Ying Ding

Ajay Jaiswal, Haoyu Ma, Tianlong Chen et al. · meta-ai

Pruning large neural networks to create high-quality, independently trainable sparse masks, which can maintain similar performance to their dense counterparts, is very desirable due to the reduced space and time complexity. As research effort is focused on increasingly sophisticated pruning methods that leads to sparse subnetworks trainable from the scratch, we argue for an orthogonal, under-explored theme: improving training techniques for pruned sub-networks, i.e. sparse training. Apart from the popular belief that only the quality of sparse masks matters for sparse training, in this paper we demonstrate an alternative opportunity: one can carefully customize the sparse training techniques to deviate from the default dense network training protocols, consisting of introducing ``ghost" neurons and skip connections at the early stage of training, and strategically modifying the initialization as well as labels. Our new sparse training recipe is generally applicable to improving training from scratch with various sparse masks. By adopting our newly curated techniques, we demonstrate significant performance gains across various popular datasets (CIFAR-10, CIFAR-100, TinyImageNet), architectures (ResNet-18/32/104, Vgg16, MobileNet), and sparse mask options (lottery ticket, SNIP/GRASP, SynFlow, or even randomly pruning), compared to the default training protocols, especially at high sparsity levels. Code is at https://github.com/VITA-Group/ToST

Ajay Jaiswal, Shiwei Liu, Tianlong Chen et al.

Large pre-trained transformers have been receiving explosive attention in the past few years, due to their wide adaptability for numerous downstream applications via fine-tuning, but their exponentially increasing parameter counts are becoming a primary hurdle to even just fine-tune them without industry-standard hardware. Recently, Lottery Ticket Hypothesis (LTH) and its variants, have been exploited to prune these large pre-trained models generating subnetworks that can achieve similar performance as their dense counterparts, but LTH pragmatism is enormously inhibited by repetitive full training and pruning routine of iterative magnitude pruning (IMP) which worsens with increasing model size. Motivated by the recent observations of model soups, which suggest that fine-tuned weights of multiple models can be merged to a better minima, we propose Instant Soup Pruning (ISP) to generate lottery ticket quality subnetworks, using a fraction of the original IMP cost by replacing the expensive intermediate pruning stages of IMP with computationally efficient weak mask generation and aggregation routine. More specifically, during the mask generation stage, ISP takes a small handful of iterations using varying training protocols and data subsets to generate many weak and noisy subnetworks, and superpose them to average out the noise creating a high-quality denoised subnetwork. Our extensive experiments and ablation on two popular large-scale pre-trained models: CLIP (unexplored in pruning till date) and BERT across multiple benchmark vision and language datasets validate the effectiveness of ISP compared to several state-of-the-art pruning methods. Codes are available at: \url{https://github.com/VITA-Group/instant_soup}

Yan Han, Gregory Holste, Ying Ding et al.

Before the recent success of deep learning methods for automated medical image analysis, practitioners used handcrafted radiomic features to quantitatively describe local patches of medical images. However, extracting discriminative radiomic features relies on accurate pathology localization, which is difficult to acquire in real-world settings. Despite advances in disease classification and localization from chest X-rays, many approaches fail to incorporate clinically-informed domain knowledge. For these reasons, we propose a Radiomics-Guided Transformer (RGT) that fuses \textit{global} image information with \textit{local} knowledge-guided radiomics information to provide accurate cardiopulmonary pathology localization and classification \textit{without any bounding box annotations}. RGT consists of an image Transformer branch, a radiomics Transformer branch, and fusion layers that aggregate image and radiomic information. Using the learned self-attention of its image branch, RGT extracts a bounding box for which to compute radiomic features, which are further processed by the radiomics branch; learned image and radiomic features are then fused and mutually interact via cross-attention layers. Thus, RGT utilizes a novel end-to-end feedback loop that can bootstrap accurate pathology localization only using image-level disease labels. Experiments on the NIH ChestXRay dataset demonstrate that RGT outperforms prior works in weakly supervised disease localization (by an average margin of 3.6\% over various intersection-over-union thresholds) and classification (by 1.1\% in average area under the receiver operating characteristic curve). We publicly release our codes and pre-trained models at \url{https://github.com/VITA-Group/chext}.

Ajay Jaiswal, Peihao Wang, Tianlong Chen et al.

Despite the enormous success of Graph Convolutional Networks (GCNs) in modeling graph-structured data, most of the current GCNs are shallow due to the notoriously challenging problems of over-smoothening and information squashing along with conventional difficulty caused by vanishing gradients and over-fitting. Previous works have been primarily focused on the study of over-smoothening and over-squashing phenomena in training deep GCNs. Surprisingly, in comparison with CNNs/RNNs, very limited attention has been given to understanding how healthy gradient flow can benefit the trainability of deep GCNs. In this paper, firstly, we provide a new perspective of gradient flow to understand the substandard performance of deep GCNs and hypothesize that by facilitating healthy gradient flow, we can significantly improve their trainability, as well as achieve state-of-the-art (SOTA) level performance from vanilla-GCNs. Next, we argue that blindly adopting the Glorot initialization for GCNs is not optimal, and derive a topology-aware isometric initialization scheme for vanilla-GCNs based on the principles of isometry. Additionally, contrary to ad-hoc addition of skip-connections, we propose to use gradient-guided dynamic rewiring of vanilla-GCNs} with skip connections. Our dynamic rewiring method uses the gradient flow within each layer during training to introduce on-demand skip-connections adaptively. We provide extensive empirical evidence across multiple datasets that our methods improve gradient flow in deep vanilla-GCNs and significantly boost their performance to comfortably compete and outperform many fancy state-of-the-art methods. Codes are available at: https://github.com/VITA-Group/GradientGCN.

Song Wang, Mingquan Lin, Ying Ding et al.

Analyzing radiology reports is a time-consuming and error-prone task, which raises the need for an efficient automated radiology report analysis system to alleviate the workloads of radiologists and encourage precise diagnosis. In this work, we present RadText, an open-source radiology text analysis system developed by Python. RadText offers an easy-to-use text analysis pipeline, including de-identification, section segmentation, sentence split and word tokenization, named entity recognition, parsing, and negation detection. RadText features a flexible modular design, provides a hybrid text processing schema, and supports raw text processing and local processing, which enables better usability and improved data privacy. RadText adopts BioC as the unified interface, and also standardizes the input / output into a structured representation compatible with Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). This allows for a more systematic approach to observational research across multiple, disparate data sources. We evaluated RadText on the MIMIC-CXR dataset, with five new disease labels we annotated for this work. RadText demonstrates highly accurate classification performances, with an average precision of, a recall of 0.94, and an F-1 score of 0.92. We have made our code, documentation, examples, and the test set available at https://github.com/bionlplab/radtext .

Ajay Jaiswal, Shiwei Liu, Tianlong Chen et al.

