Medical Imaging

Existing reconstruction models in snapshot compressive imaging systems (SCI) are trained with a single well-calibrated hardware instance, making their perfor- mance vulnerable to hardware shifts and limited in adapting to multiple hardware configurations. To facilitate cross-hardware learning, previous efforts attempt to directly collect multi-hardware data and perform centralized training, which is impractical due to severe user data privacy concerns and hardware heterogeneity across different platforms/institutions. In this study, we explicitly consider data privacy and heterogeneity in cooperatively optimizing SCI systems by proposing a Federated Hardware-Prompt learning (FedHP) framework. Rather than mitigating the client drift by rectifying the gradients, which only takes effect on the learning manifold but fails to solve the heterogeneity rooted in the input data space, FedHP learns a hardware-conditioned prompter to align inconsistent data distribution across clients, serving as an indicator of the data inconsistency among different hardware (e.g., coded apertures). Extensive experimental results demonstrate that the proposed FedHP coordinates the pre-trained model to multiple hardware con- figurations, outperforming prevalent FL frameworks for 0.35dB under challenging heterogeneous settings. Moreover, a Snapshot Spectral Heterogeneous Dataset has been built upon multiple practical SCI systems. Data and code are aveilable at https://github.com/Jiamian-Wang/FedHP-Snapshot-Compressive-Imaging.git

Deep learning has seen remarkable advancements in machine learning, yet it often demands extensive annotated data. Tasks like 3D semantic segmentation impose a substantial annotation burden, especially in domains like medicine, where expert annotations drive up the cost. Active learning (AL) holds great potential to alleviate this annotation burden in 3D medical segmentation. The majority of existing AL methods, however, are not tailored to the medical domain. While weakly-supervised methods have been explored to reduce annotation burden, the fusion of AL with weak supervision remains unexplored, despite its potential to significantly reduce annotation costs. Additionally, there is little focus on slice-based AL for 3D segmentation, which can also significantly reduce costs in comparison to conventional volume-based AL. This paper introduces a novel metric learning method for Coreset to perform slice-based active learning in 3D medical segmentation. By merging contrastive learning with inherent data groupings in medical imaging, we learn a metric that emphasizes the relevant differences in samples for training 3D medical segmentation models. We perform comprehensive evaluations using both weak and full annotations across four datasets (medical and non-medical). Our findings demonstrate that our approach surpasses existing active learning techniques on both weak and full annotations and obtains superior performance with low-annotation budgets which is crucial in medical imaging. Source code for this project is available in the supplementary materials and on GitHub: https://github.com/arvindmvepa/al-seg.

Polarimetric imaging is a challenging problem in the field of polarization-based vision, since setting a short exposure time reduces the signal-to-noise ratio, making the degree of polarization (DoP) and the angle of polarization (AoP) severely degenerated, while if setting a relatively long exposure time, the DoP and AoP would tend to be over-smoothed due to the frequently-occurring motion blur. This work proposes a polarimetric imaging framework that can produce clean and clear polarized snapshots by complementarily fusing a degraded pair of noisy and blurry ones. By adopting a neural network-based three-phase fusing scheme with specially-designed modules tailored to each phase, our framework can not only improve the image quality but also preserve the polarization properties. Experimental results show that our framework achieves state-of-the-art performance.

Classical optimization and learning-based methods are the two reigning paradigms in deformable image registration. While optimization-based methods boast generalizability across modalities and robust performance, learning-based methods promise peak performance, incorporating weak supervision and amortized optimization. However, the exact conditions for either paradigm to perform well over the other are shrouded and not explicitly outlined in the existing literature. In this paper, we make an explicit correspondence between the mutual information of the distribution of per-pixel intensity and labels, and the performance of classical registration methods. This strong correlation hints to the fact that architectural designs in learning-based methods is unlikely to affect this correlation, and therefore, the performance of learning-based methods. This hypothesis is thoroughly validated with state-of-the-art classical and learning-based methods. However, learning-based methods with weak supervision can perform high-fidelity intensity and label registration, which is not possible with classical methods. Next, we show that this high-fidelity feature learning does not translate to invariance to domain shift, and learning-based methods are sensitive to such changes in the data distribution. We reassess and recalibrate performance expectations from classical and DLIR methods under access to label supervision, training time, and its generalization capabilities under minor domain shifts.

