John V. Guttag

Angie Boggust, Harini Suresh, Hendrik Strobelt et al. · mit

Saliency methods are a common class of machine learning interpretability techniques that calculate how important each input feature is to a model's output. We find that, with the rapid pace of development, users struggle to stay informed of the strengths and limitations of new methods and, thus, choose methods for unprincipled reasons (e.g., popularity). Moreover, despite a corresponding rise in evaluation metrics, existing approaches assume universal desiderata for saliency methods (e.g., faithfulness) that do not account for diverse user needs. In response, we introduce saliency cards: structured documentation of how saliency methods operate and their performance across a battery of evaluative metrics. Through a review of 25 saliency method papers and 33 method evaluations, we identify 10 attributes that users should account for when choosing a method. We group these attributes into three categories that span the process of computing and interpreting saliency: methodology, or how the saliency is calculated; sensitivity, or the relationship between the saliency and the underlying model and data; and, perceptibility, or how an end user ultimately interprets the result. By collating this information, saliency cards allow users to more holistically assess and compare the implications of different methods. Through nine semi-structured interviews with users from various backgrounds, including researchers, radiologists, and computational biologists, we find that saliency cards provide a detailed vocabulary for discussing individual methods and allow for a more systematic selection of task-appropriate methods. Moreover, with saliency cards, we are able to analyze the research landscape in a more structured fashion to identify opportunities for new methods and evaluation metrics for unmet user needs.

Kathleen M. Lewis, Emily Mu, Adrian V. Dalca et al.

Recent vision-language models outperform vision-only models on many image classification tasks. However, because of the absence of paired text/image descriptions, it remains difficult to fine-tune these models for fine-grained image classification. In this work, we propose a method, GIST, for generating image-specific fine-grained text descriptions from image-only datasets, and show that these text descriptions can be used to improve classification. Key parts of our method include 1. prompting a pretrained large language model with domain-specific prompts to generate diverse fine-grained text descriptions for each class and 2. using a pretrained vision-language model to match each image to label-preserving text descriptions that capture relevant visual features in the image. We demonstrate the utility of GIST by fine-tuning vision-language models on the image-and-generated-text pairs to learn an aligned vision-language representation space for improved classification. We evaluate our learned representation space in full-shot and few-shot scenarios across four diverse fine-grained classification datasets, each from a different domain. Our method achieves an average improvement of $4.1\%$ in accuracy over CLIP linear probes and an average of $1.1\%$ improvement in accuracy over the previous state-of-the-art image-text classification method on the full-shot datasets. Our method achieves similar improvements across few-shot regimes. Code is available at https://github.com/emu1729/GIST.

Victor Ion Butoi, Jose Javier Gonzalez Ortiz, Tianyu Ma et al.

While deep learning models have become the predominant method for medical image segmentation, they are typically not capable of generalizing to unseen segmentation tasks involving new anatomies, image modalities, or labels. Given a new segmentation task, researchers generally have to train or fine-tune models, which is time-consuming and poses a substantial barrier for clinical researchers, who often lack the resources and expertise to train neural networks. We present UniverSeg, a method for solving unseen medical segmentation tasks without additional training. Given a query image and example set of image-label pairs that define a new segmentation task, UniverSeg employs a new Cross-Block mechanism to produce accurate segmentation maps without the need for additional training. To achieve generalization to new tasks, we have gathered and standardized a collection of 53 open-access medical segmentation datasets with over 22,000 scans, which we refer to as MegaMedical. We used this collection to train UniverSeg on a diverse set of anatomies and imaging modalities. We demonstrate that UniverSeg substantially outperforms several related methods on unseen tasks, and thoroughly analyze and draw insights about important aspects of the proposed system. The UniverSeg source code and model weights are freely available at https://universeg.csail.mit.edu

Rajiv Movva, Divya Shanmugam, Kaihua Hou et al.

Healthcare data in the United States often records only a patient's coarse race group: for example, both Indian and Chinese patients are typically coded as "Asian." It is unknown, however, whether this coarse coding conceals meaningful disparities in the performance of clinical risk scores across granular race groups. Here we show that it does. Using data from 418K emergency department visits, we assess clinical risk score performance disparities across 26 granular groups for three outcomes, five risk scores, and four performance metrics. Across outcomes and metrics, we show that the risk scores exhibit significant granular performance disparities within coarse race groups. In fact, variation in performance within coarse groups often *exceeds* the variation between coarse groups. We explore why these disparities arise, finding that outcome rates, feature distributions, and the relationships between features and outcomes all vary significantly across granular groups. Our results suggest that healthcare providers, hospital systems, and machine learning researchers should strive to collect, release, and use granular race data in place of coarse race data, and that existing analyses may significantly underestimate racial disparities in performance.

