arXiv subjects

Joyce C. Ho

Publications and source records attributed to Joyce C. Ho.

At least 19 recordsLinked to original sources

arXiv2026

How Fine-Grained Should a RAG Benchmark Be? A Hierarchical Framework for Synthetic Question Generation

Evaluating retrieval-augmented generation (RAG) systems requires benchmarks that capture diverse question characteristics, yet practitioners lack empirical guidance on which dimensions to vary and at what granularity. We present HieraRAG, a hierarchical framework for studying granularity in RAG benchmark construction, defining optimal granularity as the level that maximizes discriminative power (the standard deviation of generation quality across categories) within a given RAG configuration. As a case study, we generate 5,872 synthetic question-answer (QA) pairs from FineWeb-10BT across 3 dimensions (Question Complexity, Answer Type, Linguistic Variation) at 3 granularity levels (2, 4, and 8 categories). With a BM25+Falcon-3-10B pipeline, optimal granularity varies by dimension: complexity benefits from fine-grained distinctions (discriminative power: 0.053) while answer type and linguistic variation peak at medium granularity. We introduce a Coherence Ratio metric to quantify whether fine-grained splits cleanly subdivide parent categories, revealing structural differences across dimensions (Question Complexity: 0.40 vs. Answer Type: 1.44). Human evaluation of 110 stratified QA pairs confirms synthetic quality. While these specific findings reflect a single configuration, HieraRAG provides a portable procedure and validation metric for practitioners to determine evaluation granularity within their own RAG settings.

cs.CL↗

arXiv2026

Anatomy of a Query: W5H Dimensions and FAR Patterns for Text-to-SQL Evaluation

Natural language interfaces to databases have gained popularity, yet the theoretical foundations for evaluating and designing these systems remain underdeveloped. We present QUEST (Query Understanding Evaluation through Semantic Translation), a framework resting on two independently motivated components: the FAR structural invariant, which holds that every well-formed query reduces to Filter, Aggregate, and Return operations; and the W5H dimensional framework, which holds that all filtering criteria map to six semantic dimensions (Who, What, Where, When, Why, and How). Validated across five text-to-SQL datasets (n = 120,464), FAR conformance is universal across all domains and schema types, while W5H dimensional profiles vary substantially. Healthcare queries are strongly concentrated in temporal (WHEN: 80.4%) and person-centric (WHO: 73.0%) dimensions far exceeding general-domain benchmarks, and causal (WHY) and mechanistic (HOW) reasoning are near-zero everywhere, with apparent HOW exceptions reflecting quantitative aggregation rather than genuine procedural reasoning. These results identify a frontier that must be crossed for genuine machine reasoning over structured data.

cs.DB↗

arXiv2025

FusionDP: Foundation Model-Assisted Differentially Private Learning for Partially Sensitive Features

Ensuring the privacy of sensitive training data is crucial in privacy-preserving machine learning. However, in practical scenarios, privacy protection may be required for only a subset of features. For instance, in ICU data, demographic attributes like age and gender pose higher privacy risks due to their re-identification potential, whereas raw lab results are generally less sensitive. Traditional DP-SGD enforces privacy protection on all features in one sample, leading to excessive noise injection and significant utility degradation. We propose FusionDP, a two-step framework that enhances model utility under feature-level differential privacy. First, FusionDP leverages large foundation models to impute sensitive features given non-sensitive features, treating them as external priors that provide high-quality estimates of sensitive attributes without accessing the true values during model training. Second, we introduce a modified DP-SGD algorithm that trains models on both original and imputed features while formally preserving the privacy of the original sensitive features. We evaluate FusionDP on two modalities: a sepsis prediction task on tabular data from PhysioNet and a clinical note classification task from MIMIC-III. By comparing against privacy-preserving baselines, our results show that FusionDP significantly improves model performance while maintaining rigorous feature-level privacy, demonstrating the potential of foundation model-driven imputation to enhance the privacy-utility trade-off for various modalities.

cs.LG↗

arXiv2025

Retrieval-augmented GUI Agents with Generative Guidelines

GUI agents powered by vision-language models (VLMs) show promise in automating complex digital tasks. However, their effectiveness in real-world applications is often limited by scarce training data and the inherent complexity of these tasks, which frequently require long-tailed knowledge covering rare, unseen scenarios. We propose RAG-GUI , a lightweight VLM that leverages web tutorials at inference time. RAG-GUI is first warm-started via supervised finetuning (SFT) and further refined through self-guided rejection sampling finetuning (RSF). Designed to be model-agnostic, RAG-GUI functions as a generic plug-in that enhances any VLM-based agent. Evaluated across three distinct tasks, it consistently outperforms baseline agents and surpasses other inference baselines by 2.6% to 13.3% across two model sizes, demonstrating strong generalization and practical plug-and-play capabilities in real-world scenarios.

