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Introducing interpretability and reasoning into Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) analysis is challenging given the complexity of gigapixel slides. Traditionally MIL interpretability is limited to identifying salient regions deemed pertinent for downstream tasks offering little insight to the end-user (pathologist) regarding the rationale behind these selections. To address this we propose Self-Interpretable MIL (SI-MIL) a method intrinsically designed for interpretability from the very outset. SI-MIL employs a deep MIL framework to guide an interpretable branch grounded on handcrafted pathological features facilitating linear predictions. Beyond identifying salient regions SI-MIL uniquely provides feature-level interpretations rooted in pathological insights for WSIs. Notably SI-MIL with its linear prediction constraints challenges the prevalent myth of an inevitable trade-off between model interpretability and performance demonstrating competitive results compared to state-of-the-art methods on WSI-level prediction tasks across three cancer types. In addition we thoroughly benchmark the local- and global-interpretability of SI-MIL in terms of statistical analysis a domain expert study and desiderata of interpretability namely user-friendliness and faithfulness. 

Semi-supervised crowd counting is an important yet challenging task. A popular approach is to iteratively generate pseudo-labels for unlabeled data and add them to the training set. The key is to use uncertainty to select reliable pseudo-labels. In this paper, we propose a novel method to calibrate model uncertainty for crowd counting. Our method takes a supervised uncertainty estimation strategy to train the model through a surrogate function. This ensures the uncertainty is well controlled throughout the training. We propose a matching-based patch-wise surrogate function to better approximate uncertainty for crowd counting tasks. The proposed method pays a sufficient amount of attention to details, while maintaining a proper granularity. Altogether our method is able to generate reliable uncertainty estimation, high quality pseudolabels, and achieve state-of-the-art performance in semisupervised crowd counting. 

In digital pathology, the spatial context of cells is important for cell classification, cancer diagnosis and prognosis. To model such complex cell context, however, is challenging. Cells form different mixtures, lineages, clusters and holes. To model such structural patterns in a learnable fashion, we introduce several mathematical tools from spatial statistics and topological data analysis. We incorporate such structural descriptors into a deep generative model as both conditional inputs and a differentiable loss. This way, we are able to generate high quality multi-class cell layouts for the first time. We show that the topology-rich cell layouts can be used for data augmentation and improve the performance of downstream tasks such as cell classification. 

Multiplex Immunohistochemistry (mIHC) is a cost-effective and accessible method for in situ labeling of multiple protein biomarkers in a tissue sample. By assigning a different stain to each biomarker, it allows the visualization of different types of cells within the tumor vicinity for downstream analysis. However, to detect different types of stains in a given mIHC image is a challenging problem, especially when the number of stains is high. Previous deep-learning-based methods mostly assume full supervision; yet the annotation can be costly. In this paper, we propose a novel unsupervised stain decomposition method to detect different stains simultaneously. Our method does not require any supervision, except for color samples of different stains. A main technical challenge is that the problem is underdetermined and can have multiple solutions. To conquer this issue, we propose a novel inversion regulation technique, which eliminates most undesirable solutions. On a 7-plexed IHC images dataset, the proposed method achieves high quality stain decomposition results without human annotation.