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.

FedBRB: An Effective Solution to the Small-to-Large Scenario in Device-Heterogeneity Federated Learning

Recently, the success of large models has demonstrated the importance of scaling up model size. This has spurred interest in exploring collaborative training of large-scale models from federated learning perspective. Due to computational constraints, many institutions struggle to train a large-scale model locally. Thus, training a larger global model using only smaller local models has become an important scenario (i.e., the \textbf{small-to-large scenario}). Although recent device-heterogeneity federated learning approaches have started to explore this area, they face limitations in fully covering the parameter space of the global model. In this paper, we propose a method called \textbf{FedBRB} (\underline{B}lock-wise \underline{R}olling and weighted \underline{B}roadcast) based on the block concept. FedBRB can uses small local models to train all blocks of the large global model, and broadcasts the trained parameters to the entire space for faster information interaction. Experiments demonstrate FedBRB yields substantial performance gains, achieving state-of-the-art results in this scenario. Moreover, FedBRB using only minimal local models can even surpass baselines using larger local models.

Empowering Federated Learning for Massive Models with NVIDIA FLARE

In the ever-evolving landscape of artificial intelligence (AI) and large language models (LLMs), handling and leveraging data effectively has become a critical challenge. Most state-of-the-art machine learning algorithms are data-centric. However, as the lifeblood of model performance, necessary data cannot always be centralized due to various factors such as privacy, regulation, geopolitics, copyright issues, and the sheer effort required to move vast datasets. In this paper, we explore how federated learning enabled by NVIDIA FLARE can address these challenges with easy and scalable integration capabilities, enabling parameter-efficient and full supervised fine-tuning of LLMs for natural language processing and biopharmaceutical applications to enhance their accuracy and robustness.

FedBPT: Efficient Federated Black-box Prompt Tuning for Large Language Models

Pre-trained language models (PLM) have revolutionized the NLP landscape, achieving stellar performances across diverse tasks. These models, while benefiting from vast training data, often require fine-tuning on specific data to cater to distinct downstream tasks. However, this data adaptation process has inherent security and privacy concerns, primarily when leveraging user-generated, device-residing data. Federated learning (FL) provides a solution, allowing collaborative model fine-tuning without centralized data collection. However, applying FL to finetune PLMs is hampered by challenges, including restricted model parameter access, high computational requirements, and communication overheads. This paper introduces Federated Black-box Prompt Tuning (FedBPT), a framework designed to address these challenges. FedBPT does not require the clients to access the model parameters. By focusing on training optimal prompts and utilizing gradient-free optimization methods, FedBPT reduces the number of exchanged variables, boosts communication efficiency, and minimizes computational and storage costs. Experiments highlight the framework's ability to drastically cut communication and memory costs while maintaining competitive performance. Ultimately, FedBPT presents a promising solution for efficient, privacy-preserving fine-tuning of PLM in the age of large language models.

Disruptive Autoencoders: Leveraging Low-level features for 3D Medical Image Pre-training

Harnessing the power of pre-training on large-scale datasets like ImageNet forms a fundamental building block for the progress of representation learning-driven solutions in computer vision. Medical images are inherently different from natural images as they are acquired in the form of many modalities (CT, MR, PET, Ultrasound etc.) and contain granulated information like tissue, lesion, organs etc. These characteristics of medical images require special attention towards learning features representative of local context. In this work, we focus on designing an effective pre-training framework for 3D radiology images. First, we propose a new masking strategy called local masking where the masking is performed across channel embeddings instead of tokens to improve the learning of local feature representations. We combine this with classical low-level perturbations like adding noise and downsampling to further enable low-level representation learning. To this end, we introduce Disruptive Autoencoders, a pre-training framework that attempts to reconstruct the original image from disruptions created by a combination of local masking and low-level perturbations. Additionally, we also devise a cross-modal contrastive loss (CMCL) to accommodate the pre-training of multiple modalities in a single framework. We curate a large-scale dataset to enable pre-training of 3D medical radiology images (MRI and CT). The proposed pre-training framework is tested across multiple downstream tasks and achieves state-of-the-art performance. Notably, our proposed method tops the public test leaderboard of BTCV multi-organ segmentation challenge.

A Systematic Evaluation of Federated Learning on Biomedical Natural Language Processing

Language models (LMs) like BERT and GPT have revolutionized natural language processing (NLP). However, privacy-sensitive domains, particularly the medical field, face challenges to train LMs due to limited data access and privacy constraints imposed by regulations like the Health Insurance Portability and Accountability Act (HIPPA) and the General Data Protection Regulation (GDPR). Federated learning (FL) offers a decentralized solution that enables collaborative learning while ensuring the preservation of data privacy. In this study, we systematically evaluate FL in medicine across $2$ biomedical NLP tasks using $6$ LMs encompassing $8$ corpora. Our results showed that: 1) FL models consistently outperform LMs trained on individual client's data and sometimes match the model trained with polled data; 2) With the fixed number of total data, LMs trained using FL with more clients exhibit inferior performance, but pre-trained transformer-based models exhibited greater resilience. 3) LMs trained using FL perform nearly on par with the model trained with pooled data when clients' data are IID distributed while exhibiting visible gaps with non-IID data. Our code is available at: https://github.com/PL97/FedNLP

Communication-Efficient Vertical Federated Learning with Limited Overlapping Samples

Federated learning is a popular collaborative learning approach that enables clients to train a global model without sharing their local data. Vertical federated learning (VFL) deals with scenarios in which the data on clients have different feature spaces but share some overlapping samples. Existing VFL approaches suffer from high communication costs and cannot deal efficiently with limited overlapping samples commonly seen in the real world. We propose a practical vertical federated learning (VFL) framework called \textbf{one-shot VFL} that can solve the communication bottleneck and the problem of limited overlapping samples simultaneously based on semi-supervised learning. We also propose \textbf{few-shot VFL} to improve the accuracy further with just one more communication round between the server and the clients. In our proposed framework, the clients only need to communicate with the server once or only a few times. We evaluate the proposed VFL framework on both image and tabular datasets. Our methods can improve the accuracy by more than 46.5\% and reduce the communication cost by more than 330$\times$ compared with state-of-the-art VFL methods when evaluated on CIFAR-10. Our code will be made publicly available at \url{https://nvidia.github.io/NVFlare/research/one-shot-vfl}.