arXiv subjects

Jiayuan Ding

Publications and source records attributed to Jiayuan Ding.

At least 19 recordsLinked to original sources

arXiv2026

What the Reranker Sees: Multi-Aspect Page Annotation for Long-Document Multimodal Question Answering

Long-document visual question answering (VQA) over documents of tens to hundreds of pages mixing text, tables, charts, and figures typically follows retrieve-then-read pipelines. In our setting, the bottleneck shifts from retrieval recall to reranker-side evidence selection: on MMLongBench-Doc, BGE-M3 reaches Recall@20 = 0.86 but only F1@5 = 0.254, and even the visual retriever ColPali reaches only F1@5 = 0.332; a text-only rerank LLM seeing only raw snippets misses table, chart, and layout evidence even when the upstream retriever encoded images. We propose Trident, with two complementary components: Trident-R, a retriever-agnostic LLM reranker that converts each candidate into an LLM-readable semantic record, including a visual caption, section path, entity tags, multi-axis concept hits, and a text snippet, then performs a single adaptive-K rerank call; and Trident-S, a generation-side module that prompts the VLM under topical, entity, and structural lenses before synthesis. On two long-document datasets, the annotation+rerank protocol substantially improves retrieval F1 across five heterogeneous pools, with every reranked pool exceeding the strongest adaptive-K baseline PageIndex. An LLM rerank without the annotation barely changes first-hit ranking, indicating the lift comes from the structured annotation. Trident-S targets open-ended synthesis questions by design, adding up to 6.6 points in generation accuracy on these questions. The best Trident configuration is the strongest downstream QA pipeline in our evaluation, with rankings consistent across two LLM judges (kappa = 0.913).

cs.AI↗

arXiv2026

MatrAIx: Simulating the World with 8.3 Billion Persona Agents

Human evaluation of AI systems and digital products is costly, slow, and difficult to scale. Offline evaluations are more scalable but often abstract away human diversity and interactive behavior. We therefore introduce MatrAIx, a population-scale simulated-user evaluation infrastructure for testing AI systems and digital products with heterogeneous users. MatrAIx has three core components: First, Persona 8B contains 8.3 billion persona records represented by 1,290 categorical dimensions. Records are either sampled from a dependency graph that preserves correlated attributes or derived from human-authored profiles. We release a quality-filtered coreset of approximately 1 million personas, comprising 599,847 human-grounded and 400,000 synthetic records. Second, the MatrAIx Playground provides four environments in which diverse users evaluate and interact with digital products: Survey, AI Chatbot, Web, and App. Third, MatrAIx provides 1,010 application tasks spanning more than 25 domains, including Commerce, Software, Finance, and Healthcare. We conducted 18,189 evaluation trials across eight representative tasks. Persona agents were powered by three LLMs: Claude Opus 4.8, GPT 5.5, and Claude Haiku 4.5. The resulting feedback captures how decisions and preferences vary across persona backgrounds, including hesitation after a price increase, willingness to continue after an AI assistant fails, and latency tolerance. We conducted two main validation studies: First, a 400-trial controlled study evaluated persona adherence across ten behavioral attributes and all four environments. The declared behavior was expressed or correctly suppressed in 366 trials (91.5%). Second, human and LLM judges evaluated the extraction quality of human-grounded personas. Overall, MatrAIx provides an end-to-end infrastructure for evaluating AI systems and digital products with diverse simulated human users.

cs.AI↗

arXiv2026

Predictive single cell foundation model for gene regulation and aging with privacy-preserving tabular learning

Pre-trained foundation models (FMs) have begun transforming single-cell genomics, but scaling them raises privacy concerns. Moreover, unlike text data, single-cell data is unordered and exhibits a unique tabular structure that current single-cell FMs overlook. We introduce Tabula, a privacy-preserving FM designed with federated learning (FL) that explicitly models the tabular structure of single-cell data. To deploy Tabula, we further developed Chiron, a decentralized AI agent-enabled platform for collaborative training across institutions without sharing raw data. Beyond strong performance across downstream benchmarks, Tabula reveals combinatorial regulatory logic across diverse biological systems, including hematopoiesis, pancreatic endogenesis, neurogenesis, and cardiogenesis. Using a new scRNA-seq dataset of paired young and aged human fibroblasts, Tabula nominates rejuvenation factors through age- and identity score-guided in silico prioritization, outperforming conventional approaches. Thus, Tabula represents an important advance in single-cell foundation modeling by integrating tabular learning with FL, paving the way toward privacy-preserving virtual cells for human health.

