Hadi Salman, Payman Yadollahpour, Tom Fletcher, Kayhan Batmanghelich
The Normalizing Flow (NF) models a general probability density by estimating an invertible transformation applied on samples drawn from a known distribution. We introduce a new type of NF, called Deep Diffeomorphic Normalizing Flow (DDNF). A diffeomorphic flow is an invertible function where both the function and its inverse are smooth. We construct the flow using an ordinary differential equation (ODE) governed by a time-varying smooth vector field. We use a neural network to parametrize the smooth vector field and a recursive neural network (RNN) for approximating the solution of the ODE. Each cell in the RNN is a residual network implementing one Euler integration step. The architecture of our flow enables efficient likelihood evaluation, straightforward flow inversion, and results in highly flexible density estimation. An end-to-end trained DDNF achieves competitive results with state-of-the-art methods on a suite of density estimation and variational inference tasks. Finally, our method brings concepts from Riemannian geometry that, we believe, can open a new research direction for neural density estimation.
Nematollah Kayhan Batmanghelich, Gerald Quon, Alex Kulesza, Manolis Kellis, Polina Golland, Luke Bornn
We propose a novel diverse feature selection method based on determinantal point processes (DPPs). Our model enables one to flexibly define diversity based on the covariance of features (similar to orthogonal matching pursuit) or alternatively based on side information. We introduce our approach in the context of Bayesian sparse regression, employing a DPP as a variational approximation to the true spike and slab posterior distribution. We subsequently show how this variational DPP approximation generalizes and extends mean-field approximation, and can be learned efficiently by exploiting the fast sampling properties of DPPs. Our motivating application comes from bioinformatics, where we aim to identify a diverse set of genes whose expression profiles predict a tumor type where the diversity is defined with respect to a gene-gene interaction network. We also explore an application in spatial statistics. In both cases, we demonstrate that the proposed method yields significantly more diverse feature sets than classic sparse methods, without compromising accuracy.
Sumedha Singla, Motahhare Eslami, Brian Pollack, Stephen Wallace, Kayhan Batmanghelich
We propose a BlackBox Counterfactual Explainer, designed to explain image classification models for medical applications. Classical approaches (e.g., saliency maps) that assess feature importance do not explain "how" imaging features in important anatomical regions are relevant to the classification decision. Our framework explains the decision for a target class by gradually "exaggerating" the semantic effect of the class in a query image. We adopted a Generative Adversarial Network (GAN) to generate a progressive set of perturbations to a query image, such that the classification decision changes from its original class to its negation. We used counterfactual explanations from our framework to audit a classifier trained on a chest x-ray dataset with multiple labels. We proposed clinically-relevant quantitative metrics such as cardiothoracic ratio and the score of a healthy costophrenic recess to evaluate our explanations. We conducted a human-grounded experiment with diagnostic radiology residents to compare different styles of explanations (no explanation, saliency map, cycleGAN explanation, and our counterfactual explanation) by evaluating different aspects of explanations: (1) understandability, (2) classifier's decision justification, (3) visual quality, (d) identity preservation, and (5) overall helpfulness of an explanation to the users. Our results show that our counterfactual explanation was the only explanation method that significantly improved the users' understanding of the classifier's decision compared to the no-explanation baseline. Our metrics established a benchmark for evaluating model explanation methods in medical images. Our explanations revealed that the classifier relied on clinically relevant radiographic features for its diagnostic decisions, thus making its decision-making process more transparent to the end-user.
Yanwu Xu, Shaoan Xie, Maxwell Reynolds, Matthew Ragoza, Mingming Gong, Kayhan Batmanghelich
An organ segmentation method that can generalize to unseen contrasts and scanner settings can significantly reduce the need for retraining of deep learning models. Domain Generalization (DG) aims to achieve this goal. However, most DG methods for segmentation require training data from multiple domains during training. We propose a novel adversarial domain generalization method for organ segmentation trained on data from a \emph{single} domain. We synthesize the new domains via learning an adversarial domain synthesizer (ADS) and presume that the synthetic domains cover a large enough area of plausible distributions so that unseen domains can be interpolated from synthetic domains. We propose a mutual information regularizer to enforce the semantic consistency between images from the synthetic domains, which can be estimated by patch-level contrastive learning. We evaluate our method for various organ segmentation for unseen modalities, scanning protocols, and scanner sites.
Li Sun, Ke Yu, Kayhan Batmanghelich
Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relationship between different anatomical regions. The structure of the graph is informed by anatomical correspondences between each patient and an anatomical atlas. In addition, the graph representation has the advantage of handling any arbitrarily sized image in full resolution. Experiments on large-scale Computer Tomography (CT) datasets of lung images show that our approach compares favorably to baseline methods that do not account for the context. We use the learned embedding for staging lung tissue abnormalities related to COVID-19.