Aniruddh Raghu, Divya Shanmugam, Eugene Pomerantsev et al.

Neural network models have demonstrated impressive performance in predicting pathologies and outcomes from the 12-lead electrocardiogram (ECG). However, these models often need to be trained with large, labelled datasets, which are not available for many predictive tasks of interest. In this work, we perform an empirical study examining whether training time data augmentation methods can be used to improve performance on such data-scarce ECG prediction problems. We investigate how data augmentation strategies impact model performance when detecting cardiac abnormalities from the ECG. Motivated by our finding that the effectiveness of existing augmentation strategies is highly task-dependent, we introduce a new method, TaskAug, which defines a flexible augmentation policy that is optimized on a per-task basis. We outline an efficient learning algorithm to do so that leverages recent work in nested optimization and implicit differentiation. In experiments, considering three datasets and eight predictive tasks, we find that TaskAug is competitive with or improves on prior work, and the learned policies shed light on what transformations are most effective for different tasks. We distill key insights from our experimental evaluation, generating a set of best practices for applying data augmentation to ECG prediction problems.

Helen Lu, Divya Shanmugam, Harini Suresh et al.

Test-time augmentation -- the aggregation of predictions across transformed examples of test inputs -- is an established technique to improve the performance of image classification models. Importantly, TTA can be used to improve model performance post-hoc, without additional training. Although test-time augmentation (TTA) can be applied to any data modality, it has seen limited adoption in NLP due in part to the difficulty of identifying label-preserving transformations. In this paper, we present augmentation policies that yield significant accuracy improvements with language models. A key finding is that augmentation policy design -- for instance, the number of samples generated from a single, non-deterministic augmentation -- has a considerable impact on the benefit of TTA. Experiments across a binary classification task and dataset show that test-time augmentation can deliver consistent improvements over current state-of-the-art approaches.

Jose Javier Gonzalez Ortiz, John Guttag, Adrian Dalca

Hypernetworks, neural networks that predict the parameters of another neural network, are powerful models that have been successfully used in diverse applications from image generation to multi-task learning. Unfortunately, existing hypernetworks are often challenging to train. Training typically converges far more slowly than for non-hypernetwork models, and the rate of convergence can be very sensitive to hyperparameter choices. In this work, we identify a fundamental and previously unidentified problem that contributes to the challenge of training hypernetworks: a magnitude proportionality between the inputs and outputs of the hypernetwork. We demonstrate both analytically and empirically that this can lead to unstable optimization, thereby slowing down convergence, and sometimes even preventing any learning. We present a simple solution to this problem using a revised hypernetwork formulation that we call Magnitude Invariant Parametrizations (MIP). We demonstrate the proposed solution on several hypernetwork tasks, where it consistently stabilizes training and achieves faster convergence. Furthermore, we perform a comprehensive ablation study including choices of activation function, normalization strategies, input dimensionality, and hypernetwork architecture; and find that MIP improves training in all scenarios. We provide easy-to-use code that can turn existing networks into MIP-based hypernetworks.

Kathleen M. Lewis, John Guttag

Online clothing catalogs lack diversity in body shape and garment size. Brands commonly display their garments on models of one or two sizes, rarely including plus-size models. To our knowledge, our paper presents the first method for generating images of garments and models in a new target size to tackle the size under-representation problem. Our primary technical contribution is a conditional generative adversarial network that learns deformation fields at multiple resolutions to realistically change the size of models and garments. Results from our two user studies show SizeGAN outperforms alternative methods along three dimensions -- realism, garment faithfulness, and size -- which are all important for real world use.

Aniruddh Raghu, Payal Chandak, Ridwan Alam et al.

Self-supervised learning (SSL) for clinical time series data has received significant attention in recent literature, since these data are highly rich and provide important information about a patient's physiological state. However, most existing SSL methods for clinical time series are limited in that they are designed for unimodal time series, such as a sequence of structured features (e.g., lab values and vitals signs) or an individual high-dimensional physiological signal (e.g., an electrocardiogram). These existing methods cannot be readily extended to model time series that exhibit multimodality, with structured features and high-dimensional data being recorded at each timestep in the sequence. In this work, we address this gap and propose a new SSL method -- Sequential Multi-Dimensional SSL -- where a SSL loss is applied both at the level of the entire sequence and at the level of the individual high-dimensional data points in the sequence in order to better capture information at both scales. Our strategy is agnostic to the specific form of loss function used at each level -- it can be contrastive, as in SimCLR, or non-contrastive, as in VICReg. We evaluate our method on two real-world clinical datasets, where the time series contains sequences of (1) high-frequency electrocardiograms and (2) structured data from lab values and vitals signs. Our experimental results indicate that pre-training with our method and then fine-tuning on downstream tasks improves performance over baselines on both datasets, and in several settings, can lead to improvements across different self-supervised loss functions.

