Kayhan Batmanghelich

Ke Yu, Shantanu Ghosh, Zhexiong Liu et al. · amazon-science, cmu

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

Shantanu Ghosh, Ke Yu, Forough Arabshahi et al. · amazon-science, cmu

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}

Shantanu Ghosh, Ke Yu, Forough Arabshahi et al. · amazon-science, cmu

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, Shaoan Xie, Wenhao Wu et al. · amazon-science

Unpaired image-to-image translation (I2I) is an ill-posed problem, as an infinite number of translation functions can map the source domain distribution to the target distribution. Therefore, much effort has been put into designing suitable constraints, e.g., cycle consistency (CycleGAN), geometry consistency (GCGAN), and contrastive learning-based constraints (CUTGAN), that help better pose the problem. However, these well-known constraints have limitations: (1) they are either too restrictive or too weak for specific I2I tasks; (2) these methods result in content distortion when there is a significant spatial variation between the source and target domains. This paper proposes a universal regularization technique called maximum spatial perturbation consistency (MSPC), which enforces a spatial perturbation function (T ) and the translation operator (G) to be commutative (i.e., TG = GT ). In addition, we introduce two adversarial training components for learning the spatial perturbation function. The first one lets T compete with G to achieve maximum perturbation. The second one lets G and T compete with discriminators to align the spatial variations caused by the change of object size, object distortion, background interruptions, etc. Our method outperforms the state-of-the-art methods on most I2I benchmarks. We also introduce a new benchmark, namely the front face to profile face dataset, to emphasize the underlying challenges of I2I for real-world applications. We finally perform ablation experiments to study the sensitivity of our method to the severity of spatial perturbation and its effectiveness for distribution alignment.

Shantanu Ghosh, Kayhan Batmanghelich · amazon-science, cmu

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.

Yanwu Xu, Shaoan Xie, Maxwell Reynolds et al.

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.

Weicheng Dai, Chenyu Wang, Andy Li et al.

Generative models for volumetric medical images have found many applications in medical imaging, ranging from data augmentation to serving as priors for inverse problems. For these applications, generating high-resolution 3D images with strong controllability is essential but remains highly challenging. Existing approaches typically control generation either through radiology reports used as text prompts or through full image segmentation. While text-based prompting is flexible, it provides limited spatial control over the location, shape, and boundary of abnormalities. In contrast, segmentation-based methods receive precise spatial guidance but are restrictive in requiring full-organ annotations. In this work, we propose a flexible multimodal framework for controllable volumetric image generation that supports input from radiology reports and segmentation prompts (both optional). Our approach allows users to provide segmentation of a specific anatomy or abnormality without requiring full-organ annotations. The semantic meaning of the segmentation mask is specified through an accompanying text description, resulting in a highly flexible and scalable conditioning mechanism. We develop a memory-efficient architecture based on a modified diffusion transformer that jointly processes image and segmentation tokens. The model further incorporates gated attention to effectively attend to long radiology reports. Experiments demonstrate that our method achieves state-of-the-art perceptual and semantic scores (e.g., 24% relative improvement in mean FID), generates high-resolution anatomically consistent CT volumes, and improves data efficiency when used for data augmentation. Radiologists' evaluation further confirms strong alignment between generated and real medical images.

Yanwu Xu, Li Sun, Wei Peng et al.

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.

Nihal Murali, Aahlad Puli, Ke Yu et al.

Deep Neural Networks (DNNs) are prone to learning spurious features that correlate with the label during training but are irrelevant to the learning problem. This hurts model generalization and poses problems when deploying them in safety-critical applications. This paper aims to better understand the effects of spurious features through the lens of the learning dynamics of the internal neurons during the training process. We make the following observations: (1) While previous works highlight the harmful effects of spurious features on the generalization ability of DNNs, we emphasize that not all spurious features are harmful. Spurious features can be "benign" or "harmful" depending on whether they are "harder" or "easier" to learn than the core features for a given model. This definition is model and dataset-dependent. (2) We build upon this premise and use instance difficulty methods (like Prediction Depth (Baldock et al., 2021)) to quantify "easiness" for a given model and to identify this behavior during the training phase. (3) We empirically show that the harmful spurious features can be detected by observing the learning dynamics of the DNN's early layers. In other words, easy features learned by the initial layers of a DNN early during the training can (potentially) hurt model generalization. We verify our claims on medical and vision datasets, both simulated and real, and justify the empirical success of our hypothesis by showing the theoretical connections between Prediction Depth and information-theoretic concepts like V-usable information (Ethayarajh et al., 2021). Lastly, our experiments show that monitoring only accuracy during training (as is common in machine learning pipelines) is insufficient to detect spurious features. We, therefore, highlight the need for monitoring early training dynamics using suitable instance difficulty metrics.