Diffusion models excel in solving imaging inverse problems due to their ability to model complex image priors. However, their reliance on large, clean datasets for training limits their practical use where clean data is scarce. In this paper, we propose EMDiffusion, an expectation-maximization (EM) approach to train diffusion models from corrupted observations. Our method alternates between reconstructing clean images from corrupted data using a known diffusion model (E-step) and refining diffusion model weights based on these reconstructions (M-step). This iterative process leads the learned diffusion model to gradually converge to a local optimum, that is, to approximate the true clean data distribution. We validate our method through extensive experiments on diverse computational imaging tasks, including random inpainting, denoising, and deblurring, achieving new state-of-the-art performance.

Multiple Instance Learning (MIL) is widely used in medical imaging classification to reduce the labeling effort. While only bag labels are available for training, one typically seeks predictions at both bag and instance levels (classification and localization tasks, respectively). Early MIL methods treated the instances in a bag independently. Recent methods account for global and local dependencies among instances. Although they have yielded excellent results in classification, their performance in terms of localization is comparatively limited. We argue that these models have been designed to target the classification task, while implications at the instance level have not been deeply investigated. Motivated by a simple observation -- that neighboring instances are likely to have the same label -- we propose a novel, principled, and flexible mechanism to model local dependencies. It can be used alone or combined with any mechanism to model global dependencies (e.g., transformers). A thorough empirical validation shows that our module leads to state-of-the-art performance in localization while being competitive or superior in classification. Our code is at https://github.com/Franblueee/SmMIL.

The paper proposes a novel evaluation metric for automatic medical report generation from X-ray images, VLScore. It aims to overcome the limitations of existing evaluation methods, which either focus solely on textual similarities, ignoring clinical aspects, or concentrate only on a single clinical aspect, the pathology, neglecting all other factors. The key idea of our metric is to measure the similarity between radiology reports while considering the corresponding image. We demonstrate the benefit of our metric through evaluation on a dataset where radiologists marked errors in pairs of reports, showing notable alignment with radiologists' judgments. In addition, we provide a new dataset for evaluating metrics. This dataset includes well-designed perturbations that distinguish between significant modifications (e.g., removal of a diagnosis) and insignificant ones. It highlights the weaknesses in current evaluation metrics and provides a clear framework for analysis.

As large language models (LLMs) develop increasingly sophisticated capabilities and find applications in medical settings, it becomes important to assess their medical safety due to their far-reaching implications for personal and public health, patient safety, and human rights. However, there is little to no understanding of the notion of medical safety in the context of LLMs, let alone how to evaluate and improve it. To address this gap, we first define the notion of medical safety in LLMs based on the Principles of Medical Ethics set forth by the American Medical Association. We then leverage this understanding to introduce MedSafetyBench, the first benchmark dataset designed to measure the medical safety of LLMs. We demonstrate the utility of MedSafetyBench by using it to evaluate and improve the medical safety of LLMs. Our results show that publicly-available medical LLMs do not meet standards of medical safety and that fine-tuning them using MedSafetyBench improves their medical safety while preserving their medical performance. By introducing this new benchmark dataset, our work enables a systematic study of the state of medical safety in LLMs and motivates future work in this area, paving the way to mitigate the safety risks of LLMs in medicine. The benchmark dataset and code are available at https://github.com/AI4LIFE-GROUP/med-safety-bench.