Godfrey Tan, Massimiliano Poletto, John Guttag et al.

Role classification involves grouping hosts into related roles. It exposes the logical structure of a network, simplifies network management tasks such as policy checking and network segmentation, and can be used to improve the accuracy of network monitoring and analysis algorithms such as intrusion detection. This paper defines the role classification problem and introduces two practical algorithms that group hosts based on observed connection patterns while dealing with changes in these patterns over time. The algorithms have been implemented in a commercial network monitoring and analysis product for enterprise networks. Results from grouping two enterprise networks show that the number of groups identified by our algorithms can be two orders of magnitude smaller than the number of hosts and that the way our algorithms group hosts highly reflects the logical structure of the networks.

Jose Javier Gonzalez Ortiz, John Guttag, Adrian Dalca

Convolutional Neural Networks (CNNs) are the predominant model used for a variety of medical image analysis tasks. At inference time, these models are computationally intensive, especially with volumetric data. In principle, it is possible to trade accuracy for computational efficiency by manipulating the rescaling factor in the downsample and upsample layers of CNN architectures. However, properly exploring the accuracy-efficiency trade-off is prohibitively expensive with existing models. To address this, we introduce Scale-Space HyperNetworks (SSHN), a method that learns a spectrum of CNNs with varying internal rescaling factors. A single SSHN characterizes an entire Pareto accuracy-efficiency curve of models that match, and occasionally surpass, the outcomes of training many separate networks with fixed rescaling factors. We demonstrate the proposed approach in several medical image analysis applications, comparing SSHN against strategies with both fixed and dynamic rescaling factors. We find that SSHN consistently provides a better accuracy-efficiency trade-off at a fraction of the training cost. Trained SSHNs enable the user to quickly choose a rescaling factor that appropriately balances accuracy and computational efficiency for their particular needs at inference.

Katie Matton, Purvaja Balaji, Hamzeh Ghasemzadeh et al.

Phonotrauma refers to vocal fold tissue damage resulting from exposure to forces during voicing. It occurs on a continuum from mild to severe, and treatment options can vary based on severity. Assessment of severity involves a clinician's expert judgment, which is costly and can vary widely in reliability. In this work, we present the first method for automatically classifying phonotrauma severity from vocal fold images. To account for the ordinal nature of the labels, we adopt a widely used ordinal regression framework. To account for label uncertainty, we propose a novel modification to ordinal regression loss functions that enables them to operate on soft labels reflecting annotator rating distributions. Our proposed soft ordinal regression method achieves predictive performance approaching that of clinical experts, while producing well-calibrated uncertainty estimates. By providing an automated tool for phonotrauma severity assessment, our work can enable large-scale studies of phonotrauma, ultimately leading to improved clinical understanding and patient care.

Emily Mu, John Guttag, Maggie Makar

Given a similarity metric, contrastive methods learn a representation in which examples that are similar are pushed together and examples that are dissimilar are pulled apart. Contrastive learning techniques have been utilized extensively to learn representations for tasks ranging from image classification to caption generation. However, existing contrastive learning approaches can fail to generalize because they do not take into account the possibility of different similarity relations. In this paper, we propose a novel multi-similarity contrastive loss (MSCon), that learns generalizable embeddings by jointly utilizing supervision from multiple metrics of similarity. Our method automatically learns contrastive similarity weightings based on the uncertainty in the corresponding similarity, down-weighting uncertain tasks and leading to better out-of-domain generalization to new tasks. We show empirically that networks trained with MSCon outperform state-of-the-art baselines on in-domain and out-of-domain settings.

Amy Zhao, Guha Balakrishnan, Kathleen M. Lewis et al.

We introduce a new video synthesis task: synthesizing time lapse videos depicting how a given painting might have been created. Artists paint using unique combinations of brushes, strokes, and colors. There are often many possible ways to create a given painting. Our goal is to learn to capture this rich range of possibilities. Creating distributions of long-term videos is a challenge for learning-based video synthesis methods. We present a probabilistic model that, given a single image of a completed painting, recurrently synthesizes steps of the painting process. We implement this model as a convolutional neural network, and introduce a novel training scheme to enable learning from a limited dataset of painting time lapses. We demonstrate that this model can be used to sample many time steps, enabling long-term stochastic video synthesis. We evaluate our method on digital and watercolor paintings collected from video websites, and show that human raters find our synthetic videos to be similar to time lapse videos produced by real artists. Our code is available at https://xamyzhao.github.io/timecraft.