Graphs are omnipresent and GNNs are a powerful family of neural networks for learning over graphs. Despite their popularity, scaling GNNs either by deepening or widening suffers from prevalent issues of unhealthy gradients, over-smoothening, information squashing, which often lead to sub-standard performance. In this work, we are interested in exploring a principled way to scale GNNs capacity without deepening or widening, which can improve its performance across multiple small and large graphs. Motivated by the recent intriguing phenomenon of model soups, which suggest that fine-tuned weights of multiple large-language pre-trained models can be merged to a better minima, we argue to exploit the fundamentals of model soups to mitigate the aforementioned issues of memory bottleneck and trainability during GNNs scaling. More specifically, we propose not to deepen or widen current GNNs, but instead present a data-centric perspective of model soups tailored for GNNs, i.e., to build powerful GNNs. By dividing giant graph data, we build multiple independently and parallelly trained weaker GNNs (soup ingredient) without any intermediate communication, and combine their strength using a greedy interpolation soup procedure to achieve state-of-the-art performance. Compared to concurrent distributed GNN training works such as Jiong et. al. 2023, we train each soup ingredient by sampling different subgraphs per epoch and their respective sub-models are merged only after being fully trained (rather than intermediately so). Moreover, we provide a wide variety of model soup preparation techniques by leveraging state-of-the-art graph sampling and graph partitioning approaches that can handle large graphs. Codes are available at: \url{https://github.com/VITA-Group/graph_ladling}.

Gregory Holste, Ziyu Jiang, Ajay Jaiswal et al.

Pruning has emerged as a powerful technique for compressing deep neural networks, reducing memory usage and inference time without significantly affecting overall performance. However, the nuanced ways in which pruning impacts model behavior are not well understood, particularly for long-tailed, multi-label datasets commonly found in clinical settings. This knowledge gap could have dangerous implications when deploying a pruned model for diagnosis, where unexpected model behavior could impact patient well-being. To fill this gap, we perform the first analysis of pruning's effect on neural networks trained to diagnose thorax diseases from chest X-rays (CXRs). On two large CXR datasets, we examine which diseases are most affected by pruning and characterize class "forgettability" based on disease frequency and co-occurrence behavior. Further, we identify individual CXRs where uncompressed and heavily pruned models disagree, known as pruning-identified exemplars (PIEs), and conduct a human reader study to evaluate their unifying qualities. We find that radiologists perceive PIEs as having more label noise, lower image quality, and higher diagnosis difficulty. This work represents a first step toward understanding the impact of pruning on model behavior in deep long-tailed, multi-label medical image classification. All code, model weights, and data access instructions can be found at https://github.com/VITA-Group/PruneCXR.

Lang Zeng, Jipeng Zhang, Wei Chen et al.

The aim of dynamic prediction is to provide individualized risk predictions over time, which are updated as new data become available. In pursuit of constructing a dynamic prediction model for a progressive eye disorder, age-related macular degeneration (AMD), we propose a time-dependent Cox survival neural network (tdCoxSNN) to predict its progression using longitudinal fundus images. tdCoxSNN builds upon the time-dependent Cox model by utilizing a neural network to capture the non-linear effect of time-dependent covariates on the survival outcome. Moreover, by concurrently integrating a convolutional neural network (CNN) with the survival network, tdCoxSNN can directly take longitudinal images as input. We evaluate and compare our proposed method with joint modeling and landmarking approaches through extensive simulations. We applied the proposed approach to two real datasets. One is a large AMD study, the Age-Related Eye Disease Study (AREDS), in which more than 50,000 fundus images were captured over a period of 12 years for more than 4,000 participants. Another is a public dataset of the primary biliary cirrhosis (PBC) disease, where multiple lab tests were longitudinally collected to predict the time-to-liver transplant. Our approach demonstrates commendable predictive performance in both simulation studies and the analysis of the two real datasets.

Mufan Qiu, Genhui Zheng, Yinuo Xu et al.

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

Ajay Jaiswal, Tianlong Chen, Justin F. Rousseau et al.

Deep neural networks (DNNs) have rapidly become a \textit{de facto} choice for medical image understanding tasks. However, DNNs are notoriously fragile to the class imbalance in image classification. We further point out that such imbalance fragility can be amplified when it comes to more sophisticated tasks such as pathology localization, as imbalances in such problems can have highly complex and often implicit forms of presence. For example, different pathology can have different sizes or colors (w.r.t.the background), different underlying demographic distributions, and in general different difficulty levels to recognize, even in a meticulously curated balanced distribution of training data. In this paper, we propose to use pruning to automatically and adaptively identify \textit{hard-to-learn} (HTL) training samples, and improve pathology localization by attending them explicitly, during training in \textit{supervised, semi-supervised, and weakly-supervised} settings. Our main inspiration is drawn from the recent finding that deep classification models have difficult-to-memorize samples and those may be effectively exposed through network pruning \cite{hooker2019compressed} - and we extend such observation beyond classification for the first time. We also present an interesting demographic analysis which illustrates HTLs ability to capture complex demographic imbalances. Our extensive experiments on the Skin Lesion Localization task in multiple training settings by paying additional attention to HTLs show significant improvement of localization performance by $\sim$2-3\%.

Ajay Jaiswal, Kumar Ashutosh, Justin F Rousseau et al.

AI-powered Medical Imaging has recently achieved enormous attention due to its ability to provide fast-paced healthcare diagnoses. However, it usually suffers from a lack of high-quality datasets due to high annotation cost, inter-observer variability, human annotator error, and errors in computer-generated labels. Deep learning models trained on noisy labelled datasets are sensitive to the noise type and lead to less generalization on the unseen samples. To address this challenge, we propose a Robust Stochastic Knowledge Distillation (RoS-KD) framework which mimics the notion of learning a topic from multiple sources to ensure deterrence in learning noisy information. More specifically, RoS-KD learns a smooth, well-informed, and robust student manifold by distilling knowledge from multiple teachers trained on overlapping subsets of training data. Our extensive experiments on popular medical imaging classification tasks (cardiopulmonary disease and lesion classification) using real-world datasets, show the performance benefit of RoS-KD, its ability to distill knowledge from many popular large networks (ResNet-50, DenseNet-121, MobileNet-V2) in a comparatively small network, and its robustness to adversarial attacks (PGD, FSGM). More specifically, RoS-KD achieves >2% and >4% improvement on F1-score for lesion classification and cardiopulmonary disease classification tasks, respectively, when the underlying student is ResNet-18 against recent competitive knowledge distillation baseline. Additionally, on cardiopulmonary disease classification task, RoS-KD outperforms most of the SOTA baselines by ~1% gain in AUC score.

Li Shi, Redoan Rahman, Esther Melamed et al.