cs.CL↗

arXiv2025

AceSearcher: Bootstrapping Reasoning and Search for LLMs via Reinforced Self-Play

Search-augmented LLMs often struggle with complex reasoning tasks due to ineffective multi-hop retrieval and limited reasoning ability. We propose AceSearcher, a cooperative self-play framework that trains a single large language model (LLM) to alternate between two roles: a decomposer that breaks down complex queries and a solver that integrates retrieved contexts for answer generation. AceSearcher couples supervised fine-tuning on a diverse mixture of search, reasoning, and decomposition tasks with reinforcement fine-tuning optimized for final answer accuracy, eliminating the need for intermediate annotations. Extensive experiments on three reasoning-intensive tasks across 10 datasets show that AceSearcher outperforms state-of-the-art baselines, achieving an average exact match improvement of 7.6%. Remarkably, on document-level finance reasoning tasks, AceSearcher-32B matches the performance of the DeepSeek-V3 model using less than 5% of its parameters. Even at smaller scales (1.5B and 8B), AceSearcher often surpasses existing search-augmented LLMs with up to 9x more parameters, highlighting its exceptional efficiency and effectiveness in tackling complex reasoning tasks. Our code will be published at https://github.com/ritaranx/AceSearcher and https://huggingface.co/AceSearcher.

cs.CL↗

arXiv2025

Collab-RAG: Boosting Retrieval-Augmented Generation for Complex Question Answering via White-Box and Black-Box LLM Collaboration

Retrieval-Augmented Generation (RAG) systems often struggle to handle multi-hop question-answering tasks accurately due to irrelevant context retrieval and limited complex reasoning capabilities. We introduce Collab-RAG, a collaborative training framework that leverages mutual enhancement between a white-box small language model (SLM) and a blackbox large language model (LLM) for RAG. Specifically, the SLM decomposes complex queries into simpler sub-questions, thus enhancing the accuracy of the retrieval and facilitating more effective reasoning by the black-box LLM. Concurrently, the black-box LLM provides feedback signals to improve the SLM's decomposition capability. We observe that Collab-RAG relies solely on supervision from an affordable black-box LLM without additional distillation from frontier LLMs, yet demonstrates strong generalization across multiple black-box LLMs. Experimental evaluations across five multi-hop QA datasets demonstrate that Collab-RAG substantially outperforms existing black-box-only and SLM fine-tuning baselines by 1.8%-14.2% on average. In particular, our fine-tuned 3B SLM surpasses a frozen 32B LLM in question decomposition, highlighting the efficiency of Collab-RAG in improving reasoning and retrieval for complex questions. The code of Collab-RAG is available on https://github.com/ritaranx/Collab-RAG/.

cs.CL↗

arXiv2025

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

This comprehensive review aims to provide an overview of the current state of Healthcare Knowledge Graphs (HKGs), including their construction, utilization models, and applications across various healthcare and biomedical research domains. We thoroughly analyzed existing literature on HKGs, covering their construction methodologies, utilization techniques, and applications in basic science research, pharmaceutical research and development, clinical decision support, and public health. The review encompasses both model-free and model-based utilization approaches and the integration of HKGs with large language models (LLMs). We searched Google Scholar for relevant papers on HKGs and classified them into the following topics: HKG construction, HKG utilization, and their downstream applications in various domains. We also discussed their special challenges and the promise for future work. The review highlights the potential of HKGs to significantly impact biomedical research and clinical practice by integrating vast amounts of biomedical knowledge from multiple domains. The synergy between HKGs and LLMs offers promising opportunities for constructing more comprehensive knowledge graphs and improving the accuracy of healthcare applications. HKGs have emerged as a powerful tool for structuring medical knowledge, with broad applications across biomedical research, clinical decision-making, and public health. This survey serves as a roadmap for future research and development in the field of HKGs, highlighting the potential of combining knowledge graphs with advanced machine learning models for healthcare transformation.

cs.AI↗

arXiv2025

SimRAG: Self-Improving Retrieval-Augmented Generation for Adapting Large Language Models to Specialized Domains