Ke Yu, Li Sun, Junxiang Chen et al.

Large-scale volumetric medical images with annotation are rare, costly, and time prohibitive to acquire. Self-supervised learning (SSL) offers a promising pre-training and feature extraction solution for many downstream tasks, as it only uses unlabeled data. Recently, SSL methods based on instance discrimination have gained popularity in the medical imaging domain. However, SSL pre-trained encoders may use many clues in the image to discriminate an instance that are not necessarily disease-related. Moreover, pathological patterns are often subtle and heterogeneous, requiring the ability of the desired method to represent anatomy-specific features that are sensitive to abnormal changes in different body parts. In this work, we present a novel SSL framework, named DrasCLR, for 3D medical imaging to overcome these challenges. We propose two domain-specific contrastive learning strategies: one aims to capture subtle disease patterns inside a local anatomical region, and the other aims to represent severe disease patterns that span larger regions. We formulate the encoder using conditional hyper-parameterized network, in which the parameters are dependant on the anatomical location, to extract anatomically sensitive features. Extensive experiments on large-scale computer tomography (CT) datasets of lung images show that our method improves the performance of many downstream prediction and segmentation tasks. The patient-level representation improves the performance of the patient survival prediction task. We show how our method can detect emphysema subtypes via dense prediction. We demonstrate that fine-tuning the pre-trained model can significantly reduce annotation efforts without sacrificing emphysema detection accuracy. Our ablation study highlights the importance of incorporating anatomical context into the SSL framework.

Yanwu Xu, Mingming Gong, Shaoan Xie et al.

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.

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.

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, Rayan Syed, Chenyu Wang et al. · amazon-science, cmu

Error slice discovery is crucial to diagnose and mitigate model errors. Current clustering or discrete attribute-based slice discovery methods face key limitations: 1) clustering results in incoherent slices, while assigning discrete attributes to slices leads to incomplete coverage of error patterns due to missing or insufficient attributes; 2) these methods lack complex reasoning, preventing them from fully explaining model biases; 3) they fail to integrate \textit{domain knowledge}, limiting their usage in specialized fields \eg radiology. We propose\ladder (\underline{La}nguage-\underline{D}riven \underline{D}iscovery and \underline{E}rror \underline{R}ectification), to address the limitations by: (1) leveraging the flexibility of natural language to address incompleteness, (2) employing LLM's latent \textit{domain knowledge} and advanced reasoning to analyze sentences and derive testable hypotheses directly, identifying biased attributes, and form coherent error slices without clustering. Existing mitigation methods typically address only the worst-performing group, often amplifying errors in other subgroups. In contrast,\ladder generates pseudo attributes from the discovered hypotheses to mitigate errors across all biases without explicit attribute annotations or prior knowledge of bias. Rigorous evaluations on 6 datasets spanning natural and medical images -- comparing 200+ classifiers with diverse architectures, pretraining strategies, and LLMs -- show that\ladder consistently outperforms existing baselines in discovering and mitigating biases.

Sumedha Singla, Nihal Murali, Forough Arabshahi et al.

A highly accurate but overconfident model is ill-suited for deployment in critical applications such as healthcare and autonomous driving. The classification outcome should reflect a high uncertainty on ambiguous in-distribution samples that lie close to the decision boundary. The model should also refrain from making overconfident decisions on samples that lie far outside its training distribution, far-out-of-distribution (far-OOD), or on unseen samples from novel classes that lie near its training distribution (near-OOD). This paper proposes an application of counterfactual explanations in fixing an over-confident classifier. Specifically, we propose to fine-tune a given pre-trained classifier using augmentations from a counterfactual explainer (ACE) to fix its uncertainty characteristics while retaining its predictive performance. We perform extensive experiments with detecting far-OOD, near-OOD, and ambiguous samples. Our empirical results show that the revised model have improved uncertainty measures, and its performance is competitive to the state-of-the-art methods.