Adrian V. Dalca, John Guttag, Mert R. Sabuncu

A wide range of systems exhibit high dimensional incomplete data. Accurate estimation of the missing data is often desired, and is crucial for many downstream analyses. Many state-of-the-art recovery methods involve supervised learning using datasets containing full observations. In contrast, we focus on unsupervised estimation of missing image data, where no full observations are available - a common situation in practice. Unsupervised imputation methods for images often employ a simple linear subspace to capture correlations between data dimensions, omitting more complex relationships. In this work, we introduce a general probabilistic model that describes sparse high dimensional imaging data as being generated by a deep non-linear embedding. We derive a learning algorithm using a variational approximation based on convolutional neural networks and discuss its relationship to linear imputation models, the variational auto encoder, and deep image priors. We introduce sparsity-aware network building blocks that explicitly model observed and missing data. We analyze proposed sparsity-aware network building blocks, evaluate our method on public domain imaging datasets, and conclude by showing that our method enables imputation in an important real-world problem involving medical images. The code is freely available as part of the \verb|neuron| library at http://github.com/adalca/neuron.

Amy Zhao, Guha Balakrishnan, Frédo Durand et al.

Image segmentation is an important task in many medical applications. Methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling medical images requires significant expertise and time, and typical hand-tuned approaches for data augmentation fail to capture the complex variations in such images. We present an automated data augmentation method for synthesizing labeled medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transformations from the images, and use the model along with the labeled example to synthesize additional labeled examples. Each transformation is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. We show that training a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at https://github.com/xamyzhao/brainstorm.

Adrian V. Dalca, Guha Balakrishnan, John Guttag et al.

Traditional deformable registration techniques achieve impressive results and offer a rigorous theoretical treatment, but are computationally intensive since they solve an optimization problem for each image pair. Recently, learning-based methods have facilitated fast registration by learning spatial deformation functions. However, these approaches use restricted deformation models, require supervised labels, or do not guarantee a diffeomorphic (topology-preserving) registration. Furthermore, learning-based registration tools have not been derived from a probabilistic framework that can offer uncertainty estimates. In this paper, we present a probabilistic generative model and derive an unsupervised learning-based inference algorithm that makes use of recent developments in convolutional neural networks (CNNs). We demonstrate our method on a 3D brain registration task, and provide an empirical analysis of the algorithm. Our approach results in state of the art accuracy and very fast runtimes, while providing diffeomorphic guarantees and uncertainty estimates. Our implementation is available online at http://voxelmorph.csail.mit.edu .

Hallee E. Wong, Marianne Rakic, John Guttag et al.

Biomedical image segmentation is a crucial part of both scientific research and clinical care. With enough labelled data, deep learning models can be trained to accurately automate specific biomedical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive and requires domain expertise. We present \emph{ScribblePrompt}, a flexible neural network based interactive segmentation tool for biomedical imaging that enables human annotators to segment previously unseen structures using scribbles, clicks, and bounding boxes. Through rigorous quantitative experiments, we demonstrate that given comparable amounts of interaction, ScribblePrompt produces more accurate segmentations than previous methods on datasets unseen during training. In a user study with domain experts, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to the next best method. ScribblePrompt's success rests on a set of careful design decisions. These include a training strategy that incorporates both a highly diverse set of images and tasks, novel algorithms for simulated user interactions and labels, and a network that enables fast inference. We showcase ScribblePrompt in an interactive demo, provide code, and release a dataset of scribble annotations at https://scribbleprompt.csail.mit.edu

S. Mazdak Abulnaga, Andrew Hoopes, Neel Dey et al. · mit

We present MultiMorph, a fast and efficient method for constructing anatomical atlases on the fly. Atlases capture the canonical structure of a collection of images and are essential for quantifying anatomical variability across populations. However, current atlas construction methods often require days to weeks of computation, thereby discouraging rapid experimentation. As a result, many scientific studies rely on suboptimal, precomputed atlases from mismatched populations, negatively impacting downstream analyses. MultiMorph addresses these challenges with a feedforward model that rapidly produces high-quality, population-specific atlases in a single forward pass for any 3D brain dataset, without any fine-tuning or optimization. MultiMorph is based on a linear group-interaction layer that aggregates and shares features within the group of input images. Further, by leveraging auxiliary synthetic data, MultiMorph generalizes to new imaging modalities and population groups at test-time. Experimentally, MultiMorph outperforms state-of-the-art optimization-based and learning-based atlas construction methods in both small and large population settings, with a 100-fold reduction in time. This makes MultiMorph an accessible framework for biomedical researchers without machine learning expertise, enabling rapid, high-quality atlas generation for diverse studies.