This paper applies eXplainable Artificial Intelligence (XAI) methods to investigate the socioeconomic disparities in COVID patient mortality. An Extreme Gradient Boosting (XGBoost) prediction model is built based on a de-identified Austin area hospital dataset to predict the mortality of COVID-19 patients. We apply two XAI methods, Shapley Additive exPlanations (SHAP) and Locally Interpretable Model Agnostic Explanations (LIME), to compare the global and local interpretation of feature importance. This paper demonstrates the advantages of using XAI which shows the feature importance and decisive capability. Furthermore, we use the XAI methods to cross-validate their interpretations for individual patients. The XAI models reveal that Medicare financial class, older age, and gender have high impact on the mortality prediction. We find that LIME local interpretation does not show significant differences in feature importance comparing to SHAP, which suggests pattern confirmation. This paper demonstrates the importance of XAI methods in cross-validation of feature attributions.

Chao Min, Yi Zhao, Yi Bu et al.

Artificial Intelligence (AI), a cornerstone of 21st-century technology, has seen remarkable growth in China. In this paper, we examine China's AI development process, demonstrating that it is characterized by rapid learning and differentiation, surpassing the export-oriented growth propelled by Foreign Direct Investment seen in earlier Asian industrializers. Our data indicates that China currently leads the USA in the volume of AI-related research papers. However, when we delve into the quality of these papers based on specific metrics, the USA retains a slight edge. Nevertheless, the pace and scale of China's AI development remain noteworthy. We attribute China's accelerated AI progress to several factors, including global trends favoring open access to algorithms and research papers, contributions from China's broad diaspora and returnees, and relatively lax data protection policies. In the vein of our research, we have developed a novel measure for gauging China's imitation of US research. Our analysis shows that by 2018, the time lag between China and the USA in addressing AI research topics had evaporated. This finding suggests that China has effectively bridged a significant knowledge gap and could potentially be setting out on an independent research trajectory. While this study compares China and the USA exclusively, it's important to note that research collaborations between these two nations have resulted in more highly cited work than those produced by either country independently. This underscores the power of international cooperation in driving scientific progress in AI.

Tianhao Li, Sandesh Shetty, Advaith Kamath et al.

Large pre-trained language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology, has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Our proposed few-shot learning approach uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features. Our experiments, which involved seven rare tissues from different cancer types, demonstrated that the LLM-based prediction model achieved significant accuracy with very few or zero samples. Our proposed model, the CancerGPT (with $\sim$ 124M parameters), was even comparable to the larger fine-tuned GPT-3 model (with $\sim$ 175B parameters). Our research is the first to tackle drug pair synergy prediction in rare tissues with limited data. We are also the first to utilize an LLM-based prediction model for biological reaction prediction tasks.

Mingquan Lin, Song Wang, Ying Ding et al.

Background: The predictive Intensive Care Unit (ICU) scoring system plays an important role in ICU management because it predicts important outcomes, especially mortality. Many scoring systems have been developed and used in the ICU. These scoring systems are primarily based on the structured clinical data in the electronic health record (EHR), which may suffer the loss of important clinical information in the narratives and images. Methods: In this work, we build a deep learning based survival prediction model with multi-modality data to predict ICU mortality. Four sets of features are investigated: (1) physiological measurements of Simplified Acute Physiology Score (SAPS) II, (2) common thorax diseases pre-defined by radiologists, (3) BERT-based text representations, and (4) chest X-ray image features. We use the Medical Information Mart for Intensive Care IV (MIMIC-IV) dataset to evaluate the proposed model. Results: Our model achieves the average C-index of 0.7829 (95% confidence interval, 0.7620-0.8038), which substantially exceeds that of the baseline with SAPS-II features (0.7470 (0.7263-0.7676)). Ablation studies further demonstrate the contributions of pre-defined labels (2.00%), text features (2.44%), and image features (2.82%).

Ajay Jaiswal, Nurendra Choudhary, Ravinarayana Adkathimar et al.

Graph Neural Networks (GNNs) have attracted immense attention in the past decade due to their numerous real-world applications built around graph-structured data. On the other hand, Large Language Models (LLMs) with extensive pretrained knowledge and powerful semantic comprehension abilities have recently shown a remarkable ability to benefit applications using vision and text data. In this paper, we investigate how LLMs can be leveraged in a computationally efficient fashion to benefit rich graph-structured data, a modality relatively unexplored in LLM literature. Prior works in this area exploit LLMs to augment every node features in an ad-hoc fashion (not scalable for large graphs), use natural language to describe the complex structural information of graphs, or perform computationally expensive finetuning of LLMs in conjunction with GNNs. We propose E-LLaGNN (Efficient LLMs augmented GNNs), a framework with an on-demand LLM service that enriches message passing procedure of graph learning by enhancing a limited fraction of nodes from the graph. More specifically, E-LLaGNN relies on sampling high-quality neighborhoods using LLMs, followed by on-demand neighborhood feature enhancement using diverse prompts from our prompt catalog, and finally information aggregation using message passing from conventional GNN architectures. We explore several heuristics-based active node selection strategies to limit the computational and memory footprint of LLMs when handling millions of nodes. Through extensive experiments & ablation on popular graph benchmarks of varying scales (Cora, PubMed, ArXiv, & Products), we illustrate the effectiveness of our E-LLaGNN framework and reveal many interesting capabilities such as improved gradient flow in deep GNNs, LLM-free inference ability etc.

Xuan Wang, Zhongling Xu, Gopi Kannedhara et al.

Healthcare models are transitioning from unimodal prediction toward multimodal reasoning over heterogeneous diagnostic inputs. In computational pathology, for complex tumor subtypes where morphology alone can be challenging to distinguish, pathology reports and molecular measurements may provide additional diagnostic evidence alongside whole-slide images, yet existing models often fail to clarify how diverse signals assemble into recognizable diagnostic concepts. We propose ConceptM$^3$oE (Concept Multimodal MoE), which embeds concept formation directly within interaction-aware mixture-of-experts (MoE) pathways. The architecture decomposes evidence into modality-specific, redundant, and synergistic experts, which are then projected into structured concept bottlenecks mapping latent features to a hierarchy of morphology and biomarker concepts. To prevent the information loss typical of interpretable bottlenecks, we utilize residual pathways within each expert to allow task-relevant signals to flow both through the concepts and directly to the final task prediction, so that high performance is maintained alongside interpretability. Across an institutional pediatric brain tumor cohort and a public glioma cohort, the framework delivers competitive performance to unconstrained models while producing reasoning traces validated by an independent neuropathologist. In data-limited regimes, ConceptM$^3$oE improves limited-data performance, increasing macro-F1 from 56.41% to 66.70% at small training sizes compared to non-concept-informed baselines, while also showing faster training convergence consistent with the regularizing effect of concept learning. This work offers a scalable path toward high-performance medical AI that is inherently verifiable and better aligned with the complex decision-making of clinical practice.

Joakim Nguyen, Jian Yu, Jinrui Fang et al.