Artificial intelligence has significantly impacted medical applications, particularly with the advent of Medical Large Vision Language Models (Med-LVLMs), sparking optimism for the future of automated and personalized healthcare. However, the trustworthiness of Med-LVLMs remains unverified, posing significant risks for future model deployment. In this paper, we introduce CARES and aim to comprehensively evaluate the Trustworthiness of Med-LVLMs across the medical domain. We assess the trustworthiness of Med-LVLMs across five dimensions, including trustfulness, fairness, safety, privacy, and robustness. CARES comprises about 41K question-answer pairs in both closed and open-ended formats, covering 16 medical image modalities and 27 anatomical regions. Our analysis reveals that the models consistently exhibit concerns regarding trustworthiness, often displaying factual inaccuracies and failing to maintain fairness across different demographic groups. Furthermore, they are vulnerable to attacks and demonstrate a lack of privacy awareness. We publicly release our benchmark and code in https://github.com/richard-peng-xia/CARES.

A major challenge of the long measurement times in magnetic resonance imaging (MRI), an important medical imaging technology, is that patients may move during data acquisition. This leads to severe motion artifacts in the reconstructed images and volumes. In this paper, we propose MotionTTT a deep learning-based test-time-training (TTT) method for accurate motion estimation. The key idea is that a neural network trained for motion-free reconstruction has a small loss if there is no motion, thus optimizing over motion parameters passed through the reconstruction network enables accurate estimation of motion. The estimated motion parameters enable to correct for the motion and to reconstruct accurate motion-corrected images. Our method uses 2D reconstruction networks to estimate rigid motion in 3D, and constitutes the first deep learning based method for 3D rigid motion estimation towards 3D-motion-corrected MRI. We show that our method can provably reconstruct motion parameters for a simple signal and neural network model. We demonstrate the effectiveness of our method for both retrospectively simulated motion and prospectively collected real motion-corrupted data. Code is available at \url{https://github.com/MLI-lab/MRI_MotionTTT}.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks---which, differing from algorithms, are more flexible and can support different algorithms—including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

Medical Imaging (MI) datasets are fundamental to artificial intelligence in healthcare. The accuracy, robustness, and fairness of diagnostic algorithms depend on the data (and its quality) used to train and evaluate the models. MI datasets used to be proprietary, but have become increasingly available to the public, including on community-contributed platforms (CCPs) like Kaggle or HuggingFace. While open data is important to enhance the redistribution of data's public value, we find that the current CCP governance model fails to uphold the quality needed and recommended practices for sharing, documenting, and evaluating datasets. In this paper, we conduct an analysis of publicly available machine learning datasets on CCPs, discussing datasets' context, and identifying limitations and gaps in the current CCP landscape. We highlight differences between MI and computer vision datasets, particularly in the potentially harmful downstream effects from poor adoption of recommended dataset management practices. We compare the analyzed datasets across several dimensions, including data sharing, data documentation, and maintenance. We find vague licenses, lack of persistent identifiers and storage, duplicates, and missing metadata, with differences between the platforms. Our research contributes to efforts in responsible data curation and AI algorithms for healthcare.

Current benchmarks for evaluating large language models (LLMs) in medicine are primarily focused on question-answering involving domain knowledge and descriptive reasoning. While such qualitative capabilities are vital to medical diagnosis, in real-world scenarios, doctors frequently use clinical calculators that follow quantitative equations and rule-based reasoning paradigms for evidence-based decision support. To this end, we propose MedCalc-Bench, a first-of-its-kind dataset focused on evaluating the medical calculation capability of LLMs. MedCalc-Bench contains an evaluation set of over 1000 manually reviewed instances from 55 different medical calculation tasks. Each instance in MedCalc-Bench consists of a patient note, a question requesting to compute a specific medical value, a ground truth answer, and a step-by-step explanation showing how the answer is obtained. While our evaluation results show the potential of LLMs in this area, none of them are effective enough for clinical settings. Common issues include extracting the incorrect entities, not using the correct equation or rules for a calculation task, or incorrectly performing the arithmetic for the computation. We hope our study highlights the quantitative knowledge and reasoning gaps in LLMs within medical settings, encouraging future improvements of LLMs for various clinical calculation tasks. MedCalc-Bench is publicly available at: https://github.com/ncbi-nlp/MedCalc-Bench.

