C-FedRAG: A Confidential Federated Retrieval-Augmented Generation System

Organizations seeking to utilize Large Language Models (LLMs) for knowledge querying and analysis often encounter challenges in maintaining an LLM fine-tuned on targeted, up-to-date information that keeps answers relevant and grounded. Retrieval Augmented Generation (RAG) has quickly become a feasible solution for organizations looking to overcome the challenges of maintaining proprietary models and to help reduce LLM hallucinations in their query responses. However, RAG comes with its own issues regarding scaling data pipelines across tiered-access and disparate data sources. In many scenarios, it is necessary to query beyond a single data silo to provide richer and more relevant context for an LLM. Analyzing data sources within and across organizational trust boundaries is often limited by complex data-sharing policies that prohibit centralized data storage, therefore, inhibit the fast and effective setup and scaling of RAG solutions. In this paper, we introduce Confidential Computing (CC) techniques as a solution for secure Federated Retrieval Augmented Generation (FedRAG). Our proposed Confidential FedRAG system (C-FedRAG) enables secure connection and scaling of a RAG workflows across a decentralized network of data providers by ensuring context confidentiality. We also demonstrate how to implement a C-FedRAG system using the NVIDIA FLARE SDK and assess its performance using the MedRAG toolkit and MIRAGE benchmarking dataset.

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data$-$features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

IPMN Risk Assessment under Federated Learning Paradigm

Accurate classification of Intraductal Papillary Mucinous Neoplasms (IPMN) is essential for identifying high-risk cases that require timely intervention. In this study, we develop a federated learning framework for multi-center IPMN classification utilizing a comprehensive pancreas MRI dataset. This dataset includes 653 T1-weighted and 656 T2-weighted MRI images, accompanied by corresponding IPMN risk scores from 7 leading medical institutions, making it the largest and most diverse dataset for IPMN classification to date. We assess the performance of DenseNet-121 in both centralized and federated settings for training on distributed data. Our results demonstrate that the federated learning approach achieves high classification accuracy comparable to centralized learning while ensuring data privacy across institutions. This work marks a significant advancement in collaborative IPMN classification, facilitating secure and high-accuracy model training across multiple centers.

Adaptive Aggregation Weights for Federated Segmentation of Pancreas MRI

Federated learning (FL) enables collaborative model training across institutions without sharing sensitive data, making it an attractive solution for medical imaging tasks. However, traditional FL methods, such as Federated Averaging (FedAvg), face difficulties in generalizing across domains due to variations in imaging protocols and patient demographics across institutions. This challenge is particularly evident in pancreas MRI segmentation, where anatomical variability and imaging artifacts significantly impact performance. In this paper, we conduct a comprehensive evaluation of FL algorithms for pancreas MRI segmentation and introduce a novel approach that incorporates adaptive aggregation weights. By dynamically adjusting the contribution of each client during model aggregation, our method accounts for domain-specific differences and improves generalization across heterogeneous datasets. Experimental results demonstrate that our approach enhances segmentation accuracy and reduces the impact of domain shift compared to conventional FL methods while maintaining privacy-preserving capabilities. Significant performance improvements are observed across multiple hospitals (centers).

MAISI: Medical AI for Synthetic Imaging

Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns. This paper introduces the Medical AI for Synthetic Imaging (MAISI), an innovative approach using the diffusion model to generate synthetic 3D computed tomography (CT) images to address those challenges. MAISI leverages the foundation volume compression network and the latent diffusion model to produce high-resolution CT images (up to a landmark volume dimension of 512 x 512 x 768 ) with flexible volume dimensions and voxel spacing. By incorporating ControlNet, MAISI can process organ segmentation, including 127 anatomical structures, as additional conditions and enables the generation of accurately annotated synthetic images that can be used for various downstream tasks. Our experiment results show that MAISI's capabilities in generating realistic, anatomically accurate images for diverse regions and conditions reveal its promising potential to mitigate challenges using synthetic data.

A Short Review and Evaluation of SAM2's Performance in 3D CT Image Segmentation

Since the release of Segment Anything 2 (SAM2), the medical imaging community has been actively evaluating its performance for 3D medical image segmentation. However, different studies have employed varying evaluation pipelines, resulting in conflicting outcomes that obscure a clear understanding of SAM2's capabilities and potential applications. We shortly review existing benchmarks and point out that the SAM2 paper clearly outlines a zero-shot evaluation pipeline, which simulates user clicks iteratively for up to eight iterations. We reproduced this interactive annotation simulation on 3D CT datasets and provided the results and code~\url{https://github.com/Project-MONAI/VISTA}. Our findings reveal that directly applying SAM2 on 3D medical imaging in a zero-shot manner is far from satisfactory. It is prone to generating false positives when foreground objects disappear, and annotating more slices cannot fully offset this tendency. For smaller single-connected objects like kidney and aorta, SAM2 performs reasonably well but for most organs it is still far behind state-of-the-art 3D annotation methods. More research and innovation are needed for 3D medical imaging community to use SAM2 correctly.