Accurate diagnosis of pediatric brain tumors, starting with histopathology, presents unique challenges for deep learning, including severe data scarcity, class imbalance, and fine-grained morphologic overlap across diagnostically distinct subtypes. While pathology foundation models have advanced patch-level representation learning, their effective adaptation to weakly supervised pediatric brain tumor classification under limited data remains underexplored. In this work, we introduce an expert-guided contrastive fine-tuning framework for pediatric brain tumor diagnosis from whole-slide images (WSI). Our approach integrates contrastive learning into slide-level multiple instance learning (MIL) to explicitly regularize the geometry of slide-level representations during downstream fine-tuning. We propose both a general supervised contrastive setting and an expert-guided variant that incorporates clinically informed hard negatives targeting diagnostically confusable subtypes. Through comprehensive experiments on pediatric brain tumor WSI classification under realistic low-sample and class-imbalanced conditions, we demonstrate that contrastive fine-tuning yields measurable improvements in fine-grained diagnostic distinctions. Our experimental analyses reveal complementary strengths across different contrastive strategies, with expert-guided hard negatives promoting more compact intra-class representations and improved inter-class separation. This work highlights the importance of explicitly shaping slide-level representations for robust fine-grained classification in data-scarce pediatric pathology settings.

Dawei Li, Shu Yang, Zhen Tan et al.

Recent advancements in large language models (LLMs) have achieved promising performances across various applications. Nonetheless, the ongoing challenge of integrating long-tail knowledge continues to impede the seamless adoption of LLMs in specialized domains. In this work, we introduce DALK, a.k.a. Dynamic Co-Augmentation of LLMs and KG, to address this limitation and demonstrate its ability on studying Alzheimer's Disease (AD), a specialized sub-field in biomedicine and a global health priority. With a synergized framework of LLM and KG mutually enhancing each other, we first leverage LLM to construct an evolving AD-specific knowledge graph (KG) sourced from AD-related scientific literature, and then we utilize a coarse-to-fine sampling method with a novel self-aware knowledge retrieval approach to select appropriate knowledge from the KG to augment LLM inference capabilities. The experimental results, conducted on our constructed AD question answering (ADQA) benchmark, underscore the efficacy of DALK. Additionally, we perform a series of detailed analyses that can offer valuable insights and guidelines for the emerging topic of mutually enhancing KG and LLM. We will release the code and data at https://github.com/David-Li0406/DALK.

Redoan Rahman, Jooyeong Kang, Justin F Rousseau et al.

This paper applies multiple machine learning (ML) algorithms to a dataset of de-identified COVID-19 patients provided by the COVID-19 Research Database. The dataset consists of 20,878 COVID-positive patients, among which 9,177 patients died in the year 2020. This paper aims to understand and interpret the association of socio-economic characteristics of patients with their mortality instead of maximizing prediction accuracy. According to our analysis, a patients households annual and disposable income, age, education, and employment status significantly impacts a machine learning models prediction. We also observe several individual patient data, which gives us insight into how the feature values impact the prediction for that data point. This paper analyzes the global and local interpretation of machine learning models on socio-economic data of COVID patients.

Bernardo Consoli, Xizhi Wu, Song Wang et al.

Extracting social determinants of health (SDoH) from unstructured medical notes depends heavily on labor-intensive annotations, which are typically task-specific, hampering reusability and limiting sharing. In this study we introduced SDoH-GPT, a simple and effective few-shot Large Language Model (LLM) method leveraging contrastive examples and concise instructions to extract SDoH without relying on extensive medical annotations or costly human intervention. It achieved tenfold and twentyfold reductions in time and cost respectively, and superior consistency with human annotators measured by Cohen's kappa of up to 0.92. The innovative combination of SDoH-GPT and XGBoost leverages the strengths of both, ensuring high accuracy and computational efficiency while consistently maintaining 0.90+ AUROC scores. Testing across three distinct datasets has confirmed its robustness and accuracy. This study highlights the potential of leveraging LLMs to revolutionize medical note classification, demonstrating their capability to achieve highly accurate classifications with significantly reduced time and cost.

Lang Zeng, Weijing Tang, Zhao Ren et al.

The stochastic gradient descent (SGD) algorithm has been widely used to optimize deep Cox neural network (Cox-NN) by updating model parameters using mini-batches of data. We show that SGD aims to optimize the average of mini-batch partial-likelihood, which is different from the standard partial-likelihood. This distinction requires developing new statistical properties for the global optimizer, namely, the mini-batch maximum partial-likelihood estimator (mb-MPLE). We establish that mb-MPLE for Cox-NN is consistent and achieves the optimal minimax convergence rate up to a polylogarithmic factor. For Cox regression with linear covariate effects, we further show that mb-MPLE is $\sqrt{n}$-consistent and asymptotically normal with asymptotic variance approaching the information lower bound as batch size increases, which is confirmed by simulation studies. Additionally, we offer practical guidance on using SGD, supported by theoretical analysis and numerical evidence. For Cox-NN, we demonstrate that the ratio of the learning rate to the batch size is critical in SGD dynamics, offering insight into hyperparameter tuning. For Cox regression, we characterize the iterative convergence of SGD, ensuring that the global optimizer, mb-MPLE, can be approximated with sufficiently many iterations. Finally, we demonstrate the effectiveness of mb-MPLE in a large-scale real-world application where the standard MPLE is intractable.

Tianqi Shang, Weiqing He, Tianlong Chen et al.

Social determinants of health (SDoH) play a crucial role in patient health outcomes, yet their integration into biomedical knowledge graphs remains underexplored. This study addresses this gap by constructing an SDoH-enriched knowledge graph using the MIMIC-III dataset and PrimeKG. We introduce a novel fairness formulation for graph embeddings, focusing on invariance with respect to sensitive SDoH information. Via employing a heterogeneous-GCN model for drug-disease link prediction, we detect biases related to various SDoH factors. To mitigate these biases, we propose a post-processing method that strategically reweights edges connected to SDoHs, balancing their influence on graph representations. This approach represents one of the first comprehensive investigations into fairness issues within biomedical knowledge graphs incorporating SDoH. Our work not only highlights the importance of considering SDoH in medical informatics but also provides a concrete method for reducing SDoH-related biases in link prediction tasks, paving the way for more equitable healthcare recommendations. Our code is available at \url{https://github.com/hwq0726/SDoH-KG}.

Muhammad Zain Raza, Jiawei Xu, Terence Lim et al.

Thematic Analysis (TA) is a fundamental method in healthcare research for analyzing transcript data, but it is resource-intensive and difficult to scale for large, complex datasets. This study investigates the potential of large language models (LLMs) to augment the inductive TA process in high-stakes healthcare settings. Focusing on interview transcripts from parents of children with Anomalous Aortic Origin of a Coronary Artery (AAOCA), a rare congenital heart disease, we propose an LLM-Enhanced Thematic Analysis (LLM-TA) pipeline. Our pipeline integrates an affordable state-of-the-art LLM (GPT-4o mini), LangChain, and prompt engineering with chunking techniques to analyze nine detailed transcripts following the inductive TA framework. We evaluate the LLM-generated themes against human-generated results using thematic similarity metrics, LLM-assisted assessments, and expert reviews. Results demonstrate that our pipeline outperforms existing LLM-assisted TA methods significantly. While the pipeline alone has not yet reached human-level quality in inductive TA, it shows great potential to improve scalability, efficiency, and accuracy while reducing analyst workload when working collaboratively with domain experts. We provide practical recommendations for incorporating LLMs into high-stakes TA workflows and emphasize the importance of close collaboration with domain experts to address challenges related to real-world applicability and dataset complexity. https://github.com/jiaweixu98/LLM-TA

Awais Naeem, Tianhao Li, Huang-Ru Liao et al.