Yanwu Xu, Mingming Gong, Shaoan Xie, Wei Wei, Matthias Grundmann, Kayhan Batmanghelich, Tingbo Hou
Despite the proliferation of generative models, achieving fast sampling during inference without compromising sample diversity and quality remains challenging. Existing models such as Denoising Diffusion Probabilistic Models (DDPM) deliver high-quality, diverse samples but are slowed by an inherently high number of iterative steps. The Denoising Diffusion Generative Adversarial Networks (DDGAN) attempted to circumvent this limitation by integrating a GAN model for larger jumps in the diffusion process. However, DDGAN encountered scalability limitations when applied to large datasets. To address these limitations, we introduce a novel approach that tackles the problem by matching implicit and explicit factors. More specifically, our approach involves utilizing an implicit model to match the marginal distributions of noisy data and the explicit conditional distribution of the forward diffusion. This combination allows us to effectively match the joint denoising distributions. Unlike DDPM but similar to DDGAN, we do not enforce a parametric distribution for the reverse step, enabling us to take large steps during inference. Similar to the DDPM but unlike DDGAN, we take advantage of the exact form of the diffusion process. We demonstrate that our proposed method obtains comparable generative performance to diffusion-based models and vastly superior results to models with a small number of sampling steps.
Shantanu Ghosh, Ke Yu, Forough Arabshahi, Kayhan Batmanghelich
ML model design either starts with an interpretable model or a Blackbox and explains it post hoc. Blackbox models are flexible but difficult to explain, while interpretable models are inherently explainable. Yet, interpretable models require extensive ML knowledge and tend to be less flexible and underperforming than their Blackbox variants. This paper aims to blur the distinction between a post hoc explanation of a Blackbox and constructing interpretable models. Beginning with a Blackbox, we iteratively carve out a mixture of interpretable experts (MoIE) and a residual network. Each interpretable model specializes in a subset of samples and explains them using First Order Logic (FOL), providing basic reasoning on concepts from the Blackbox. We route the remaining samples through a flexible residual. We repeat the method on the residual network until all the interpretable models explain the desired proportion of data. Our extensive experiments show that our route, interpret, and repeat approach (1) identifies a diverse set of instance-specific concepts with high concept completeness via MoIE without compromising in performance, (2) identifies the relatively ``harder'' samples to explain via residuals, (3) outperforms the interpretable by-design models by significant margins during test-time interventions, and (4) fixes the shortcut learned by the original Blackbox. The code for MoIE is publicly available at: \url{https://github.com/batmanlab/ICML-2023-Route-interpret-repeat}
Ke Yu, Shyam Visweswaran, Kayhan Batmanghelich
Learning accurate drug representations is essential for task such as computational drug repositioning. A drug hierarchy is a valuable source that encodes knowledge of relations among drugs in a tree-like structure where drugs that act on the same organs, treat the same disease, or bind to the same biological target are grouped together. However, its utility in learning drug representations has not yet been explored, and currently described drug representations cannot place novel molecules in a drug hierarchy. Here, we develop a semi-supervised drug embedding that incorporates two sources of information: (1) underlying chemical grammar that is inferred from chemical structures of drugs and drug-like molecules (unsupervised), and (2) hierarchical relations that are encoded in an expert-crafted hierarchy of approved drugs (supervised). We use the Variational Auto-Encoder (VAE) framework to encode the chemical structures of molecules and use the drug-drug similarity information obtained from the hierarchy to induce the clustering of drugs in hyperbolic space. The hyperbolic space is amenable for encoding hierarchical relations. Our qualitative results support that the learned drug embedding can induce the hierarchical relations among drugs. We demonstrate that the learned drug embedding can be used for drug repositioning.
Shantanu Ghosh, Ke Yu, Kayhan Batmanghelich
Building generalizable AI models is one of the primary challenges in the healthcare domain. While radiologists rely on generalizable descriptive rules of abnormality, Neural Network (NN) models suffer even with a slight shift in input distribution (e.g., scanner type). Fine-tuning a model to transfer knowledge from one domain to another requires a significant amount of labeled data in the target domain. In this paper, we develop an interpretable model that can be efficiently fine-tuned to an unseen target domain with minimal computational cost. We assume the interpretable component of NN to be approximately domain-invariant. However, interpretable models typically underperform compared to their Blackbox (BB) variants. We start with a BB in the source domain and distill it into a \emph{mixture} of shallow interpretable models using human-understandable concepts. As each interpretable model covers a subset of data, a mixture of interpretable models achieves comparable performance as BB. Further, we use the pseudo-labeling technique from semi-supervised learning (SSL) to learn the concept classifier in the target domain, followed by fine-tuning the interpretable models in the target domain. We evaluate our model using a real-life large-scale chest-X-ray (CXR) classification dataset. The code is available at: \url{https://github.com/batmanlab/MICCAI-2023-Route-interpret-repeat-CXRs}.
