arXiv subjects

Dongjie Wang

Publications and source records attributed to Dongjie Wang.

At least 19 recordsLinked to original sources

arXiv2026

Import What You Need: Learning When and How to Augment EHR Graphs with External Knowledge

Longitudinal prediction from electronic health records (EHRs) is limited by the sparsity and irregularity in patient trajectories, and knowledge augmentation with external knowledge graphs (KGs) offers a promising way to alleviate these issues. However, KG expansion often follows predefined rules, with limited control over whether and how to augment each visit as a patient's state evolves. We propose ReTA, a Reinforcement learning-based dynamic Topology Augmentation framework that casts KG import as a per-visit, budget-aware policy. ReTA first constructs an offline refined pool of KG-grounded templates, then learns a policy to select one augment action per visit from three options: Soft Import, which enriches node features without modifying graph topology, Hard Import, which grafts a compact KG subgraph onto the visit graph to create message-passing shortcuts, and Skip, which leaves the visit unaugmented when the base encoder is already confident. To stabilize learning, ReTA employs a decoupled encoder that processes semantic and structural signals in separate channels and fuses them via adaptive gating. Experiments on MIMIC-III and MIMIC-IV across diagnosis prediction, mortality, and readmission show that ReTA consistently outperforms strong baselines while remaining efficient, with larger gains under sparse supervision. ReTA transfers across datasets and knowledge graphs and yields interpretable augmentation patterns.

cs.LG↗

arXiv2026

TimesJev: Thinking Fast on Time Series with System 1 Sufficiency

Large language models (LLMs) have recently shown strong potential for time series reasoning, while models that reason over time series are usually with long chains of thought. However, this process often consumes thousands of tokens, directly leading to substantial latency during inference. In contrast, System 1 models such as Jev make decisions instantly and can naturally be an alternative, but raw time series are not compatible with the embedding space of these models, thus hindering the reasoning performance, especially when input series contain thousands of numeric points. In this paper, we make a very early attempt to propose a time series System 1 model, namely TimesJev. Specifically, we first formalize System 1 sufficiency in time series reasoning, which motivates a compressed representation for time series with key frequency patterns preserved. To construct this representation, we derive a dimension reduction objective that combines (i) a sufficiency divergence that measures the core information lost during compression, and (ii) a realizability divergence that quantifies the incompatibility of the System 1 model to the optimal prediction given this representation. We optimize this objective by learning time series compression with a gating mechanism for sufficiency, and then aligning the selected representation with the embedding space for realizability. Finally, experiments on 13 datasets demonstrate that TimesJev outperforms reasoning models by over 62% with 62.9% less inference time than their fine-tuned versions on average.

cs.AI↗

arXiv2026

An Efficient Quantum Spectral-Galerkin Method for Linear Elliptic Equations

This paper presents an efficient quantum spectral-Galerkin method for constant-coefficient second-order linear elliptic equations. The method employs a boundary-adapted Jacobi tensor-product basis that incorporates the boundary condition into the approximation space and produces Galerkin systems with polynomially bounded condition numbers and sparsity. For analytic solutions satisfying a suitable uniform regularity condition, spectral convergence allows the normalized Galerkin coefficient state to be prepared with complexity $\mathrm{poly}(d,\log(1/ε))$, where $d$ is the spatial dimension and $ε$ is the error tolerance, under standard sparse-access and state-preparation assumptions. At the state-preparation level, this improves the precision dependence over fixed-order finite-difference and finite-element discretizations. We further show how to estimate prescribed linear functionals of the solution, with an additional $O(1/ε)$ factor arising from norm and inner-product estimation.

physics.comp-ph↗

arXiv2026

Ozone: A Unified Platform for Transportation Research

Transportation research increasingly depends on heterogeneous data from roadside cameras, UAV imagery, LiDAR, and in-vehicle sensors. Differences in data representations, model interfaces, and evaluation protocols complicate cross-dataset benchmarking and reproducibility. We present Ozone, a unified transportation research platform organized around Hardware, Data, Model, and Evaluation layers, with a Prototype layer supporting deployment-oriented applications. Its data layer links vehicle trajectories, traffic conflicts, reconstructed crashes, and digital-twin maps through a shared trajectory schema. The source inventory spans 19 trajectory datasets recorded at 59 sites in eight countries, with completed converters for 12 sources and adaptation ongoing for seven. The converters align coordinate systems, object classes, oriented bounding boxes, and kinematic fields. A shared implementation of surrogate safety measures supports conflict extraction, while map and motion constraints link crash reports to reconstructed trajectories. CARLA digital-twin maps and SUMO traffic logic connect these records to simulation, model development, and evaluation. Validation on 500 vehicles from four datasets reports mean position, heading, and speed errors below 0.15 m, 2.5°, and 0.3 m/s. A workflow study reports an 85 % reduction in experiment setup time. Case studies demonstrate human-factor experiments and automated-driving safety testing, while the model interfaces support traffic modeling and world-model research. The source code and datasets are publicly available.