Color video snapshot compressive imaging (SCI) employs computational imaging techniques to capture multiple sequential video frames in a single Bayer-patterned measurement. With the increasing popularity of quad-Bayer pattern in mainstream smartphone cameras for capturing high-resolution videos, mobile photography has become more accessible to a wider audience. However, existing color video SCI reconstruction algorithms are designed based on the traditional Bayer pattern. When applied to videos captured by quad-Bayer cameras, these algorithms often result in color distortion and ineffective demosaicing, rendering them impractical for primary equipment. To address this challenge, we propose the MambaSCI method, which leverages the Mamba and UNet architectures for efficient reconstruction of quad-Bayer patterned color video SCI. To the best of our knowledge, our work presents the first algorithm for quad-Bayer patterned SCI reconstruction, and also the initial application of the Mamba model to this task. Specifically, we customize Residual-Mamba-Blocks, which residually connect the Spatial-Temporal Mamba (STMamba), Edge-Detail-Reconstruction (EDR) module, and Channel Attention (CA) module. Respectively, STMamba is used to model long-range spatial-temporal dependencies with linear complexity, EDR is for better edge-detail reconstruction, and CA is used to compensate for the missing channel information interaction in Mamba model. Experiments demonstrate that MambaSCI surpasses state-of-the-art methods with lower computational and memory costs. PyTorch style pseudo-code for the core modules is provided in the supplementary materials. Code is at https://github.com/PAN083/MambaSCI.

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Non-line-of-sight (NLOS) imaging allows for seeing hidden scenes around corners through active sensing. Most previous algorithms for NLOS reconstruction require dense transients acquired through regular scans over a large relay surface, which limits their applicability in realistic scenarios with irregular relay surfaces. In this paper, we propose an unsupervised learning-based framework for NLOS imaging from irregularly undersampled transients~(IUT). Our method learns implicit priors from noisy irregularly undersampled transients without requiring paired data, which is difficult and expensive to acquire and align. To overcome the ambiguity of the measurement consistency constraint in inferring the albedo volume, we design a virtual scanning process that enables the network to learn within both range and null spaces for high-quality reconstruction. We devise a physics-guided SURE-based denoiser to enhance robustness to ubiquitous noise in low-photon imaging conditions. Extensive experiments on both simulated and real-world data validate the performance and generalization of our method. Compared with the state-of-the-art (SOTA) method, our method achieves higher fidelity, greater robustness, and remarkably faster inference times by orders of magnitude. The code and model are available at https://github.com/XingyuCuii/Virtual-Scanning-NLOS.

Dynamic reconstruction in confocal non-line-of-sight imaging encounters great challenges since the dense raster-scanning manner limits the practical frame rate. A fewer pioneer works reconstruct high-resolution volumes from the under-scanning transient measurements but overlook temporal consistency among transient frames. To fully exploit multi-frame information, we propose the first spatial-temporal Mamba (ST-Mamba) based method tailored for dynamic reconstruction of transient videos. Our method capitalizes on neighbouring transient frames to aggregate the target 3D hidden volume. Specifically, the interleaved features extracted from the input transient frames are fed to the proposed ST-Mamba blocks, which leverage the time-resolving causality in transient measurement. The cross ST-Mamba blocks are then devised to integrate the adjacent transient features. The target high-resolution transient frame is subsequently recovered by the transient spreading module. After transient fusion and recovery, a physical-based network is employed to reconstruct the hidden volume. To tackle the substantial noise inherent in transient videos, we propose a wave-based loss function to impose constraints within the phasor field. Besides, we introduce a new dataset, comprising synthetic videos for training and real-world videos for evaluation. Extensive experiments showcase the superior performance of our method on both synthetic data and real world data captured by different imaging setups. The code and data are available at https://github.com/Depth2World/Dynamic_NLOS.