Accurate diagnosis and prognosis assisted by pathology images are essential for cancer treatment selection and planning. Despite the recent trend of adopting deep-learning approaches for analyzing complex pathology images, they fall short as they often overlook the domain-expert understanding of tissue structure and cell composition. In this work, we focus on a challenging Open-ended Pathology VQA (PathVQA-Open) task and propose a novel framework named Path-RAG, which leverages HistoCartography to retrieve relevant domain knowledge from pathology images and significantly improves performance on PathVQA-Open. Admitting the complexity of pathology image analysis, Path-RAG adopts a human-centered AI approach by retrieving domain knowledge using HistoCartography to select the relevant patches from pathology images. Our experiments suggest that domain guidance can significantly boost the accuracy of LLaVA-Med from 38% to 47%, with a notable gain of 28% for H&E-stained pathology images in the PathVQA-Open dataset. For longer-form question and answer pairs, our model consistently achieves significant improvements of 32.5% in ARCH-Open PubMed and 30.6% in ARCH-Open Books on H\&E images. Our code and dataset is available here (https://github.com/embedded-robotics/path-rag).

Javad M Alizadeh, Genhui Zheng, Chiu C Tan et al.

People experiencing homelessness (PEH) face substantial barriers to accessing timely, accurate information about community services. DreamKG addresses this through a knowledge graph-augmented conversational system that grounds responses in verified, up-to-date data about Philadelphia organizations, services, locations, and hours. Unlike standard large language models (LLMs) prone to hallucinations, DreamKG combines Neo4j knowledge graphs with structured query understanding to handle location-aware and time-sensitive queries reliably. The system performs spatial reasoning for distance-based recommendations and temporal filtering for operating hours. Preliminary evaluation shows 59% superiority over Google Search AI on relevant queries and 84% rejection of irrelevant queries. This demonstration highlights the potential of hybrid architectures that combines LLM flexibility with knowledge graph reliability to improve service accessibility for vulnerable populations effectively.

Song Wang, Liyan Tang, Mingquan Lin et al.

Radiology report generation aims to produce computer-aided diagnoses to alleviate the workload of radiologists and has drawn increasing attention recently. However, previous deep learning methods tend to neglect the mutual influences between medical findings, which can be the bottleneck that limits the quality of generated reports. In this work, we propose to mine and represent the associations among medical findings in an informative knowledge graph and incorporate this prior knowledge with radiology report generation to help improve the quality of generated reports. Experiment results demonstrate the superior performance of our proposed method on the IU X-ray dataset with a ROUGE-L of 0.384$\pm$0.007 and CIDEr of 0.340$\pm$0.011. Compared with previous works, our model achieves an average of 1.6% improvement (2.0% and 1.5% improvements in CIDEr and ROUGE-L, respectively). The experiments suggest that prior knowledge can bring performance gains to accurate radiology report generation. We will make the code publicly available at https://github.com/bionlplab/report_generation_amia2022.

Yan Han, Chongyan Chen, Liyan Tang et al.

Chest X-ray becomes one of the most common medical diagnoses due to its noninvasiveness. The number of chest X-ray images has skyrocketed, but reading chest X-rays still have been manually performed by radiologists, which creates huge burnouts and delays. Traditionally, radiomics, as a subfield of radiology that can extract a large number of quantitative features from medical images, demonstrates its potential to facilitate medical imaging diagnosis before the deep learning era. In this paper, we develop an end-to-end framework, ChexRadiNet, that can utilize the radiomics features to improve the abnormality classification performance. Specifically, ChexRadiNet first applies a light-weight but efficient triplet-attention mechanism to classify the chest X-rays and highlight the abnormal regions. Then it uses the generated class activation map to extract radiomic features, which further guides our model to learn more robust image features. After a number of iterations and with the help of radiomic features, our framework can converge to more accurate image regions. We evaluate the ChexRadiNet framework using three public datasets: NIH ChestX-ray, CheXpert, and MIMIC-CXR. We find that ChexRadiNet outperforms the state-of-the-art on both disease detection (0.843 in AUC) and localization (0.679 in T(IoU) = 0.1). We will make the code publicly available at https://github.com/bionlplab/lung_disease_detection_amia2021, with the hope that this method can facilitate the development of automatic systems with a higher-level understanding of the radiological world.

Jian Yu, Joakim Nguyen, Jinrui Fang et al.

Accurate classification of pediatric central nervous system tumors remains challenging due to histological complexity and limited training data. While pathology foundation models have advanced whole-slide image (WSI) analysis, they often fail to leverage the rich, complementary information found in clinical text and tissue microarchitecture. To this end, we propose PathMoE, an interpretable multimodal framework that integrates H\&E slides, pathology reports, and nuclei-level cell graphs via an interaction-aware mixture-of-experts architecture built on state-of-the-art foundation models for each modality. By training specialized experts to capture modality uniqueness, redundancy, and synergy, PathMoE employs an input-dependent gating mechanism that dynamically weights these interactions, providing sample-level interpretability. We evaluate our framework on two dataset-specific classification tasks on an internal pediatric brain tumor dataset (PBT) and external TCGA datasets. PathMoE improves macro-F1 from 0.762 to 0.799 (+0.037) on PBT when integrating WSI, text, and graph modalities; on TCGA, augmenting WSI with graph knowledge improves macro-F1 from 0.668 to 0.709 (+0.041). These results demonstrate significant performance gains over state-of-the-art image-only baselines while revealing the specific modality interactions driving individual predictions. This interpretability is particularly critical for rare tumor subtypes, where transparent model reasoning is essential for clinical trust and diagnostic validation.

Chi-Yang Hsu, Kyle Cox, Jiawei Xu et al.

We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a deeper understanding of gene sets, significantly surpassing GSEA by 40.28% and LLM baselines by 5.38% based on cosine similarity to human annotations. Our analysis further provides insights into future directions of biological processes naming, and implications for bioinformatics and precision medicine.

Shrey Pandit, Jiawei Xu, Junyuan Hong et al.