cs.DB↗

arXiv2026

When Do LLMs Help with Feature Selection? A Systematic Empirical Study

Large language models (LLMs) can leverage semantic feature names alongside summary statistics for tabular feature selection, yet it remains unclear when such information improves subset selection relative to established statistical methods. We investigate this question within an 18-dataset framework comprising 10 datasets for Group Relative Policy Optimization (GRPO) training, 2 for checkpoint validation, and 6 held-out evaluation datasets. We compare five classical baselines, frozen Qwen2.5-7B and Llama-3.3-70B selectors, and two GRPO-adapted Qwen2.5-7B models, reporting classification ROC-AUC and regression R^2 separately and using dataset-wise ranks for cross-task comparison. Across five seeded evaluation partitions, classical selectors generally achieve higher predictive performance than the tested 7B LLM/RL selectors, including under a pre-specified ~33% feature budget with strict train-only classical fitting, while the 7B selectors retain compact subsets. A cardinality-matched semantic sensitivity experiment shows that, for Zero-shot Qwen-7B, informative feature names improve regression performance over anonymized and shuffled alternatives (+0.1964 and +0.1606 mean R^2), whereas aggregate classification differences are smaller (+0.0159 and +0.0084 ROC-AUC) and dataset-dependent. These results characterize when semantic information benefits LLM-based feature selection and show that classical selectors remain strong baselines for predictive tabular feature selection.

cs.LG↗

arXiv2026

Cite What You Explore: Budget-Aware LLM Reasoning over Medical KGs with Verifiable Evidence

Post-discharge risk prediction from electronic health records (EHRs) is difficult because many dependencies that link discharge-time observations to downstream complications, such as comorbidity cascades and drug-disease interactions, are absent from the record. External medical knowledge graphs (KGs) can supply these missing dependencies, but tracing them demands three properties: KG exploration must remain cost-bounded, retrieved evidence must be differentiated by source quality, and the resulting rationale must be citable for retrospective review. Large language models (LLMs) can plan and verify over structured evidence, making them natural candidates for KG reasoning, but existing LLM-based methods do not satisfy these three properties jointly. In this paper, we propose BAR, a Budget-Aware LLM Reasoning framework over medical KGs with three contributions. First, BAR refines the raw KG into disease-specific evidence graphs whose edges carry support scores and provenance records, turning the KG into a quality-annotated reasoning space rather than a static feature source. Second, an LLM then reasons over this graph through a plan-navigate-verify loop that decomposes the question into steps, retrieves evidence under a patient-specific budget, and revises when verification fails. Third, a reasoning policy is trained with a reward that compares predictions with and without acquired evidence, combined with acquisition cost and citation-integrity terms. Across 8 diseases and 3 prediction horizons on MIMIC-III and MIMIC-IV, BAR improves AUPRC by 3.4 points over the strongest baseline, raises citation precision from 59.8% to 77.9%, and consumes only 62-65% of the budget cap.

cs.LG↗

arXiv2026

RASPER: Reward-Aligned Summarization of Clinical Notes for EHR Outcome Prediction

Unstructured discharge notes in Electronic Health Records (EHRs) often carry signal complementary to structured medical codes, holding patient-specific evidence that standardized cohort-level codes alone cannot capture. However, this evidence in notes is frequently buried in lengthy, noisy text that is not intentionally written with any specific clinical prediction in mind. Summarization is an obvious mitigation, but generic summaries, tuned for fluency rather than the outcome, routinely omit decisive evidence while retaining plausible but uninformative detail. To this end, we propose RASPER, a Reward-Aligned Summarizer for Prediction in EHR, that optimizes note summarization directly against the downstream clinical task. RASPER employs a tunable LLM-based summarizer to extract task-relevant evidence from discharge notes and trains it via reinforcement learning from prediction feedback, using a reward derived from the downstream predictor's loss. To ground the summarizer, a longitudinal encoder converts structured codes into soft prompts that incorporate each patient's clinical context into note summarization. By rewarding the quality of the resulting multimodal prediction, RASPER encourages the summarizer to retain patient-specific evidence that complements, rather than duplicates, information captured by structured codes. RASPER consistently outperforms strong baselines on both readmission prediction and medication recommendation across MIMIC-III and MIMIC-IV.

