MEDFuse: Multimodal EHR Data Fusion with Masked Lab-Test Modeling and Large Language Models

Electronic health records (EHRs) are multimodal by nature, consisting of structured tabular features like lab tests and unstructured clinical notes. In real-life clinical practice, doctors use complementary multimodal EHR data sources to get a clearer picture of patients' health and support clinical decision-making. However, most EHR predictive models do not reflect these procedures, as they either focus on a single modality or overlook the inter-modality interactions/redundancy. In this work, we propose MEDFuse, a Multimodal EHR Data Fusion framework that incorporates masked lab-test modeling and large language models (LLMs) to effectively integrate structured and unstructured medical data. MEDFuse leverages multimodal embeddings extracted from two sources: LLMs fine-tuned on free clinical text and masked tabular transformers trained on structured lab test results. We design a disentangled transformer module, optimized by a mutual information loss to 1) decouple modality-specific and modality-shared information and 2) extract useful joint representation from the noise and redundancy present in clinical notes. Through comprehensive validation on the public MIMIC-III dataset and the in-house FEMH dataset, MEDFuse demonstrates great potential in advancing clinical predictions, achieving over 90% F1 score in the 10-disease multi-label classification task.

Efficient In-Context Medical Segmentation with Meta-driven Visual Prompt Selection

In-context learning (ICL) with Large Vision Models (LVMs) presents a promising avenue in medical image segmentation by reducing the reliance on extensive labeling. However, the ICL performance of LVMs highly depends on the choices of visual prompts and suffers from domain shifts. While existing works leveraging LVMs for medical tasks have focused mainly on model-centric approaches like fine-tuning, we study an orthogonal data-centric perspective on how to select good visual prompts to facilitate generalization to medical domain. In this work, we propose a label-efficient in-context medical segmentation method by introducing a novel Meta-driven Visual Prompt Selection mechanism (MVPS), where a prompt retriever obtained from a meta-learning framework actively selects the optimal images as prompts to promote model performance and generalizability. Evaluated on 8 datasets and 4 tasks across 3 medical imaging modalities, our proposed approach demonstrates consistent gains over existing methods under different scenarios, improving both computational and label efficiency. Finally, we show that MVPS is a flexible, finetuning-free module that could be easily plugged into different backbones and combined with other model-centric approaches.

Adam-mini: Use Fewer Learning Rates To Gain More

We propose Adam-mini, an optimizer that achieves on-par or better performance than AdamW with 45% to 50% less memory footprint. Adam-mini reduces memory by cutting down the learning rate resources in Adam (i.e., $1/\sqrt{v}$). We find that $\geq$ 90% of these learning rates in $v$ could be harmlessly removed if we (1) carefully partition the parameters into blocks following our proposed principle on Hessian structure; (2) assign a single but good learning rate to each parameter block. We further find that, for each of these parameter blocks, there exists a single high-quality learning rate that can outperform Adam, provided that sufficient resources are available to search it out. We then provide one cost-effective way to find good learning rates and propose Adam-mini. Empirically, we verify that Adam-mini performs on par or better than AdamW on various language models sized from 125M to 7B for pre-training, supervised fine-tuning, and RLHF. The reduced memory footprint of Adam-mini also alleviates communication overheads among GPUs and CPUs, thereby increasing throughput. For instance, Adam-mini achieves 49.6% higher throughput than AdamW when pre-training Llama2-7B on $2\times$ A800-80GB GPUs, which saves 33% wall-clock time for pre-training.

Analyzing Diversity in Healthcare LLM Research: A Scientometric Perspective

The deployment of large language models (LLMs) in healthcare has demonstrated substantial potential for enhancing clinical decision-making, administrative efficiency, and patient outcomes. However, the underrepresentation of diverse groups in the development and application of these models can perpetuate biases, leading to inequitable healthcare delivery. This paper presents a comprehensive scientometric analysis of LLM research for healthcare, including data from January 1, 2021, to June 16, 2024. By analyzing metadata from PubMed and Dimensions, including author affiliations, countries, and funding sources, we assess the diversity of contributors to LLM research. Our findings highlight significant gender and geographic disparities, with a predominance of male authors and contributions primarily from high-income countries (HICs). We introduce a novel journal diversity index based on Gini impurity to measure the inclusiveness of scientific publications. Our results underscore the necessity for greater representation in order to ensure the equitable application of LLMs in healthcare. We propose actionable strategies to enhance diversity and inclusivity in artificial intelligence research, with the ultimate goal of fostering a more inclusive and equitable future in healthcare innovation.

Multimodal Deep Learning for Low-Resource Settings: A Vector Embedding Alignment Approach for Healthcare Applications

Large-scale multi-modal deep learning models have revolutionized domains such as healthcare, highlighting the importance of computational power. However, in resource-constrained regions like Low and Middle-Income Countries (LMICs), limited access to GPUs and data poses significant challenges, often leaving CPUs as the sole resource. To address this, we advocate for leveraging vector embeddings to enable flexible and efficient computational methodologies, democratizing multimodal deep learning across diverse contexts. Our paper investigates the efficiency and effectiveness of using vector embeddings from single-modal foundation models and multi-modal Vision-Language Models (VLMs) for multimodal deep learning in low-resource environments, particularly in healthcare. Additionally, we propose a simple yet effective inference-time method to enhance performance by aligning image-text embeddings. Comparing these approaches with traditional methods, we assess their impact on computational efficiency and model performance using metrics like accuracy, F1-score, inference time, training time, and memory usage across three medical modalities: BRSET (ophthalmology), HAM10000 (dermatology), and SatelliteBench (public health). Our findings show that embeddings reduce computational demands without compromising model performance. Furthermore, our alignment method improves performance in medical tasks. This research promotes sustainable AI practices by optimizing resources in constrained environments, highlighting the potential of embedding-based approaches for efficient multimodal learning. Vector embeddings democratize multimodal deep learning in LMICs, particularly in healthcare, enhancing AI adaptability in varied use cases.