Data Alchemy: Mitigating Cross-Site Model Variability Through Test Time Data Calibration

Deploying deep learning-based imaging tools across various clinical sites poses significant challenges due to inherent domain shifts and regulatory hurdles associated with site-specific fine-tuning. For histopathology, stain normalization techniques can mitigate discrepancies, but they often fall short of eliminating inter-site variations. Therefore, we present Data Alchemy, an explainable stain normalization method combined with test time data calibration via a template learning framework to overcome barriers in cross-site analysis. Data Alchemy handles shifts inherent to multi-site data and minimizes them without needing to change the weights of the normalization or classifier networks. Our approach extends to unseen sites in various clinical settings where data domain discrepancies are unknown. Extensive experiments highlight the efficacy of our framework in tumor classification in hematoxylin and eosin-stained patches. Our explainable normalization method boosts classification tasks' area under the precision-recall curve(AUPR) by 0.165, 0.545 to 0.710. Additionally, Data Alchemy further reduces the multisite classification domain gap, by improving the 0.710 AUPR an additional 0.142, elevating classification performance further to 0.852, from 0.545. Our Data Alchemy framework can popularize precision medicine with minimal operational overhead by allowing for the seamless integration of pre-trained deep learning-based clinical tools across multiple sites.

HoloHisto: End-to-end Gigapixel WSI Segmentation with 4K Resolution Sequential Tokenization

In digital pathology, the traditional method for deep learning-based image segmentation typically involves a two-stage process: initially segmenting high-resolution whole slide images (WSI) into smaller patches (e.g., 256x256, 512x512, 1024x1024) and subsequently reconstructing them to their original scale. This method often struggles to capture the complex details and vast scope of WSIs. In this paper, we propose the holistic histopathology (HoloHisto) segmentation method to achieve end-to-end segmentation on gigapixel WSIs, whose maximum resolution is above 80,000$\times$70,000 pixels. HoloHisto fundamentally shifts the paradigm of WSI segmentation to an end-to-end learning fashion with 1) a large (4K) resolution base patch for elevated visual information inclusion and efficient processing, and 2) a novel sequential tokenization mechanism to properly model the contextual relationships and efficiently model the rich information from the 4K input. To our best knowledge, HoloHisto presents the first holistic approach for gigapixel resolution WSI segmentation, supporting direct I/O of complete WSI and their corresponding gigapixel masks. Under the HoloHisto platform, we unveil a random 4K sampler that transcends ultra-high resolution, delivering 31 and 10 times more pixels than standard 2D and 3D patches, respectively, for advancing computational capabilities. To facilitate efficient 4K resolution dense prediction, we leverage sequential tokenization, utilizing a pre-trained image tokenizer to group image features into a discrete token grid. To assess the performance, our team curated a new kidney pathology image segmentation (KPIs) dataset with WSI-level glomeruli segmentation from whole mouse kidneys. From the results, HoloHisto-4K delivers remarkable performance gains over previous state-of-the-art models.

FinTruthQA: A Benchmark Dataset for Evaluating the Quality of Financial Information Disclosure

Accurate and transparent financial information disclosure is crucial in the fields of accounting and finance, ensuring market efficiency and investor confidence. Among many information disclosure platforms, the Chinese stock exchanges' investor interactive platform provides a novel and interactive way for listed firms to disclose information of interest to investors through an online question-and-answer (Q&A) format. However, it is common for listed firms to respond to questions with limited or no substantive information, and automatically evaluating the quality of financial information disclosure on large amounts of Q&A pairs is challenging. This paper builds a benchmark FinTruthQA, that can evaluate advanced natural language processing (NLP) techniques for the automatic quality assessment of information disclosure in financial Q&A data. FinTruthQA comprises 6,000 real-world financial Q&A entries and each Q&A was manually annotated based on four conceptual dimensions of accounting. We benchmarked various NLP techniques on FinTruthQA, including statistical machine learning models, pre-trained language model and their fine-tuned versions, as well as the large language model GPT-4. Experiments showed that existing NLP models have strong predictive ability for real question identification and question relevance tasks, but are suboptimal for answer relevance and answer readability tasks. By establishing this benchmark, we provide a robust foundation for the automatic evaluation of information disclosure, significantly enhancing the transparency and quality of financial reporting. FinTruthQA can be used by auditors, regulators, and financial analysts for real-time monitoring and data-driven decision-making, as well as by researchers for advanced studies in accounting and finance, ultimately fostering greater trust and efficiency in the financial markets.

VISTA3D: Versatile Imaging SegmenTation and Annotation model for 3D Computed Tomography

Segmentation foundation models have attracted great interest, however, none of them are adequate enough for the use cases in 3D computed tomography scans (CT) images. Existing works finetune on medical images with 2D foundation models trained on natural images, but interactive segmentation, especially in 2D, is too time-consuming for 3D scans and less useful for large cohort analysis. Models that can perform out-of-the-box automatic segmentation are more desirable. However, the model trained in this way lacks the ability to perform segmentation on unseen objects like novel tumors. Thus for 3D medical image analysis, an ideal segmentation solution might expect two features: accurate out-of-the-box performance covering major organ classes, and effective adaptation or zero-shot ability to novel structures. In this paper, we discuss what features a 3D CT segmentation foundation model should have, and introduce VISTA3D, Versatile Imaging SegmenTation and Annotation model. The model is trained systematically on 11454 volumes encompassing 127 types of human anatomical structures and various lesions and provides accurate out-of-the-box segmentation. The model's design also achieves state-of-the-art zero-shot interactive segmentation in 3D. The novel model design and training recipe represent a promising step toward developing a versatile medical image foundation model. Code and model weights will be released shortly. The early version of online demo can be tried on https://build.nvidia.com/nvidia/vista-3d.