cs.AI↗

arXiv2026

SoftGene: Protein Language Model-Enhanced Soft Prompting for Interpretable Gene Set Annotation

Gene set analysis is a cornerstone of functional genomics, yet it remains labor-intensive and heavily dependent on manual curation and expert biological interpretation. While Large Language Models (LLMs) have emerged as powerful tools for genomic reasoning and annotation, most existing approaches rely on symbolic gene names and fail to capture domain-specific biological structure, particularly protein sequence information that governs molecular activity, interactions, and downstream gene function. In this work, we propose SoftGene, a novel framework for LLM-based gene set annotation that leverages the hierarchical structure of gene sets. First, we use a hierarchical attention-based encoder built on ESM, a protein language model, to represent each gene set using protein-level amino acid sequence information. Second, we construct a hybrid prompting scheme that combines soft prompts derived from gene set embeddings with hard prompts containing auxiliary context generated by an LLM, and feed the resulting prompt into a local LLM for annotation. We evaluate our framework on two benchmark datasets: Gene Ontology (GO) and the Molecular Signatures Database (MSigDB). Our results show that integrating protein-sequence representations with textual context improves gene set annotation overall, while per-domain analyses reveal that the contribution of protein embeddings varies across biological domains.

cs.AI↗

arXiv2026

City Editing: Hierarchical Agentic Execution for Dependency-Aware Urban Geospatial Modification

Urban renewal requires incremental modifications to existing geospatial plans, yet manually updating complex layouts under spatial constraints is labor-intensive and error-prone. To tackle this, we propose CEAE, a hierarchical agentic framework that formulates urban renewal as machine-executable GeoJSON editing from natural-language instructions. CEAE decomposes instructions into hierarchical geometric intents, executing edits from coarse to fine while preserving spatial consistency through a self-reflective execution-validation loop. Experimental results show that CEAE outperforms baselines in execution validity, robustness, and geometric accuracy.

cs.MA↗

arXiv2026

Hierarchical and Permutation-Invariant Feature Transformation Learning via Policy-Guided Embedding Search

Feature transformation improves predictive performance on tabular data by constructing informative abstractions from raw features. Recent generative approaches encode transformation knowledge into continuous embedding spaces for efficient exploration of candidate strategies, but face three key limitations: (1) overlooking hierarchical relationships between low-level features, operations, and high-level abstractions; (2) enforcing order-sensitive embeddings on inherently permutation-invariant transformation sequences, thereby introducing systematic bias; and (3) relying on gradient-based search, which is ill-suited to non-convex transformation spaces. We propose a framework with two complementary components. First, a permutation-invariant hierarchical module captures interactions across features, operations, and abstraction levels, with a self-attention pooling mechanism that maps semantically equivalent structures to consistent embeddings aligned with downstream performance. Second, a policy-guided multi-objective reinforcement learning strategy initializes the search from empirically strong seeds and jointly optimizes predictive accuracy and transformation efficiency. Extensive experiments on diverse tabular benchmarks demonstrate the effectiveness and robustness of our framework against strong baselines. Our code and data are publicly available at: https://github.com/RayLiu1103/PHER.

cs.LG↗

arXiv2026

REFINE: LLM Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation

Learning rich medical concept representations is essential for EHR prediction. Text-attributed knowledge graphs (TKGs) provide a natural foundation by organizing heterogeneous medical relations together with textual semantics. However, most existing encoders process concepts uniformly across patients, despite the fact that a code's meaning and predictive value depend on patient-specific clinical context and trajectory. Learning patient-personalized concept representations from TKGs introduces two key challenges: (1) deciding how much KG context to incorporate for each observed code, and (2) aligning semantic information with the patient-specific relational structure. We propose REFINE, a KG-aware budgeted LLM graph refinement framework for patient-personalized medical concept encoding. Starting from a global TKG, REFINE constructs patient-specific temporal graphs. A sequential reinforcement learning policy selects a personalized KG expansion budget for each observed code. The resulting patient graph is processed by a heterogeneous GNN to capture relation-aware structural dependencies, while a frozen LLM uses graph-aware soft prompts to semantically refine concept representations. Experiments on MIMIC-III and MIMIC-IV show that REFINE consistently improves diverse EHR backbones, outperforms strong baselines, and demonstrates robust gains across component ablation, KG selection, and data insufficiency.

