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Ying Ding

Publications and source records attributed to Ying Ding.

At least 19 recordsLinked to original sources
arXiv2026

Agent-Enhanced Heterogeneous Graph RAG for Academic Question Answering

Academic question answering requires reasoning over heterogeneous scholarly graphs, where queries range from simple attribute lookups to multi-hop inference across author--paper--venue structures. Existing retrieval-augmented generation (RAG) systems struggle in this setting due to three limitations: (1) fixed retrieval strategies that do not adapt to varying query complexity, (2) the absence of sufficiency evaluation leading to incomplete or misaligned evidence, and (3) a lack of structured verification against graph facts. To address these issues, we propose an agentic heterogeneous graph RAG method that transforms the three core stages of the RAG pipeline into explicit agentic decision steps. A query-aware retrieval agent analyzes query type and selects an appropriate graph traversal strategy; a sufficiency-aware reranking agent assesses evidence completeness and adaptively expands the retrieved subgraph; and a graph-grounded verification agent checks entity, relation, and attribute correctness before finalizing the answer. Experiments on heterogeneous graphs constructed from OpenAlex and DBLP suggest that our method consistently outperforms strong LLM, graph-augmented RAG, and agent-based baselines.

cs.SI↗
arXiv2026

SEER: Long-Context Reasoning via Selective Visual-Text Compression

Long-context reasoning remains computationally expensive for large language models due to the quadratic complexity of attention over text tokens. Visual-text compression offers a promising alternative by rendering text into images and processing them with vision-language models, often reducing token usage. However, existing approaches apply uniform compression regardless of query relevance, potentially sacrificing precision where detailed extraction is required. We present SEER, a framework that learns to select query-relevant images through visual scanning and retrieve textual content only where needed, combining the efficiency of visual compression with the precision of text-based reasoning. Through supervised fine-tuning on tool-interaction trajectories, SEER learns adaptive tool invocation for selection and retrieval. Experiments on long-context benchmarks show that SEER improves extraction precision through selective text retrieval while retaining average prompt-token savings relative to full-text baselines. On LongBench, SEER achieves 51.11% average accuracy, outperforming the visual-text baseline Glyph-9B by 2.33 points and Qwen3-8B by 3.49 points. Code can be accessed at https://github.com/jiaweixu98/SEER

cs.CL↗
arXiv2026

EndoMD-SLAM: Endoscopic Gaussian Splatting SLAM under Optical Degradation with Memory and Static-Transient Decomposition

Dense 3D reconstruction is critical for clinical endoscopic navigation and documentation. While Gaussian Splatting SLAM systems show promise in this domain, they fundamentally rely on strict multi-view photometric consistency. In routine procedures, this assumption is severely violated by intermittent optical degradations like moving debris and water flushing. Standard systems erroneously fuse these cameraattached artifacts into the persistent 3D geometry, causing severe tracking drift and irreversible map corruption. To address this limitation, we propose EndoMD-SLAM, a framework designed to maintain stability under optical degradation through specialized tracking and mapping mechanisms. On the tracking side, a memory-driven gating mechanism detects unreliable observations to suspend map updates and utilizes historical keyframes for drift-aware relocalization. On the mapping side, a self-supervised static-transient decomposition isolates visual contaminants into a dedicated transient field. This explicit separation prevents artifacts from structurally entangling with the persistent anatomical map. We curate a degradationfocused benchmark from colonoscopy videos to systematically evaluate these failure modes. Extensive experiments show that while standard baselines fail under severe optical degradation, EndoMD-SLAM preserves geometric integrity, reducing absolute trajectory error by 91% and improving rendering fidelity by 9.9 dB PSNR.

cs.CV↗
arXiv2026

Grounded in Consensus, In Step With Emerging Science: A Consensus-Anchored Multi-Corpus Clinical Chatbot for Long COVID

Long COVID (LC) poses a challenge for clinical decision support because relevant evidence is distributed across sources with different update cycles, evidentiary roles, and levels of clinical maturity. We present a clinician-facing chatbot that organizes four sources within a retrieval-augmented workflow: expert-curated consensus guidance, current PubMed literature, registered interventional trials, and evidence from living systematic reviews. Consensus guidance is always included to frame responses, while the remaining sources are retrieved in parallel when selected by the user. In an exploratory automated evaluation on 50 clinician-facing questions, our chatbot showed comparable mean ratings to OpenEvidence, with numerically higher scores and lower score variability in an LLM-judged comparison.

cs.IR↗
arXiv2026

CalVerT: Augmenting Agents with Calibrated Verifier Telemetry Improves Action and Learning in Knowledge-Intensive Tasks

LLM agents in knowledge intensive question answering take retrieval and reasoning actions with incomplete knowledge about whether their current answer is uncertain, unsupported, or already complete. This produces two failure modes: committing to confident but unsupported answers, which hurts accuracy, and over-retrieving when the evidence in hand already suffices, resulting in wasted compute. To give agents a more complete picture of the state space they are operating in, we introduce calibrated verifier telemetry (CalVerT), which augments the agent's state with additional telemetry: a calibrated self-confidence score and a grounding verifier score. We show that CalVerT can improve agents in both training-free and training-based settings. On four QA benchmarks, we find that CalVerT raises F1 by triggering retrieval in cases where agents over-rely on parametric knowledge, while cutting redundant retrieval in cases where agents have sufficient context to answer. We show that CalVerT can augment existing QA frameworks without training. Moreover, CalVerT also improves trained systems: by simply augmenting an agent's state with telemetry, we observe improvements after reinforcement learning, as compared to an agent with identical training but no CalVerT telemetry.

