Robust Learning via Conditional Prevalence Adjustment

Healthcare data often come from multiple sites in which the correlations between confounding variables can vary widely. If deep learning models exploit these unstable correlations, they might fail catastrophically in unseen sites. Although many methods have been proposed to tackle unstable correlations, each has its limitations. For example, adversarial training forces models to completely ignore unstable correlations, but doing so may lead to poor predictive performance. Other methods (e.g. Invariant risk minimization [4]) try to learn domain-invariant representations that rely only on stable associations by assuming a causal data-generating process (input X causes class label Y ). Thus, they may be ineffective for anti-causal tasks (Y causes X), which are common in computer vision. We propose a method called CoPA (Conditional Prevalence-Adjustment) for anti-causal tasks. CoPA assumes that (1) generation mechanism is stable, i.e. label Y and confounding variable(s) Z generate X, and (2) the unstable conditional prevalence in each site E fully accounts for the unstable correlations between X and Y . Our crucial observation is that confounding variables are routinely recorded in healthcare settings and the prevalence can be readily estimated, for example, from a set of (Y, Z) samples (no need for corresponding samples of X). CoPA can work even if there is a single training site, a scenario which is often overlooked by existing methods. Our experiments on synthetic and real data show CoPA beating competitive baselines.

A Framework for Interpretability in Machine Learning for Medical Imaging

Interpretability for machine learning models in medical imaging (MLMI) is an important direction of research. However, there is a general sense of murkiness in what interpretability means. Why does the need for interpretability in MLMI arise? What goals does one actually seek to address when interpretability is needed? To answer these questions, we identify a need to formalize the goals and elements of interpretability in MLMI. By reasoning about real-world tasks and goals common in both medical image analysis and its intersection with machine learning, we identify four core elements of interpretability: localization, visual recognizability, physical attribution, and transparency. Overall, this paper formalizes interpretability needs in the context of medical imaging, and our applied perspective clarifies concrete MLMI-specific goals and considerations in order to guide method design and improve real-world usage. Our goal is to provide practical and didactic information for model designers and practitioners, inspire developers of models in the medical imaging field to reason more deeply about what interpretability is achieving, and suggest future directions of interpretability research.

Learning Invariant Representations with a Nonparametric Nadaraya-Watson Head

Machine learning models will often fail when deployed in an environment with a data distribution that is different than the training distribution. When multiple environments are available during training, many methods exist that learn representations which are invariant across the different distributions, with the hope that these representations will be transportable to unseen domains. In this work, we present a nonparametric strategy for learning invariant representations based on the recently-proposed Nadaraya-Watson (NW) head. The NW head makes a prediction by comparing the learned representations of the query to the elements of a support set that consists of labeled data. We demonstrate that by manipulating the support set, one can encode different causal assumptions. In particular, restricting the support set to a single environment encourages the model to learn invariant features that do not depend on the environment. We present a causally-motivated setup for our modeling and training strategy and validate on three challenging real-world domain generalization tasks in computer vision.

A robust and interpretable deep learning framework for multi-modal registration via keypoints

We present KeyMorph, a deep learning-based image registration framework that relies on automatically detecting corresponding keypoints. State-of-the-art deep learning methods for registration often are not robust to large misalignments, are not interpretable, and do not incorporate the symmetries of the problem. In addition, most models produce only a single prediction at test-time. Our core insight which addresses these shortcomings is that corresponding keypoints between images can be used to obtain the optimal transformation via a differentiable closed-form expression. We use this observation to drive the end-to-end learning of keypoints tailored for the registration task, and without knowledge of ground-truth keypoints. This framework not only leads to substantially more robust registration but also yields better interpretability, since the keypoints reveal which parts of the image are driving the final alignment. Moreover, KeyMorph can be designed to be equivariant under image translations and/or symmetric with respect to the input image ordering. Finally, we show how multiple deformation fields can be computed efficiently and in closed-form at test time corresponding to different transformation variants. We demonstrate the proposed framework in solving 3D affine and spline-based registration of multi-modal brain MRI scans. In particular, we show registration accuracy that surpasses current state-of-the-art methods, especially in the context of large displacements. Our code is available at https://github.com/evanmy/keymorph.