Hallee E. Wong, Jose Javier Gonzalez Ortiz, John Guttag et al.

Medical researchers and clinicians often need to perform novel segmentation tasks on a set of related images. Existing methods for segmenting a new dataset are either interactive, requiring substantial human effort for each image, or require an existing set of previously labeled images. We introduce a system, MultiverSeg, that enables practitioners to rapidly segment an entire new dataset without requiring access to any existing labeled data from that task or domain. Along with the image to segment, the model takes user interactions such as clicks, bounding boxes or scribbles as input, and predicts a segmentation. As the user segments more images, those images and segmentations become additional inputs to the model, providing context. As the context set of labeled images grows, the number of interactions required to segment each new image decreases. We demonstrate that MultiverSeg enables users to interactively segment new datasets efficiently, by amortizing the number of interactions per image to achieve an accurate segmentation. Compared to using a state-of-the-art interactive segmentation method, MultiverSeg reduced the total number of clicks by 36% and scribble steps by 25% to achieve 90% Dice on sets of images from unseen tasks. We release code and model weights at https://multiverseg.csail.mit.edu

Marianne Rakic, Hallee E. Wong, Jose Javier Gonzalez Ortiz et al.

Existing learning-based solutions to medical image segmentation have two important shortcomings. First, for most new segmentation task, a new model has to be trained or fine-tuned. This requires extensive resources and machine learning expertise, and is therefore often infeasible for medical researchers and clinicians. Second, most existing segmentation methods produce a single deterministic segmentation mask for a given image. In practice however, there is often considerable uncertainty about what constitutes the correct segmentation, and different expert annotators will often segment the same image differently. We tackle both of these problems with Tyche, a model that uses a context set to generate stochastic predictions for previously unseen tasks without the need to retrain. Tyche differs from other in-context segmentation methods in two important ways. (1) We introduce a novel convolution block architecture that enables interactions among predictions. (2) We introduce in-context test-time augmentation, a new mechanism to provide prediction stochasticity. When combined with appropriate model design and loss functions, Tyche can predict a set of plausible diverse segmentation candidates for new or unseen medical images and segmentation tasks without the need to retrain.

Andrew Hoopes, Malte Hoffmann, Douglas N. Greve et al.

We introduce HyperMorph, a framework that facilitates efficient hyperparameter tuning in learning-based deformable image registration. Classical registration algorithms perform an iterative pair-wise optimization to compute a deformation field that aligns two images. Recent learning-based approaches leverage large image datasets to learn a function that rapidly estimates a deformation for a given image pair. In both strategies, the accuracy of the resulting spatial correspondences is strongly influenced by the choice of certain hyperparameter values. However, an effective hyperparameter search consumes substantial time and human effort as it often involves training multiple models for different fixed hyperparameter values and may lead to suboptimal registration. We propose an amortized hyperparameter learning strategy to alleviate this burden by learning the impact of hyperparameters on deformation fields. We design a meta network, or hypernetwork, that predicts the parameters of a registration network for input hyperparameters, thereby comprising a single model that generates the optimal deformation field corresponding to given hyperparameter values. This strategy enables fast, high-resolution hyperparameter search at test-time, reducing the inefficiency of traditional approaches while increasing flexibility. We also demonstrate additional benefits of HyperMorph, including enhanced robustness to model initialization and the ability to rapidly identify optimal hyperparameter values specific to a dataset, image contrast, task, or even anatomical region, all without the need to retrain models. We make our code publicly available at http://hypermorph.voxelmorph.net.

Aniruddh Raghu, John Guttag, Katherine Young et al.

The impact of machine learning models on healthcare will depend on the degree of trust that healthcare professionals place in the predictions made by these models. In this paper, we present a method to provide people with clinical expertise with domain-relevant evidence about why a prediction should be trusted. We first design a probabilistic model that relates meaningful latent concepts to prediction targets and observed data. Inference of latent variables in this model corresponds to both making a prediction and providing supporting evidence for that prediction. We present a two-step process to efficiently approximate inference: (i) estimating model parameters using variational learning, and (ii) approximating maximum a posteriori estimation of latent variables in the model using a neural network, trained with an objective derived from the probabilistic model. We demonstrate the method on the task of predicting mortality risk for patients with cardiovascular disease. Specifically, using electrocardiogram and tabular data as input, we show that our approach provides appropriate domain-relevant supporting evidence for accurate predictions.

