Pathology image analysis crucially relies on the availability and quality of annotated pathological samples, which are very difficult to collect and need lots of human effort. To address this issue, beyond traditional preprocess data augmentation methods, mixing-based approaches are effective and practical. However, previous mixing-based data augmentation methods do not thoroughly explore the essential characteristics of pathology images, including the local specificity, global distribution, and inner/outer-sample instance relationship. To further understand the pathology characteristics and make up effective pseudo samples, we propose the CellMix framework with a novel distribution-based in-place shuffle strategy. We split the images into patches with respect to the granularity of pathology instances and do the shuffle process across the same batch. In this way, we generate new samples while keeping the absolute relationship of pathology instances intact. Furthermore, to deal with the perturbations and distribution-based noise, we devise a loss-drive strategy inspired by curriculum learning during the training process, making the model fit the augmented data adaptively. It is worth mentioning that we are the first to explore data augmentation techniques in the pathology image field. Experiments show SOTA results on 7 different datasets. We conclude that this novel instance relationship-based strategy can shed light on general data augmentation for pathology image analysis. The code is available at //github.com/sagizty/CellMix.
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The "pre-training $\rightarrow$ downstream adaptation" presents both new opportunities and challenges for Continual Learning (CL). Although the recent state-of-the-art in CL is achieved through Parameter-Efficient-Tuning (PET) adaptation paradigm, only prompt has been explored, limiting its application to Transformers only. In this paper, we position prompting as one instantiation of PET, and propose a unified CL framework with general PET, dubbed as Learning-Accumulation-Ensemble (LAE). PET, e.g., using Adapter, LoRA, or Prefix, can adapt a pre-trained model to downstream tasks with fewer parameters and resources. Given a PET method, our LAE framework incorporates it for CL with three novel designs. 1) Learning: the pre-trained model adapts to the new task by tuning an online PET module, along with our adaptation speed calibration to align different PET modules, 2) Accumulation: the task-specific knowledge learned by the online PET module is accumulated into an offline PET module through momentum update, 3) Ensemble: During inference, we respectively construct two experts with online/offline PET modules (which are favored by the novel/historical tasks) for prediction ensemble. We show that LAE is compatible with a battery of PET methods and gains strong CL capability. For example, LAE with Adaptor PET surpasses the prior state-of-the-art by 1.3% and 3.6% in last-incremental accuracy on CIFAR100 and ImageNet-R datasets, respectively.
Tumour heterogeneity in breast cancer poses challenges in predicting outcome and response to therapy. Spatial transcriptomics technologies may address these challenges, as they provide a wealth of information about gene expression at the cell level, but they are expensive, hindering their use in large-scale clinical oncology studies. Predicting gene expression from hematoxylin and eosin stained histology images provides a more affordable alternative for such studies. Here we present BrST-Net, a deep learning framework for predicting gene expression from histopathology images using spatial transcriptomics data. Using this framework, we trained and evaluated 10 state-of-the-art deep learning models without utilizing pretrained weights for the prediction of 250 genes. To enhance the generalisation performance of the main network, we introduce an auxiliary network into the framework. Our methodology outperforms previous studies, with 237 genes identified with positive correlation, including 24 genes with a median correlation coefficient greater than 0.50. This is a notable improvement over previous studies, which could predict only 102 genes with positive correlation, with the highest correlation values ranging from 0.29 to 0.34.
As it is cumbersome and expensive to acquire a huge amount of data for training neural dialog models, data augmentation is proposed to effectively utilize existing training samples. However, current data augmentation techniques on the dialog generation task mostly augment all cases in the training dataset without considering the intrinsic attributes between different cases. We argue that not all cases are beneficial for augmentation task, and the cases suitable for augmentation should obey the following two attributes: (1) low-quality (the dialog model cannot generate a high-quality response for the case), (2) representative (the case should represent the property of the whole dataset). Herein, we explore this idea by proposing a Selective Data Augmentation framework (SDA) for the response generation task. SDA employs a dual adversarial network to select the lowest quality and most representative data points for augmentation in one stage. Extensive experiments conducted on two publicly available datasets, i.e., DailyDialog and OpenSubtitles, show that our framework can improve the response generation performance with respect to various metrics.
Self-supervised learning in vision-language processing exploits semantic alignment between imaging and text modalities. Prior work in biomedical VLP has mostly relied on the alignment of single image and report pairs even though clinical notes commonly refer to prior images. This does not only introduce poor alignment between the modalities but also a missed opportunity to exploit rich self-supervision through existing temporal content in the data. In this work, we explicitly account for prior images and reports when available during both training and fine-tuning. Our approach, named BioViL-T, uses a CNN-Transformer hybrid multi-image encoder trained jointly with a text model. It is designed to be versatile to arising challenges such as pose variations and missing input images across time. The resulting model excels on downstream tasks both in single- and multi-image setups, achieving state-of-the-art performance on (I) progression classification, (II) phrase grounding, and (III) report generation, whilst offering consistent improvements on disease classification and sentence-similarity tasks. We release a novel multi-modal temporal benchmark dataset, MS-CXR-T, to quantify the quality of vision-language representations in terms of temporal semantics. Our experimental results show the advantages of incorporating prior images and reports to make most use of the data.