cs.LG↗

arXiv2026

A Simple Plug-in for Improving Eviction-Based KV Cache Compression

KV cache growth is a major bottleneck for long-context inference in large language models. Existing methods are often dominated by binary eviction or representation approximation, which may underutilize tokens that are not critical for exact retention but are still reconstructable. We present VECTOR, a plug-and-play augmentation for eviction-based pipelines that introduces three-way token routing: retention, approximation, and eviction. VECTOR combines an importance signal from the base scorer with a reconstructability signal from an offline-calibrated regression-based value estimation. By leveraging reconstructability, VECTOR recovers useful value information that would otherwise be irreversibly lost under binary eviction, while preserving key vectors for attention routing stability. Experimental results show that VECTOR improves quality-memory trade-offs under medium-to-high compression, with especially clear gains in stricter budget regimes.

cs.LG↗

arXiv2026

Crafting Reversible SFT Behaviors in Large Language Models

Supervised fine-tuning (SFT) induces new behaviors in large language models, yet imposes no structural constraint on how these behaviors are distributed within the model. Existing behavior interpretation methods, such as circuit attribution approaches, identify sparse subnetworks correlated with SFT-induced behaviors post-hoc. However, such correlations do not imply *causal necessity*, limiting the ability to selectively control SFT-induced behaviors at inference time. We pursue an alternative by asking: can an SFT-induced behavior be deliberately compressed into a sparse, mechanistically necessary subnetwork, termed a *carrier*, while remaining controllable at inference time without weight modification? We propose (a) **Loss-Constrained Dual Descent (LCDD)**, which constructs such carriers by jointly optimizing routing masks and model weights under an explicit utility budget, and (b) **SFT-Eraser**, a soft prompt optimized via activation matching on extracted carrier channels, to reverse the SFT-induced behavior. Across safety, fixed-response, and style behaviors on multiple model families, LCDD yields sparse carriers that preserve target behaviors while enabling strong reversion when triggered by SFT-Eraser. Ablations further establish that the sparse structure is the key precondition for reversal: the same trigger optimization fails on standard SFT models, confirming that structure rather than trigger design is the operative factor. These results provide direct evidence that the learned carriers are causally necessary for the behaviors, pointing to a new direction for systematically localizing and selectively suppressing SFT-induced behaviors in deployed models.

cs.LG↗

arXiv2026

Perfecting Human-AI Interaction at Clinical Scale. Turning Production Signals into Safer, More Human Conversations

Healthcare conversational AI agents shouldn't be optimized only for clean benchmark accuracy in production-first regime; they must be optimized for the lived reality of patient conversations, where audio is imperfect, intent is indirect, language shifts mid-call, and compliance hinges on how guidance is delivered. We present a production-validated framework grounded in real-time signals from 115M+ live patient-AI interactions and clinician-led testing (7K+ licensed clinicians; 500K+ test calls). These in-the-wild cues -- paralinguistics, turn-taking dynamics, clarification triggers, escalation markers, multilingual continuity, and workflow confirmations -- reveal failure modes that curated data misses and provide actionable training and evaluation signals for safety and reliability. We further show why healthcare-grade safety cannot rely on a single LLM: long-horizon dialogue and limited attention demand redundancy via governed orchestration, independent checks, and verification. Many apparent "reasoning" errors originate upstream, motivating vertical integration across contextual ASR, clarification/repair, ambient speech handling, and latency-aware model/hardware choices. Treating interaction intelligence (tone, pacing, empathy, clarification, turn-taking) as first-class safety variables, we drive measurable gains in safety, documentation, task completion, and equity in building the safest generative AI solution for autonomous patient-facing care. Deployed across more than 10 million real patient calls, Polaris attains a clinical safety score of 99.9%, while significantly improving patient experience with average patient rating of 8.95 and reducing ASR errors by 50% over enterprise ASR. These results establish real-world interaction intelligence as a critical -- and previously underexplored -- determinant of safety and reliability in patient-facing clinical AI systems.

