FairMedFM: Fairness Benchmarking for Medical Imaging Foundation Models

The advent of foundation models (FMs) in healthcare offers unprecedented opportunities to enhance medical diagnostics through automated classification and segmentation tasks. However, these models also raise significant concerns about their fairness, especially when applied to diverse and underrepresented populations in healthcare applications. Currently, there is a lack of comprehensive benchmarks, standardized pipelines, and easily adaptable libraries to evaluate and understand the fairness performance of FMs in medical imaging, leading to considerable challenges in formulating and implementing solutions that ensure equitable outcomes across diverse patient populations. To fill this gap, we introduce FairMedFM, a fairness benchmark for FM research in medical imaging.FairMedFM integrates with 17 popular medical imaging datasets, encompassing different modalities, dimensionalities, and sensitive attributes. It explores 20 widely used FMs, with various usages such as zero-shot learning, linear probing, parameter-efficient fine-tuning, and prompting in various downstream tasks -- classification and segmentation. Our exhaustive analysis evaluates the fairness performance over different evaluation metrics from multiple perspectives, revealing the existence of bias, varied utility-fairness trade-offs on different FMs, consistent disparities on the same datasets regardless FMs, and limited effectiveness of existing unfairness mitigation methods. Checkout FairMedFM's project page and open-sourced codebase, which supports extendible functionalities and applications as well as inclusive for studies on FMs in medical imaging over the long term.

Synthesizing Multimodal Electronic Health Records via Predictive Diffusion Models

Synthesizing electronic health records (EHR) data has become a preferred strategy to address data scarcity, improve data quality, and model fairness in healthcare. However, existing approaches for EHR data generation predominantly rely on state-of-the-art generative techniques like generative adversarial networks, variational autoencoders, and language models. These methods typically replicate input visits, resulting in inadequate modeling of temporal dependencies between visits and overlooking the generation of time information, a crucial element in EHR data. Moreover, their ability to learn visit representations is limited due to simple linear mapping functions, thus compromising generation quality. To address these limitations, we propose a novel EHR data generation model called EHRPD. It is a diffusion-based model designed to predict the next visit based on the current one while also incorporating time interval estimation. To enhance generation quality and diversity, we introduce a novel time-aware visit embedding module and a pioneering predictive denoising diffusion probabilistic model (PDDPM). Additionally, we devise a predictive U-Net (PU-Net) to optimize P-DDPM.We conduct experiments on two public datasets and evaluate EHRPD from fidelity, privacy, and utility perspectives. The experimental results demonstrate the efficacy and utility of the proposed EHRPD in addressing the aforementioned limitations and advancing EHR data generation.

PatentGPT: A Large Language Model for Intellectual Property

In recent years, large language models have attracted significant attention due to their exceptional performance across a multitude of natural language process tasks, and have been widely applied in various fields. However, the application of large language models in the Intellectual Property (IP) space is challenging due to the strong need for specialized knowledge, privacy protection, processing of extremely long text in this field. In this technical report, we present for the first time a low-cost, standardized procedure for training IP-oriented LLMs, meeting the unique requirements of the IP domain. Using this standard process, we have trained the PatentGPT series models based on open-source pretrained models. By evaluating them on the open-source IP-oriented benchmark MOZIP, our domain-specific LLMs outperforms GPT-4, indicating the effectiveness of the proposed training procedure and the expertise of the PatentGPT models in the IP demain. What is impressive is that our model significantly outperformed GPT-4 on the 2019 China Patent Agent Qualification Examination by achieving a score of 65, reaching the level of human experts. Additionally, the PatentGPT model, which utilizes the SMoE architecture, achieves performance comparable to that of GPT-4 in the IP domain and demonstrates a better cost-performance ratio on long-text tasks, potentially serving as an alternative to GPT-4 within the IP domain.

FineRec:Exploring Fine-grained Sequential Recommendation

Sequential recommendation is dedicated to offering items of interest for users based on their history behaviors. The attribute-opinion pairs, expressed by users in their reviews for items, provide the potentials to capture user preferences and item characteristics at a fine-grained level. To this end, we propose a novel framework FineRec that explores the attribute-opinion pairs of reviews to finely handle sequential recommendation. Specifically, we utilize a large language model to extract attribute-opinion pairs from reviews. For each attribute, a unique attribute-specific user-opinion-item graph is created, where corresponding opinions serve as the edges linking heterogeneous user and item nodes. To tackle the diversity of opinions, we devise a diversity-aware convolution operation to aggregate information within the graphs, enabling attribute-specific user and item representation learning. Ultimately, we present an interaction-driven fusion mechanism to integrate attribute-specific user/item representations across all attributes for generating recommendations. Extensive experiments conducted on several realworld datasets demonstrate the superiority of our FineRec over existing state-of-the-art methods. Further analysis also verifies the effectiveness of our fine-grained manner in handling the task.

Recent Advances in Predictive Modeling with Electronic Health Records

The development of electronic health records (EHR) systems has enabled the collection of a vast amount of digitized patient data. However, utilizing EHR data for predictive modeling presents several challenges due to its unique characteristics. With the advancements in machine learning techniques, deep learning has demonstrated its superiority in various applications, including healthcare. This survey systematically reviews recent advances in deep learning-based predictive models using EHR data. Specifically, we begin by introducing the background of EHR data and providing a mathematical definition of the predictive modeling task. We then categorize and summarize predictive deep models from multiple perspectives. Furthermore, we present benchmarks and toolkits relevant to predictive modeling in healthcare. Finally, we conclude this survey by discussing open challenges and suggesting promising directions for future research.