Harini Suresh, Kathleen M. Lewis, John V. Guttag et al.

Interpretability methods aim to help users build trust in and understand the capabilities of machine learning models. However, existing approaches often rely on abstract, complex visualizations that poorly map to the task at hand or require non-trivial ML expertise to interpret. Here, we present two visual analytics modules that facilitate an intuitive assessment of model reliability. To help users better characterize and reason about a model's uncertainty, we visualize raw and aggregate information about a given input's nearest neighbors. Using an interactive editor, users can manipulate this input in semantically-meaningful ways, determine the effect on the output, and compare against their prior expectations. We evaluate our interface using an electrocardiogram beat classification case study. Compared to a baseline feature importance interface, we find that 14 physicians are better able to align the model's uncertainty with domain-relevant factors and build intuition about its capabilities and limitations.

Andrew Hoopes, Malte Hoffmann, Bruce Fischl et al.

We present HyperMorph, a learning-based strategy for deformable image registration that removes the need to tune important registration hyperparameters during training. Classical registration methods solve an optimization problem to find a set of spatial correspondences between two images, while learning-based methods leverage a training dataset to learn a function that generates these correspondences. The quality of the results for both types of techniques depends greatly on the choice of hyperparameters. Unfortunately, hyperparameter tuning is time-consuming and typically involves training many separate models with various hyperparameter values, potentially leading to suboptimal results. To address this inefficiency, we introduce amortized hyperparameter learning for image registration, a novel strategy to learn the effects of hyperparameters on deformation fields. The proposed framework learns a hypernetwork that takes in an input hyperparameter and modulates a registration network to produce the optimal deformation field for that hyperparameter value. In effect, this strategy trains a single, rich model that enables rapid, fine-grained discovery of hyperparameter values from a continuous interval at test-time. We demonstrate that this approach can be used to optimize multiple hyperparameters considerably faster than existing search strategies, leading to a reduced computational and human burden as well as increased flexibility. We also show several important benefits, including increased robustness to initialization and the ability to rapidly identify optimal hyperparameter values specific to a registration task, dataset, or even a single anatomical region, all without retraining the HyperMorph model. Our code is publicly available at http://voxelmorph.mit.edu.

Roshni Sahoo, Divya Shanmugam, John Guttag

Current unsupervised domain adaptation methods can address many types of distribution shift, but they assume data from the source domain is freely available. As the use of pre-trained models becomes more prevalent, it is reasonable to assume that source data is unavailable. We propose an unsupervised method for adapting a source classifier to a target domain that varies from the source domain along natural axes, such as brightness and contrast. Our method only requires access to unlabeled target instances and the source classifier. We validate our method in scenarios where the distribution shift involves brightness, contrast, and rotation and show that it outperforms fine-tuning baselines in scenarios with limited labeled data.

Marianne Rakic, John Guttag, Adrian V. Dalca

Changes over time in brain anatomy can provide important insight for treatment design or scientific analyses. We present a method that predicts how a brain MRI for an individual will change over time. We model changes using a diffeomorphic deformation field that we predict using function using convolutional neural networks. Given a predicted deformation field, a baseline scan can be warped to give a prediction of the brain scan at a future time. We demonstrate the method using the ADNI cohort, and analyze how performance is affected by model variants and the subject-specific information provided. We show that the model provides good predictions and that external clinical data can improve predictions.

Ava P. Soleimany, Harini Suresh, Jose Javier Gonzalez Ortiz et al.

Global eradication of malaria depends on the development of drugs effective against the silent, yet obligate liver stage of the disease. The gold standard in drug development remains microscopic imaging of liver stage parasites in in vitro cell culture models. Image analysis presents a major bottleneck in this pipeline since the parasite has significant variability in size, shape, and density in these models. As with other highly variable datasets, traditional segmentation models have poor generalizability as they rely on hand-crafted features; thus, manual annotation of liver stage malaria images remains standard. To address this need, we develop a convolutional neural network architecture that utilizes spatial dropout sampling for parasite segmentation and epistemic uncertainty estimation in images of liver stage malaria. Our pipeline produces high-precision segmentations nearly identical to expert annotations, generalizes well on a diverse dataset of liver stage malaria parasites, and promotes independence between learned feature maps to model the uncertainty of generated predictions.

Guha Balakrishnan, Adrian V. Dalca, Amy Zhao et al.

