To pretrain or not to pretrain? A case study of domain-specific pretraining for semantic segmentation in histopathology

Annotating medical imaging datasets is costly, so fine-tuning (or transfer learning) is the most effective method for digital pathology vision applications such as disease classification and semantic segmentation. However, due to texture bias in models trained on real-world images, transfer learning for histopathology applications might result in underperforming models, which necessitates the need for using unlabeled histopathology data and self-supervised methods to discover domain-specific characteristics. Here, we tested the premise that histopathology-specific pretrained models provide better initializations for pathology vision tasks, i.e., gland and cell segmentation. In this study, we compare the performance of gland and cell segmentation tasks with domain-specific and non-domain-specific pretrained weights. Moreover, we investigate the data size at which domain-specific pretraining produces a statistically significant difference in performance. In addition, we investigated whether domain-specific initialization improves the effectiveness of out-of-domain testing on distinct datasets but the same task. The results indicate that performance gain using domain-specific pretraining depends on both the task and the size of the training dataset. In instances with limited dataset sizes, a significant improvement in gland segmentation performance was also observed, whereas models trained on cell segmentation datasets exhibit no improvement

ADASSM: Adversarial Data Augmentation in Statistical Shape Models From Images

Statistical shape models (SSM) have been well-established as an excellent tool for identifying variations in the morphology of anatomy across the underlying population. Shape models use consistent shape representation across all the samples in a given cohort, which helps to compare shapes and identify the variations that can detect pathologies and help in formulating treatment plans. In medical imaging, computing these shape representations from CT/MRI scans requires time-intensive preprocessing operations, including but not limited to anatomy segmentation annotations, registration, and texture denoising. Deep learning models have demonstrated exceptional capabilities in learning shape representations directly from volumetric images, giving rise to highly effective and efficient Image-to-SSM. Nevertheless, these models are data-hungry and due to the limited availability of medical data, deep learning models tend to overfit. Offline data augmentation techniques, that use kernel density estimation based (KDE) methods for generating shape-augmented samples, have successfully aided Image-to-SSM networks in achieving comparable accuracy to traditional SSM methods. However, these augmentation methods focus on shape augmentation, whereas deep learning models exhibit image-based texture bias results in sub-optimal models. This paper introduces a novel strategy for on-the-fly data augmentation for the Image-to-SSM framework by leveraging data-dependent noise generation or texture augmentation. The proposed framework is trained as an adversary to the Image-to-SSM network, augmenting diverse and challenging noisy samples. Our approach achieves improved accuracy by encouraging the model to focus on the underlying geometry rather than relying solely on pixel values

Multi-Set Inoculation: Assessing Model Robustness Across Multiple Challenge Sets

Language models, given their black-box nature, often exhibit sensitivity to input perturbations, leading to trust issues due to hallucinations. To bolster trust, it's essential to understand these models' failure modes and devise strategies to enhance their performance. In this study, we propose a framework to study the effect of input perturbations on language models of different scales, from pre-trained models to large language models (LLMs). We use fine-tuning to train a robust model to perturbations, and we investigate whether exposure to one perturbation improves or degrades the model's performance on other perturbations. To address multi-perturbation robustness, we suggest three distinct training strategies. We also extend the framework to LLMs via a chain of thought(COT) prompting with exemplars. We instantiate our framework for the Tabular-NLI task and show that the proposed strategies train the model robust to different perturbations without losing accuracy on a given dataset.Comment: 13 pages, 2 Figure, 12 Table

InfoSync: Information Synchronization across Multilingual Semi-structured Tables

Information Synchronization of semi-structured data across languages is challenging. For instance, Wikipedia tables in one language should be synchronized across languages. To address this problem, we introduce a new dataset InfoSyncC and a two-step method for tabular synchronization. InfoSync contains 100K entity-centric tables (Wikipedia Infoboxes) across 14 languages, of which a subset (3.5K pairs) are manually annotated. The proposed method includes 1) Information Alignment to map rows and 2) Information Update for updating missing/outdated information for aligned tables across multilingual tables. When evaluated on InfoSync, information alignment achieves an F1 score of 87.91 (en non-en). To evaluate information updation, we perform human-assisted Wikipedia edits on Infoboxes for 603 table pairs. Our approach obtains an acceptance rate of 77.28% on Wikipedia, showing the effectiveness of the proposed method.Comment: 22 pages, 7 figures, 20 tables, ACL 2023 (Toronto, Canada

Unsupervised Domain Adaptation for Semantic Segmentation via Feature-space Density Matching

Semantic segmentation is a critical step in automated image interpretation and analysis where pixels are classified into one or more predefined semantically meaningful classes. Deep learning approaches for semantic segmentation rely on harnessing the power of annotated images to learn features indicative of these semantic classes. Nonetheless, they often fail to generalize when there is a significant domain (i.e., distributional) shift between the training (i.e., source) data and the dataset(s) encountered when deployed (i.e., target), necessitating manual annotations for the target data to achieve acceptable performance. This is especially important in medical imaging because different image modalities have significant intra- and inter-site variations due to protocol and vendor variability. Current techniques are sensitive to hyperparameter tuning and target dataset size. This paper presents an unsupervised domain adaptation approach for semantic segmentation that alleviates the need for annotating target data. Using kernel density estimation, we match the target data distribution to the source data in the feature space. We demonstrate that our results are comparable or superior on multiple-site prostate MRI and histopathology images, which mitigates the need for annotating target data