Chenyu Wang, Weicheng Dai, Han Liu et al.

Vision--language models (VLMs) for radiology report generation (RRG) can produce long-form chest CT reports from volumetric scans and show strong potential to improve radiology workflow efficiency and consistency. However, existing methods face two key limitations: (i) training supervision is often coarse, aligning a whole CT volume with a full free-text report without explicit alignment for fine-grained attributes or pathology locations; and (ii) evaluation is typically holistic (lexical overlap, entity matching, or LLM-as-a-judge scores) and not diagnostic for spatial grounding. We propose \emph{Discriminative Cue-Prompting with Prompt Dropout (DCP-PD)}, a plug-and-play framework that distills fine-grained cues from free-text reports and uses them to guide report generation while mitigating shortcut reliance via prompt dropout. DCP-PD achieves state-of-the-art performance on CT-RATE, improving macro F1 from $=0.501$ to $0.603$ (20% relative), and substantially boosts out-of-distribution performance on Rad-ChestCT from F1 $=0.266$ to $0.503$ (89% relative). Finally, we introduce a hierarchical, location-aware question-set protocol (presence $\rightarrow$ laterality $\rightarrow$ lobe) to directly assess pathology-location grounding, showing that fine-grained spatial localization remains challenging even for models that score highly on current benchmarks.

Ibrahim Ethem Hamamci, Sezgin Er, Chenyu Wang et al.

Advancements in medical imaging AI, particularly in 3D imaging, have been limited due to the scarcity of comprehensive datasets. We introduce CT-RATE, a public dataset that pairs 3D medical images with corresponding textual reports. CT-RATE comprises 25,692 non-contrast 3D chest CT scans from 21,304 unique patients. Each scan is accompanied by its corresponding radiology report. Leveraging CT-RATE, we develop CT-CLIP, a CT-focused contrastive language-image pretraining framework designed for broad applications without the need for task-specific training. We demonstrate how CT-CLIP can be used in multi-abnormality detection and case retrieval, and outperforms state-of-the-art fully supervised models across all key metrics. By combining CT-CLIP's vision encoder with a pretrained large language model, we create CT-CHAT, a vision-language foundational chat model for 3D chest CT volumes. Finetuned on over 2.7 million question-answer pairs derived from the CT-RATE dataset, CT-CHAT underscores the necessity for specialized methods in 3D medical imaging. Collectively, the open-source release of CT-RATE, CT-CLIP, and CT-CHAT not only addresses critical challenges in 3D medical imaging but also lays the groundwork for future innovations in medical AI and improved patient care.

Maxwell Reynolds, Chaitanya Srinivasan, Vijay Cherupally et al.

Discovery of sensitive and biologically grounded biomarkers is essential for early detection and monitoring of Alzheimer's disease (AD). Structural MRI is widely available but typically relies on hand-crafted features such as cortical thickness or volume. We ask whether self-supervised learning (SSL) can uncover more powerful biomarkers from the same data. Existing SSL methods underperform FreeSurfer-derived features in disease classification, conversion prediction, and amyloid status prediction. We introduce Residual Noise Contrastive Estimation (R-NCE), a new SSL framework that integrates auxiliary FreeSurfer features while maximizing additional augmentation-invariant information. R-NCE outperforms traditional features and existing SSL methods across multiple benchmarks, including AD conversion prediction. To assess biological relevance, we derive Brain Age Gap (BAG) measures and perform genome-wide association studies. R-NCE-BAG shows high heritability and associations with MAPT and IRAG1, with enrichment in astrocytes and oligodendrocytes, indicating sensitivity to neurodegenerative and cerebrovascular processes.

Ke Yu, Stephen Albro, Giulia DeSalvo et al.

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.

Shantanu Ghosh, Clare B. Poynton, Shyam Visweswaran et al. · amazon-science, cmu

The lack of large and diverse training data on Computer-Aided Diagnosis (CAD) in breast cancer detection has been one of the concerns that impedes the adoption of the system. Recently, pre-training with large-scale image text datasets via Vision-Language models (VLM) (\eg CLIP) partially addresses the issue of robustness and data efficiency in computer vision (CV). This paper proposes Mammo-CLIP, the first VLM pre-trained on a substantial amount of screening mammogram-report pairs, addressing the challenges of dataset diversity and size. Our experiments on two public datasets demonstrate strong performance in classifying and localizing various mammographic attributes crucial for breast cancer detection, showcasing data efficiency and robustness similar to CLIP in CV. We also propose Mammo-FActOR, a novel feature attribution method, to provide spatial interpretation of representation with sentence-level granularity within mammography reports. Code is available publicly: \url{https://github.com/batmanlab/Mammo-CLIP}.