Objective: Reproducibility is critical for translating machine learning-based (ML) solutions in computational pathology (CompPath) into practice. However, an increasing number of studies report difficulties in reproducing ML results. The NCI Imaging Data Commons (IDC) is a public repository of >120 cancer image collections, including >38,000 whole-slide images (WSIs), that is designed to be used with cloud-based ML services. Here, we explore the potential of the IDC to facilitate reproducibility of CompPath research. Materials and Methods: The IDC realizes the FAIR principles: All images are encoded according to the DICOM standard, persistently identified, discoverable via rich metadata, and accessible via open tools. Taking advantage of this, we implemented two experiments in which a representative ML-based method for classifying lung tumor tissue was trained and/or evaluated on different datasets from the IDC. To assess reproducibility, the experiments were run multiple times with independent but identically configured sessions of common ML services. Results: The AUC values of different runs of the same experiment were generally consistent and in the same order of magnitude as a similar, previously published study. However, there were occasional small variations in AUC values of up to 0.044, indicating a practical limit to reproducibility. Discussion and conclusion: By realizing the FAIR principles, the IDC enables other researchers to reuse exactly the same datasets. Cloud-based ML services enable others to run CompPath experiments in an identically configured computing environment without having to own high-performance hardware. The combination of both makes it possible to approach the reproducibility limit.
Recent studies on contrastive learning have achieved remarkable performance solely by leveraging few labels in the context of medical image segmentation. Existing methods mainly focus on instance discrimination and invariant mapping. However, they face three common pitfalls: (1) tailness: medical image data usually follows an implicit long-tail class distribution. Blindly leveraging all pixels in training hence can lead to the data imbalance issues, and cause deteriorated performance; (2) consistency: it remains unclear whether a segmentation model has learned meaningful and yet consistent anatomical features due to the intra-class variations between different anatomical features; and (3) diversity: the intra-slice correlations within the entire dataset have received significantly less attention. This motivates us to seek a principled approach for strategically making use of the dataset itself to discover similar yet distinct samples from different anatomical views. In this paper, we introduce a novel semi-supervised 2D medical image segmentation framework termed Mine yOur owN Anatomy (MONA), and make three contributions. First, prior work argues that every pixel equally matters to the model training; we observe empirically that this alone is unlikely to define meaningful anatomical features, mainly due to lacking the supervision signal. We show two simple solutions towards learning invariances - through the use of stronger data augmentations and nearest neighbors. Second, we construct a set of objectives that encourage the model to be capable of decomposing medical images into a collection of anatomical features in an unsupervised manner. Lastly, we both empirically and theoretically, demonstrate the efficacy of our MONA on three benchmark datasets with different labeled settings, achieving new state-of-the-art under different labeled semi-supervised settings
In this work, we leverage visual prompting (VP) to improve adversarial robustness of a fixed, pre-trained model at testing time. Compared to conventional adversarial defenses, VP allows us to design universal (i.e., data-agnostic) input prompting templates, which have plug-and-play capabilities at testing time to achieve desired model performance without introducing much computation overhead. Although VP has been successfully applied to improving model generalization, it remains elusive whether and how it can be used to defend against adversarial attacks. We investigate this problem and show that the vanilla VP approach is not effective in adversarial defense since a universal input prompt lacks the capacity for robust learning against sample-specific adversarial perturbations. To circumvent it, we propose a new VP method, termed Class-wise Adversarial Visual Prompting (C-AVP), to generate class-wise visual prompts so as to not only leverage the strengths of ensemble prompts but also optimize their interrelations to improve model robustness. Our experiments show that C-AVP outperforms the conventional VP method, with 2.1X standard accuracy gain and 2X robust accuracy gain. Compared to classical test-time defenses, C-AVP also yields a 42X inference time speedup.
Images can convey rich semantics and induce various emotions in viewers. Recently, with the rapid advancement of emotional intelligence and the explosive growth of visual data, extensive research efforts have been dedicated to affective image content analysis (AICA). In this survey, we will comprehensively review the development of AICA in the recent two decades, especially focusing on the state-of-the-art methods with respect to three main challenges -- the affective gap, perception subjectivity, and label noise and absence. We begin with an introduction to the key emotion representation models that have been widely employed in AICA and description of available datasets for performing evaluation with quantitative comparison of label noise and dataset bias. We then summarize and compare the representative approaches on (1) emotion feature extraction, including both handcrafted and deep features, (2) learning methods on dominant emotion recognition, personalized emotion prediction, emotion distribution learning, and learning from noisy data or few labels, and (3) AICA based applications. Finally, we discuss some challenges and promising research directions in the future, such as image content and context understanding, group emotion clustering, and viewer-image interaction.
TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classication
Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively.
Most previous event extraction studies have relied heavily on features derived from annotated event mentions, thus cannot be applied to new event types without annotation effort. In this work, we take a fresh look at event extraction and model it as a grounding problem. We design a transferable neural architecture, mapping event mentions and types jointly into a shared semantic space using structural and compositional neural networks, where the type of each event mention can be determined by the closest of all candidate types . By leveraging (1)~available manual annotations for a small set of existing event types and (2)~existing event ontologies, our framework applies to new event types without requiring additional annotation. Experiments on both existing event types (e.g., ACE, ERE) and new event types (e.g., FrameNet) demonstrate the effectiveness of our approach. \textit{Without any manual annotations} for 23 new event types, our zero-shot framework achieved performance comparable to a state-of-the-art supervised model which is trained from the annotations of 500 event mentions.
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