In the present study, we introduce an innovative structure for 3D medical image segmentation that effectively integrates 2D U-Net-derived skip connections into the architecture of 3D convolutional neural networks (3D CNNs). Conventional 3D segmentation techniques predominantly depend on isotropic 3D convolutions for the extraction of volumetric features, which frequently engenders inefficiencies due to the varying information density across the three orthogonal axes in medical imaging modalities such as computed tomography (CT) and magnetic resonance imaging (MRI). This disparity leads to a decline in axial-slice plane feature extraction efficiency, with slice plane features being comparatively underutilized relative to features in the time-axial. To address this issue, we introduce the U-shaped Connection (uC), utilizing simplified 2D U-Net in place of standard skip connections to augment the extraction of the axial-slice plane features while concurrently preserving the volumetric context afforded by 3D convolutions. Based on uC, we further present uC 3DU-Net, an enhanced 3D U-Net backbone that integrates the uC approach to facilitate optimal axial-slice plane feature utilization. Through rigorous experimental validation on five publicly accessible datasets—FLARE2021, OIMHS, FeTA2021, AbdomenCT-1K, and BTCV, the proposed method surpasses contemporary state-of-the-art models. Notably, this performance is achieved while reducing the number of parameters and computational complexity. This investigation underscores the efficacy of incorporating 2D convolutions within the framework of 3D CNNs to overcome the intrinsic limitations of volumetric segmentation, thereby potentially expanding the frontiers of medical image analysis. Our implementation is available at https://github.com/IMOP-lab/U-Shaped-Connection.

Electronic health records (EHRs) are stored in various database systems with different database models on heterogeneous storage architectures, such as relational databases, document stores, or graph databases. These different database models have a big impact on query complexity and performance. While this has been a known fact in database research, its implications for the growing number of Text-to-Query systems have surprisingly not been investigated so far. In this paper, we present SM3-Text-to-Query, the first multi-model medical Text-to-Query benchmark based on synthetic patient data from Synthea, following the SNOMED-CT taxonomy---a widely used knowledge graph ontology covering medical terminology. SM3-Text-to-Query provides data representations for relational databases (PostgreSQL), document stores (MongoDB), and graph databases (Neo4j and GraphDB (RDF)), allowing the evaluation across four popular query languages, namely SQL, MQL, Cypher, and SPARQL. We systematically and manually develop 408 template questions, which we augment to construct a benchmark of 10K diverse natural language question/query pairs for these four query languages (40K pairs overall). On our dataset, we evaluate several common in-context-learning (ICL) approaches for a set of representative closed and open-source LLMs. Our evaluation sheds light on the trade-offs between database models and query languages for different ICL strategies and LLMs. Last, SM3-Text-to-Query is easily extendable to additional query languages or real, standard-based patient databases.

Learning an ordering of items based on pairwise comparisons is useful when items are difficult to rate consistently on an absolute scale, for example, when annotators have to make subjective assessments. When exhaustive comparison is infeasible, actively sampling item pairs can reduce the number of annotations necessary for learning an accurate ordering. However, many algorithms ignore shared structure between items, limiting their sample efficiency and precluding generalization to new items. It is also common to disregard how noise in comparisons varies between item pairs, despite it being informative of item similarity. In this work, we study active preference learning for ordering items with contextual attributes, both in- and out-of-sample. We give an upper bound on the expected ordering error of a logistic preference model as a function of which items have been compared. Next, we propose an active learning strategy that samples items to minimize this bound by accounting for aleatoric and epistemic uncertainty in comparisons. We evaluate the resulting algorithm, and a variant aimed at reducing model misspecification, in multiple realistic ordering tasks with comparisons made by human annotators. Our results demonstrate superior sample efficiency and generalization compared to non-contextual ranking approaches and active preference learning baselines.