Chenyu Wang, Weichao Zhou, Shantanu Ghosh et al. · amazon-science, cmu

Radiology report generation (RRG) has shown great potential in assisting radiologists by automating the labor-intensive task of report writing. While recent advancements have improved the quality and coherence of generated reports, ensuring their factual correctness remains a critical challenge. Although generative medical Vision Large Language Models (VLLMs) have been proposed to address this issue, these models are prone to hallucinations and can produce inaccurate diagnostic information. To address these concerns, we introduce a novel Semantic Consistency-Based Uncertainty Quantification framework that provides both report-level and sentence-level uncertainties. Unlike existing approaches, our method does not require modifications to the underlying model or access to its inner state, such as output token logits, thus serving as a plug-and-play module that can be seamlessly integrated with state-of-the-art models. Extensive experiments demonstrate the efficacy of our method in detecting hallucinations and enhancing the factual accuracy of automatically generated radiology reports. By abstaining from high-uncertainty reports, our approach improves factuality scores by $10$\%, achieved by rejecting $20$\% of reports using the \texttt{Radialog} model on the MIMIC-CXR dataset. Furthermore, sentence-level uncertainty flags the lowest-precision sentence in each report with an $82.9$\% success rate. Our implementation is open-source and available at https://github.com/BU-DEPEND-Lab/SCUQ-RRG.

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}.

Joshua Robinson, Li Sun, Ke Yu et al.

The generalization of representations learned via contrastive learning depends crucially on what features of the data are extracted. However, we observe that the contrastive loss does not always sufficiently guide which features are extracted, a behavior that can negatively impact the performance on downstream tasks via "shortcuts", i.e., by inadvertently suppressing important predictive features. We find that feature extraction is influenced by the difficulty of the so-called instance discrimination task (i.e., the task of discriminating pairs of similar points from pairs of dissimilar ones). Although harder pairs improve the representation of some features, the improvement comes at the cost of suppressing previously well represented features. In response, we propose implicit feature modification (IFM), a method for altering positive and negative samples in order to guide contrastive models towards capturing a wider variety of predictive features. Empirically, we observe that IFM reduces feature suppression, and as a result improves performance on vision and medical imaging tasks. The code is available at: \url{https://github.com/joshr17/IFM}.

Huan Fu, Mingming Gong, Chaohui Wang et al.

Monocular depth estimation, which plays a crucial role in understanding 3D scene geometry, is an ill-posed problem. Recent methods have gained significant improvement by exploring image-level information and hierarchical features from deep convolutional neural networks (DCNNs). These methods model depth estimation as a regression problem and train the regression networks by minimizing mean squared error, which suffers from slow convergence and unsatisfactory local solutions. Besides, existing depth estimation networks employ repeated spatial pooling operations, resulting in undesirable low-resolution feature maps. To obtain high-resolution depth maps, skip-connections or multi-layer deconvolution networks are required, which complicates network training and consumes much more computations. To eliminate or at least largely reduce these problems, we introduce a spacing-increasing discretization (SID) strategy to discretize depth and recast depth network learning as an ordinal regression problem. By training the network using an ordinary regression loss, our method achieves much higher accuracy and \dd{faster convergence in synch}. Furthermore, we adopt a multi-scale network structure which avoids unnecessary spatial pooling and captures multi-scale information in parallel. The method described in this paper achieves state-of-the-art results on four challenging benchmarks, i.e., KITTI [17], ScanNet [9], Make3D [50], and NYU Depth v2 [42], and win the 1st prize in Robust Vision Challenge 2018. Code has been made available at: https://github.com/hufu6371/DORN.