Advancements in Large Language Models (LLMs) and their increasing use in medical question-answering necessitate rigorous evaluation of their reliability. A critical challenge lies in hallucination, where models generate plausible yet factually incorrect outputs. In the medical domain, this poses serious risks to patient safety and clinical decision-making. To address this, we introduce MedHallu, the first benchmark specifically designed for medical hallucination detection. MedHallu comprises 10,000 high-quality question-answer pairs derived from PubMedQA, with hallucinated answers systematically generated through a controlled pipeline. Our experiments show that state-of-the-art LLMs, including GPT-4o, Llama-3.1, and the medically fine-tuned UltraMedical, struggle with this binary hallucination detection task, with the best model achieving an F1 score as low as 0.625 for detecting "hard" category hallucinations. Using bidirectional entailment clustering, we show that harder-to-detect hallucinations are semantically closer to ground truth. Through experiments, we also show incorporating domain-specific knowledge and introducing a "not sure" category as one of the answer categories improves the precision and F1 scores by up to 38% relative to baselines.

Seungjun Yi, Joakim Nguyen, Huimin Xu et al.

Congenital heart disease (CHD) presents complex, lifelong challenges often underrepresented in traditional clinical metrics. While unstructured narratives offer rich insights into patient and caregiver experiences, manual thematic analysis (TA) remains labor-intensive and unscalable. We propose a fully automated large language model (LLM) pipeline that performs end-to-end TA on clinical narratives, which eliminates the need for manual coding or full transcript review. Our system employs a novel multi-agent framework, where specialized LLM agents assume roles to enhance theme quality and alignment with human analysis. To further improve thematic relevance, we optionally integrate reinforcement learning from human feedback (RLHF). This supports scalable, patient-centered analysis of large qualitative datasets and allows LLMs to be fine-tuned for specific clinical contexts.

Francis Tang, Ying Ding

Time series data plays a critical role across diverse domains such as healthcare, energy, and finance, where tasks like classification, anomaly detection, and forecasting are essential for informed decision-making. Recently, large language models (LLMs) have gained prominence for their ability to handle complex data and extract meaningful insights. This study investigates whether LLMs are effective for time series data analysis by comparing their performance with non-LLM-based approaches across three tasks: classification, anomaly detection, and forecasting. Through a series of experiments using GPT4TS and autoregressive models, we evaluate their performance on benchmark datasets and assess their accuracy, precision, and ability to generalize. Our findings indicate that while LLM-based methods excel in specific tasks like anomaly detection, their benefits are less pronounced in others, such as forecasting, where simpler models sometimes perform comparably or better. This research highlights the role of LLMs in time series analysis and lays the groundwork for future studies to systematically explore their applications and limitations in handling temporal data.

Huimin Xu, Seungjun Yi, Terence Lim et al.

Thematic analysis (TA) is a widely used qualitative approach for uncovering latent meanings in unstructured text data. TA provides valuable insights in healthcare but is resource-intensive. Large Language Models (LLMs) have been introduced to perform TA, yet their applications in healthcare remain unexplored. Here, we propose TAMA: A Human-AI Collaborative Thematic Analysis framework using Multi-Agent LLMs for clinical interviews. We leverage the scalability and coherence of multi-agent systems through structured conversations between agents and coordinate the expertise of cardiac experts in TA. Using interview transcripts from parents of children with Anomalous Aortic Origin of a Coronary Artery (AAOCA), a rare congenital heart disease, we demonstrate that TAMA outperforms existing LLM-assisted TA approaches, achieving higher thematic hit rate, coverage, and distinctiveness. TAMA demonstrates strong potential for automated TA in clinical settings by leveraging multi-agent LLM systems with human-in-the-loop integration by enhancing quality while significantly reducing manual workload.

Jinrui Fang, Runhan Chen, Xu Yang et al.

Large language models (LLMs) achieve high accuracy in medical diagnosis when all clinical information is provided in a single turn, yet how they behave under multi-turn evidence accumulation closer to real clinical reasoning remains unexplored. We introduce MINT (Medical Incremental N-Turn Benchmark), a high-fidelity, multi-turn medical diagnosis benchmark comprising 1,035 cases with clinically labeled evidence shards, controlled turn granularity, and information-preserving decomposition. Through systematic evaluation of 11 LLMs on MINT, we uncover three persistent behavioral patterns that significantly impact diagnostic decisions: (1) intent to answer, models rush to answer before sufficient evidence has been observed, with over 55% of answers committed within the first two turns; (2) self-correction, incorrect-to-correct answer revisions occur at up to 10.6 times the rate of correct-to-incorrect flips, revealing a latent capacity for self-correction that premature commitment forecloses; and (3) strong lures, clinically salient information such as laboratory results trigger premature answering even when models are explicitly instructed to wait. We translate these findings into clinically actionable guidance: deferring the diagnostic question to later turns reduces premature answering and improves accuracy at the first point of commitment by up to 62.6%, while reserving salient clinical evidence for later turns prevents a catastrophic accuracy drop of up to 23.3% caused by premature commitment. Our work provides both a controlled evaluation framework and concrete recommendations for improving the reliability of LLMs in multi-turn medical diagnosis.

Kyle Cox, Jiawei Xu, Yikun Han et al.

An interesting behavior in large language models (LLMs) is prompt sensitivity. When provided with different but semantically equivalent versions of the same prompt, models may produce very different distributions of answers. This suggests that the uncertainty reflected in a model's output distribution for one prompt may not reflect the model's uncertainty about the meaning of the prompt. We model prompt sensitivity as a type of generalization error, and show that sampling across the semantic ``concept space'' with paraphrasing perturbations improves uncertainty calibration without compromising accuracy. Additionally, we introduce a new metric for uncertainty decomposition in black-box LLMs that improves upon entropy-based decomposition by modeling semantic continuities in natural language generation. We show that this decomposition metric can be used to quantify how much LLM uncertainty is attributed to prompt sensitivity. Our work introduces a new way to improve uncertainty calibration in prompt-sensitive language models, and provides evidence that some LLMs fail to exhibit consistent general reasoning about the meanings of their inputs.

Seungjun Yi, Joakim Nguyen, Terence Lim et al.

This position paper examines how large language models (LLMs) can support thematic analysis of unstructured clinical transcripts, a widely used but resource-intensive method for uncovering patterns in patient and provider narratives. We conducted a systematic review of recent studies applying LLMs to thematic analysis, complemented by an interview with a practicing clinician. Our findings reveal that current approaches remain fragmented across multiple dimensions including types of thematic analysis, datasets, prompting strategies and models used, most notably in evaluation. Existing evaluation methods vary widely (from qualitative expert review to automatic similarity metrics), hindering progress and preventing meaningful benchmarking across studies. We argue that establishing standardized evaluation practices is critical for advancing the field. To this end, we propose an evaluation framework centered on three dimensions: validity, reliability, and interpretability.

Shrey Pandit, Ashwin Vinod, Liu Leqi et al.