cs.HC↗

arXiv2026

MIXRAG : Mixture-of-Experts Retrieval-Augmented Generation for Textual Graph Understanding and Question Answering

Large Language Models (LLMs) have achieved impressive performance across a wide range of applications. However, they often suffer from hallucinations in knowledge-intensive domains due to their reliance on static pretraining corpora. To address this limitation, Retrieval-Augmented Generation (RAG) enhances LLMs by incorporating external knowledge sources during inference. Among these sources, textual graphs provide structured and semantically rich information that supports more precise and interpretable reasoning. This has led to growing interest in graph-based RAG systems. Despite their potential, most existing approaches rely on a single retriever to identify relevant subgraphs, which limits their ability to capture the diverse aspects of complex queries. Moreover, these systems often struggle to accurately judge the relevance of retrieved content, making them prone to distraction by irrelevant noise. To address these challenges, in this paper, we propose MIXRAG, a Mixture-of-Experts Graph-RAG framework that introduces multiple specialized graph retrievers and a dynamic routing controller to better handle diverse query intents. Each retriever is trained to focus on a specific aspect of graph semantics, such as entities, relations, or subgraph topology. A Mixture-of-Experts module adaptively selects and fuses relevant retrievers based on the input query. To reduce noise in the retrieved information, we introduce a query-aware GraphEncoder that carefully analyzes relationships within the retrieved subgraphs, highlighting the most relevant parts while down-weighting unnecessary noise. Empirical results demonstrate that our method achieves state-of-the-art performance and consistently outperforms various baselines. MIXRAG is effective across a wide range of graph-based tasks in different domains. The code will be released upon paper acceptance.

cs.IR↗

arXiv2025

TRAJECT-Bench:A Trajectory-Aware Benchmark for Evaluating Agentic Tool Use

Large language model (LLM)-based agents increasingly rely on tool use to complete real-world tasks. While existing works evaluate the LLMs' tool use capability, they largely focus on the final answers yet overlook the detailed tool usage trajectory, i.e., whether tools are selected, parameterized, and ordered correctly. We introduce TRAJECT-Bench, a trajectory-aware benchmark to comprehensively evaluate LLMs' tool use capability through diverse tasks with fine-grained evaluation metrics. TRAJECT-Bench pairs high-fidelity, executable tools across practical domains with tasks grounded in production-style APIs, and synthesizes trajectories that vary in breadth (parallel calls) and depth (interdependent chains). Besides final accuracy, TRAJECT-Bench also reports trajectory-level diagnostics, including tool selection and argument correctness, and dependency/order satisfaction. Analyses reveal failure modes such as similar tool confusion and parameter-blind selection, and scaling behavior with tool diversity and trajectory length where the bottleneck of transiting from short to mid-length trajectories is revealed, offering actionable guidance for LLMs' tool use.

cs.AI↗

arXiv2025

Retrieval-Augmented Generation with Graphs (GraphRAG)

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

cs.IR↗

arXiv2024

MMedAgent: Learning to Use Medical Tools with Multi-modal Agent

Multi-Modal Large Language Models (MLLMs), despite being successful, exhibit limited generality and often fall short when compared to specialized models. Recently, LLM-based agents have been developed to address these challenges by selecting appropriate specialized models as tools based on user inputs. However, such advancements have not been extensively explored within the medical domain. To bridge this gap, this paper introduces the first agent explicitly designed for the medical field, named \textbf{M}ulti-modal \textbf{Med}ical \textbf{Agent} (MMedAgent). We curate an instruction-tuning dataset comprising six medical tools solving seven tasks across five modalities, enabling the agent to choose the most suitable tools for a given task. Comprehensive experiments demonstrate that MMedAgent achieves superior performance across a variety of medical tasks compared to state-of-the-art open-source methods and even the closed-source model, GPT-4o. Furthermore, MMedAgent exhibits efficiency in updating and integrating new medical tools. Codes and models are all available.