Xinliu Zhong, Kayhan Batmanghelich, Li Sun

Vision-language models pre-trained on large scale of unlabeled biomedical images and associated reports learn generalizable semantic representations. These multi-modal representations can benefit various downstream tasks in the biomedical domain. Contrastive learning is widely used to pre-train vision-language models for general natural images and associated captions. Despite its popularity, we found biomedical texts have complex and domain-specific semantics that are often neglected by common contrastive methods. To address this issue, we propose a novel method, perturbed report discrimination, for pre-train biomedical vision-language models. First, we curate a set of text perturbation methods that keep the same words, but disrupt the semantic structure of the sentence. Next, we apply different types of perturbation to reports, and use the model to distinguish the original report from the perturbed ones given the associated image. Parallel to this, we enhance the sensitivity of our method to higher level of granularity for both modalities by contrasting attention-weighted image sub-regions and sub-words in the image-text pairs. We conduct extensive experiments on multiple downstream tasks, and our method outperforms strong baseline methods. The results demonstrate that our approach learns more semantic meaningful and robust multi-modal representations.

Chenyu Wang, Tianle Chen, H. M. Sabbir Ahmad et al.

Uncertainty quantification (UQ) is vital for ensuring that vision-language models (VLMs) behave safely and reliably. A central challenge is to localize uncertainty to its source, determining whether it arises from the image, the text, or misalignment between the two. We introduce VLM-UQBench, a benchmark for modality-specific and cross-modal data uncertainty in VLMs, It consists of 600 real-world samples drawn from the VizWiz dataset, curated into clean, image-, text-, and cross-modal uncertainty subsets, and a scalable perturbation pipeline with 8 visual, 5 textual, and 3 cross-modal perturbations. We further propose two simple metrics that quantify the sensitivity of UQ scores to these perturbations and their correlation with hallucinations, and use them to evaluate a range of UQ methods across four VLMs and three datasets. Empirically, we find that: (i) existing UQ methods exhibit strong modality-specific specialization and substantial dependence on the underlying VLM, (ii) modality-specific uncertainty frequently co-occurs with hallucinations while current UQ scores provide only weak and inconsistent risk signals, and (iii) although UQ methods can rival reasoning-based chain-of-thought baselines on overt, group-level ambiguity, they largely fail to detect the subtle, instance-level ambiguity introduced by our perturbation pipeline. These results highlight a significant gap between current UQ practices and the fine-grained, modality-aware uncertainty required for reliable VLM deployment.

Shantanu Ghosh, Vedant Parthesh Joshi, Rayan Syed et al.

Breast cancer is one of the leading causes of death among women worldwide. We introduce Mammo-FM, the first foundation model specifically for mammography, pretrained on the largest and most diverse dataset to date - 140,677 patients (821,326 mammograms) across four U.S. institutions. Mammo-FM provides a unified foundation for core clinical tasks in breast imaging, including cancer diagnosis, pathology localization, structured report generation, and cancer risk prognosis within a single framework. Its alignment between images and text enables both visual and textual interpretability, improving transparency and clinical auditability, which are essential for real-world adoption. We rigorously evaluate Mammo-FM across diagnosis, prognosis, and report-generation tasks in in- and out-of-distribution datasets. Despite operating on native-resolution mammograms and using only one-third of the parameters of state-of-the-art generalist FMs, Mammo-FM consistently outperforms them across multiple public and private benchmarks. These results highlight the efficiency and value of domain-specific foundation models designed around the full spectrum of tasks within a clinical domain and emphasize the importance of rigorous, domain-aligned evaluation.

Katelyn Morrison, Arpit Mathur, Aidan Bradshaw et al.

As text-to-image generative models rapidly improve, AI researchers are making significant advances in developing domain-specific models capable of generating complex medical imagery from text prompts. Despite this, these technical advancements have overlooked whether and how medical professionals would benefit from and use text-to-image generative AI (GenAI) in practice. By developing domain-specific GenAI without involving stakeholders, we risk the potential of building models that are either not useful or even more harmful than helpful. In this paper, we adopt a human-centered approach to responsible model development by involving stakeholders in evaluating and reflecting on the promises, risks, and challenges of a novel text-to-CT Scan GenAI model. Through exploratory model prompting activities, we uncover the perspectives of medical students, radiology trainees, and radiologists on the role that text-to-CT Scan GenAI can play across medical education, training, and practice. This human-centered approach additionally enabled us to surface technical challenges and domain-specific risks of generating synthetic medical images. We conclude by reflecting on the implications of medical text-to-image GenAI.

Li Sun, Florian Luisier, Kayhan Batmanghelich et al.