Aligning large language models (LLMs) to accurately detect hallucinations remains a significant challenge due to the sophisticated nature of hallucinated text. Recognizing that hallucinated samples typically exhibit higher deceptive quality than traditional negative samples, we use these carefully engineered hallucinations as negative examples in the DPO alignment procedure. Our method incorporates a curriculum learning strategy, gradually transitioning the training from easier samples, identified based on the greatest reduction in probability scores from independent fact checking models, to progressively harder ones. This structured difficulty scaling ensures stable and incremental learning. Experimental evaluation demonstrates that our HaluCheck models, trained with curriculum DPO approach and high quality negative samples, significantly improves model performance across various metrics, achieving improvements of upto 24% on difficult benchmarks like MedHallu and HaluEval. Additionally, HaluCheck models demonstrate robustness in zero-shot settings, significantly outperforming larger state-of-the-art models across various benchmarks.

Song Wang, Yiliang Zhou, Ziqiang Han et al.

Data accuracy is essential for scientific research and policy development. The National Violent Death Reporting System (NVDRS) data is widely used for discovering the patterns and causes of death. Recent studies suggested the annotation inconsistencies within the NVDRS and the potential impact on erroneous suicide-cause attributions. We present an empirical Natural Language Processing (NLP) approach to detect annotation inconsistencies and adopt a cross-validation-like paradigm to identify problematic instances. We analyzed 267,804 suicide death incidents between 2003 and 2020 from the NVDRS. Our results showed that incorporating the target state's data into training the suicide-crisis classifier brought an increase of 5.4% to the F-1 score on the target state's test set and a decrease of 1.1% on other states' test set. To conclude, we demonstrated the annotation inconsistencies in NVDRS's death investigation notes, identified problematic instances, evaluated the effectiveness of correcting problematic instances, and eventually proposed an NLP improvement solution.

Mingfei Lu, Mengjia Wu, Feng Liu et al.

Memory is critical for enabling large language model (LLM) based agents to maintain coherent behavior over long-horizon interactions. However, existing agent memory systems suffer from two key gaps: they rely on a one-size-fits-all memory structure and do not model memory structure selection as a context-adaptive decision, limiting their ability to handle heterogeneous interaction patterns and resulting in suboptimal performance. We propose a unified framework, FluxMem, that enables adaptive memory organization for LLM agents. Our framework equips agents with multiple complementary memory structures. It explicitly learns to select among these structures based on interaction-level features, using offline supervision derived from downstream response quality and memory utilization. To support robust long-horizon memory evolution, we further introduce a three-level memory hierarchy and a Beta Mixture Model-based probabilistic gate for distribution-aware memory fusion, replacing brittle similarity thresholds. Experiments on two long-horizon benchmarks, PERSONAMEM and LoCoMo, demonstrate that our method achieves average improvements of 9.18% and 6.14%.

Haoling Wang, Lang Zeng, Tao Sun et al.

Predicting time-to-event outcomes when event times are interval censored is challenging because the exact event time is unobserved. Many existing survival analysis approaches for interval-censored data rely on strong model assumptions or cannot handle high-dimensional predictors. We develop ICODEN, an ordinary differential equation-based neural network for interval-censored data that models the hazard function through deep neural networks and obtains the cumulative hazard by solving an ordinary differential equation. ICODEN does not require the proportional hazards assumption or a prespecified parametric form for the hazard function, thereby permitting flexible survival modeling. Across simulation settings with proportional or non-proportional hazards and both linear and nonlinear covariate effects, ICODEN consistently achieves satisfactory predictive accuracy and remains stable as the number of predictors increases. Applications to data from multiple phases of the Alzheimer's Disease Neuroimaging Initiative (ADNI) and to two Age-Related Eye Disease Studies (AREDS and AREDS2) for age-related macular degeneration (AMD) demonstrate ICODEN's robust prediction performance. In both applications, predicting time-to-AD or time-to-late AMD, ICODEN effectively uses hundreds to more than 1,000 SNPs and supports data-driven subgroup identification with differential progression risk profiles. These results establish ICODEN as a practical assumption-lean tool for prediction with interval-censored survival data in high-dimensional biomedical settings.

Deepthi Potluri, Aby Mammen Mathew, Jeffrey B DeWitt et al.

Access to the right evidence does not guarantee that large language models (LLMs) will reason with it correctly. This gap between retrieval and reasoning is especially concerning in clinical settings, where outputs must align with structured protocols. We study this gap using Written Exposure Therapy (WET) guidelines as a testbed. In evaluating model responses to curated clinician-vetted questions, we find that errors persist even when authoritative passages are provided. To address this, we propose an evaluation framework that measures accuracy, consistency, and fidelity of reasoning. Our results highlight both the potential and the risks: retrieval-augmented generation (RAG) can constrain outputs, but safe deployment requires assessing reasoning as rigorously as retrieval.

Philip DiGiacomo, Haoyang Wang, Jinrui Fang et al.

As AI chatbots gain adoption in clinical medicine, developing effective frameworks for complex, emerging diseases presents significant challenges. We developed and evaluated six Retrieval-Augmented Generation (RAG) corpus configurations for Long COVID (LC) clinical question answering, ranging from expert-curated sources to large-scale literature databases. Our evaluation employed an LLM-as-a-judge framework across faithfulness, relevance, and comprehensiveness metrics using LongCOVID-CQ, a novel dataset of expert-generated clinical questions. Our RAG corpus configuration combining clinical guidelines with high-quality systematic reviews consistently outperformed both narrow single-guideline approaches and large-scale literature databases. Our findings suggest that for emerging diseases, retrieval grounded in curated secondary reviews provides an optimal balance between narrow consensus documents and unfiltered primary literature, supporting clinical decision-making while avoiding information overload and oversimplified guidance. We propose Guide-RAG, a chatbot system and accompanying evaluation framework that integrates both curated expert knowledge and comprehensive literature databases to effectively answer LC clinical questions.

Seungjun Yi, Joakim Nguyen, Huimin Xu et al.

Thematic Analysis (TA) is a widely used qualitative method that provides a structured yet flexible framework for identifying and reporting patterns in clinical interview transcripts. However, manual thematic analysis is time-consuming and limits scalability. Recent advances in LLMs offer a pathway to automate thematic analysis, but alignment with human results remains limited. To address these limitations, we propose SFT-TA, an automated thematic analysis framework that embeds supervised fine-tuned (SFT) agents within a multi-agent system. Our framework outperforms existing frameworks and the gpt-4o baseline in alignment with human reference themes. We observed that SFT agents alone may underperform, but achieve better results than the baseline when embedded within a multi-agent system. Our results highlight that embedding SFT agents in specific roles within a multi-agent system is a promising pathway to improve alignment with desired outputs for thematic analysis.

Song Wang, Yishu Wei, Haotian Ma et al.