Automated Fusion of Multimodal Electronic Health Records for Better Medical Predictions

The widespread adoption of Electronic Health Record (EHR) systems in healthcare institutes has generated vast amounts of medical data, offering significant opportunities for improving healthcare services through deep learning techniques. However, the complex and diverse modalities and feature structures in real-world EHR data pose great challenges for deep learning model design. To address the multi-modality challenge in EHR data, current approaches primarily rely on hand-crafted model architectures based on intuition and empirical experiences, leading to sub-optimal model architectures and limited performance. Therefore, to automate the process of model design for mining EHR data, we propose a novel neural architecture search (NAS) framework named AutoFM, which can automatically search for the optimal model architectures for encoding diverse input modalities and fusion strategies. We conduct thorough experiments on real-world multi-modal EHR data and prediction tasks, and the results demonstrate that our framework not only achieves significant performance improvement over existing state-of-the-art methods but also discovers meaningful network architectures effectively.

Hierarchical Pretraining on Multimodal Electronic Health Records

Pretraining has proven to be a powerful technique in natural language processing (NLP), exhibiting remarkable success in various NLP downstream tasks. However, in the medical domain, existing pretrained models on electronic health records (EHR) fail to capture the hierarchical nature of EHR data, limiting their generalization capability across diverse downstream tasks using a single pretrained model. To tackle this challenge, this paper introduces a novel, general, and unified pretraining framework called MEDHMP, specifically designed for hierarchically multimodal EHR data. The effectiveness of the proposed MEDHMP is demonstrated through experimental results on eight downstream tasks spanning three levels. Comparisons against eighteen baselines further highlight the efficacy of our approach.

MedDiffusion: Boosting Health Risk Prediction via Diffusion-based Data Augmentation

Health risk prediction is one of the fundamental tasks under predictive modeling in the medical domain, which aims to forecast the potential health risks that patients may face in the future using their historical Electronic Health Records (EHR). Researchers have developed several risk prediction models to handle the unique challenges of EHR data, such as its sequential nature, high dimensionality, and inherent noise. These models have yielded impressive results. Nonetheless, a key issue undermining their effectiveness is data insufficiency. A variety of data generation and augmentation methods have been introduced to mitigate this issue by expanding the size of the training data set through the learning of underlying data distributions. However, the performance of these methods is often limited due to their task-unrelated design. To address these shortcomings, this paper introduces a novel, end-to-end diffusion-based risk prediction model, named MedDiffusion. It enhances risk prediction performance by creating synthetic patient data during training to enlarge sample space. Furthermore, MedDiffusion discerns hidden relationships between patient visits using a step-wise attention mechanism, enabling the model to automatically retain the most vital information for generating high-quality data. Experimental evaluation on four real-world medical datasets demonstrates that MedDiffusion outperforms 14 cutting-edge baselines in terms of PR-AUC, F1, and Cohen's Kappa. We also conduct ablation studies and benchmark our model against GAN-based alternatives to further validate the rationality and adaptability of our model design. Additionally, we analyze generated data to offer fresh insights into the model's interpretability.

Client-Level Differential Privacy via Adaptive Intermediary in Federated Medical Imaging

Despite recent progress in enhancing the privacy of federated learning (FL) via differential privacy (DP), the trade-off of DP between privacy protection and performance is still underexplored for real-world medical scenario. In this paper, we propose to optimize the trade-off under the context of client-level DP, which focuses on privacy during communications. However, FL for medical imaging involves typically much fewer participants (hospitals) than other domains (e.g., mobile devices), thus ensuring clients be differentially private is much more challenging. To tackle this problem, we propose an adaptive intermediary strategy to improve performance without harming privacy. Specifically, we theoretically find splitting clients into sub-clients, which serve as intermediaries between hospitals and the server, can mitigate the noises introduced by DP without harming privacy. Our proposed approach is empirically evaluated on both classification and segmentation tasks using two public datasets, and its effectiveness is demonstrated with significant performance improvements and comprehensive analytical studies. Code is available at: https://github.com/med-air/Client-DP-FL.

3DSAM-adapter: Holistic Adaptation of SAM from 2D to 3D for Promptable Medical Image Segmentation

Despite that the segment anything model (SAM) achieved impressive results on general-purpose semantic segmentation with strong generalization ability on daily images, its demonstrated performance on medical image segmentation is less precise and not stable, especially when dealing with tumor segmentation tasks that involve objects of small sizes, irregular shapes, and low contrast. Notably, the original SAM architecture is designed for 2D natural images, therefore would not be able to extract the 3D spatial information from volumetric medical data effectively. In this paper, we propose a novel adaptation method for transferring SAM from 2D to 3D for promptable medical image segmentation. Through a holistically designed scheme for architecture modification, we transfer the SAM to support volumetric inputs while retaining the majority of its pre-trained parameters for reuse. The fine-tuning process is conducted in a parameter-efficient manner, wherein most of the pre-trained parameters remain frozen, and only a few lightweight spatial adapters are introduced and tuned. Regardless of the domain gap between natural and medical data and the disparity in the spatial arrangement between 2D and 3D, the transformer trained on natural images can effectively capture the spatial patterns present in volumetric medical images with only lightweight adaptations. We conduct experiments on four open-source tumor segmentation datasets, and with a single click prompt, our model can outperform domain state-of-the-art medical image segmentation models on 3 out of 4 tasks, specifically by 8.25%, 29.87%, and 10.11% for kidney tumor, pancreas tumor, colon cancer segmentation, and achieve similar performance for liver tumor segmentation. We also compare our adaptation method with existing popular adapters, and observed significant performance improvement on most datasets.