Current state-of-the-art models for natural language understanding require a preprocessing step to convert raw text into discrete tokens. This process known as tokenization relies on a pre-built vocabulary of words or sub-word morphemes. This fixed vocabulary limits the model's robustness to spelling errors and its capacity to adapt to new domains. In this work, we introduce a novel open-vocabulary language model that adopts a hierarchical two-level approach: one at the word level and another at the sequence level. Concretely, we design an intra-word module that uses a shallow Transformer architecture to learn word representations from their characters, and a deep inter-word Transformer module that contextualizes each word representation by attending to the entire word sequence. Our model thus directly operates on character sequences with explicit awareness of word boundaries, but without biased sub-word or word-level vocabulary. Experiments on various downstream tasks show that our method outperforms strong baselines. We also demonstrate that our hierarchical model is robust to textual corruption and domain shift.

Reuben Dorent, Aaron Kujawa, Marina Ivory et al.

Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.

Yanwu Xu, Mingming Gong, Shaoan Xie et al.

Deep learning has achieved remarkable success in medicalimage segmentation, but it usually requires a large numberof images labeled with fine-grained segmentation masks, andthe annotation of these masks can be very expensive andtime-consuming. Therefore, recent methods try to use un-supervised domain adaptation (UDA) methods to borrow in-formation from labeled data from other datasets (source do-mains) to a new dataset (target domain). However, due tothe absence of labels in the target domain, the performance ofUDA methods is much worse than that of the fully supervisedmethod. In this paper, we propose a weakly supervised do-main adaptation setting, in which we can partially label newdatasets with bounding boxes, which are easier and cheaperto obtain than segmentation masks. Accordingly, we proposea new weakly-supervised domain adaptation method calledBox-Adapt, which fully explores the fine-grained segmenta-tion mask in the source domain and the weak bounding boxin the target domain. Our Box-Adapt is a two-stage methodthat first performs joint training on the source and target do-mains, and then conducts self-training with the pseudo-labelsof the target domain. We demonstrate the effectiveness of ourmethod in the liver segmentation task. Weakly supervised do-main adaptation

Sumedha Singla, Stephen Wallace, Sofia Triantafillou et al.

Model explainability is essential for the creation of trustworthy Machine Learning models in healthcare. An ideal explanation resembles the decision-making process of a domain expert and is expressed using concepts or terminology that is meaningful to the clinicians. To provide such an explanation, we first associate the hidden units of the classifier to clinically relevant concepts. We take advantage of radiology reports accompanying the chest X-ray images to define concepts. We discover sparse associations between concepts and hidden units using a linear sparse logistic regression. To ensure that the identified units truly influence the classifier's outcome, we adopt tools from Causal Inference literature and, more specifically, mediation analysis through counterfactual interventions. Finally, we construct a low-depth decision tree to translate all the discovered concepts into a straightforward decision rule, expressed to the radiologist. We evaluated our approach on a large chest x-ray dataset, where our model produces a global explanation consistent with clinical knowledge.

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.

Sumedha Singla, Motahhare Eslami, Brian Pollack et al.

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.

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.

Li Sun, Junxiang Chen, Yanwu Xu et al.

Generative Adversarial Networks (GAN) have many potential medical imaging applications, including data augmentation, domain adaptation, and model explanation. Due to the limited memory of Graphical Processing Units (GPUs), most current 3D GAN models are trained on low-resolution medical images, these models either cannot scale to high-resolution or are prone to patchy artifacts. In this work, we propose a novel end-to-end GAN architecture that can generate high-resolution 3D images. We achieve this goal by using different configurations between training and inference. During training, we adopt a hierarchical structure that simultaneously generates a low-resolution version of the image and a randomly selected sub-volume of the high-resolution image. The hierarchical design has two advantages: First, the memory demand for training on high-resolution images is amortized among sub-volumes. Furthermore, anchoring the high-resolution sub-volumes to a single low-resolution image ensures anatomical consistency between sub-volumes. During inference, our model can directly generate full high-resolution images. We also incorporate an encoder with a similar hierarchical structure into the model to extract features from the images. Experiments on 3D thorax CT and brain MRI demonstrate that our approach outperforms state of the art in image generation. We also demonstrate clinical applications of the proposed model in data augmentation and clinical-relevant feature extraction.