We introduce visual deprojection: the task of recovering an image or video that has been collapsed along a dimension. Projections arise in various contexts, such as long-exposure photography, where a dynamic scene is collapsed in time to produce a motion-blurred image, and corner cameras, where reflected light from a scene is collapsed along a spatial dimension because of an edge occluder to yield a 1D video. Deprojection is ill-posed-- often there are many plausible solutions for a given input. We first propose a probabilistic model capturing the ambiguity of the task. We then present a variational inference strategy using convolutional neural networks as functional approximators. Sampling from the inference network at test time yields plausible candidates from the distribution of original signals that are consistent with a given input projection. We evaluate the method on several datasets for both spatial and temporal deprojection tasks. We first demonstrate the method can recover human gait videos and face images from spatial projections, and then show that it can recover videos of moving digits from dramatically motion-blurred images obtained via temporal projection.

Adrian V. Dalca, Marianne Rakic, John Guttag et al.

We develop a learning framework for building deformable templates, which play a fundamental role in many image analysis and computational anatomy tasks. Conventional methods for template creation and image alignment to the template have undergone decades of rich technical development. In these frameworks, templates are constructed using an iterative process of template estimation and alignment, which is often computationally very expensive. Due in part to this shortcoming, most methods compute a single template for the entire population of images, or a few templates for specific sub-groups of the data. In this work, we present a probabilistic model and efficient learning strategy that yields either universal or conditional templates, jointly with a neural network that provides efficient alignment of the images to these templates. We demonstrate the usefulness of this method on a variety of domains, with a special focus on neuroimaging. This is particularly useful for clinical applications where a pre-existing template does not exist, or creating a new one with traditional methods can be prohibitively expensive. Our code and atlases are available online as part of the VoxelMorph library at http://voxelmorph.csail.mit.edu.

Harini Suresh, John V. Guttag

As machine learning (ML) increasingly affects people and society, awareness of its potential unwanted consequences has also grown. To anticipate, prevent, and mitigate undesirable downstream consequences, it is critical that we understand when and how harm might be introduced throughout the ML life cycle. In this paper, we provide a framework that identifies seven distinct potential sources of downstream harm in machine learning, spanning data collection, development, and deployment. In doing so, we aim to facilitate more productive and precise communication around these issues, as well as more direct, application-grounded ways to mitigate them.

Divya Shanmugam, Davis Blalock, John Guttag

Patients who suffer an acute coronary syndrome are at elevated risk for adverse cardiovascular events such as myocardial infarction and cardiovascular death. Accurate assessment of this risk is crucial to their course of care. We focus on estimating a patient's risk of cardiovascular death after an acute coronary syndrome based on a patient's raw electrocardiogram (ECG) signal. Learning from this signal is challenging for two reasons: 1) positive examples signifying a downstream cardiovascular event are scarce, causing drastic class imbalance, and 2) each patient's ECG signal consists of thousands of heartbeats, accompanied by a single label for the downstream outcome. Machine learning has been previously applied to this task, but most approaches rely on hand-crafted features and domain knowledge. We propose a method that learns a representation from the raw ECG signal by using a multiple instance learning framework. We present a learned risk score for cardiovascular death that outperforms existing risk metrics in predicting cardiovascular death within 30, 60, 90, and 365 days on a dataset of 5000 patients.

Harini Suresh, Jen J. Gong, John Guttag

Machine learning approaches have been effective in predicting adverse outcomes in different clinical settings. These models are often developed and evaluated on datasets with heterogeneous patient populations. However, good predictive performance on the aggregate population does not imply good performance for specific groups. In this work, we present a two-step framework to 1) learn relevant patient subgroups, and 2) predict an outcome for separate patient populations in a multi-task framework, where each population is a separate task. We demonstrate how to discover relevant groups in an unsupervised way with a sequence-to-sequence autoencoder. We show that using these groups in a multi-task framework leads to better predictive performance of in-hospital mortality both across groups and overall. We also highlight the need for more granular evaluation of performance when dealing with heterogeneous populations.

Guha Balakrishnan, Amy Zhao, Adrian V. Dalca et al.

We address the computational problem of novel human pose synthesis. Given an image of a person and a desired pose, we produce a depiction of that person in that pose, retaining the appearance of both the person and background. We present a modular generative neural network that synthesizes unseen poses using training pairs of images and poses taken from human action videos. Our network separates a scene into different body part and background layers, moves body parts to new locations and refines their appearances, and composites the new foreground with a hole-filled background. These subtasks, implemented with separate modules, are trained jointly using only a single target image as a supervised label. We use an adversarial discriminator to force our network to synthesize realistic details conditioned on pose. We demonstrate image synthesis results on three action classes: golf, yoga/workouts and tennis, and show that our method produces accurate results within action classes as well as across action classes. Given a sequence of desired poses, we also produce coherent videos of actions.

