Scarcity of labeled histopathology data limits the applicability of deep learning methods to under-profiled cancer types and labels. Transfer learning allows researchers to overcome the limitations of small datasets by pre-training machine learning models on larger datasets similar to the small target dataset. However, similarity between datasets is often determined heuristically. In this paper, we propose a principled notion of distance between histopathology datasets based on a hierarchical generalization of optimal transport distances. Our method does not require any training, is agnostic to model type, and preserves much of the hierarchical structure in histopathology datasets imposed by tiling. We apply our method to H&E stained slides from The Cancer Genome Atlas from six different cancer types. We show that our method outperforms a baseline distance in a cancer-type prediction task. Our results also show that our optimal transport distance predicts difficulty of transferability in a tumor vs.normal prediction setting.
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Recent advances in Deep Learning and Computer Vision have alleviated many of the bottlenecks, allowing algorithms to be label-free with better performance. Specifically, Transformers provide a global perspective of the image, which Convolutional Neural Networks (CNN) lack by design. Here we present Cross Architectural Self-Supervision, a novel self-supervised learning approach which leverages transformers and CNN simultaneously, while also being computationally accessible to general practitioners via easily available cloud services. Compared to existing state-of-the-art self-supervised learning approaches, we empirically show CASS trained CNNs, and Transformers gained an average of 8.5% with 100% labelled data, 7.3% with 10% labelled data, and 11.5% with 1% labelled data, across three diverse datasets. Notably, one of the employed datasets included histopathology slides of an autoimmune disease, a topic underrepresented in Medical Imaging and has minimal data. In addition, our findings reveal that CASS is twice as efficient as other state-of-the-art methods in terms of training time.
To avoid the curse of dimensionality, a common approach to clustering high-dimensional data is to first project the data into a space of reduced dimension, and then cluster the projected data. Although effective, this two-stage approach prevents joint optimization of the dimensionality-reduction and clustering models, and obscures how well the complete model describes the data. Here, we show how a family of such two-stage models can be combined into a single, hierarchical model that we call a hierarchical mixture of Gaussians (HMoG). An HMoG simultaneously captures both dimensionality-reduction and clustering, and its performance is quantified in closed-form by the likelihood function. By formulating and extending existing models with exponential family theory, we show how to maximize the likelihood of HMoGs with expectation-maximization. We apply HMoGs to synthetic data and RNA sequencing data, and demonstrate how they exceed the limitations of two-stage models. Ultimately, HMoGs are a rigorous generalization of a common statistical framework, and provide researchers with a method to improve model performance when clustering high-dimensional data.
As modern complex neural networks keep breaking records and solving harder problems, their predictions also become less and less intelligible. The current lack of interpretability often undermines the deployment of accurate machine learning tools in sensitive settings. In this work, we present a model-agnostic explanation method for image classification based on a hierarchical extension of Shapley coefficients--Hierarchical Shap (h-Shap)--that resolves some of the limitations of current approaches. Unlike other Shapley-based explanation methods, h-Shap is scalable and can be computed without the need of approximation. Under certain distributional assumptions, such as those common in multiple instance learning, h-Shap retrieves the exact Shapley coefficients with an exponential improvement in computational complexity. We compare our hierarchical approach with popular Shapley-based and non-Shapley-based methods on a synthetic dataset, a medical imaging scenario, and a general computer vision problem, showing that h-Shap outperforms the state of the art in both accuracy and runtime. Code and experiments are made publicly available.
Modern deep neural networks struggle to transfer knowledge and generalize across diverse domains when deployed to real-world applications. Currently, domain generalization (DG) is introduced to learn a universal representation from multiple domains to improve the network generalization ability on unseen domains. However, previous DG methods only focus on the data-level consistency scheme without considering the synergistic regularization among different consistency schemes. In this paper, we present a novel Hierarchical Consistency framework for Domain Generalization (HCDG) by integrating Extrinsic Consistency and Intrinsic Consistency synergistically. Particularly, for the Extrinsic Consistency, we leverage the knowledge across multiple source domains to enforce data-level consistency. To better enhance such consistency, we design a novel Amplitude Gaussian-mixing strategy into Fourier-based data augmentation called DomainUp. For the Intrinsic Consistency, we perform task-level consistency for the same instance under the dual-task scenario. We evaluate the proposed HCDG framework on two medical image segmentation tasks, i.e., optic cup/disc segmentation on fundus images and prostate MRI segmentation. Extensive experimental results manifest the effectiveness and versatility of our HCDG framework.
