SQA). To this end, we develop novel multi-modal transformer-based architectures and we demonstrate how our pre-training method can benefit their performance. Quantitative and qualitative experimental results show that Multi-CLIP outperforms state-of-the-art works across the downstream tasks of 3D-VQA and 3D-SQA and leads to a well-structured 3D scene feature space.
PDF The first two authors contributed equally
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ContraBAR: Contrastive Bayes-Adaptive Deep RL
Authors:Era Choshen, Aviv Tamar
In meta reinforcement learning (meta RL), an agent seeks a Bayes-optimal policy — the optimal policy when facing an unknown task that is sampled from some known task distribution. Previous approaches tackled this problem by inferring a belief over task parameters, using variational inference methods. Motivated by recent successes of contrastive learning approaches in RL, such as contrastive predictive coding (CPC), we investigate whether contrastive methods can be used for learning Bayes-optimal behavior. We begin by proving that representations learned by CPC are indeed sufficient for Bayes optimality. Based on this observation, we propose a simple meta RL algorithm that uses CPC in lieu of variational belief inference. Our method, ContraBAR, achieves comparable performance to state-of-the-art in domains with state-based observation and circumvents the computational toll of future observation reconstruction, enabling learning in domains with image-based observations. It can also be combined with image augmentations for domain randomization and used seamlessly in both online and offline meta RL settings.
PDF ICML 2023. Pytorch code available at https://github.com/ec2604/ContraBAR
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ReContrast: Domain-Specific Anomaly Detection via Contrastive Reconstruction
Authors:Jia Guo, Shuai Lu, Lize Jia, Weihang Zhang, Huiqi Li
Most advanced unsupervised anomaly detection (UAD) methods rely on modeling feature representations of frozen encoder networks pre-trained on large-scale datasets, e.g. ImageNet. However, the features extracted from the encoders that are borrowed from natural image domains coincide little with the features required in the target UAD domain, such as industrial inspection and medical imaging. In this paper, we propose a novel epistemic UAD method, namely ReContrast, which optimizes the entire network to reduce biases towards the pre-trained image domain and orients the network in the target domain. We start with a feature reconstruction approach that detects anomalies from errors. Essentially, the elements of contrastive learning are elegantly embedded in feature reconstruction to prevent the network from training instability, pattern collapse, and identical shortcut, while simultaneously optimizing both the encoder and decoder on the target domain. To demonstrate our transfer ability on various image domains, we conduct extensive experiments across two popular industrial defect detection benchmarks and three medical image UAD tasks, which shows our superiority over current state-of-the-art methods.
PDF under review
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Asymmetric Patch Sampling for Contrastive Learning
Authors:Chengchao Shen, Jianzhong Chen, Shu Wang, Hulin Kuang, Jin Liu, Jianxin Wang
Asymmetric appearance between positive pair effectively reduces the risk of representation degradation in contrastive learning. However, there are still a mass of appearance similarities between positive pair constructed by the existing methods, which inhibits the further representation improvement. In this paper, we propose a novel asymmetric patch sampling strategy for contrastive learning, to further boost the appearance asymmetry for better representations. Specifically, dual patch sampling strategies are applied to the given image, to obtain asymmetric positive pairs. First, sparse patch sampling is conducted to obtain the first view, which reduces spatial redundancy of image and allows a more asymmetric view. Second, a selective patch sampling is proposed to construct another view with large appearance discrepancy relative to the first one. Due to the inappreciable appearance similarity between positive pair, the trained model is encouraged to capture the similarity on semantics, instead of low-level ones. Experimental results demonstrate that our proposed method significantly outperforms the existing self-supervised methods on both ImageNet-1K and CIFAR dataset, e.g., 2.5% finetune accuracy improvement on CIFAR100. Furthermore, our method achieves state-of-the-art performance on downstream tasks, object detection and instance segmentation on COCO.Additionally, compared to other self-supervised methods, our method is more efficient on both memory and computation during training. The source code is available at https://github.com/visresearch/aps.
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Devil is in Channels: Contrastive Single Domain Generalization for Medical Image Segmentation
Authors:Shishuai Hu, Zehui Liao, Yong Xia
Deep learning-based medical image segmentation models suffer from performance degradation when deployed to a new healthcare center. To address this issue, unsupervised domain adaptation and multi-source domain generalization methods have been proposed, which, however, are less favorable for clinical practice due to the cost of acquiring target-domain data and the privacy concerns associated with redistributing the data from multiple source domains. In this paper, we propose a \textbf{C}hannel-level \textbf{C}ontrastive \textbf{S}ingle \textbf{D}omain \textbf{G}eneralization (\textbf{C$^2$SDG}) model for medical image segmentation. In C$^2$SDG, the shallower features of each image and its style-augmented counterpart are extracted and used for contrastive training, resulting in the disentangled style representations and structure representations. The segmentation is performed based solely on the structure representations. Our method is novel in the contrastive perspective that enables channel-wise feature disentanglement using a single source domain. We evaluated C$^2$SDG against six SDG methods on a multi-domain joint optic cup and optic disc segmentation benchmark. Our results suggest the effectiveness of each module in C$^2$SDG and also indicate that C$^2$SDG outperforms the baseline and all competing methods with a large margin. The code will be available at \url{https://github.com/ShishuaiHu/CCSDG}.
PDF 12 pages, 5 figures
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Factorized Contrastive Learning: Going Beyond Multi-view Redundancy
Authors:Paul Pu Liang, Zihao Deng, Martin Ma, James Zou, Louis-Philippe Morency, Ruslan Salakhutdinov
In a wide range of multimodal tasks, contrastive learning has become a particularly appealing approach since it can successfully learn representations from abundant unlabeled data with only pairing information (e.g., image-caption or video-audio pairs). Underpinning these approaches is the assumption of multi-view redundancy - that shared information between modalities is necessary and sufficient for downstream tasks. However, in many real-world settings, task-relevant information is also contained in modality-unique regions: information that is only present in one modality but still relevant to the task. How can we learn self-supervised multimodal representations to capture both shared and unique information relevant to downstream tasks? This paper proposes FactorCL, a new multimodal representation learning method to go beyond multi-view redundancy. FactorCL is built from three new contributions: (1) factorizing task-relevant information into shared and unique representations, (2) capturing task-relevant information via maximizing MI lower bounds and removing task-irrelevant information via minimizing MI upper bounds, and (3) multimodal data augmentations to approximate task relevance without labels. On large-scale real-world datasets, FactorCL captures both shared and unique information and achieves state-of-the-art results on six benchmarks.
PDF Code available at: https://github.com/pliang279/FactorCL
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