Biomedical Visual Instruction Tuning with Clinician Preference Alignment

Recent advancements in multimodal foundation models have showcased impressive capabilities in understanding and reasoning with visual and textual information. Adapting these foundation models trained for general usage to specialized domains like biomedicine requires large-scale domain-specific instruction datasets. While existing works have explored curating such datasets automatically, the resultant datasets are not explicitly aligned with domain expertise. In this work, we propose a data-centric framework, Biomedical Visual Instruction Tuning with Clinician Preference Alignment (BioMed-VITAL), that incorporates clinician preferences into both stages of generating and selecting instruction data for tuning biomedical multimodal foundation models. First, during the generation stage, we prompt the GPT-4V generator with a diverse set of clinician-selected demonstrations for preference-aligned data candidate generation. Then, during the selection phase, we train a separate selection model, which explicitly distills clinician and policy-guided model preferences into a rating function to select high-quality data for medical instruction tuning. Results show that the model tuned with the instruction-following data from our method demonstrates a significant improvement in open visual chat (18.5% relatively) and medical VQA (win rate up to 81.73%). Our instruction-following data and models are available at BioMed-VITAL.github.io.

TACCO: Task-guided Co-clustering of Clinical Concepts and Patient Visits for Disease Subtyping based on EHR Data

The growing availability of well-organized Electronic Health Records (EHR) data has enabled the development of various machine learning models towards disease risk prediction. However, existing risk prediction methods overlook the heterogeneity of complex diseases, failing to model the potential disease subtypes regarding their corresponding patient visits and clinical concept subgroups. In this work, we introduce TACCO, a novel framework that jointly discovers clusters of clinical concepts and patient visits based on a hypergraph modeling of EHR data. Specifically, we develop a novel self-supervised co-clustering framework that can be guided by the risk prediction task of specific diseases. Furthermore, we enhance the hypergraph model of EHR data with textual embeddings and enforce the alignment between the clusters of clinical concepts and patient visits through a contrastive objective. Comprehensive experiments conducted on the public MIMIC-III dataset and Emory internal CRADLE dataset over the downstream clinical tasks of phenotype classification and cardiovascular risk prediction demonstrate an average 31.25% performance improvement compared to traditional ML baselines and a 5.26% improvement on top of the vanilla hypergraph model without our co-clustering mechanism. In-depth model analysis, clustering results analysis, and clinical case studies further validate the improved utilities and insightful interpretations delivered by TACCO. Code is available at https://github.com/PericlesHat/TACCO.

LLMs-based Few-Shot Disease Predictions using EHR: A Novel Approach Combining Predictive Agent Reasoning and Critical Agent Instruction

Electronic health records (EHRs) contain valuable patient data for health-related prediction tasks, such as disease prediction. Traditional approaches rely on supervised learning methods that require large labeled datasets, which can be expensive and challenging to obtain. In this study, we investigate the feasibility of applying Large Language Models (LLMs) to convert structured patient visit data (e.g., diagnoses, labs, prescriptions) into natural language narratives. We evaluate the zero-shot and few-shot performance of LLMs using various EHR-prediction-oriented prompting strategies. Furthermore, we propose a novel approach that utilizes LLM agents with different roles: a predictor agent that makes predictions and generates reasoning processes and a critic agent that analyzes incorrect predictions and provides guidance for improving the reasoning of the predictor agent. Our results demonstrate that with the proposed approach, LLMs can achieve decent few-shot performance compared to traditional supervised learning methods in EHR-based disease predictions, suggesting its potential for health-oriented applications.

Microstructures and Accuracy of Graph Recall by Large Language Models

Graphs data is crucial for many applications, and much of it exists in the relations described in textual format. As a result, being able to accurately recall and encode a graph described in earlier text is a basic yet pivotal ability that LLMs need to demonstrate if they are to perform reasoning tasks that involve graph-structured information. Human performance at graph recall has been studied by cognitive scientists for decades, and has been found to often exhibit certain structural patterns of bias that align with human handling of social relationships. To date, however, we know little about how LLMs behave in analogous graph recall tasks: do their recalled graphs also exhibit certain biased patterns, and if so, how do they compare with humans and affect other graph reasoning tasks? In this work, we perform the first systematical study of graph recall by LLMs, investigating the accuracy and biased microstructures (local structural patterns) in their recall. We find that LLMs not only underperform often in graph recall, but also tend to favor more triangles and alternating 2-paths. Moreover, we find that more advanced LLMs have a striking dependence on the domain that a real-world graph comes from -- by yielding the best recall accuracy when the graph is narrated in a language style consistent with its original domain.

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in \url{https://github.com/ritaranx/ClinGen}.