Ke Yu, Shyam Visweswaran, Kayhan Batmanghelich

Learning accurate drug representation is essential for tasks such as computational drug repositioning and prediction of drug side-effects. A drug hierarchy is a valuable source that encodes human knowledge of drug relations 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 molecular 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 knowledge-based drug-drug similarity to induce the clustering of drugs in hyperbolic space. The hyperbolic space is amenable for encoding hierarchical concepts. Both quantitative and qualitative results support that the learned drug embedding can accurately reproduce the chemical structure and induce the hierarchical relations among drugs. Furthermore, our approach can infer the pharmacological properties of novel molecules by retrieving similar drugs from the embedding space. We demonstrate that the learned drug embedding can be used to find new uses for existing drugs and to discover side-effects. We show that it significantly outperforms baselines in both tasks.

Sumedha Singla, Brian Pollack, Junxiang Chen et al.

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.

Junxiang Chen, Kayhan Batmanghelich

Recent work by Locatello et al. (2018) has shown that an inductive bias is required to disentangle factors of interest in Variational Autoencoder (VAE). Motivated by a real-world problem, we propose a setting where such bias is introduced by providing pairwise ordinal comparisons between instances, based on the desired factor to be disentangled. For example, a doctor compares pairs of patients based on the level of severity of their illnesses, and the desired factor is a quantitive level of the disease severity. In a real-world application, the pairwise comparisons are usually noisy. Our method, Robust Ordinal VAE (ROVAE), incorporates the noisy pairwise ordinal comparisons in the disentanglement task. We introduce non-negative random variables in ROVAE, such that it can automatically determine whether each pairwise ordinal comparison is trustworthy and ignore the noisy comparisons. Experimental results demonstrate that ROVAE outperforms existing methods and is more robust to noisy pairwise comparisons in both benchmark datasets and a real-world application.

Yipeng Mou, Mingming Gong, Huan Fu et al.

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.

Mingming Gong, Yanwu Xu, Chunyuan Li et al.

Conditional generative models enjoy remarkable progress over the past few years. One of the popular conditional models is Auxiliary Classifier GAN (AC-GAN), which generates highly discriminative images by extending the loss function of GAN with an auxiliary classifier. However, the diversity of the generated samples by AC-GAN tends to decrease as the number of classes increases, hence limiting its power on large-scale data. In this paper, we identify the source of the low diversity issue theoretically and propose a practical solution to solve the problem. We show that the auxiliary classifier in AC-GAN imposes perfect separability, which is disadvantageous when the supports of the class distributions have significant overlap. To address the issue, we propose Twin Auxiliary Classifiers Generative Adversarial Net (TAC-GAN) that further benefits from a new player that interacts with other players (the generator and the discriminator) in GAN. Theoretically, we demonstrate that TAC-GAN can effectively minimize the divergence between the generated and real-data distributions. Extensive experimental results show that our TAC-GAN can successfully replicate the true data distributions on simulated data, and significantly improves the diversity of class-conditional image generation on real datasets.

Junxiang Chen, Kayhan Batmanghelich

Recently, researches related to unsupervised disentanglement learning with deep generative models have gained substantial popularity. However, without introducing supervision, there is no guarantee that the factors of interest can be successfully recovered. Motivated by a real-world problem, we propose a setting where the user introduces weak supervision by providing similarities between instances based on a factor to be disentangled. The similarity is provided as either a binary (yes/no) or a real-valued label describing whether a pair of instances are similar or not. We propose a new method for weakly supervised disentanglement of latent variables within the framework of Variational Autoencoder. Experimental results demonstrate that utilizing weak supervision improves the performance of the disentanglement method substantially.

Yanwu Xu, Mingming Gong, Junxiang Chen et al.

Majority of state-of-the-art deep learning methods are discriminative approaches, which model the conditional distribution of labels given inputs features. The success of such approaches heavily depends on high-quality labeled instances, which are not easy to obtain, especially as the number of candidate classes increases. In this paper, we study the complementary learning problem. Unlike ordinary labels, complementary labels are easy to obtain because an annotator only needs to provide a yes/no answer to a randomly chosen candidate class for each instance. We propose a generative-discriminative complementary learning method that estimates the ordinary labels by modeling both the conditional (discriminative) and instance (generative) distributions. Our method, we call Complementary Conditional GAN (CCGAN), improves the accuracy of predicting ordinary labels and can generate high-quality instances in spite of weak supervision. In addition to the extensive empirical studies, we also theoretically show that our model can retrieve the true conditional distribution from the complementarily-labeled data.