Retrieval-augmented generation (RAG) enhances the question-answering (QA) abilities of large language models (LLMs) by integrating external knowledge. However, adapting general-purpose RAG systems to specialized fields such as science and medicine poses unique challenges due to distribution shifts and limited access to domain-specific data. To tackle this, we propose SimRAG, a self-training approach that equips the LLM with joint capabilities of question answering and question generation for domain adaptation. Our method first fine-tunes the LLM on instruction-following, question-answering, and search-related data. Then, it prompts the same LLM to generate diverse domain-relevant questions from unlabeled corpora, with an additional filtering strategy to retain high-quality synthetic examples. By leveraging these self-generated synthetic examples, the LLM can improve their performance on domain-specific RAG tasks. Experiments on 11 datasets, spanning two backbone sizes and three domains, demonstrate that SimRAG outperforms baselines by 1.2\%--8.6\%.

cs.CL↗

arXiv2024

Is thermography a viable solution for detecting pressure injuries in dark skin patients?

Pressure injury (PI) detection is challenging, especially in dark skin tones, due to the unreliability of visual inspection. Thermography has been suggested as a viable alternative as temperature differences in the skin can indicate impending tissue damage. Although deep learning models have demonstrated considerable promise toward reliably detecting PI, the existing work fails to evaluate the performance on darker skin tones and varying data collection protocols. In this paper, we introduce a new thermal and optical imaging dataset of 35 participants focused on darker skin tones where temperature differences are induced through cooling and cupping protocols. We vary the image collection process to include different cameras, lighting, patient pose, and camera distance. We compare the performance of a small convolutional neural network (CNN) trained on either the thermal or the optical images on all skin tones. Our preliminary results suggest that thermography-based CNN is robust to data collection protocols for all skin tones.

cs.CV↗

arXiv2024

BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers

Developing effective biomedical retrieval models is important for excelling at knowledge-intensive biomedical tasks but still challenging due to the deficiency of sufficient publicly annotated biomedical data and computational resources. We present BMRetriever, a series of dense retrievers for enhancing biomedical retrieval via unsupervised pre-training on large biomedical corpora, followed by instruction fine-tuning on a combination of labeled datasets and synthetic pairs. Experiments on 5 biomedical tasks across 11 datasets verify BMRetriever's efficacy on various biomedical applications. BMRetriever also exhibits strong parameter efficiency, with the 410M variant outperforming baselines up to 11.7 times larger, and the 2B variant matching the performance of models with over 5B parameters. The training data and model checkpoints are released at \url{https://huggingface.co/BMRetriever} to ensure transparency, reproducibility, and application to new domains.

cs.CL↗

arXiv2024

RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records

We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks. The code will be published at \url{https://github.com/ritaranx/RAM-EHR}.

cs.CL↗

arXiv2024

Large Language Models for Integrating Social Determinant of Health Data: A Case Study on Heart Failure 30-Day Readmission Prediction

Social determinants of health (SDOH) $-$ the myriad of circumstances in which people live, grow, and age $-$ play an important role in health outcomes. However, existing outcome prediction models often only use proxies of SDOH as features. Recent open data initiatives present an opportunity to construct a more comprehensive view of SDOH, but manually integrating the most relevant data for individual patients becomes increasingly challenging as the volume and diversity of public SDOH data grows. Large language models (LLMs) have shown promise at automatically annotating structured data. Here, we conduct an end-to-end case study evaluating the feasibility of using LLMs to integrate SDOH data, and the utility of these SDOH features for clinical prediction. We first manually label 700+ variables from two publicly-accessible SDOH data sources to one of five semantic SDOH categories. Then, we benchmark performance of 9 open-source LLMs on this classification task. Finally, we train ML models to predict 30-day hospital readmission among 39k heart failure (HF) patients, and we compare the prediction performance of the categorized SDOH variables with standard clinical variables. Additionally, we investigate the impact of few-shot LLM prompting on LLM annotation performance, and perform a metadata ablation study on prompts to evaluate which information helps LLMs accurately annotate these variables. We find that some open-source LLMs can effectively, accurately annotate SDOH variables with zero-shot prompting without the need for fine-tuning. Crucially, when combined with standard clinical features, the LLM-annotated Neighborhood and Built Environment subset of the SDOH variables shows the best performance predicting 30-day readmission of HF patients.