cs.CL↗

arXiv2024

Copyright Protection in Generative AI: A Technical Perspective

Generative AI has witnessed rapid advancement in recent years, expanding their capabilities to create synthesized content such as text, images, audio, and code. The high fidelity and authenticity of contents generated by these Deep Generative Models (DGMs) have sparked significant copyright concerns. There have been various legal debates on how to effectively safeguard copyrights in DGMs. This work delves into this issue by providing a comprehensive overview of copyright protection from a technical perspective. We examine from two distinct viewpoints: the copyrights pertaining to the source data held by the data owners and those of the generative models maintained by the model builders. For data copyright, we delve into methods data owners can protect their content and DGMs can be utilized without infringing upon these rights. For model copyright, our discussion extends to strategies for preventing model theft and identifying outputs generated by specific models. Finally, we highlight the limitations of existing techniques and identify areas that remain unexplored. Furthermore, we discuss prospective directions for the future of copyright protection, underscoring its importance for the sustainable and ethical development of Generative AI.

cs.CR↗

arXiv2024

Polaris: A Safety-focused LLM Constellation Architecture for Healthcare

We develop Polaris, the first safety-focused LLM constellation for real-time patient-AI healthcare conversations. Unlike prior LLM works in healthcare focusing on tasks like question answering, our work specifically focuses on long multi-turn voice conversations. Our one-trillion parameter constellation system is composed of several multibillion parameter LLMs as co-operative agents: a stateful primary agent that focuses on driving an engaging conversation and several specialist support agents focused on healthcare tasks performed by nurses to increase safety and reduce hallucinations. We develop a sophisticated training protocol for iterative co-training of the agents that optimize for diverse objectives. We train our models on proprietary data, clinical care plans, healthcare regulatory documents, medical manuals, and other medical reasoning documents. We align our models to speak like medical professionals, using organic healthcare conversations and simulated ones between patient actors and experienced nurses. This allows our system to express unique capabilities such as rapport building, trust building, empathy and bedside manner. Finally, we present the first comprehensive clinician evaluation of an LLM system for healthcare. We recruited over 1100 U.S. licensed nurses and over 130 U.S. licensed physicians to perform end-to-end conversational evaluations of our system by posing as patients and rating the system on several measures. We demonstrate Polaris performs on par with human nurses on aggregate across dimensions such as medical safety, clinical readiness, conversational quality, and bedside manner. Additionally, we conduct a challenging task-based evaluation of the individual specialist support agents, where we demonstrate our LLM agents significantly outperform a much larger general-purpose LLM (GPT-4) as well as from its own medium-size class (LLaMA-2 70B).

cs.AI↗

arXiv2024

Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation

Spatially resolved transcriptomics brings exciting breakthroughs to single-cell analysis by providing physical locations along with gene expression. However, as a cost of the extremely high spatial resolution, the cellular level spatial transcriptomic data suffer significantly from missing values. While a standard solution is to perform imputation on the missing values, most existing methods either overlook spatial information or only incorporate localized spatial context without the ability to capture long-range spatial information. Using multi-head self-attention mechanisms and positional encoding, transformer models can readily grasp the relationship between tokens and encode location information. In this paper, by treating single cells as spatial tokens, we study how to leverage transformers to facilitate spatial tanscriptomics imputation. In particular, investigate the following two key questions: (1) $\textit{how to encode spatial information of cells in transformers}$, and (2) $\textit{ how to train a transformer for transcriptomic imputation}$. By answering these two questions, we present a transformer-based imputation framework, SpaFormer, for cellular-level spatial transcriptomic data. Extensive experiments demonstrate that SpaFormer outperforms existing state-of-the-art imputation algorithms on three large-scale datasets while maintaining superior computational efficiency.