cs.LG↗

arXiv2026

LEMMA-RCA: A Large Multi-modal Multi-domain Dataset for Root Cause Analysis

Root cause analysis (RCA) is crucial for enhancing the reliability and performance of complex systems. However, progress in this field has been hindered by the lack of large-scale, open-source datasets tailored for RCA. To bridge this gap, we introduce LEMMA-RCA, a large dataset designed for diverse RCA tasks across multiple domains and modalities. LEMMA-RCA features various real-world fault scenarios from Information Technology (IT) and Operational Technology (OT) systems, including microservices, water distribution, and water treatment systems, with hundreds of system entities involved. We evaluate the performance of six baseline methods on LEMMA-RCA across various settings, including offline and online models, as well as single and multi-modal settings. Our study demonstrates the utility of LEMMA-RCA in facilitating fair evaluation and promoting the development of more robust RCA techniques. The dataset is publicly available at https://www.lemmarca.info, with archival metadata and access instructions deposited under DOI: https://doi.org/10.5281/zenodo.20516735.

cs.AI↗

arXiv2026

Iterative Feature Space Optimization through Incremental Adaptive Evaluation

Iterative feature space optimization involves systematically evaluating and adjusting the feature space to improve downstream task performance. However, existing works suffer from three key limitations:1) overlooking differences among data samples leads to evaluation bias; 2) tailoring feature spaces to specific machine learning models results in overfitting and poor generalization; 3) requiring the evaluator to be retrained from scratch during each optimization iteration significantly reduces the overall efficiency of the optimization process. To bridge these gaps, we propose a gEneralized Adaptive feature Space Evaluator (EASE) to efficiently produce optimal and generalized feature spaces. This framework consists of two key components: Feature-Sample Subspace Generator and Contextual Attention Evaluator. The first component aims to decouple the information distribution within the feature space to mitigate evaluation bias. To achieve this, we first identify features most relevant to prediction tasks and samples most challenging for evaluation based on feedback from the subsequent evaluator. This decoupling strategy makes the evaluator consistently target the most challenging aspects of the feature space. The second component intends to incrementally capture evolving patterns of the feature space for efficient evaluation. We propose a weighted-sharing multi-head attention mechanism to encode key characteristics of the feature space into an embedding vector for evaluation. Moreover, the evaluator is updated incrementally, retaining prior evaluation knowledge while incorporating new insights, as consecutive feature spaces during the optimization process share partial information. Extensive experiments on fourteen real-world datasets demonstrate the effectiveness of the proposed framework. Our code and data are publicly available.

cs.LG↗

arXiv2026

PageLLM: A Multi-Grained Reward Framework for Whole-Page Optimization with Large Language Models

Whole-page optimization (WPO) decides how search and recommendation results are surfaced to users, and large language models (LLMs) open a new route to it by treating page generation as sequence generation. Adapting LLMs to web-scale WPO, however, remains bottlenecked by the need for costly human annotations and by the mismatched granularity between page-level coherence and item-level placement. In this work we show that these two challenges are coupled: implicit user feedback alone suffices for alignment, provided the reward signal is decoupled into two complementary granularities. We propose PageLLM, a reward-based fine-tuning framework that (i) turns implicit feedback into four contrastive preference-pair families covering relevance, ranking, diversity, and redundancy, (ii) learns a coarse page-level reward and a fine item-level reward that captures engagement-sensitive position swaps, and (iii) combines both rewards in PPO-based RLHF over a pre-trained LLM. Extensive experiments on seven Amazon categories against eleven baselines show that neither reward alone is sufficient -- dropping the page-level or item-level signal reduces NDCG@100 by 17.8% and 15.2% respectively, whereas the joint reward improves NDCG@100 by up to 46.8%. Deployed in a 10M-user online A/B test, PageLLM raises GMV by 0.44% and click-through rate by 0.14%, confirming that multi-grained rewards from implicit feedback scale to production WPO. Code and data are available at an anonymized repository.

cs.LG↗

arXiv2026

Text-Attributed Knowledge Graph Enrichment with Large Language Models for Medical Concept Representation