A Simple Nadaraya-Watson Head can offer Explainable and Calibrated Classification

In this paper, we empirically analyze a simple, non-learnable, and nonparametric Nadaraya-Watson (NW) prediction head that can be used with any neural network architecture. In the NW head, the prediction is a weighted average of labels from a support set. The weights are computed from distances between the query feature and support features. This is in contrast to the dominant approach of using a learnable classification head (e.g., a fully-connected layer) on the features, which can be challenging to interpret and can yield poorly calibrated predictions. Our empirical results on an array of computer vision tasks demonstrate that the NW head can yield better calibration than its parametric counterpart, while having comparable accuracy and with minimal computational overhead. To further increase inference-time efficiency, we propose a simple approach that involves a clustering step run on the training set to create a relatively small distilled support set. In addition to using the weights as a means of interpreting model predictions, we further present an easy-to-compute "support influence function," which quantifies the influence of a support element on the prediction for a given query. As we demonstrate in our experiments, the influence function can allow the user to debug a trained model. We believe that the NW head is a flexible, interpretable, and highly useful building block that can be used in a range of applications.

Computing Multiple Image Reconstructions with a Single Hypernetwork

Deep learning based techniques achieve state-of-the-art results in a wide range of image reconstruction tasks like compressed sensing. These methods almost always have hyperparameters, such as the weight coefficients that balance the different terms in the optimized loss function. The typical approach is to train the model for a hyperparameter setting determined with some empirical or theoretical justification. Thus, at inference time, the model can only compute reconstructions corresponding to the pre-determined hyperparameter values. In this work, we present a hypernetwork-based approach, called HyperRecon, to train reconstruction models that are agnostic to hyperparameter settings. At inference time, HyperRecon can efficiently produce diverse reconstructions, which would each correspond to different hyperparameter values. In this framework, the user is empowered to select the most useful output(s) based on their own judgement. We demonstrate our method in compressed sensing, super-resolution and denoising tasks, using two large-scale and publicly-available MRI datasets. Our code is available at https://github.com/alanqrwang/hyperrecon.

Hyper-Convolutions via Implicit Kernels for Medical Imaging

The convolutional neural network (CNN) is one of the most commonly used architectures for computer vision tasks. The key building block of a CNN is the convolutional kernel that aggregates information from the pixel neighborhood and shares weights across all pixels. A standard CNN's capacity, and thus its performance, is directly related to the number of learnable kernel weights, which is determined by the number of channels and the kernel size (support). In this paper, we present the \textit{hyper-convolution}, a novel building block that implicitly encodes the convolutional kernel using spatial coordinates. Hyper-convolutions decouple kernel size from the total number of learnable parameters, enabling a more flexible architecture design. We demonstrate in our experiments that replacing regular convolutions with hyper-convolutions can improve performance with less parameters, and increase robustness against noise. We provide our code here: \emph{https://github.com/tym002/Hyper-Convolution}

Joint Optimization of Hadamard Sensing and Reconstruction in Compressed Sensing Fluorescence Microscopy

Compressed sensing fluorescence microscopy (CS-FM) proposes a scheme whereby less measurements are collected during sensing and reconstruction is performed to recover the image. Much work has gone into optimizing the sensing and reconstruction portions separately. We propose a method of jointly optimizing both sensing and reconstruction end-to-end under a total measurement constraint, enabling learning of the optimal sensing scheme concurrently with the parameters of a neural network-based reconstruction network. We train our model on a rich dataset of confocal, two-photon, and wide-field microscopy images comprising of a variety of biological samples. We show that our method outperforms several baseline sensing schemes and a regularized regression reconstruction algorithm.

Regularization-Agnostic Compressed Sensing MRI Reconstruction with Hypernetworks

Reconstructing under-sampled k-space measurements in Compressed Sensing MRI (CS-MRI) is classically solved with regularized least-squares. Recently, deep learning has been used to amortize this optimization by training reconstruction networks on a dataset of under-sampled measurements. Here, a crucial design choice is the regularization function(s) and corresponding weight(s). In this paper, we explore a novel strategy of using a hypernetwork to generate the parameters of a separate reconstruction network as a function of the regularization weight(s), resulting in a regularization-agnostic reconstruction model. At test time, for a given under-sampled image, our model can rapidly compute reconstructions with different amounts of regularization. We analyze the variability of these reconstructions, especially in situations when the overall quality is similar. Finally, we propose and empirically demonstrate an efficient and data-driven way of maximizing reconstruction performance given limited hypernetwork capacity. Our code is publicly available at https://github.com/alanqrwang/RegAgnosticCSMRI.