cs.CL↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

cs.CL↗

arXiv2024

Multimodal Fusion of EHR in Structures and Semantics: Integrating Clinical Records and Notes with Hypergraph and LLM

Electronic Health Records (EHRs) have become increasingly popular to support clinical decision-making and healthcare in recent decades. EHRs usually contain heterogeneous information, such as structural data in tabular form and unstructured data in textual notes. Different types of information in EHRs can complement each other and provide a more complete picture of the health status of a patient. While there has been a lot of research on representation learning of structured EHR data, the fusion of different types of EHR data (multimodal fusion) is not well studied. This is mostly because of the complex medical coding systems used and the noise and redundancy present in the written notes. In this work, we propose a new framework called MINGLE, which integrates both structures and semantics in EHR effectively. Our framework uses a two-level infusion strategy to combine medical concept semantics and clinical note semantics into hypergraph neural networks, which learn the complex interactions between different types of data to generate visit representations for downstream prediction. Experiment results on two EHR datasets, the public MIMIC-III and private CRADLE, show that MINGLE can effectively improve predictive performance by 11.83% relatively, enhancing semantic integration as well as multimodal fusion for structural and textual EHR data.

cs.LG↗

arXiv2023

A Deep Reinforcement Learning Approach for Interactive Search with Sentence-level Feedback

Interactive search can provide a better experience by incorporating interaction feedback from the users. This can significantly improve search accuracy as it helps avoid irrelevant information and captures the users' search intents. Existing state-of-the-art (SOTA) systems use reinforcement learning (RL) models to incorporate the interactions but focus on item-level feedback, ignoring the fine-grained information found in sentence-level feedback. Yet such feedback requires extensive RL action space exploration and large amounts of annotated data. This work addresses these challenges by proposing a new deep Q-learning (DQ) approach, DQrank. DQrank adapts BERT-based models, the SOTA in natural language processing, to select crucial sentences based on users' engagement and rank the items to obtain more satisfactory responses. We also propose two mechanisms to better explore optimal actions. DQrank further utilizes the experience replay mechanism in DQ to store the feedback sentences to obtain a better initial ranking performance. We validate the effectiveness of DQrank on three search datasets. The results show that DQRank performs at least 12% better than the previous SOTA RL approaches. We also conduct detailed ablation studies. The ablation results demonstrate that each model component can efficiently extract and accumulate long-term engagement effects from the users' sentence-level feedback. This structure offers new technologies with promised performance to construct a search system with sentence-level interaction.

cs.LG↗

arXiv2023

Weakly-Supervised Scientific Document Classification via Retrieval-Augmented Multi-Stage Training

Scientific document classification is a critical task for a wide range of applications, but the cost of obtaining massive amounts of human-labeled data can be prohibitive. To address this challenge, we propose a weakly-supervised approach for scientific document classification using label names only. In scientific domains, label names often include domain-specific concepts that may not appear in the document corpus, making it difficult to match labels and documents precisely. To tackle this issue, we propose WANDER, which leverages dense retrieval to perform matching in the embedding space to capture the semantics of label names. We further design the label name expansion module to enrich the label name representations. Lastly, a self-training step is used to refine the predictions. The experiments on three datasets show that WANDER outperforms the best baseline by 11.9% on average. Our code will be published at https://github.com/ritaranx/wander.

cs.CL↗

arXiv2022

Communication Efficient Generalized Tensor Factorization for Decentralized Healthcare Networks

Tensor factorization has been proved as an efficient unsupervised learning approach for health data analysis, especially for computational phenotyping, where the high-dimensional Electronic Health Records (EHRs) with patients' history of medical procedures, medications, diagnosis, lab tests, etc., are converted to meaningful and interpretable medical concepts. Federated tensor factorization distributes the tensor computation to multiple workers under the coordination of a central server, which enables jointly learning the phenotypes across multiple hospitals while preserving the privacy of the patient information. However, existing federated tensor factorization algorithms encounter the single-point-failure issue with the involvement of the central server, which is not only easily exposed to external attacks but also limits the number of clients sharing information with the server under restricted uplink bandwidth. In this paper, we propose CiderTF, a communication-efficient decentralized generalized tensor factorization, which reduces the uplink communication cost by leveraging a four-level communication reduction strategy designed for a generalized tensor factorization, which has the flexibility of modeling different tensor distribution with multiple kinds of loss functions. Experiments on two real-world EHR datasets demonstrate that CiderTF achieves comparable convergence with a communication reduction up to 99.99%.

cs.LG↗