cs.CL↗
arXiv2026

EmoPatient: An Emotion-Directed Patient Simulator for Realistic Palliative Care Communication Training

Effective communication during palliative care discussions is a critical clinical skill, yet training clinicians to manage complex patient emotions remains challenging. Large language model (LLM)-based patient simulators provide a scalable approach for communication training, but most existing systems treat patient emotion as static and fail to capture the dynamic emotional shifts observed in clinical interactions. We present EmoPatient, an emotion-directed patient simulator designed to generate evolving emotional responses during palliative care discussions. The system introduces an Emotion Director agent that estimates the patient's emotional state and generates turn-level control signals for emotional intensity, regulatory stability, and interactional guidance. We evaluate EmoPatient through controlled multi-turn physician-patient dialogue simulations and compare it with baseline simulators. Results show improvements across four theory-informed emotional realism metrics and robustness across conversational personality variants, suggesting that modeling emotional dynamics can improve the realism of LLM-based patient simulators for palliative care communication training.

cs.HC↗
arXiv2026

Chreode: A Cell World Model for One-Step Temporal Dynamics and Perturbation Prediction

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 / Schr\"odinger-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.

cs.LG↗
arXiv2026

ConceptM$^3$oE: Concept-Guided Multimodal Mixture of Experts for Interpretable Computational Pathology

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.

cs.AI↗
arXiv2026

Clinically-Informed Modeling for Pediatric Brain Tumor Classification from Whole-Slide Histopathology Images

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.

cs.CV↗
arXiv2026

DreamKG: A KG-Augmented Conversational System for People Experiencing Homelessness

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.

cs.AI↗
arXiv2026

Benchmarking Multi-turn Medical Diagnosis: Hold, Lure, and Self-Correction

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.

cs.CL↗
arXiv2026

Resonant Parameters of Vector Charmonium-like States above 4.4 GeV

We analysis the $\sqrt{s}$-dependent line shapes of the $e^+e^-\to D_s^{+}D_{s1}^{*-}(2536)$, $D_s^{+}D_{s2}^{*-}(2573)$, $\phi\chi_{c1,2}$, $K^+K^-J/\psi$, $K_S^0 K_S^0 J/\psi$, and $K^+K^-\psi(2S)$ cross sections measured by the BESIII experiment using the four resonant structures $\psi(4230)$, $\psi(4500)$, $\psi(4660)$, and $\psi(4710)$, by performing a simultaneous $\chi^2$-minimized fit. Their masses and widths are obtained. We find that the processes $e^+e^-\to D_s^{+}D_{s1}^{*-}(2536)$, $e^+e^-\to D_s^{+}D_{s2}^{*-}(2573)$, and $e^+e^-\to \phi\chi_{c1,2}$ are all dominantly produced via the $\psi(4660)$ and $\psi(4710)$ decays.

hep-ex↗
arXiv2026

Automated Thematic Analysis for Clinical Qualitative Data: Iterative Codebook Refinement with Full Provenance

Thematic analysis (TA) is widely used in health research to extract patterns from patient interviews, yet manual TA faces challenges in scalability and reproducibility. LLM-based automation can help, but existing approaches produce codebooks with limited generalizability and lack analytic auditability. We present an automated TA framework combining iterative codebook refinement with full provenance tracking. Evaluated on five corpora spanning clinical interviews, social media, and public transcripts, the framework achieves the highest composite quality score on four of five datasets compared to six baselines. Iterative refinement yields statistically significant improvements on four datasets with large effect sizes, driven by gains in code reusability and distributional consistency while preserving descriptive quality. On two clinical corpora (pediatric cardiology), generated themes align with expert-annotated themes.

cs.CL↗
arXiv2026

PathMoE: Interpretable Multimodal Interaction Experts for Pediatric Brain Tumor Classification

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.

cs.CV↗
arXiv2026

Choosing How to Remember: Adaptive Memory Structures for LLM Agents

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%.

cs.AI↗
arXiv2026

ICODEN: Ordinary Differential Equation Neural Networks for Interval-Censored Data

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.

cs.LG↗
arXiv2026

Rethinking the Value of Multi-Agent Workflow: A Strong Single Agent Baseline

Recent advances in LLM-based multi-agent systems (MAS) show that workflows composed of multiple LLM agents with distinct roles, tools, and communication patterns can outperform single-LLM baselines on complex tasks. However, most frameworks are homogeneous, where all agents share the same base LLM and differ only in prompts, tools, and positions in the workflow. This raises the question of whether such workflows can be simulated by a single agent through multi-turn conversations. We investigate this across seven benchmarks spanning coding, mathematics, general question answering, domain-specific reasoning, and real-world planning and tool use. Our results show that a single agent can reach the performance of homogeneous workflows with an efficiency advantage from KV cache reuse, and can even match the performance of an automatically optimized heterogeneous workflow. Building on this finding, we propose \textbf{OneFlow}, an algorithm that automatically tailors workflows for single-agent execution, reducing inference costs compared to existing automatic multi-agent design frameworks without trading off accuracy. These results position the single-LLM implementation of multi-agent workflows as a strong baseline for MAS research. We also note that single-LLM methods cannot capture heterogeneous workflows due to the lack of KV cache sharing across different LLMs, highlighting future opportunities in developing \textit{truly} heterogeneous multi-agent systems.

cs.MA↗