In electronic health record (EHR) mining, learning high-quality representations of medical concepts (e.g., standardized diagnosis, medication, and procedure codes) is fundamental for downstream clinical prediction. However, ro bust concept representation learning is hindered by two key challenges: (i) clinically important cross-type dependencies (e.g., diagnosis medication and medication-procedure relations) are often missing or incomplete in existing ontology resources, limiting the ability to model complex EHR patterns; and (ii) rich clinical semantics are often missing from structured resources, and even when available as text, are difficult to integrate with KG structure for representation learning. To address these challenges, we present MedCo, an LLM empowered graph learning framework for medical concept representation. MedCo first builds a global knowledge graph (KG) over medical codes by combining statistically reliable associations mined from EHRs with type-constrained LLM prompting to infer semantic relations. It then utilizes LLMs to enrich the KG into a text-attributed graph by generating node descriptions and edge rationales, providing semantic signals for both concepts and their relationships. Finally, MedCo jointly trains a LoRA-tuned LLaMA text encoder with a heterogeneous GNN, fusing text semantics and graph structure into unified concept embeddings. Extensive experiments on MIMIC-III and MIMIC-IV show that MedCo consistently improves prediction performance and serves as an effective plug-in concept encoder for standard EHR pipelines.

cs.LG↗

arXiv2026

RePrompT: Recurrent Prompt Tuning for Integrating Structured EHR Encoders with Large Language Models

Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured EHRs (e.g., standardized diagnosis and medication codes) presents two key challenges. First, translating time-stamped EHR sequences into plain text can obscure both temporal structure and code identities, weakening the ability to capture code co-occurrence and longitudinal regularities. Second, unlike cohort-trained predictive models that learn a shared, task-aligned representation space across patients, LLMs are often applied in a case-isolated inference setting where each patient is processed independently without leveraging population-level patterns. To address these challenges, we introduce RePrompT, a time-aware LLM framework that integrates structured EHR encoders through prompt tuning, without modifying underlying architectures. Specifically, RePrompT recurrently incorporates latent states from prior visits to preserve longitudinal information, and injects population-level information through trainable prompt tokens derived from a cohort-trained, task-aligned EHR encoder. Experiments on MIMIC-III and MIMIC-IV demonstrate that RePrompT consistently outperforms both EHR-based and LLM-based baselines across multiple clinical prediction tasks.

cs.CL↗

arXiv2026

A Comprehensive Survey on Vector Database: Storage and Retrieval Technique, Challenge

As high-dimensional vector data increasingly surpasses the processing capabilities of traditional database management systems, Vector Databases (VDBs) have emerged and become tightly integrated with large language models, being widely applied in modern artificial intelligence systems. However, existing research has primarily focused on underlying technologies such as approximate nearest neighbor search, with relatively few studies providing a systematic architectural-level review of VDBs or analyzing how these core technologies collectively support the overall capacity of VDBs. This survey aims to offer a comprehensive overview of the core designs and algorithms of VDBs, establishing a holistic understanding of this rapidly evolving field. First, we systematically review the key technologies and design principles of VDBs from the two core dimensions of storage and retrieval, tracing their technological evolution. Next, we conduct an in-depth comparison of several mainstream VDB architectures, summarizing their strengths, limitations, and typical application scenarios. Finally, we explore emerging directions for integrating VDBs with large language models, including open research challenges and trends such as novel indexing strategies. This survey serves as a systematic reference guide for researchers and practitioners, helping readers quickly grasp the technological landscape and development trends in the field of vector databases, and promoting further innovation in both theoretical and applied aspects.

cs.DB↗

arXiv2026

Neural Structure Embedding for Symbolic Regression via Continuous Structure Search and Coefficient Optimization

Symbolic regression aims to discover human-interpretable equations that explain observational data. However, existing approaches rely heavily on discrete structure search (e.g., genetic programming), which often leads to high computational cost, unstable performance, and limited scalability to large equation spaces. To address these challenges, we propose SRCO, a unified embedding-driven framework for symbolic regression that transforms symbolic structures into a continuous, optimizable representation space. The framework consists of three key components: (1) structure embedding: we first generate a large pool of exploratory equations using traditional symbolic regression algorithms and train a Transformer model to compress symbolic structures into a continuous embedding space; (2) continuous structure search: the embedding space enables efficient exploration using gradient-based or sampling-based optimization, significantly reducing the cost of navigating the combinatorial structure space; and (3) coefficient optimization: for each discovered structure, we treat symbolic coefficients as learnable parameters and apply gradient optimization to obtain accurate numerical values. Experiments on synthetic and real-world datasets show that our approach consistently outperforms state-of-the-art methods in equation accuracy, robustness, and search efficiency. This work introduces a new paradigm for symbolic regression by bridging symbolic equation discovery with continuous embedding learning and optimization.

cs.LG↗