q-bio.GN↗

arXiv2023

Single-Cell Multimodal Prediction via Transformers

The recent development of multimodal single-cell technology has made the possibility of acquiring multiple omics data from individual cells, thereby enabling a deeper understanding of cellular states and dynamics. Nevertheless, the proliferation of multimodal single-cell data also introduces tremendous challenges in modeling the complex interactions among different modalities. The recently advanced methods focus on constructing static interaction graphs and applying graph neural networks (GNNs) to learn from multimodal data. However, such static graphs can be suboptimal as they do not take advantage of the downstream task information; meanwhile GNNs also have some inherent limitations when deeply stacking GNN layers. To tackle these issues, in this work, we investigate how to leverage transformers for multimodal single-cell data in an end-to-end manner while exploiting downstream task information. In particular, we propose a scMoFormer framework which can readily incorporate external domain knowledge and model the interactions within each modality and cross modalities. Extensive experiments demonstrate that scMoFormer achieves superior performance on various benchmark datasets. Remarkably, scMoFormer won a Kaggle silver medal with the rank of 24/1221 (Top 2%) without ensemble in a NeurIPS 2022 competition. Our implementation is publicly available at Github.

q-bio.GN↗

arXiv2023

Are Message Passing Neural Networks Really Helpful for Knowledge Graph Completion?

Knowledge graphs (KGs) facilitate a wide variety of applications. Despite great efforts in creation and maintenance, even the largest KGs are far from complete. Hence, KG completion (KGC) has become one of the most crucial tasks for KG research. Recently, considerable literature in this space has centered around the use of Message Passing (Graph) Neural Networks (MPNNs), to learn powerful embeddings. The success of these methods is naturally attributed to the use of MPNNs over simpler multi-layer perceptron (MLP) models, given their additional message passing (MP) component. In this work, we find that surprisingly, simple MLP models are able to achieve comparable performance to MPNNs, suggesting that MP may not be as crucial as previously believed. With further exploration, we show careful scoring function and loss function design has a much stronger influence on KGC model performance. This suggests a conflation of scoring function design, loss function design, and MP in prior work, with promising insights regarding the scalability of state-of-the-art KGC methods today, as well as careful attention to more suitable MP designs for KGC tasks tomorrow. Our codes are publicly available at: https://github.com/Juanhui28/Are_MPNNs_helpful.

cs.AI↗

arXiv2023

Empowering Graph Representation Learning with Test-Time Graph Transformation

As powerful tools for representation learning on graphs, graph neural networks (GNNs) have facilitated various applications from drug discovery to recommender systems. Nevertheless, the effectiveness of GNNs is immensely challenged by issues related to data quality, such as distribution shift, abnormal features and adversarial attacks. Recent efforts have been made on tackling these issues from a modeling perspective which requires additional cost of changing model architectures or re-training model parameters. In this work, we provide a data-centric view to tackle these issues and propose a graph transformation framework named GTrans which adapts and refines graph data at test time to achieve better performance. We provide theoretical analysis on the design of the framework and discuss why adapting graph data works better than adapting the model. Extensive experiments have demonstrated the effectiveness of GTrans on three distinct scenarios for eight benchmark datasets where suboptimal data is presented. Remarkably, GTrans performs the best in most cases with improvements up to 2.8%, 8.2% and 3.8% over the best baselines on three experimental settings. Code is released at https://github.com/ChandlerBang/GTrans.

cs.LG↗

arXiv2022

Deep Learning in Single-Cell Analysis

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.

q-bio.QM↗

arXiv2022

Graph Neural Networks for Multimodal Single-Cell Data Integration

Recent advances in multimodal single-cell technologies have enabled simultaneous acquisitions of multiple omics data from the same cell, providing deeper insights into cellular states and dynamics. However, it is challenging to learn the joint representations from the multimodal data, model the relationship between modalities, and, more importantly, incorporate the vast amount of single-modality datasets into the downstream analyses. To address these challenges and correspondingly facilitate multimodal single-cell data analyses, three key tasks have been introduced: $\textit{modality prediction}$, $\textit{modality matching}$ and $\textit{joint embedding}$. In this work, we present a general Graph Neural Network framework $\textit{scMoGNN}$ to tackle these three tasks and show that $\textit{scMoGNN}$ demonstrates superior results in all three tasks compared with the state-of-the-art and conventional approaches. Our method is an official winner in the overall ranking of $\textit{Modality prediction}$ from NeurIPS 2021 Competition, and all implementations of our methods have been integrated into DANCE package~\url{https://github.com/OmicsML/dance}.

cs.LG↗