DF-DM: A foundational process model for multimodal data fusion in the artificial intelligence era

In the big data era, integrating diverse data modalities poses significant challenges, particularly in complex fields like healthcare. This paper introduces a new process model for multimodal Data Fusion for Data Mining, integrating embeddings and the Cross-Industry Standard Process for Data Mining with the existing Data Fusion Information Group model. Our model aims to decrease computational costs, complexity, and bias while improving efficiency and reliability. We also propose "disentangled dense fusion", a novel embedding fusion method designed to optimize mutual information and facilitate dense inter-modality feature interaction, thereby minimizing redundant information. We demonstrate the model's efficacy through three use cases: predicting diabetic retinopathy using retinal images and patient metadata, domestic violence prediction employing satellite imagery, internet, and census data, and identifying clinical and demographic features from radiography images and clinical notes. The model achieved a Macro F1 score of 0.92 in diabetic retinopathy prediction, an R-squared of 0.854 and sMAPE of 24.868 in domestic violence prediction, and a macro AUC of 0.92 and 0.99 for disease prediction and sex classification, respectively, in radiological analysis. These results underscore the Data Fusion for Data Mining model's potential to significantly impact multimodal data processing, promoting its adoption in diverse, resource-constrained settings.

The Role of Linguistic Priors in Measuring Compositional Generalization of Vision-Language Models

Compositionality is a common property in many modalities including natural languages and images, but the compositional generalization of multi-modal models is not well-understood. In this paper, we identify two sources of visual-linguistic compositionality: linguistic priors and the interplay between images and texts. We show that current attempts to improve compositional generalization rely on linguistic priors rather than on information in the image. We also propose a new metric for compositionality without such linguistic priors.

BenchMD: A Benchmark for Modality-Agnostic Learning on Medical Images and Sensors

Medical data poses a daunting challenge for AI algorithms: it exists in many different modalities, experiences frequent distribution shifts, and suffers from a scarcity of examples and labels. Recent advances, including transformers and self-supervised learning, promise a more universal approach that can be applied flexibly across these diverse conditions. To measure and drive progress in this direction, we present BenchMD: a benchmark that tests how modality-agnostic methods, including architectures and training techniques (e.g. self-supervised learning, ImageNet pretraining), perform on a diverse array of clinically-relevant medical tasks. BenchMD combines 19 publicly available datasets for 7 medical modalities, including 1D sensor data, 2D images, and 3D volumetric scans. Our benchmark reflects real-world data constraints by evaluating methods across a range of dataset sizes, including challenging few-shot settings that incentivize the use of pretraining. Finally, we evaluate performance on out-of-distribution data collected at different hospitals than the training data, representing naturally-occurring distribution shifts that frequently degrade the performance of medical AI models. Our baseline results demonstrate that no modality-agnostic technique achieves strong performance across all modalities, leaving ample room for improvement on the benchmark. Code is released at https://github.com/rajpurkarlab/BenchMD .

Hiding Data Helps: On the Benefits of Masking for Sparse Coding

Sparse coding refers to modeling a signal as sparse linear combinations of the elements of a learned dictionary. Sparse coding has proven to be a successful and interpretable approach in many applications, such as signal processing, computer vision, and medical imaging. While this success has spurred much work on sparse coding with provable guarantees, work on the setting where the learned dictionary is larger (or \textit{over-realized}) with respect to the ground truth is comparatively nascent. Existing theoretical results in the over-realized regime are limited to the case of noise-less data. In this paper, we show that for over-realized sparse coding in the presence of noise, minimizing the standard dictionary learning objective can fail to recover the ground-truth dictionary, regardless of the magnitude of the signal in the data-generating process. Furthermore, drawing from the growing body of work on self-supervised learning, we propose a novel masking objective and we prove that minimizing this new objective can recover the ground-truth dictionary. We corroborate our theoretical results with experiments across several parameter regimes, showing that our proposed objective enjoys better empirical performance than the standard reconstruction objective.

Provably Learning Diverse Features in Multi-View Data with Midpoint Mixup

Mixup is a data augmentation technique that relies on training using random convex combinations of data points and their labels. In recent years, Mixup has become a standard primitive used in the training of state-of-the-art image classification models due to its demonstrated benefits over empirical risk minimization with regards to generalization and robustness. In this work, we try to explain some of this success from a feature learning perspective. We focus our attention on classification problems in which each class may have multiple associated features (or views) that can be used to predict the class correctly. Our main theoretical results demonstrate that, for a non-trivial class of data distributions with two features per class, training a 2-layer convolutional network using empirical risk minimization can lead to learning only one feature for almost all classes while training with a specific instantiation of Mixup succeeds in learning both features for every class. We also show empirically that these theoretical insights extend to the practical settings of image benchmarks modified to have additional synthetic features.