Open Visual Knowledge Extraction via Relation-Oriented Multimodality Model Prompting

Images contain rich relational knowledge that can help machines understand the world. Existing methods on visual knowledge extraction often rely on the pre-defined format (e.g., sub-verb-obj tuples) or vocabulary (e.g., relation types), restricting the expressiveness of the extracted knowledge. In this work, we take a first exploration to a new paradigm of open visual knowledge extraction. To achieve this, we present OpenVik which consists of an open relational region detector to detect regions potentially containing relational knowledge and a visual knowledge generator that generates format-free knowledge by prompting the large multimodality model with the detected region of interest. We also explore two data enhancement techniques for diversifying the generated format-free visual knowledge. Extensive knowledge quality evaluations highlight the correctness and uniqueness of the extracted open visual knowledge by OpenVik. Moreover, integrating our extracted knowledge across various visual reasoning applications shows consistent improvements, indicating the real-world applicability of OpenVik.

Dynamic Brain Transformer with Multi-level Attention for Functional Brain Network Analysis

Recent neuroimaging studies have highlighted the importance of network-centric brain analysis, particularly with functional magnetic resonance imaging. The emergence of Deep Neural Networks has fostered a substantial interest in predicting clinical outcomes and categorizing individuals based on brain networks. However, the conventional approach involving static brain network analysis offers limited potential in capturing the dynamism of brain function. Although recent studies have attempted to harness dynamic brain networks, their high dimensionality and complexity present substantial challenges. This paper proposes a novel methodology, Dynamic bRAin Transformer (DART), which combines static and dynamic brain networks for more effective and nuanced brain function analysis. Our model uses the static brain network as a baseline, integrating dynamic brain networks to enhance performance against traditional methods. We innovatively employ attention mechanisms, enhancing model explainability and exploiting the dynamic brain network's temporal variations. The proposed approach offers a robust solution to the low signal-to-noise ratio of blood-oxygen-level-dependent signals, a recurring issue in direct DNN modeling. It also provides valuable insights into which brain circuits or dynamic networks contribute more to final predictions. As such, DRAT shows a promising direction in neuroimaging studies, contributing to the comprehensive understanding of brain organization and the role of neural circuits.

A Survey on Knowledge Graphs for Healthcare: Resources, Applications, and Promises

Healthcare knowledge graphs (HKGs) have emerged as a promising tool for organizing medical knowledge in a structured and interpretable way, which provides a comprehensive view of medical concepts and their relationships. However, challenges such as data heterogeneity and limited coverage remain, emphasizing the need for further research in the field of HKGs. This survey paper serves as the first comprehensive overview of HKGs. We summarize the pipeline and key techniques for HKG construction (i.e., from scratch and through integration), as well as the common utilization approaches (i.e., model-free and model-based). To provide researchers with valuable resources, we organize existing HKGs (The resource is available at https://github.com/lujiaying/Awesome-HealthCare-KnowledgeBase) based on the data types they capture and application domains, supplemented with pertinent statistical information. In the application section, we delve into the transformative impact of HKGs across various healthcare domains, spanning from fine-grained basic science research to high-level clinical decision support. Lastly, we shed light on the opportunities for creating comprehensive and accurate HKGs in the era of large language models, presenting the potential to revolutionize healthcare delivery and enhance the interpretability and reliability of clinical prediction.

R-Mixup: Riemannian Mixup for Biological Networks

Biological networks are commonly used in biomedical and healthcare domains to effectively model the structure of complex biological systems with interactions linking biological entities. However, due to their characteristics of high dimensionality and low sample size, directly applying deep learning models on biological networks usually faces severe overfitting. In this work, we propose R-MIXUP, a Mixup-based data augmentation technique that suits the symmetric positive definite (SPD) property of adjacency matrices from biological networks with optimized training efficiency. The interpolation process in R-MIXUP leverages the log-Euclidean distance metrics from the Riemannian manifold, effectively addressing the swelling effect and arbitrarily incorrect label issues of vanilla Mixup. We demonstrate the effectiveness of R-MIXUP with five real-world biological network datasets on both regression and classification tasks. Besides, we derive a commonly ignored necessary condition for identifying the SPD matrices of biological networks and empirically study its influence on the model performance. The code implementation can be found in Appendix E.

PV2TEA: Patching Visual Modality to Textual-Established Information Extraction

Information extraction, e.g., attribute value extraction, has been extensively studied and formulated based only on text. However, many attributes can benefit from image-based extraction, like color, shape, pattern, among others. The visual modality has long been underutilized, mainly due to multimodal annotation difficulty. In this paper, we aim to patch the visual modality to the textual-established attribute information extractor. The cross-modality integration faces several unique challenges: (C1) images and textual descriptions are loosely paired intra-sample and inter-samples; (C2) images usually contain rich backgrounds that can mislead the prediction; (C3) weakly supervised labels from textual-established extractors are biased for multimodal training. We present PV2TEA, an encoder-decoder architecture equipped with three bias reduction schemes: (S1) Augmented label-smoothed contrast to improve the cross-modality alignment for loosely-paired image and text; (S2) Attention-pruning that adaptively distinguishes the visual foreground; (S3) Two-level neighborhood regularization that mitigates the label textual bias via reliability estimation. Empirical results on real-world e-Commerce datasets demonstrate up to 11.74% absolute (20.97% relatively) F1 increase over unimodal baselines.