We initiate a comprehensive experimental study of objective-based hierarchical clustering methods on massive datasets consisting of deep embedding vectors from computer vision and NLP applications. This includes a large variety of image embedding (ImageNet, ImageNetV2, NaBirds), word embedding (Twitter, Wikipedia), and sentence embedding (SST-2) vectors from several popular recent models (e.g. ResNet, ResNext, Inception V3, SBERT). Our study includes datasets with up to $4.5$ million entries with embedding dimensions up to $2048$. In order to address the challenge of scaling up hierarchical clustering to such large datasets we propose a new practical hierarchical clustering algorithm B++&C. It gives a 5%/20% improvement on average for the popular Moseley-Wang (MW) / Cohen-Addad et al. (CKMM) objectives (normalized) compared to a wide range of classic methods and recent heuristics. We also introduce a theoretical algorithm B2SAT&C which achieves a $0.74$-approximation for the CKMM objective in polynomial time. This is the first substantial improvement over the trivial $2/3$-approximation achieved by a random binary tree. Prior to this work, the best poly-time approximation of $\approx 2/3 + 0.0004$ was due to Charikar et al. (SODA'19).
Image classifiers often rely overly on peripheral attributes that have a strong correlation with the target class (i.e., dataset bias) when making predictions. Recently, a myriad of studies focus on mitigating such dataset bias, the task of which is referred to as debiasing. However, these debiasing methods often have inconsistent experimental settings (e.g., datasets and neural network architectures). Additionally, most of the previous studies in debiasing do not specify how they select their model parameters which involve early stopping and hyper-parameter tuning. The goal of this paper is to standardize the inconsistent experimental settings and propose a consistent model parameter selection criterion for debiasing. Based on such unified experimental settings and model parameter selection criterion, we build a benchmark named DebiasBench which includes five datasets and seven debiasing methods. We carefully conduct extensive experiments in various aspects and show that different state-of-the-art methods work best in different datasets, respectively. Even, the vanilla method, the method with no debiasing module, also shows competitive results in datasets with low bias severity. We publicly release the implementation of existing debiasing methods in DebiasBench to encourage future researchers in debiasing to conduct fair comparisons and further push the state-of-the-art performances.
In machine learning, an agent needs to estimate uncertainty to efficiently explore and adapt and to make effective decisions. A common approach to uncertainty estimation maintains an ensemble of models. In recent years, several approaches have been proposed for training ensembles, and conflicting views prevail with regards to the importance of various ingredients of these approaches. In this paper, we aim to address the benefits of two ingredients -- prior functions and bootstrapping -- which have come into question. We show that prior functions can significantly improve an ensemble agent's joint predictions across inputs and that bootstrapping affords additional benefits if the signal-to-noise ratio varies across inputs. Our claims are justified by both theoretical and experimental results.
Optimal transport (OT) is a versatile framework for comparing probability measures, with many applications to statistics, machine learning, and applied mathematics. However, OT distances suffer from computational and statistical scalability issues to high dimensions, which motivated the study of regularized OT methods like slicing, smoothing, and entropic penalty. This work establishes a unified framework for deriving limit distributions of empirical regularized OT distances, semiparametric efficiency of the plug-in empirical estimator, and bootstrap consistency. We apply the unified framework to provide a comprehensive statistical treatment of: (i) average- and max-sliced $p$-Wasserstein distances, for which several gaps in existing literature are closed; (ii) smooth distances with compactly supported kernels, the analysis of which is motivated by computational considerations; and (iii) entropic OT, for which our method generalizes existing limit distribution results and establishes, for the first time, efficiency and bootstrap consistency. While our focus is on these three regularized OT distances as applications, the flexibility of the proposed framework renders it applicable to broad classes of functionals beyond these examples.
Mini-batch optimal transport (m-OT) has been successfully used in practical applications that involve probability measures with a very high number of supports. The m-OT solves several smaller optimal transport problems and then returns the average of their costs and transportation plans. Despite its scalability advantage, the m-OT does not consider the relationship between mini-batches which leads to undesirable estimation. Moreover, the m-OT does not approximate a proper metric between probability measures since the identity property is not satisfied. To address these problems, we propose a novel mini-batch scheme for optimal transport, named Batch of Mini-batches Optimal Transport (BoMb-OT), that finds the optimal coupling between mini-batches and it can be seen as an approximation to a well-defined distance on the space of probability measures. Furthermore, we show that the m-OT is a limit of the entropic regularized version of the BoMb-OT when the regularized parameter goes to infinity. Finally, we carry out experiments on various applications including deep generative models, deep domain adaptation, approximate Bayesian computation, color transfer, and gradient flow to show that the BoMb-OT can be widely applied and performs well in various applications.
Multi-label text classification refers to the problem of assigning each given document its most relevant labels from the label set. Commonly, the metadata of the given documents and the hierarchy of the labels are available in real-world applications. However, most existing studies focus on only modeling the text information, with a few attempts to utilize either metadata or hierarchy signals, but not both of them. In this paper, we bridge the gap by formalizing the problem of metadata-aware text classification in a large label hierarchy (e.g., with tens of thousands of labels). To address this problem, we present the MATCH solution -- an end-to-end framework that leverages both metadata and hierarchy information. To incorporate metadata, we pre-train the embeddings of text and metadata in the same space and also leverage the fully-connected attentions to capture the interrelations between them. To leverage the label hierarchy, we propose different ways to regularize the parameters and output probability of each child label by its parents. Extensive experiments on two massive text datasets with large-scale label hierarchies demonstrate the effectiveness of MATCH over state-of-the-art deep learning baselines.
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