Shantanu Ghosh, Ke Yu, Forough Arabshahi, Kayhan Batmanghelich
We use concept-based interpretable models to mitigate shortcut learning. Existing methods lack interpretability. Beginning with a Blackbox, we iteratively carve out a mixture of interpretable experts (MoIE) and a residual network. Each expert explains a subset of data using First Order Logic (FOL). While explaining a sample, the FOL from biased BB-derived MoIE detects the shortcut effectively. Finetuning the BB with Metadata Normalization (MDN) eliminates the shortcut. The FOLs from the finetuned-BB-derived MoIE verify the elimination of the shortcut. Our experiments show that MoIE does not hurt the accuracy of the original BB and eliminates shortcuts effectively.
Yanwu Xu, Li Sun, Wei Peng, Shuyue Jia, Katelyn Morrison, Adam Perer, Afrooz Zandifar, Shyam Visweswaran, Motahhare Eslami, Kayhan Batmanghelich
This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.
Kayhan Batmanghelich, Ardavan Saeedi, Karthik Narasimhan, Sam Gershman
Traditional topic models do not account for semantic regularities in language. Recent distributional representations of words exhibit semantic consistency over directional metrics such as cosine similarity. However, neither categorical nor Gaussian observational distributions used in existing topic models are appropriate to leverage such correlations. In this paper, we propose to use the von Mises-Fisher distribution to model the density of words over a unit sphere. Such a representation is well-suited for directional data. We use a Hierarchical Dirichlet Process for our base topic model and propose an efficient inference algorithm based on Stochastic Variational Inference. This model enables us to naturally exploit the semantic structures of word embeddings while flexibly discovering the number of topics. Experiments demonstrate that our method outperforms competitive approaches in terms of topic coherence on two different text corpora while offering efficient inference.
Xiyu Yu, Tongliang Liu, Mingming Gong, Kun Zhang, Kayhan Batmanghelich, Dacheng Tao
Transfer learning aims to improve learning in target domain by borrowing knowledge from a related but different source domain. To reduce the distribution shift between source and target domains, recent methods have focused on exploring invariant representations that have similar distributions across domains. However, when learning this invariant knowledge, existing methods assume that the labels in source domain are uncontaminated, while in reality, we often have access to source data with noisy labels. In this paper, we first show how label noise adversely affect the learning of invariant representations and the correcting of label shift in various transfer learning scenarios. To reduce the adverse effects, we propose a novel Denoising Conditional Invariant Component (DCIC) framework, which provably ensures (1) extracting invariant representations given examples with noisy labels in source domain and unlabeled examples in target domain; (2) estimating the label distribution in target domain with no bias. Experimental results on both synthetic and real-world data verify the effectiveness of the proposed method.
Li Sun, Ke Yu, Kayhan Batmanghelich
Supervised learning method requires a large volume of annotated datasets. Collecting such datasets is time-consuming and expensive. Until now, very few annotated COVID-19 imaging datasets are available. Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relationship between different anatomical regions. The structure of the graph is informed by anatomical correspondences between each patient and an anatomical atlas. In addition, the graph representation has the advantage of handling any arbitrarily sized image in full resolution. Experiments on large-scale Computer Tomography (CT) datasets of lung images show that our approach compares favorably to baseline methods that do not account for the context. We use the learnt embedding to quantify the clinical progression of COVID-19 and show that our method generalizes well to COVID-19 patients from different hospitals. Qualitative results suggest that our model can identify clinically relevant regions in the images.
Sumedha Singla, Brian Pollack, Junxiang Chen, Kayhan Batmanghelich
As machine learning methods see greater adoption and implementation in high stakes applications such as medical image diagnosis, the need for model interpretability and explanation has become more critical. Classical approaches that assess feature importance (e.g. saliency maps) do not explain how and why a particular region of an image is relevant to the prediction. We propose a method that explains the outcome of a classification black-box by gradually exaggerating the semantic effect of a given class. Given a query input to a classifier, our method produces a progressive set of plausible variations of that query, which gradually changes the posterior probability from its original class to its negation. These counter-factually generated samples preserve features unrelated to the classification decision, such that a user can employ our method as a "tuning knob" to traverse a data manifold while crossing the decision boundary. Our method is model agnostic and only requires the output value and gradient of the predictor with respect to its input.