Davis W Blalock, John V Guttag

Vectors of data are at the heart of machine learning and data mining. Recently, vector quantization methods have shown great promise in reducing both the time and space costs of operating on vectors. We introduce a vector quantization algorithm that can compress vectors over 12x faster than existing techniques while also accelerating approximate vector operations such as distance and dot product computations by up to 10x. Because it can encode over 2GB of vectors per second, it makes vector quantization cheap enough to employ in many more circumstances. For example, using our technique to compute approximate dot products in a nested loop can multiply matrices faster than a state-of-the-art BLAS implementation, even when our algorithm must first compress the matrices. In addition to showing the above speedups, we demonstrate that our approach can accelerate nearest neighbor search and maximum inner product search by over 100x compared to floating point operations and up to 10x compared to other vector quantization methods. Our approximate Euclidean distance and dot product computations are not only faster than those of related algorithms with slower encodings, but also faster than Hamming distance computations, which have direct hardware support on the tested platforms. We also assess the errors of our algorithm's approximate distances and dot products, and find that it is competitive with existing, slower vector quantization algorithms.

Ronnachai Jaroensri, Amy Zhao, Guha Balakrishnan et al.

For many movement disorders, such as Parkinson's disease and ataxia, disease progression is visually assessed by a clinician using a numerical disease rating scale. These tests are subjective, time-consuming, and must be administered by a professional. This can be problematic where specialists are not available, or when a patient is not consistently evaluated by the same clinician. We present an automated method for quantifying the severity of motion impairment in patients with ataxia, using only video recordings. We consider videos of the finger-to-nose test, a common movement task used as part of the assessment of ataxia progression during the course of routine clinical checkups. Our method uses neural network-based pose estimation and optical flow techniques to track the motion of the patient's hand in a video recording. We extract features that describe qualities of the motion such as speed and variation in performance. Using labels provided by an expert clinician, we train a supervised learning model that predicts severity according to the Brief Ataxia Rating Scale (BARS). The performance of our system is comparable to that of a group of ataxia specialists in terms of mean error and correlation, and our system's predictions were consistently within the range of inter-rater variability. This work demonstrates the feasibility of using computer vision and machine learning to produce consistent and clinically useful measures of motor impairment.

Davis W. Blalock, John V. Guttag

Thanks to the rise of wearable and connected devices, sensor-generated time series comprise a large and growing fraction of the world's data. Unfortunately, extracting value from this data can be challenging, since sensors report low-level signals (e.g., acceleration), not the high-level events that are typically of interest (e.g., gestures). We introduce a technique to bridge this gap by automatically extracting examples of real-world events in low-level data, given only a rough estimate of when these events have taken place. By identifying sets of features that repeat in the same temporal arrangement, we isolate examples of such diverse events as human actions, power consumption patterns, and spoken words with up to 96% precision and recall. Our method is fast enough to run in real time and assumes only minimal knowledge of which variables are relevant or the lengths of events. Our evaluation uses numerous publicly available datasets and over 1 million samples of manually labeled sensor data.

Marzyeh Ghassemi, Zeeshan Syed, Daryush D. Mehta et al.

Voice disorders affect an estimated 14 million working-aged Americans, and many more worldwide. We present the first large scale study of vocal misuse based on long-term ambulatory data collected by an accelerometer placed on the neck. We investigate an unsupervised data mining approach to uncovering latent information about voice misuse. We segment signals from over 253 days of data from 22 subjects into over a hundred million single glottal pulses (closures of the vocal folds), cluster segments into symbols, and use symbolic mismatch to uncover differences between patients and matched controls, and between patients pre- and post-treatment. Our results show significant behavioral differences between patients and controls, as well as between some pre- and post-treatment patients. Our proposed approach provides an objective basis for helping diagnose behavioral voice disorders, and is a first step towards a more data-driven understanding of the impact of voice therapy.

Yun Liu, Kun-Ta Chuang, Fu-Wen Liang et al.

In many domains such as medicine, training data is in short supply. In such cases, external knowledge is often helpful in building predictive models. We propose a novel method to incorporate publicly available domain expertise to build accurate models. Specifically, we use word2vec models trained on a domain-specific corpus to estimate the relevance of each feature's text description to the prediction problem. We use these relevance estimates to rescale the features, causing more important features to experience weaker regularization. We apply our method to predict the onset of five chronic diseases in the next five years in two genders and two age groups. Our rescaling approach improves the accuracy of the model, particularly when there are few positive examples. Furthermore, our method selects 60% fewer features, easing interpretation by physicians. Our method is applicable to other domains where feature and outcome descriptions are available.