Background: Understanding social determinants of health (SDoH) factors contributing to suicide incidents is crucial for early intervention and prevention. However, data-driven approaches to this goal face challenges such as long-tailed factor distributions, analyzing pivotal stressors preceding suicide incidents, and limited model explainability. Methods: We present a multi-stage large language model framework to enhance SDoH factor extraction from unstructured text. Our approach was compared to other state-of-the-art language models (i.e., pre-trained BioBERT and GPT-3.5-turbo) and reasoning models (i.e., DeepSeek-R1). We also evaluated how the model's explanations help people annotate SDoH factors more quickly and accurately. The analysis included both automated comparisons and a pilot user study. Results: We show that our proposed framework demonstrated performance boosts in the overarching task of extracting SDoH factors and in the finer-grained tasks of retrieving relevant context. Additionally, we show that fine-tuning a smaller, task-specific model achieves comparable or better performance with reduced inference costs. The multi-stage design not only enhances extraction but also provides intermediate explanations, improving model explainability. Conclusions: Our approach improves both the accuracy and transparency of extracting suicide-related SDoH from unstructured texts. These advancements have the potential to support early identification of individuals at risk and inform more effective prevention strategies.

Jiawei Xu, Yonggeon Lee, Anthony Elkommos Youssef et al.

This study addresses the challenge of predicting post-stroke rigidity by emphasizing feature interactions through graph-based explainable AI. Post-stroke rigidity, characterized by increased muscle tone and stiffness, significantly affects survivors' mobility and quality of life. Despite its prevalence, early prediction remains limited, delaying intervention. We analyze 519K stroke hospitalization records from the Healthcare Cost and Utilization Project dataset, where 43% of patients exhibited rigidity. We compare traditional approaches such as Logistic Regression, XGBoost, and Transformer with graph-based models like Graphormer and Graph Attention Network. These graph models inherently capture feature interactions and incorporate intrinsic or post-hoc explainability. Our results show that graph-based methods outperform others (AUROC 0.75), identifying key predictors such as NIH Stroke Scale and APR-DRG mortality risk scores. They also uncover interactions missed by conventional models. This research provides a novel application of graph-based XAI in stroke prognosis, with potential to guide early identification and personalized rehabilitation strategies.

Jinhao Duan, Xinyu Zhao, Zhuoxuan Zhang et al.

Although Large Language Models (LLMs) succeed in human-guided conversations such as instruction following and question answering, the potential of LLM-guided conversations-where LLMs direct the discourse and steer the conversation's objectives-remains under-explored. In this study, we first characterize LLM-guided conversation into three fundamental components: (i) Goal Navigation; (ii) Context Management; (iii) Empathetic Engagement, and propose GuideLLM as an installation. We then implement an interviewing environment for the evaluation of LLM-guided conversation. Specifically, various topics are involved in this environment for comprehensive interviewing evaluation, resulting in around 1.4k turns of utterances, 184k tokens, and over 200 events mentioned during the interviewing for each chatbot evaluation. We compare GuideLLM with 6 state-of-the-art LLMs such as GPT-4o and Llama-3-70b-Instruct, from the perspective of interviewing quality, and autobiography generation quality. For automatic evaluation, we derive user proxies from multiple autobiographies and employ LLM-as-a-judge to score LLM behaviors. We further conduct a human-involved experiment by employing 45 human participants to chat with GuideLLM and baselines. We then collect human feedback, preferences, and ratings regarding the qualities of conversation and autobiography. Experimental results indicate that GuideLLM significantly outperforms baseline LLMs in automatic evaluation and achieves consistent leading performances in human ratings.

Junyi Chen, Mengjia Wu, Qian Liu et al.

The degraded performance and group unfairness caused by confounding sensitive attributes in rumor detection remains relatively unexplored. To address this, we propose a two-step framework. Initially, it identifies confounding sensitive attributes that limit rumor detection performance and cause unfairness across groups. Subsequently, we aim to learn equally informative representations through invariant learning. Our method considers diverse sets of groups without sensitive attribute annotations. Experiments show our method easily integrates with existing rumor detectors, significantly improving both their detection performance and fairness.

Zhuoyi Shang, Yanwei Liu, Jinxia Liu et al.

For general users, training a neural network from scratch is usually challenging and labor-intensive. Fortunately, neural network zoos enable them to find a well-performing model for directly use or fine-tuning it in their local environments. Although current model retrieval solutions attempt to convert neural network models into vectors to avoid complex multiple inference processes required for model selection, it is still difficult to choose a suitable model due to inaccurate vectorization and biased correlation alignment between the query dataset and models. From the perspective of knowledge consistency, i.e., whether the knowledge possessed by the model can meet the needs of query tasks, we propose a model retrieval scheme, named Know2Vec, that acts as a black-box retrieval proxy for model zoo. Know2Vec first accesses to models via a black-box interface in advance, capturing vital decision knowledge from models while ensuring their privacy. Next, it employs an effective encoding technique to transform the knowledge into precise model vectors. Secondly, it maps the user's query task to a knowledge vector by probing the semantic relationships within query samples. Furthermore, the proxy ensures the knowledge-consistency between query vector and model vectors within their alignment space, which is optimized through the supervised learning with diverse loss functions, and finally it can identify the most suitable model for a given task during the inference stage. Extensive experiments show that our Know2Vec achieves superior retrieval accuracy against the state-of-the-art methods in diverse neural network retrieval tasks.

Mingquan Lin, Tianhao Li, Zhaoyi Sun et al.

Purpose: Limited studies exploring concrete methods or approaches to tackle and enhance model fairness in the radiology domain. Our proposed AI model utilizes supervised contrastive learning to minimize bias in CXR diagnosis. Materials and Methods: In this retrospective study, we evaluated our proposed method on two datasets: the Medical Imaging and Data Resource Center (MIDRC) dataset with 77,887 CXR images from 27,796 patients collected as of April 20, 2023 for COVID-19 diagnosis, and the NIH Chest X-ray (NIH-CXR) dataset with 112,120 CXR images from 30,805 patients collected between 1992 and 2015. In the NIH-CXR dataset, thoracic abnormalities include atelectasis, cardiomegaly, effusion, infiltration, mass, nodule, pneumonia, pneumothorax, consolidation, edema, emphysema, fibrosis, pleural thickening, or hernia. Our proposed method utilizes supervised contrastive learning with carefully selected positive and negative samples to generate fair image embeddings, which are fine-tuned for subsequent tasks to reduce bias in chest X-ray (CXR) diagnosis. We evaluated the methods using the marginal AUC difference ($δ$ mAUC). Results: The proposed model showed a significant decrease in bias across all subgroups when compared to the baseline models, as evidenced by a paired T-test (p<0.0001). The $δ$ mAUC obtained by our method were 0.0116 (95\% CI, 0.0110-0.0123), 0.2102 (95% CI, 0.2087-0.2118), and 0.1000 (95\% CI, 0.0988-0.1011) for sex, race, and age on MIDRC, and 0.0090 (95\% CI, 0.0082-0.0097) for sex and 0.0512 (95% CI, 0.0512-0.0532) for age on NIH-CXR, respectively. Conclusion: Employing supervised contrastive learning can mitigate bias in CXR diagnosis, addressing concerns of fairness and reliability in deep learning-based diagnostic methods.