Yanwu Xu, Mingming Gong, Tongliang Liu et al.

In recent years, the learned local descriptors have outperformed handcrafted ones by a large margin, due to the powerful deep convolutional neural network architectures such as L2-Net [1] and triplet based metric learning [2]. However, there are two problems in the current methods, which hinders the overall performance. Firstly, the widely-used margin loss is sensitive to incorrect correspondences, which are prevalent in the existing local descriptor learning datasets. Second, the L2 distance ignores the fact that the feature vectors have been normalized to unit norm. To tackle these two problems and further boost the performance, we propose a robust angular loss which 1) uses cosine similarity instead of L2 distance to compare descriptors and 2) relies on a robust loss function that gives smaller penalty to triplets with negative relative similarity. The resulting descriptor shows robustness on different datasets, reaching the state-of-the-art result on Brown dataset , as well as demonstrating excellent generalization ability on the Hpatches dataset and a Wide Baseline Stereo dataset.

Spyridon Bakas, Mauricio Reyes, Andras Jakab et al.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.

Hadi Salman, Payman Yadollahpour, Tom Fletcher et al.

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.

Huan Fu, Mingming Gong, Chaohui Wang et al.

Unsupervised domain mapping aims to learn a function to translate domain X to Y by a function GXY in the absence of paired examples. Finding the optimal GXY without paired data is an ill-posed problem, so appropriate constraints are required to obtain reasonable solutions. One of the most prominent constraints is cycle consistency, which enforces the translated image by GXY to be translated back to the input image by an inverse mapping GYX. While cycle consistency requires the simultaneous training of GXY and GY X, recent studies have shown that one-sided domain mapping can be achieved by preserving pairwise distances between images. Although cycle consistency and distance preservation successfully constrain the solution space, they overlook the special properties that simple geometric transformations do not change the semantic structure of images. Based on this special property, we develop a geometry-consistent generative adversarial network (GcGAN), which enables one-sided unsupervised domain mapping. GcGAN takes the original image and its counterpart image transformed by a predefined geometric transformation as inputs and generates two images in the new domain coupled with the corresponding geometry-consistency constraint. The geometry-consistency constraint reduces the space of possible solutions while keep the correct solutions in the search space. Quantitative and qualitative comparisons with the baseline (GAN alone) and the state-of-the-art methods including CycleGAN and DistanceGAN demonstrate the effectiveness of our method.

Mingming Gong, Kun Zhang, Biwei Huang et al.

An essential problem in domain adaptation is to understand and make use of distribution changes across domains. For this purpose, we first propose a flexible Generative Domain Adaptation Network (G-DAN) with specific latent variables to capture changes in the generating process of features across domains. By explicitly modeling the changes, one can even generate data in new domains using the generating process with new values for the latent variables in G-DAN. In practice, the process to generate all features together may involve high-dimensional latent variables, requiring dealing with distributions in high dimensions and making it difficult to learn domain changes from few source domains. Interestingly, by further making use of the causal representation of joint distributions, we then decompose the joint distribution into separate modules, each of which involves different low-dimensional latent variables and can be learned separately, leading to a Causal G-DAN (CG-DAN). This improves both statistical and computational efficiency of the learning procedure. Finally, by matching the feature distribution in the target domain, we can recover the target-domain joint distribution and derive the learning machine for the target domain. We demonstrate the efficacy of both G-DAN and CG-DAN in domain generation and cross-domain prediction on both synthetic and real data experiments.

Xiyu Yu, Tongliang Liu, Mingming Gong et al.

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.

Kun Zhang, Mingming Gong, Joseph Ramsey et al.

Measurement error in the observed values of the variables can greatly change the output of various causal discovery methods. This problem has received much attention in multiple fields, but it is not clear to what extent the causal model for the measurement-error-free variables can be identified in the presence of measurement error with unknown variance. In this paper, we study precise sufficient identifiability conditions for the measurement-error-free causal model and show what information of the causal model can be recovered from observed data. In particular, we present two different sets of identifiability conditions, based on the second-order statistics and higher-order statistics of the data, respectively. The former was inspired by the relationship between the generating model of the measurement-error-contaminated data and the factor analysis model, and the latter makes use of the identifiability result of the over-complete independent component analysis problem.