Shantanu Ghosh, Kayhan Batmanghelich
Discovering a high-performing sparse network within a massive neural network is advantageous for deploying them on devices with limited storage, such as mobile phones. Additionally, model explainability is essential to fostering trust in AI. The Lottery Ticket Hypothesis (LTH) finds a network within a deep network with comparable or superior performance to the original model. However, limited study has been conducted on the success or failure of LTH in terms of explainability. In this work, we examine why the performance of the pruned networks gradually increases or decreases. Using Grad-CAM and Post-hoc concept bottleneck models (PCBMs), respectively, we investigate the explainability of pruned networks in terms of pixels and high-level concepts. We perform extensive experiments across vision and medical imaging datasets. As more weights are pruned, the performance of the network degrades. The discovered concepts and pixels from the pruned networks are inconsistent with the original network -- a possible reason for the drop in performance.
Ke Yu, Stephen Albro, Giulia DeSalvo, Suraj Kothawade, Abdullah Rashwan, Sasan Tavakkol, Kayhan Batmanghelich, Xiaoqi Yin
Training high-quality instance segmentation models requires an abundance of labeled images with instance masks and classifications, which is often expensive to procure. Active learning addresses this challenge by striving for optimum performance with minimal labeling cost by selecting the most informative and representative images for labeling. Despite its potential, active learning has been less explored in instance segmentation compared to other tasks like image classification, which require less labeling. In this study, we propose a post-hoc active learning algorithm that integrates uncertainty-based sampling with diversity-based sampling. Our proposed algorithm is not only simple and easy to implement, but it also delivers superior performance on various datasets. Its practical application is demonstrated on a real-world overhead imagery dataset, where it increases the labeling efficiency fivefold.
Ke Yu, Shantanu Ghosh, Zhexiong Liu, Christopher Deible, Kayhan Batmanghelich
Creating a large-scale dataset of abnormality annotation on medical images is a labor-intensive and costly task. Leveraging weak supervision from readily available data such as radiology reports can compensate lack of large-scale data for anomaly detection methods. However, most of the current methods only use image-level pathological observations, failing to utilize the relevant anatomy mentions in reports. Furthermore, Natural Language Processing (NLP)-mined weak labels are noisy due to label sparsity and linguistic ambiguity. We propose an Anatomy-Guided chest X-ray Network (AGXNet) to address these issues of weak annotation. Our framework consists of a cascade of two networks, one responsible for identifying anatomical abnormalities and the second responsible for pathological observations. The critical component in our framework is an anatomy-guided attention module that aids the downstream observation network in focusing on the relevant anatomical regions generated by the anatomy network. We use Positive Unlabeled (PU) learning to account for the fact that lack of mention does not necessarily mean a negative label. Our quantitative and qualitative results on the MIMIC-CXR dataset demonstrate the effectiveness of AGXNet in disease and anatomical abnormality localization. Experiments on the NIH Chest X-ray dataset show that the learned feature representations are transferable and can achieve the state-of-the-art performances in disease classification and competitive disease localization results. Our code is available at https://github.com/batmanlab/AGXNet
Yipeng Mou, Mingming Gong, Huan Fu, Kayhan Batmanghelich, Kun Zhang, Dacheng Tao
Majority of state-of-the-art monocular depth estimation methods are supervised learning approaches. The success of such approaches heavily depends on the high-quality depth labels which are expensive to obtain. Some recent methods try to learn depth networks by leveraging unsupervised cues from monocular videos which are easier to acquire but less reliable. In this paper, we propose to resolve this dilemma by transferring knowledge from synthetic videos with easily obtainable ground-truth depth labels. Due to the stylish difference between synthetic and real images, we propose a temporally-consistent domain adaptation (TCDA) approach that simultaneously explores labels in the synthetic domain and temporal constraints in the videos to improve style transfer and depth prediction. Furthermore, we make use of the ground-truth optical flow and pose information in the synthetic data to learn moving mask and pose prediction networks. The learned moving masks can filter out moving regions that produces erroneous temporal constraints and the estimated poses provide better initializations for estimating temporal constraints. Experimental results demonstrate the effectiveness of our method and comparable performance against state-of-the-art.
Rohit Jena, Sumedha Singla, Kayhan Batmanghelich
Vessel segmentation is an essential task in many clinical applications. Although supervised methods have achieved state-of-art performance, acquiring expert annotation is laborious and mostly limited for two-dimensional datasets with a small sample size. On the contrary, unsupervised methods rely on handcrafted features to detect tube-like structures such as vessels. However, those methods require complex pipelines involving several hyper-parameters and design choices rendering the procedure sensitive, dataset-specific, and not generalizable. We propose a self-supervised method with a limited number of hyper-parameters that is generalizable across modalities. Our method uses tube-like structure properties, such as connectivity, profile consistency, and bifurcation, to introduce inductive bias into a learning algorithm. To model those properties, we generate a vector field that we refer to as a flow. Our experiments on various public datasets in 2D and 3D show that our method performs better than unsupervised methods while learning useful transferable features from unlabeled data. Unlike generic self-supervised methods, the learned features learn vessel-relevant features that are transferable for supervised approaches, which is essential when the number of annotated data is limited.